Serialized Form (computational omics utilities 4.5.7 API)

Package com.compomics.software.dialogs
- Class com.compomics.software.dialogs.JavaHomeDialog extends JDialog implements Serializable
  - Serialized Fields
    - javaHomeOrMemoryDialogParent
```
JavaHomeOrMemoryDialogParent javaHomeOrMemoryDialogParent
```
      Reference to the JavaHomeOrMemoryDialogParent.
    - welcomeDialog
```
JDialog welcomeDialog
```
      A reference to the Welcome Dialog.
    - toolName
```
String toolName
```
      The name of the tool, e.g., PeptideShaker.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - browseButton
```
JButton browseButton
```
    - cancelButton
```
JButton cancelButton
```
    - jSeparator1
```
JSeparator jSeparator1
```
    - javaHomeHelpJButton
```
JButton javaHomeHelpJButton
```
    - javaHomeLabel
```
JLabel javaHomeLabel
```
    - javaHomeTxt
```
JTextField javaHomeTxt
```
    - okButton
```
JButton okButton
```
- Class com.compomics.software.dialogs.JavaMemoryDialog extends JDialog implements Serializable
  - Serialized Fields
    - javaHomeOrMemoryDialogParent
```
JavaHomeOrMemoryDialogParent javaHomeOrMemoryDialogParent
```
      Reference to the JavaHomeOrMemoryDialogParent.
    - welcomeDialog
```
JDialog welcomeDialog
```
      A reference to the Welcome Dialog.
    - toolName
```
String toolName
```
      The name of the tool, e.g., PeptideShaker.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - jSeparator1
```
JSeparator jSeparator1
```
    - javaOptionsHelpJButton
```
JButton javaOptionsHelpJButton
```
    - mbLabel
```
JLabel mbLabel
```
    - memoryLimitLabel
```
JLabel memoryLimitLabel
```
    - memoryTxt
```
JTextField memoryTxt
```
    - okButton
```
JButton okButton
```
- Class com.compomics.software.dialogs.JavaSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    - javaHomeOrMemoryDialogParent
```
JavaHomeOrMemoryDialogParent javaHomeOrMemoryDialogParent
```
      Reference to the JavaHomeOrMemoryDialogParent.
    - frameParent
```
JFrame frameParent
```
      The frame parent.
    - toolName
```
String toolName
```
      The name of the tool, e.g., PeptideShaker.
    - welcomeDialog
```
JDialog welcomeDialog
```
      A reference to the Welcome Dialog.
    - backgroundsPanel
```
JPanel backgroundsPanel
```
    - bitLabel
```
JLabel bitLabel
```
    - bitPanel
```
JPanel bitPanel
```
    - bitRecommendationLabel
```
JLabel bitRecommendationLabel
```
    - javaHelpJLabel
```
JLabel javaHelpJLabel
```
    - javaHomeLabel
```
JLabel javaHomeLabel
```
    - javaHomePanel
```
JPanel javaHomePanel
```
    - memoryLabel
```
JLabel memoryLabel
```
    - memoryPanel
```
JPanel memoryPanel
```
    - memoryRecommendationLabel
```
JLabel memoryRecommendationLabel
```
    - okButton
```
JButton okButton
```
    - versionLabel
```
JLabel versionLabel
```
    - versionPanel
```
JPanel versionPanel
```
    - versionRecommendationLabel1
```
JLabel versionRecommendationLabel1
```
    - versionRecommendationLabel2
```
JLabel versionRecommendationLabel2
```
- Class com.compomics.software.dialogs.PeptideShakerSetupDialog extends JDialog implements Serializable
  - Serialized Fields
    - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
      The utilities preferences.
    - lastSelectedFolder
```
String lastSelectedFolder
```
      The selected folder.
    - dialogCanceled
```
boolean dialogCanceled
```
      Set to true if the dialog was canceled.
    - parentFrame
```
JFrame parentFrame
```
      The parent frame. Can be null.
    - parentDialog
```
JDialog parentDialog
```
      The parent dialog. Can be null.
    - progressDialog
```
ProgressDialogX progressDialog
```
      The progress dialog.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - browseButton
```
JButton browseButton
```
    - cancelButton
```
JButton cancelButton
```
    - jLabel2
```
JLabel jLabel2
```
    - okButton
```
JButton okButton
```
    - peptideShakerButton
```
JButton peptideShakerButton
```
    - peptideShakerDownloadLinkLabel
```
JLabel peptideShakerDownloadLinkLabel
```
    - peptideShakerDownloadPanel
```
JPanel peptideShakerDownloadPanel
```
    - peptideShakerInfoLabel
```
JLabel peptideShakerInfoLabel
```
    - peptideShakerInstallationPanel
```
JPanel peptideShakerInstallationPanel
```
    - peptideShakerJarFileHelpLabel
```
JLabel peptideShakerJarFileHelpLabel
```
    - peptideShakernstallationJTextField
```
JTextField peptideShakernstallationJTextField
```
- Class com.compomics.software.dialogs.ProteoWizardSetupDialog extends JDialog implements Serializable
  - Serialized Fields
    - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
      The utilities preferences.
    - lastSelectedFolder
```
String lastSelectedFolder
```
      The selected folder.
    - dialogCanceled
```
boolean dialogCanceled
```
      Set to true if the dialog was canceled.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - browseButton
```
JButton browseButton
```
    - cancelButton
```
JButton cancelButton
```
    - downloadLinkLabel
```
JLabel downloadLinkLabel
```
    - downloadPanel
```
JPanel downloadPanel
```
    - folderHelpLabel
```
JLabel folderHelpLabel
```
    - iconButton
```
JButton iconButton
```
    - infoLabel
```
JLabel infoLabel
```
    - installationJTextField
```
JTextField installationJTextField
```
    - installationPanel
```
JPanel installationPanel
```
    - jLabel2
```
JLabel jLabel2
```
    - okButton
```
JButton okButton
```
- Class com.compomics.software.dialogs.ReporterSetupDialog extends JDialog implements Serializable
  - Serialized Fields
    - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
      The utilities preferences.
    - lastSelectedFolder
```
String lastSelectedFolder
```
      The selected folder.
    - dialogCanceled
```
boolean dialogCanceled
```
      Set to true if the dialog was canceled.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - browseButton
```
JButton browseButton
```
    - cancelButton
```
JButton cancelButton
```
    - jLabel2
```
JLabel jLabel2
```
    - okButton
```
JButton okButton
```
    - reporterButton
```
JButton reporterButton
```
    - reporterDownloadLinkLabel
```
JLabel reporterDownloadLinkLabel
```
    - reporterDownloadPanel
```
JPanel reporterDownloadPanel
```
    - reporterInfoLabel
```
JLabel reporterInfoLabel
```
    - reporterInstallationJTextField
```
JTextField reporterInstallationJTextField
```
    - reporterInstallationPanel
```
JPanel reporterInstallationPanel
```
    - reporterJarFileHelpLabel
```
JLabel reporterJarFileHelpLabel
```
- Class com.compomics.software.dialogs.SearchGuiSetupDialog extends JDialog implements Serializable
  - Serialized Fields
    - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
      The utilities preferences.
    - lastSelectedFolder
```
String lastSelectedFolder
```
      The selected folder.
    - dialogCanceled
```
boolean dialogCanceled
```
      Set to true if the dialog was canceled.
    - progressDialog
```
ProgressDialogX progressDialog
```
      The progress dialog.
    - parentFrame
```
JFrame parentFrame
```
      The parent frame. Can be null.
    - parentDialog
```
JDialog parentDialog
```
      The parent dialog. Can be null.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - browseButton
```
JButton browseButton
```
    - cancelButton
```
JButton cancelButton
```
    - jLabel2
```
JLabel jLabel2
```
    - okButton
```
JButton okButton
```
    - searchGuiButton
```
JButton searchGuiButton
```
    - searchGuiDownloadLinkLabel
```
JLabel searchGuiDownloadLinkLabel
```
    - searchGuiDownloadPanel
```
JPanel searchGuiDownloadPanel
```
    - searchGuiInfoLabel
```
JLabel searchGuiInfoLabel
```
    - searchGuiInstallationJTextField
```
JTextField searchGuiInstallationJTextField
```
    - searchGuiInstallationPanel
```
JPanel searchGuiInstallationPanel
```
    - searchGuiJarFileHelpLabel
```
JLabel searchGuiJarFileHelpLabel
```
Package com.compomics.software.settings.gui
- Class com.compomics.software.settings.gui.PathSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    - canceled
```
boolean canceled
```
      Boolean indicating whether the process was canceled by the user.
    - originalKeyToPathMap
```
HashMap<K,V> originalKeyToPathMap
```
      Original map of the paths to set.
    - keyToPathMap
```
HashMap<K,V> keyToPathMap
```
      Map of the paths to set.
    - keyList
```
ArrayList<E> keyList
```
      List of paths.
    - nameToKey
```
HashMap<K,V> nameToKey
```
      Name to key map.
    - toolName
```
String toolName
```
      The tool name.
    - pathsToolTips
```
ArrayList<E> pathsToolTips
```
      Tooltips for the paths.
    - pathTableToolTips
```
ArrayList<E> pathTableToolTips
```
      The path table column header tooltips.
    - cancelButton
```
JButton cancelButton
```
    - editPathMenuItem
```
JMenuItem editPathMenuItem
```
    - helpLabel
```
JLabel helpLabel
```
    - informationPanel
```
JPanel informationPanel
```
    - informationScrollPane
```
JScrollPane informationScrollPane
```
    - informationTxt
```
JTextArea informationTxt
```
    - okButton
```
JButton okButton
```
    - pathSettingsJPanel
```
JPanel pathSettingsJPanel
```
    - pathSettingsPopupMenu
```
JPopupMenu pathSettingsPopupMenu
```
    - pathTable
```
JTable pathTable
```
    - pathTableScrollPane
```
JScrollPane pathTableScrollPane
```
    - setDefaultPath
```
JMenuItem setDefaultPath
```
    - tablePanel
```
JPanel tablePanel
```
Package com.compomics.util
- Class com.compomics.util.AlternateRowColoursJTable extends JTable implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iEvenRowColor
```
Color iEvenRowColor
```
      The background colour for the even rows. A value of 'null' means use the default background colour for JTable.
    - iUnevenRowColor
```
Color iUnevenRowColor
```
      The background colour for the uneven rows. A value of 'null' (default here) means use the default background colour for JTable.
Package com.compomics.util.db
- Class com.compomics.util.db.DBResultSet extends AbstractTableModel implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iColCount
```
int iColCount
```
      The number of columns in this resultset.
    - iRowCount
```
int iRowCount
```
      The number of rows in this resultset.
    - iColNames
```
String[] iColNames
```
      The column names in this resultset.
    - iData
```
Object[][] iData
```
      The data.
- Class com.compomics.util.db.GeneratorException extends Exception implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iNested
```
Exception iNested
```
      The nested exception.
- Class com.compomics.util.db.ObjectsDB extends Object implements Serializable
  
  serialVersionUID:
  
  -8595805180622832745L
  - Serialized Fields
    - dbName
```
String dbName
```
      The name of the database.
    - path
```
String path
```
      The path to the database.
    - dbConnection
```
Connection dbConnection
```
      The connection, shall not be accessed outside this class.
    - longTableNames
```
ArrayList<E> longTableNames
```
      List of keys too long to create a table.
    - longKeysMap
```
HashMap<K,V> longKeysMap
```
      Map of the keys too long to be stored in the database indexed by table name.
    - objectsCache
```
ObjectsCache objectsCache
```
      The cache to be used for the objects.
    - debugSpeedWriter
```
BufferedWriter debugSpeedWriter
```
      The writer used to send the output to file.
    - debugContentWriter
```
BufferedWriter debugContentWriter
```
      The writer used to send the output to file.
    - debugFolder
```
File debugFolder
```
      The debug folder.
    - busy
```
boolean busy
```
      A boolean indicating whether the database is being queried.
    - tableQueueUpdating
```
String tableQueueUpdating
```
      The name of the table currently updating in the queue.
    - tableQueue
```
ArrayList<E> tableQueue
```
      A queue of entire tables to load.
    - contentQueue
```
HashMap<K,V> contentQueue
```
      A queue of table components to load.
    - contentTableQueue
```
ArrayList<E> contentTableQueue
```
      A queue of tables of content to load.
    - debugSpeed
```
boolean debugSpeed
```
      Debug, if true will output a table containing statistics on the speed of the objects I/O.
    - debugContent
```
boolean debugContent
```
      Debug, if true will output a table containing details on the objects stored.
    - debugInteractions
```
boolean debugInteractions
```
      Debug, if true, all interaction with the database will be logged in the System.out stream.
    - useSQLite
```
boolean useSQLite
```
      If true, SQLite is used as the database, if false Derby is used.

Package com.compomics.util.examples

Class com.compomics.util.examples.HelpWindow extends JFrame implements Serializable
- Serialized Fields
  - closeJButton
```
JButton closeJButton
```
  - textEditorScrollPane
```
JScrollPane textEditorScrollPane
```
  - textJEditorPane
```
JEditorPane textJEditorPane
```
Class com.compomics.util.examples.MirroredSpectraTestDialog extends JDialog implements Serializable
- Serialized Fields
  - backgroundPanel
```
JPanel backgroundPanel
```

Class com.compomics.util.examples.UtilitiesDemo extends JFrame implements Serializable

Serialized Fields

peffAnnotationsColorMap
```
HashMap<K,V> peffAnnotationsColorMap
```
The PEFF annotations color map.
peffAnnotationsTooltipMap
```
HashMap<K,V> peffAnnotationsTooltipMap
```
The PEFF annotations tooltip map.
peffFormat
```
boolean peffFormat
```
If true, the format shown is PEFF, if false FASTA is assumed.
keyValuePairs
```
TreeMap<K,V> keyValuePairs
```
The map of the PEFF key value pairs.
currentSequenceFile
```
File currentSequenceFile
```
The current PEFF (or FASTA) sequence file.
currentPeffBufferedReader
```
BufferedReader currentPeffBufferedReader
```
The current PEFF (or FASTA) buffered reader.
currentSequence
```
String currentSequence
```
The current PEFF (or FASTA) sequence.
currentSequenceLine
```
String currentSequenceLine
```
The current PEFF (or FASTA) sequence line.
linkedSpectrumPanels
```
HashMap<K,V> linkedSpectrumPanels
```
A hashmap of both the linked spectra.
allAnnotations
```
HashMap<K,V> allAnnotations
```
A hashmap of all spectrum panel annotations.
spectrumAPanel
```
SpectrumPanel spectrumAPanel
```
The first spectrum panel.
spectrumBPanel
```
SpectrumPanel spectrumBPanel
```
The second spectrum panel
spectrumPanelMaxPadding
```
int spectrumPanelMaxPadding
```
The maximum padding allowed in the spectrum panels. Increase if font size on the y-axis becomes too small.
chromatogramPanelMaxPadding
```
int chromatogramPanelMaxPadding
```
The maximum padding allowed in the chromatogram panels. Increase if font size on the y-axis becomes too small.
mascotEnzymeReader
```
MascotEnzymeReader mascotEnzymeReader
```
Used to read the enzyme details from file.
cleanProteinSequence
```
String cleanProteinSequence
```
Used for the in silico digestion example.
selectedAnnotationTypes
```
HashMap<K,V> selectedAnnotationTypes
```
The tag colors for PEFF formatting.
sequenceAnnotationColumnHeaderTooltips
```
ArrayList<E> sequenceAnnotationColumnHeaderTooltips
```
Sequence annotation column header tooltips.
sparklineColor
```
Color sparklineColor
```
The color used for the sparkline bar chart plots.
H2OIonsJCheckBox
```
JCheckBox H2OIonsJCheckBox
```
NH3IonsJCheckBox
```
JCheckBox NH3IonsJCheckBox
```
aIonsJCheckBox
```
JCheckBox aIonsJCheckBox
```
allPeaksJCheckBox
```
JCheckBox allPeaksJCheckBox
```
bIonsJCheckBox
```
JCheckBox bIonsJCheckBox
```
backgroundPanel
```
JPanel backgroundPanel
```
browseJButton
```
JButton browseJButton
```
cIonsJCheckBox
```
JCheckBox cIonsJCheckBox
```
chargeOneJCheckBox
```
JCheckBox chargeOneJCheckBox
```
chargeOverTwoJCheckBox
```
JCheckBox chargeOverTwoJCheckBox
```
chargePeptideAJSpinner
```
JSpinner chargePeptideAJSpinner
```
chargePeptideBJSpinner
```
JSpinner chargePeptideBJSpinner
```
chargeTwoJCheckBox
```
JCheckBox chargeTwoJCheckBox
```
chromatogramAJPanel
```
JPanel chromatogramAJPanel
```
chromatogramJPanel
```
JPanel chromatogramJPanel
```
chromatogramPanelHelpJLabel
```
JLabel chromatogramPanelHelpJLabel
```
chromatogramPanelInfoJLabel
```
JLabel chromatogramPanelInfoJLabel
```
enzymesJComboBox
```
JComboBox<E> enzymesJComboBox
```
exportJButton
```
JButton exportJButton
```
inSilicoDigestionHelpJLabel
```
JLabel inSilicoDigestionHelpJLabel
```
informationJEditorPane
```
JEditorPane informationJEditorPane
```
informationJPanel
```
JPanel informationJPanel
```
informationJScrollPane
```
JScrollPane informationJScrollPane
```
inhibitorsJTextField
```
JTextField inhibitorsJTextField
```
ionSelectionJPanel
```
JPanel ionSelectionJPanel
```
isotopicDistributionAJPanel
```
JPanel isotopicDistributionAJPanel
```

isotopicDistributionCalculatorHelpJLabel

JLabel isotopicDistributionCalculatorHelpJLabel

isotopicDistributionCalculatorInfoJLabel

JLabel isotopicDistributionCalculatorInfoJLabel

isotopicDistributionJPanel
```
JPanel isotopicDistributionJPanel
```
jLabel1
```
JLabel jLabel1
```
jLabel10
```
JLabel jLabel10
```
jLabel11
```
JLabel jLabel11
```
jLabel12
```
JLabel jLabel12
```
jLabel13
```
JLabel jLabel13
```
jLabel14
```
JLabel jLabel14
```
jLabel15
```
JLabel jLabel15
```
jLabel16
```
JLabel jLabel16
```
jLabel17
```
JLabel jLabel17
```
jLabel18
```
JLabel jLabel18
```
jLabel19
```
JLabel jLabel19
```
jLabel2
```
JLabel jLabel2
```
jLabel20
```
JLabel jLabel20
```
jLabel21
```
JLabel jLabel21
```
jLabel24
```
JLabel jLabel24
```
jLabel3
```
JLabel jLabel3
```
jLabel4
```
JLabel jLabel4
```
jLabel5
```
JLabel jLabel5
```
jLabel6
```
JLabel jLabel6
```
jLabel7
```
JLabel jLabel7
```
jLabel8
```
JLabel jLabel8
```
jLabel9
```
JLabel jLabel9
```
jPanel1
```
JPanel jPanel1
```
jPanel10
```
JPanel jPanel10
```
jPanel11
```
JPanel jPanel11
```
jPanel12
```
JPanel jPanel12
```
jPanel2
```
JPanel jPanel2
```
jPanel3
```
JPanel jPanel3
```
jPanel4
```
JPanel jPanel4
```
jPanel5
```
JPanel jPanel5
```
jPanel6
```
JPanel jPanel6
```
jPanel7
```
JPanel jPanel7
```
jPanel8
```
JPanel jPanel8
```
jRadioButton1
```
JRadioButton jRadioButton1
```
jSeparator1
```
JSeparator jSeparator1
```
jSeparator2
```
JSeparator jSeparator2
```
jSeparator3
```
JSeparator jSeparator3
```
jSeparator4
```
JSeparator jSeparator4
```
jSeparator5
```
JSeparator jSeparator5
```
jSeparator6
```
JSeparator jSeparator6
```
jSeparator9
```
JSeparator jSeparator9
```
jTabbedPane
```
JTabbedPane jTabbedPane
```
linkedSpectraJCheckBox
```
JCheckBox linkedSpectraJCheckBox
```
lowerMassJSpinner
```
JSpinner lowerMassJSpinner
```
missedCleavagesJSpinner
```
JSpinner missedCleavagesJSpinner
```
nextJButton
```
JButton nextJButton
```
otherIonsJCheckBox
```
JCheckBox otherIonsJCheckBox
```
peffAnnotationPanel
```
JPanel peffAnnotationPanel
```
peffAnnotationsJTable
```
JTable peffAnnotationsJTable
```
peffAnnotationsScrollPane
```
JScrollPane peffAnnotationsScrollPane
```
peffHeaderJTable
```
JTable peffHeaderJTable
```
peffHeaderScrollPane
```
JScrollPane peffHeaderScrollPane
```
peptideAColorJPanel
```
JPanel peptideAColorJPanel
```

peptideACompositionJTextField

JTextField peptideACompositionJTextField

peptideAJScrollPane
```
JScrollPane peptideAJScrollPane
```
peptideAJTable
```
JTable peptideAJTable
```
peptideAMzJTextField
```
JTextField peptideAMzJTextField
```
peptideBColorJPanel
```
JPanel peptideBColorJPanel
```

peptideBCompositionJTextField

JTextField peptideBCompositionJTextField

peptideBJScrollPane
```
JScrollPane peptideBJScrollPane
```
peptideBJTable
```
JTable peptideBJTable
```
peptideBMzJTextField
```
JTextField peptideBMzJTextField
```
peptideSequenceAJTextField
```
JTextField peptideSequenceAJTextField
```
peptideSequenceBJTextField
```
JTextField peptideSequenceBJTextField
```
peptidesJPanel
```
JPanel peptidesJPanel
```
peptidesJTable
```
JTable peptidesJTable
```
peptidesScrollPane
```
JScrollPane peptidesScrollPane
```
positionJTextField
```
JTextField positionJTextField
```
profileSpectrumJCheckBox
```
JCheckBox profileSpectrumJCheckBox
```
proteinCoverageJScrollPane
```
JScrollPane proteinCoverageJScrollPane
```
proteinDetailsScrollPane
```
JScrollPane proteinDetailsScrollPane
```
proteinDigestionJLabel
```
JLabel proteinDigestionJLabel
```
proteinDigestionJPanel
```
JPanel proteinDigestionJPanel
```
proteinHeaderJTable
```
JTable proteinHeaderJTable
```

proteinSequenceCoverageJEditorPane

JEditorPane proteinSequenceCoverageJEditorPane

sequenceCoverageJPanel
```
JPanel sequenceCoverageJPanel
```
sequenceFileJTextField
```
JTextField sequenceFileJTextField
```
sequenceJTabbedPane
```
JTabbedPane sequenceJTabbedPane
```

silacLabelPeptideAJComboBox

JComboBox<E> silacLabelPeptideAJComboBox

silacLabelPeptideBJComboBox

JComboBox<E> silacLabelPeptideBJComboBox

siteJTextField
```
JTextField siteJTextField
```
spectraJPanel
```
JPanel spectraJPanel
```
spectrumAJPanel
```
JPanel spectrumAJPanel
```
spectrumBJPanel
```
JPanel spectrumBJPanel
```
spectrumJPanel
```
JPanel spectrumJPanel
```
spectrumPanelHelpJLabel
```
JLabel spectrumPanelHelpJLabel
```
spectrumPanelInfoJLabel
```
JLabel spectrumPanelInfoJLabel
```
upperMassJSpinner
```
JSpinner upperMassJSpinner
```
xIonsJCheckBox
```
JCheckBox xIonsJCheckBox
```
yIonsJCheckBox
```
JCheckBox yIonsJCheckBox
```
zIonsJCheckBox
```
JCheckBox zIonsJCheckBox
```

Package com.compomics.util.experiment
- Class com.compomics.util.experiment.MsExperiment extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  4330394623824512352L
  - Serialized Fields
    - reference
```
String reference
```
      Reference of the experiment.
    - samples
```
HashMap<K,V> samples
```
      The samples analyzed.
    - analysis
```
HashMap<K,V> analysis
```
      The analysis.
- Class com.compomics.util.experiment.ProteomicAnalysis extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -6738411343333889777L
  - Serialized Fields
    - index
```
int index
```
      The analysis index.
    - quantification
```
HashMap<K,V> quantification
```
      Quantification results indexed by the method used.
    - identification
```
HashMap<K,V> identification
```
      Identification results.
- Class com.compomics.util.experiment.SampleAnalysisSet extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -5399187779025810060L
  - Serialized Fields
    - sample
```
Sample sample
```
      The reference sample.
    - analysis
```
HashMap<K,V> analysis
```
      The various analysis indexed by replicates indexes.
- Class com.compomics.util.experiment.ShotgunProtocol extends Object implements Serializable
  - Serialized Fields
    - enzyme
```
Enzyme enzyme
```
      The enzyme used for digestion.
    - enrichedPtms
```
ArrayList<E> enrichedPtms
```
      The PTMs enriched for.
    - labellingPtms
```
HashMap<K,V> labellingPtms
```
      The PTMs resulting of a labeling in a map: name of the PTM - boolean indicating whether the labeling is complete.
    - ms1Resolution
```
Double ms1Resolution
```
      The MS1 resolution.
    - ms1ResolutionPpm
```
boolean ms1ResolutionPpm
```
      Boolean indicating whether the MS1 resolution is in ppm.
    - fragmentationMethod
```
FragmentationMethod fragmentationMethod
```
      The fragmentation method used.
    - ms2Resolution
```
Double ms2Resolution
```
      The MS2 resolution.
    - ms2ResolutionPpm
```
boolean ms2ResolutionPpm
```
      Boolean indicating whether the MS2 resolution is in ppm.
Package com.compomics.util.experiment.biology
- Class com.compomics.util.experiment.biology.AminoAcid extends Object implements Serializable
  
  serialVersionUID:
  
  -3158896310928354857L
  - Serialized Fields
    - singleLetterCode
```
String singleLetterCode
```
      Single letter code of the amino acid.
    - threeLetterCode
```
String threeLetterCode
```
      Three letter code of the amino acid.
    - name
```
String name
```
      Name of the amino acid.
    - averageMass
```
double averageMass
```
      Average mass of the amino acid.
    - monoisotopicMass
```
Double monoisotopicMass
```
      Deprecated. use the atomchain
      
      Monoisotopic mass of the amino acid.
    - monoisotopicAtomChain
```
AtomChain monoisotopicAtomChain
```
      The monoisotopic atom chain.
    - indistinguishableAACacheMass
```
Double indistinguishableAACacheMass
```
      The mass tolerance used for the indistinguishable amino acids in cache.
    - subAminoAcidsWithoutCombination
```
char[] subAminoAcidsWithoutCombination
```
      The sub amino acids.
    - subAminoAcidsWithCombination
```
char[] subAminoAcidsWithCombination
```
      The sub amino acids.
    - aminoAcidCombinations
```
char[] aminoAcidCombinations
```
      The amino acid combinations.
    - standardGeneticCode
```
String[] standardGeneticCode
```
      The standard genetic code.
- Class com.compomics.util.experiment.biology.AminoAcidPattern extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -2823716418631089876L
  - Serialized Fields
    - target
```
Integer target
```
      The index of the amino acid of interest if there is one. Can be a modification site or a cleavage site. For trypsin: 0.
    - length
```
int length
```
      The length of the pattern, -1 if not set.
    - residueTargeted
```
HashMap<K,V> residueTargeted
```
      The list of targeted amino acids at a given index represented by their single letter code. For trypsin: 0 > {R, K} 1 > {all but P}
    - targetModifications
```
HashMap<K,V> targetModifications
```
      The modifications carried by the amino acid sequence at target amino acids.
- Class com.compomics.util.experiment.biology.AminoAcidSequence extends ExperimentObject implements Serializable
  - Serialized Fields
    - sequence
```
String sequence
```
      The sequence as string.
    - sequenceStringBuilder
```
StringBuilder sequenceStringBuilder
```
      The sequence as string builder.
    - aminoAcidPattern
```
AminoAcidPattern aminoAcidPattern
```
      The sequence as amino acid pattern.
    - modifications
```
HashMap<K,V> modifications
```
      The modifications carried by the amino acid sequence at target amino acids. 1 is the first amino acid.
- Class com.compomics.util.experiment.biology.Atom extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  1059024301538472131L
  - Serialized Fields
    - monoisotopicMass
```
Double monoisotopicMass
```
      The monoisotopic mass. Access is faster then querying the isotope map.
    - isotopeMap
```
HashMap<K,V> isotopeMap
```
      Map of the isotope masses relative to the monoisotopic peak (+1 for carbon 13).
    - representativeComposition
```
HashMap<K,V> representativeComposition
```
      Map of the isotope representative composition of the stable isotopes.
    - name
```
String name
```
      The name of the atom.
    - letter
```
String letter
```
      The single letter code of the atom.
- Class com.compomics.util.experiment.biology.AtomChain extends Object implements Serializable
  
  serialVersionUID:
  
  2222259572093523514L
  - Serialized Fields
    - atomChain
```
ArrayList<E> atomChain
```
      The chain of atoms.
    - mass
```
Double mass
```
      The mass of the atom chain.
    - addition
```
Boolean addition
```
      If true, the atom chain consists of additions, i.e., all atoms are added when calculating the mass, false, means that all atoms are subtracted. This variable also impacts the toString method.
- Class com.compomics.util.experiment.biology.AtomImpl extends Object implements Serializable
  - Serialized Fields
    - atom
```
Atom atom
```
      The reference atom.
    - isotope
```
Integer isotope
```
      The isotope, 0 for monoisotope.
- Class com.compomics.util.experiment.biology.Enzyme extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -1852087173903613377L
  - Serialized Fields
    - id
```
int id
```
    - name
```
String name
```
    - aminoAcidBefore
```
ArrayList<E> aminoAcidBefore
```
    - aminoAcidAfter
```
ArrayList<E> aminoAcidAfter
```
    - restrictionBefore
```
ArrayList<E> restrictionBefore
```
    - restrictionAfter
```
ArrayList<E> restrictionAfter
```
    - isSemiSpecific
```
Boolean isSemiSpecific
```
      If true, the enzyme is considered as semi-specific, meaning that only one end of the resulting peptide has to be enzymatic.
    - isWholeProtein
```
Boolean isWholeProtein
```
      If true, the enzyme does not cleave, i.e., the whole protein sequence is used.
- Class com.compomics.util.experiment.biology.Ion extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -1505719074403886934L
  - Serialized Fields
    - neutralLossesAsString
```
String neutralLossesAsString
```
      Cache for the neutral losses as string.
    - type
```
Ion.IonType type
```
      Type of ion.
    - theoreticMass
```
Double theoreticMass
```
      The theoretic mass.
    - atomChain
```
AtomChain atomChain
```
      The atomic composition of the ion.
- Class com.compomics.util.experiment.biology.MassGap extends ExperimentObject implements Serializable
  - Serialized Fields
    - value
```
double value
```
      The value of the mass gap.
- Class com.compomics.util.experiment.biology.NeutralLoss extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  5540846193082177391L
  - Serialized Fields
    - mass
```
Double mass
```
      Deprecated. use the composition instead.
      
      The mass lost.
    - composition
```
AtomChain composition
```
      The composition of the ion.
    - name
```
String name
```
      The name of the neutral loss.
    - fixed
```
Boolean fixed
```
      Boolean indicating whether the neutral loss will always be accounted for.
- Class com.compomics.util.experiment.biology.Peptide extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  5632064601627536034L
  - Serialized Fields
    - sequence
```
String sequence
```
      The peptide sequence.
    - sequenceWithLowerCasePtms
```
String sequenceWithLowerCasePtms
```
      The peptide sequence with the modified residues indicated in lower case.
    - mass
```
Double mass
```
      The peptide mass.
    - parentProteins
```
ArrayList<E> parentProteins
```
      The parent proteins.
    - modifications
```
ArrayList<E> modifications
```
      The modifications carried by the peptide.
- Class com.compomics.util.experiment.biology.Protein extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  1987224639519365761L
  - Serialized Fields
    - accession
```
String accession
```
      The protein accession.
    - decoy
```
boolean decoy
```
      Boolean indicating if the protein is not existing (decoy protein for instance).
    - sequence
```
String sequence
```
      The protein sequence.
    - databaseType
```
Header.DatabaseType databaseType
```
      The protein database type.
- Class com.compomics.util.experiment.biology.PTM extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -545472596243822505L
  - Serialized Fields
    - type
```
int type
```
      The modification type according to static field.
    - name
```
String name
```
      Name of the modification.
    - shortName
```
String shortName
```
      Short name of the modification.
    - mass
```
Double mass
```
      Mass difference produced by this modification. Null if not set.
    - neutralLosses
```
ArrayList<E> neutralLosses
```
      List of known neutral losses for this modification.
    - reporterIons
```
ArrayList<E> reporterIons
```
      List of known reporter ions for this modification.
    - pattern
```
AminoAcidPattern pattern
```
      The amino acid pattern targeted by this modification (can be set using the AminoAcidPatternDialog).
    - atomChainAdded
```
AtomChain atomChainAdded
```
      The composition of the molecule added.
    - atomChainRemoved
```
AtomChain atomChainRemoved
```
      The composition of the molecule removed.
    - cvTerm
```
CvTerm cvTerm
```
      The CV term associated with this PTM. Null if not set.
- Class com.compomics.util.experiment.biology.PTMFactory extends Object implements Serializable
  - Serialized Fields
    - ptmMap
```
HashMap<K,V> ptmMap
```
      A map linking indexes with modifications.
    - defaultMods
```
ArrayList<E> defaultMods
```
      List of the indexes of default modifications.
    - userMods
```
ArrayList<E> userMods
```
      List of the indexes of user modifications.
    - userColors
```
HashMap<K,V> userColors
```
      Mapping of the expected modification names to the color used.
    - defaultModsSorted
```
boolean defaultModsSorted
```
      Set to true if the default mods are sorted alphabetically.
    - usersModsSorted
```
boolean usersModsSorted
```
      Set to true if the users mods are sorted alphabetically.
- Class com.compomics.util.experiment.biology.Sample extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  303393644914835325L
  - Serialized Fields
    - reference
```
String reference
```
      Sample reference.
Package com.compomics.util.experiment.biology.aminoacids
- Class com.compomics.util.experiment.biology.aminoacids.Alanine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  2553535668713619525L
- Class com.compomics.util.experiment.biology.aminoacids.Arginine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -5308475190007072857L
- Class com.compomics.util.experiment.biology.aminoacids.Asparagine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  5951975489690885808L
- Class com.compomics.util.experiment.biology.aminoacids.AsparticAcid extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -8410332876209882538L
- Class com.compomics.util.experiment.biology.aminoacids.B extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -584166511231722270L
- Class com.compomics.util.experiment.biology.aminoacids.Cysteine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  9171494537928740228L
- Class com.compomics.util.experiment.biology.aminoacids.GlutamicAcid extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  6850534412637609745L
- Class com.compomics.util.experiment.biology.aminoacids.Glutamine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -1552736259723394861L
- Class com.compomics.util.experiment.biology.aminoacids.Glycine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  2128316713069027803L
- Class com.compomics.util.experiment.biology.aminoacids.Histidine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -669587024023052011L
- Class com.compomics.util.experiment.biology.aminoacids.Isoleucine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -514676021245212886L
- Class com.compomics.util.experiment.biology.aminoacids.J extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  1963175809911841522L
- Class com.compomics.util.experiment.biology.aminoacids.Leucine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -656824121858821632L
- Class com.compomics.util.experiment.biology.aminoacids.Lysine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  3427548228986235710L
- Class com.compomics.util.experiment.biology.aminoacids.Methionine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  1841628592146093511L
- Class com.compomics.util.experiment.biology.aminoacids.Phenylalanine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -939609662176974248L
- Class com.compomics.util.experiment.biology.aminoacids.Proline extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  3754407258673679661L
- Class com.compomics.util.experiment.biology.aminoacids.Pyrrolysine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  8680204019988094523L
- Class com.compomics.util.experiment.biology.aminoacids.Selenocysteine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -2123392615229813870L
- Class com.compomics.util.experiment.biology.aminoacids.Serine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -2201410868329421240L
- Class com.compomics.util.experiment.biology.aminoacids.Threonine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  172831874616867727L
- Class com.compomics.util.experiment.biology.aminoacids.Tryptophan extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -6773437038176247799L
- Class com.compomics.util.experiment.biology.aminoacids.Tyrosine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  7542892886050340088L
- Class com.compomics.util.experiment.biology.aminoacids.Valine extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -5155418025636472676L
- Class com.compomics.util.experiment.biology.aminoacids.X extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -2618109862080991929L
- Class com.compomics.util.experiment.biology.aminoacids.Z extends AminoAcid implements Serializable
  
  serialVersionUID:
  
  -7714841171012071337L
Package com.compomics.util.experiment.biology.atoms
- Class com.compomics.util.experiment.biology.atoms.Carbon extends Atom implements Serializable
- Class com.compomics.util.experiment.biology.atoms.Helium extends Atom implements Serializable
- Class com.compomics.util.experiment.biology.atoms.Hydrogen extends Atom implements Serializable
- Class com.compomics.util.experiment.biology.atoms.Iodine extends Atom implements Serializable
- Class com.compomics.util.experiment.biology.atoms.Lithium extends Atom implements Serializable
- Class com.compomics.util.experiment.biology.atoms.Nitrogen extends Atom implements Serializable
- Class com.compomics.util.experiment.biology.atoms.Oxygen extends Atom implements Serializable
- Class com.compomics.util.experiment.biology.atoms.Phosphorus extends Atom implements Serializable
- Class com.compomics.util.experiment.biology.atoms.Selenium extends Atom implements Serializable
- Class com.compomics.util.experiment.biology.atoms.Sodium extends Atom implements Serializable
- Class com.compomics.util.experiment.biology.atoms.Sulfur extends Atom implements Serializable
Package com.compomics.util.experiment.biology.genes
- Class com.compomics.util.experiment.biology.genes.GeneMaps extends Object implements Serializable
  - Serialized Fields
    - ensemblVersionsMap
```
HashMap<K,V> ensemblVersionsMap
```
      The Ensembl versions for each species.
    - geneNameToEnsemblIdMap
```
HashMap<K,V> geneNameToEnsemblIdMap
```
      Gene name to EnsemblId map.
    - geneNameToChromosomeMap
```
HashMap<K,V> geneNameToChromosomeMap
```
      Gene name to chromosome name map.
    - proteinToGoMap
```
HashMap<K,V> proteinToGoMap
```
      Protein accession to GO terms map.
    - goAccessionToProteinMap
```
HashMap<K,V> goAccessionToProteinMap
```
      GO term to protein accession map.
    - goNamesMap
```
HashMap<K,V> goNamesMap
```
      GO term accession to name map.
Package com.compomics.util.experiment.biology.ions
- Class com.compomics.util.experiment.biology.ions.ElementaryIon extends Ion implements Serializable
  
  serialVersionUID:
  
  -1578136397635015592L
  - Serialized Fields
    - name
```
String name
```
      The name of the ion.
    - subType
```
int subType
```
      The subtype identifier.
- Class com.compomics.util.experiment.biology.ions.Glycan extends Ion implements Serializable
  
  serialVersionUID:
  
  -2278483206647518565L
  - Serialized Fields
    - theoreticMasses
```
HashMap<K,V> theoreticMasses
```
      Masses of this glycan.
    - name
```
String name
```
      The glycan short name which can be displayed on a spectrum.
    - longName
```
String longName
```
      The glycan full name.
- Class com.compomics.util.experiment.biology.ions.ImmoniumIon extends Ion implements Serializable
  
  serialVersionUID:
  
  -3403620196563864756L
  - Serialized Fields
    - subType
```
int subType
```
      Subtype of immonium ion.
- Class com.compomics.util.experiment.biology.ions.PeptideFragmentIon extends Ion implements Serializable
  
  serialVersionUID:
  
  8283809283803740651L
  - Serialized Fields
    - neutralLosses
```
ArrayList<E> neutralLosses
```
      The neutral losses found on the ion.
    - number
```
int number
```
      Position of the ion in the peptide for peptide ions.
    - subType
```
int subType
```
      The type of fragment.
- Class com.compomics.util.experiment.biology.ions.PrecursorIon extends Ion implements Serializable
  
  serialVersionUID:
  
  -2630586959372309153L
  - Serialized Fields
    - neutralLosses
```
ArrayList<E> neutralLosses
```
      the neutral losses found on the ion.
- Class com.compomics.util.experiment.biology.ions.RelatedIon extends Ion implements Serializable
  
  serialVersionUID:
  
  -4605345486425465764L
  - Serialized Fields
    - aminoAcidTarget
```
AminoAcid aminoAcidTarget
```
      The amino acid target.
    - subType
```
int subType
```
      The sub type.
- Class com.compomics.util.experiment.biology.ions.ReporterIon extends Ion implements Serializable
  
  serialVersionUID:
  
  1109011048958734120L
  - Serialized Fields
    - name
```
String name
```
      Ion name for user defined ions.
- Class com.compomics.util.experiment.biology.ions.TagFragmentIon extends Ion implements Serializable
  - Serialized Fields
    - neutralLosses
```
ArrayList<E> neutralLosses
```
      The neutral losses found on the ion.
    - number
```
int number
```
      Position of the ion in the tag of amino acids considering gaps as an amino acid. 0 based.
    - subNumber
```
int subNumber
```
      Position of the ion in the current sequence of amino acids. 0 based.
    - subType
```
int subType
```
      The type of fragment.
    - massGap
```
double massGap
```
      Mass gap before this ion.
Package com.compomics.util.experiment.biology.mutations
- Class com.compomics.util.experiment.biology.mutations.MutationMatrix extends Object implements Serializable
  - Serialized Fields
    - name
```
String name
```
      The name of this mutation matrix.
    - description
```
String description
```
      The description of the mutation matrix.
    - mutations
```
HashMap<K,V> mutations
```
      Map of the possible amino acid mutations: original aa > mutated aa.
    - mutationsMasses
```
HashMap<K,V> mutationsMasses
```
      Map of the possible amino acid mutations: original aa > delta mass (mutated - original) > mutated aa.
    - minDelta
```
Double minDelta
```
      The minimum difference between an original amino acid and the mutated version.
    - maxDelta
```
Double maxDelta
```
      The maximum difference between an original amino acid and the mutated version.
    - mutationsReverse
```
HashMap<K,V> mutationsReverse
```
      Reverse map of the possible amino acid mutations: mutated aa > original aa.
Package com.compomics.util.experiment.identification
- Class com.compomics.util.experiment.identification.Identification extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -2551700699384242554L
  - Serialized Fields
    - proteinIdentification
```
HashSet<E> proteinIdentification
```
      List of the keys of all imported proteins.
    - peptideIdentification
```
HashSet<E> peptideIdentification
```
      List of the keys of all imported peptides.
    - spectrumIdentificationMap
```
HashMap<K,V> spectrumIdentificationMap
```
      List of all imported PSMs indexed by mgf file name.
    - proteinMap
```
HashMap<K,V> proteinMap
```
      A map linking protein accessions to all their protein matches keys.
    - methodUsed
```
int methodUsed
```
      The method used.
    - dbDirectory
```
String dbDirectory
```
      The directory where the database stored.
    - identificationDB
```
IdentificationDB identificationDB
```
      The identificationDB object interacting with the database.
    - reference
```
String reference
```
      The reference of the identification.
    - orderedSpectrumFileNames
```
ArrayList<E> orderedSpectrumFileNames
```
      The ordered list of spectrum file names.
- Class com.compomics.util.experiment.identification.IdentificationDB extends Object implements Serializable
  
  serialVersionUID:
  
  691986038787590646L
  - Serialized Fields
    - dbName
```
String dbName
```
      The name which will be used for the database.
    - rawAssumptionsTables
```
ArrayList<E> rawAssumptionsTables
```
      List of all raw assumptions tables.
    - assumptionsTables
```
ArrayList<E> assumptionsTables
```
      List of all assumptions tables.
    - psmTables
```
ArrayList<E> psmTables
```
      List of all psms tables.
    - psmParametersTables
```
ArrayList<E> psmParametersTables
```
      List of all psm parameters tables.
    - peptideParametersTables
```
ArrayList<E> peptideParametersTables
```
      List of all peptide parameters tables.
    - proteinParametersTables
```
ArrayList<E> proteinParametersTables
```
      List of all proteins parameters tables.
    - objectsDB
```
ObjectsDB objectsDB
```
      The database which will contain the objects.
- Class com.compomics.util.experiment.identification.IdentificationMatch extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -9132138792119651421L
- Class com.compomics.util.experiment.identification.IdentificationMethod extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  4601179275244591663L
  - Serialized Fields
    - index
```
int index
```
      index of the method
- Class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  496273793273328259L
  - Serialized Fields
    - rank
```
int rank
```
      The rank of the peptide assumption for the concerned spectrum.
    - advocate
```
int advocate
```
      The advocate supporting this assumption.
    - identificationCharge
```
Charge identificationCharge
```
      The charge used for identification.
    - score
```
Double score
```
      The (advocate specific) score used to rank this assumption.
    - identificationFile
```
String identificationFile
```
      The identification file.
    - rawScore
```
Double rawScore
```
      The raw score as provided by the identification algorithm.
    - aminoAcidScores
```
ArrayList<E> aminoAcidScores
```
      The individual amino acid scores. Null if not set.
Package com.compomics.util.experiment.identification.amino_acid_tags
- Class com.compomics.util.experiment.identification.amino_acid_tags.Tag extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  1625541843008045218L
  - Serialized Fields
    - content
```
ArrayList<E> content
```
      The content of the tag.
Package com.compomics.util.experiment.identification.filtering
- Class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter extends Object implements Serializable
  
  serialVersionUID:
  
  8416219001106063781L
  - Serialized Fields
    - minPepLength
```
int minPepLength
```
      The minimal peptide length allowed.
    - maxPepLength
```
int maxPepLength
```
      The maximal peptide length allowed.
    - maxMassDeviation
```
double maxMassDeviation
```
      The maximal m/z deviation allowed.
    - isPpm
```
boolean isPpm
```
      Boolean indicating the unit of the allowed m/z deviation (true: ppm, false: Da).
    - unknownPtm
```
boolean unknownPtm
```
      Boolean indicating whether peptides presenting unknown PTMs should be ignored.
    - minMissedCleavages
```
Integer minMissedCleavages
```
      The minimum number of missed cleavages allowed. Null means no lower limit.
    - maxMissedCleavages
```
Integer maxMissedCleavages
```
      The maximum number of missed cleavages allowed. Null means no upper limit.
    - minIsotopes
```
Integer minIsotopes
```
      The minimum number of isotopes allowed. Null means no lower limit.
    - maxIsotopes
```
Integer maxIsotopes
```
      The maximum number of isotopes allowed. Null means no upper limit.
Package com.compomics.util.experiment.identification.identification_parameters
- Class com.compomics.util.experiment.identification.identification_parameters.PtmSettings extends Object implements Serializable
  
  serialVersionUID:
  
  342611308111304721L
  - Serialized Fields
    - fixedModifications
```
ArrayList<E> fixedModifications
```
      List of the expected fixed modifications.
    - variableModifications
```
ArrayList<E> variableModifications
```
      List of the expected variable modifications.
    - refinementVariableModifications
```
ArrayList<E> refinementVariableModifications
```
      List of variable modifications searched during the second pass search.
    - refinementFixedModifications
```
ArrayList<E> refinementFixedModifications
```
      List of variable modifications searched during the second pass search.
    - colors
```
HashMap<K,V> colors
```
      Mapping of the expected modification names to the color used.
    - backUp
```
HashMap<K,V> backUp
```
      Back-up mapping of the PTMs for portability.
- Class com.compomics.util.experiment.identification.identification_parameters.SearchParameters extends Object implements Serializable
  
  serialVersionUID:
  
  -2773993307168773763L
  - Serialized Fields
    - marshallableParameterType
```
String marshallableParameterType
```
      Name of the type of marshalled parameter.
    - precursorAccuracyType
```
SearchParameters.MassAccuracyType precursorAccuracyType
```
      The precursor accuracy type. Default is ppm.
    - fragmentAccuracyType
```
SearchParameters.MassAccuracyType fragmentAccuracyType
```
      The fragment accuracy type. Default is Da.
    - precursorTolerance
```
Double precursorTolerance
```
      The precursor mass tolerance.
    - precursorToleranceDalton
```
Double precursorToleranceDalton
```
      The precursor mass tolerance in Dalton.
    - fragmentIonMZTolerance
```
Double fragmentIonMZTolerance
```
      The MS2 ion tolerance.
    - ptmSettings
```
PtmSettings ptmSettings
```
      The expected modifications. Modified peptides will be grouped and displayed according to this classification.
    - enzyme
```
Enzyme enzyme
```
      The enzyme used for digestion.
    - nMissedCleavages
```
Integer nMissedCleavages
```
      The allowed number of missed cleavages.
    - fastaFile
```
File fastaFile
```
      The sequence database file used for identification.
    - parametersFile
```
File parametersFile
```
      Deprecated. the file is now handled outside the parameters.
      
      The corresponding file.
    - fractionMolecularWeightRanges
```
HashMap<K,V> fractionMolecularWeightRanges
```
      The list of fraction molecular weights. The key is the fraction file path.
    - forwardIon
```
Integer forwardIon
```
      The first kind of ions searched for (typically a, b or c).
    - rewindIon
```
Integer rewindIon
```
      The second kind of ions searched for (typically x, y or z).
    - minChargeSearched
```
Charge minChargeSearched
```
      The minimal charge searched (in absolute value).
    - maxChargeSearched
```
Charge maxChargeSearched
```
      The minimal charge searched (in absolute value).
    - minIsotopicCorrection
```
Integer minIsotopicCorrection
```
      The minimal isotope correction.
    - maxIsotopicCorrection
```
Integer maxIsotopicCorrection
```
      The maximal isotope correction.
    - algorithmParameters
```
HashMap<K,V> algorithmParameters
```
      The algorithm specific parameters.
Package com.compomics.util.experiment.identification.identification_parameters.tool_specific
- Class com.compomics.util.experiment.identification.identification_parameters.tool_specific.AndromedaParameters extends Object implements Serializable
  
  serialVersionUID:
  
  9056661756332085205L
  - Serialized Fields
    - maxPeptideMass
```
Double maxPeptideMass
```
      The maximal peptide mass.
    - maxCombinations
```
Integer maxCombinations
```
      The maximum number of combinations.
    - topPeaks
```
Integer topPeaks
```
      The top peaks number.
    - topPeaksWindow
```
Integer topPeaksWindow
```
      The top peaks window size.
    - includeWater
```
Boolean includeWater
```
      Boolean indicating whether water losses should be accounted for.
    - includeAmmonia
```
Boolean includeAmmonia
```
      Boolean indicating whether ammonia losses should be accounted for.
    - dependentLosses
```
Boolean dependentLosses
```
      Boolean indicating whether neutral losses should be sequence dependent.
    - fragmentAll
```
Boolean fragmentAll
```
      Boolean indicating whether the fragment all option should be used.
    - empiricalCorrection
```
Boolean empiricalCorrection
```
      Boolean indicating whether the empirical correction should be used.
    - higherCharge
```
Boolean higherCharge
```
      Boolean indicating whether the higher charge option should be used.
    - fragmentationMethod
```
FragmentationMethod fragmentationMethod
```
      The fragmentation method used.
    - maxNumberOfModifications
```
Integer maxNumberOfModifications
```
      The maximal number of modifications.
    - minPeptideLengthNoEnzyme
```
Integer minPeptideLengthNoEnzyme
```
      The minimal peptide length when no enzyme is used.
    - maxPeptideLengthNoEnzyme
```
Integer maxPeptideLengthNoEnzyme
```
      The maximal peptide length when no enzyme is used.
    - equalIL
```
Boolean equalIL
```
      Boolean indicating whether I and L should be considered indistinguishable.
    - numberOfCandidates
```
Integer numberOfCandidates
```
      The number of candidates to report.
    - ptmIndexes
```
HashMap<K,V> ptmIndexes
```
      Map of the Andromeda indexes used for user modifications in this search.
- Class com.compomics.util.experiment.identification.identification_parameters.tool_specific.CometParameters extends Object implements Serializable
  
  serialVersionUID:
  
  -2996752557726296967L
  - Serialized Fields
    - numberOfSpectrumMatches
```
Integer numberOfSpectrumMatches
```
      The maximum number of spectrum matches.
    - maxVariableMods
```
Integer maxVariableMods
```
      The maximum number of variable modifications per peptide.
    - requireVariableMods
```
Boolean requireVariableMods
```
      Controls whether the peptides must contain at least one variable modification i.e. force all reported peptides to have a variable modification.
    - minPeaks
```
Integer minPeaks
```
      The minimum allowed number of peaks in a spectrum.
    - minPeakIntensity
```
Double minPeakIntensity
```
      The minimum peak intensity.
    - removePrecursor
```
Integer removePrecursor
```
      Remove precursor peak. An input value of 0 will not perform any precursor removal. An input value of 1 will remove all peaks around the precursor m/z. An input value of 2 will remove all charge reduced precursor peaks as expected to be present for ETD/ECD spectra.
    - removePrecursorTolerance
```
Double removePrecursorTolerance
```
      This parameter specifies the mass tolerance (in Da) around each precursor m/z that would be removed when the remove_precursor_peak option is invoked.
    - lowerClearMzRange
```
Double lowerClearMzRange
```
      Defines the lower m/z value to clear out in each MS/MS spectra.
    - upperClearMzRange
```
Double upperClearMzRange
```
      Defines the upper m/z value to clear out in each MS/MS spectra.
    - enzymeType
```
Integer enzymeType
```
      The enzyme type: 1 for a semi-enzyme search, 2 for a full-enzyme search, 8 for a semi-enzyme search, unspecific cleavage on peptide's C-terminus and 9 for a semi-enzyme search, unspecific cleavage on peptide's N-terminus.
    - isotopeCorrection
```
Integer isotopeCorrection
```
      Isotope correction setting. 0: performs no isotope error searches, 1: searches -1, 0, +1, +2, and +3 isotope offsets 2: searches -8, -4, 0, +4, +8 isotope offsets (for +4/+8 stable isotope labeling).
    - minPrecursorMass
```
Double minPrecursorMass
```
      The minimum precursor mass.
    - maxPrecursorMass
```
Double maxPrecursorMass
```
      The maximum precursor mass.
    - maxFragmentCharge
```
Integer maxFragmentCharge
```
      The maximum fragment charge.
    - removeMethionine
```
Boolean removeMethionine
```
      This parameter controls whether Comet will automatically remove the N-terminal methionine from a sequence entry.
    - batchSize
```
Integer batchSize
```
      When this parameter is set to a non-zero value, say 5000, this causes Comet to load and search about 5000 spectra at a time, looping through sets of 5000 spectra until all data have been analyzed. Set this parameter to 0 to load and search all spectra at once.
    - theoreticalFragmentIonsSumOnly
```
Boolean theoreticalFragmentIonsSumOnly
```
      The correlation score type. This parameter specifies how theoretical fragment ion peaks are represented.
    - fragmentBinOffset
```
Double fragmentBinOffset
```
      The fragment bin offset.
    - useSparseMatrix
```
Boolean useSparseMatrix
```
      Deprecated. from Comet release 2015.02 all searches use this internal data representation by default
      
      Controls whether or not internal sparse matrix data representation is used.
    - selectedOutputFormat
```
CometParameters.CometOutputFormat selectedOutputFormat
```
      The selected output format.
    - printExpectScore
```
Boolean printExpectScore
```
      A boolean flag this determines whether or not the expectation score (E-value) is reported in .out and SQT formats. Note that the E-value is always reported in pepXML output. This parameter is only relevant for results reported in .out and SQT formats.
- Class com.compomics.util.experiment.identification.identification_parameters.tool_specific.DirecTagParameters extends Object implements Serializable
  
  serialVersionUID:
  
  -3107089648450731330L
  - Serialized Fields
    - ticCutoffPercentage
```
double ticCutoffPercentage
```
      In order to maximize the effectiveness of the MVH scoring algorithm, an important step in preprocessing the experimental spectra is filtering out noise peaks. Noise peaks are filtered out by sorting the original peaks in descending order of intensity, and then picking peaks from that list until the cumulative ion current of the picked peaks divided by the total ion current (TIC) is greater than or equal to this parameter. Lower percentages mean that less of the spectrums total intensity will be allowed to pass through preprocessing. See the section on Advanced Usage for tips on how to use this parameter optimally. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - maxPeakCount
```
int maxPeakCount
```
      Another way of increasing the effectiveness of the MVH scoring algorithm when used for tagging is to set an upper bound on the number of peaks in a spectrum before generating tags. This step tends to get rid of most noise peaks and makes tagging much more feasible because so many fewer false positives are generated. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - numIntensityClasses
```
int numIntensityClasses
```
      Before scoring any candidates, experimental spectra have their peaks stratified into the number of intensity classes specified by this parameter. Spectra that are very dense in peaks will likely benefit from more intensity classes in order to best take advantage of the variation in peak intensities. Spectra that are very sparse will not see much benefit from using many intensity classes. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - adjustPrecursorMass
```
boolean adjustPrecursorMass
```
      If true, the preprocessing step will correct the precursor mass by adjusting it through a specified range in steps of a specified length, finally choosing the optimal adjustment. The optimal adjustment is the one that maximizes the sum of products of all complementary peaks in the spectrum. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - minPrecursorAdjustment
```
double minPrecursorAdjustment
```
      When adjusting the precursor mass, this parameter sets the lower mass limit of adjustment allowable from the original precursor mass, measured in Daltons. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - maxPrecursorAdjustment
```
double maxPrecursorAdjustment
```
      When adjusting the precursor mass, this parameter sets the upper mass limit of adjustment allowable from the original precursor mass, measured in Daltons. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - precursorAdjustmentStep
```
double precursorAdjustmentStep
```
      When adjusting the precursor mass, this parameter sets the size of the steps between adjustments, measured in Daltons. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - numChargeStates
```
int numChargeStates
```
      Controls the number of charge states that DirecTag will handle during all stages of the program. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - outputSuffix
```
String outputSuffix
```
      The output of a DirecTag job will be a TAGS file for each input file. The string specified by this parameter will be appended to each TAGS filename. It is useful for differentiating jobs within a single directory. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - useChargeStateFromMS
```
boolean useChargeStateFromMS
```
      If true, DirecTag will use the charge state from the input data if it is available. If false, or if charge state is not available from a particular spectrum, DirecTag will use its internal algorithm to determine charge state. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - duplicateSpectra
```
boolean duplicateSpectra
```
      If DirecTag determines a spectrum to be multiply charged and this parameter is true, the spectrum will be copied and treated as if it was all possible charge states from +2 to +<NumChargeStates>. If this parameter is false, the spectrum will simply be treated as a +2. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - deisotopingMode
```
int deisotopingMode
```
      Deisotoping a spectrum (consolidating isotopic peak intensities into the monoisotopic peaks intensity) during preprocessing will significantly improve precursor adjustment, and it may be desirable to keep the deisotoped spectrum around for candidate scoring as well. Set to 0, no deisotoping will be used. Set to 1, deisotoping will be used for precursor adjustment only. Set to 2, deisotoping will be used for both precursor adjustment and for candidate scoring. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - isotopeMzTolerance
```
double isotopeMzTolerance
```
      When deisotoping a spectrum, an isotopic peak is one that is the mass of a neutron higher than another peak, tolerating variation based on the value of this parameter. Deisotoping actually traverses the spectrum at multiple charge states, starting from the highest (NumChargeStates) and ending at the lowest. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - complementMzTolerance
```
double complementMzTolerance
```
      When adjusting the precursor mass, this parameter controls how much tolerance there is on each side of the calculated m/z when looking for a peaks complement. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - tagLength
```
int tagLength
```
      A sequence tag is generated from the gaps between a number of peaks equal to this parameter plus one. Longer tag lengths are more specific, but harder to find because many consecutive ion fragments are rare. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - maxDynamicMods
```
int maxDynamicMods
```
      This parameter sets the maximum number of modified residues that may be in any candidate sequence. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - maxTagCount
```
int maxTagCount
```
      This parameter sets the maximum number of sequence tags to report for each spectrum. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - intensityScoreWeight
```
double intensityScoreWeight
```
      This parameter controls how intensity scores are combined to form a total score. DirecTag scores tags on the basis of their peak intensities. Tags that contain intense peaks are more likely to be correct than those that contain average peaks. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - mzFidelityScoreWeight
```
double mzFidelityScoreWeight
```
      This parameter controls how mzFidelity scores are combined to form a total score. m/z fidelity for a tag can be characterized through SSE. DirecTag evaluates the consistency of fragment ion m/z values for each tag. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - complementScoreWeight
```
double complementScoreWeight
```
      This parameter controls how complement scores are combined to form a total score. Peaks that match to complementary ions within the spectrum are more trustworthy than other peaks. DirecTag assesses the number and concordance of complementary ions for each tag. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag)
    - variablePtms
```
ArrayList<E> variablePtms
```
      The variable PTMs in the order used.
- Class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsAmandaParameters extends Object implements Serializable
  
  serialVersionUID:
  
  -8458620189315975268L
  - Serialized Fields
    - generateDecoy
```
boolean generateDecoy
```
      Defines whether a decoy database shall be created and searched against. Decoy FASTS files are generated by reverting protein sequences, accessions are marked with the prefix “REV_”.
    - instrumentID
```
String instrumentID
```
      The MS Amanda instrument ID.
    - maxRank
```
Integer maxRank
```
      The maximum rank.
    - monoisotopic
```
boolean monoisotopic
```
      Defines whether monoisotopic mass values shall be used (in contrast to average mass values).
    - lowMemoryMode
```
Boolean lowMemoryMode
```
      Defines whether the low memory mode is used.
- Class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MsgfParameters extends Object implements Serializable
  
  serialVersionUID:
  
  -2656523093031942973L
  - Serialized Fields
    - searchDecoyDatabase
```
boolean searchDecoyDatabase
```
      Indicates whether MS-GF+ is to create and search a decoy database or not.
    - instrumentID
```
int instrumentID
```
      The MS-GF+ instrument ID: 0: Low-res LCQ/LTQ (Default), 1: High-res LTQ, 2: TOF, 3: Q-Exactive.
    - fragmentationType
```
int fragmentationType
```
      The MS-GF+ fragmentation type ID: 0: As written in the spectrum or CID if no info (Default), 1: CID, 2: ETD, 3: HCD.
    - protocol
```
int protocol
```
      The MS-GF+ protocol ID: 0: Automatic (Default), 1: Phosphorylation, 2: iTRAQ, 3: iTRAQPhospho, 4: TMT, 5: Standard.
    - minPeptideLength
```
Integer minPeptideLength
```
      The minimum peptide length.
    - maxPeptideLength
```
Integer maxPeptideLength
```
      The maximal peptide length.
    - numberOfSpectrumMarches
```
Integer numberOfSpectrumMarches
```
      The maximum number of spectrum matches.
    - additionalOutput
```
boolean additionalOutput
```
      Output additional features.
    - lowerIsotopeErrorRange
```
Integer lowerIsotopeErrorRange
```
      Deprecated. now a generic search setting
      
      The lower isotope error range.
    - upperIsotopeErrorRange
```
Integer upperIsotopeErrorRange
```
      Deprecated. now a generic search setting
      
      The upper isotope error range.
    - numberTolerableTermini
```
Integer numberTolerableTermini
```
      The number of tolerable termini. E.g. For trypsin, 0: non-tryptic, 1: semi-tryptic, 2: fully-tryptic peptides only.
    - numberOfPtmsPerPeptide
```
Integer numberOfPtmsPerPeptide
```
      The maximum number of PTMs per peptide.
- Class com.compomics.util.experiment.identification.identification_parameters.tool_specific.MyriMatchParameters extends Object implements Serializable
  
  serialVersionUID:
  
  8755937399680481097L
  - Serialized Fields
    - minPeptideLength
```
Integer minPeptideLength
```
      The minimum peptide length.
    - maxPeptideLength
```
Integer maxPeptideLength
```
      The maximal peptide length.
    - numberOfSpectrumMatches
```
Integer numberOfSpectrumMatches
```
      The maximum number of spectrum matches.
    - ticCutoffPercentage
```
Double ticCutoffPercentage
```
      The TicCutoffPercentage.
    - maxDynamicMods
```
Integer maxDynamicMods
```
      The maximum number of variable modifications.
    - minTerminiCleavages
```
Integer minTerminiCleavages
```
      By default, when generating peptides from the protein database, a peptide must start and end at a valid cleavage site. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified in the CleavageRules parameter. This parameter is useful to turn a tryptic digest into a semi-tryptic digest.
    - minPrecursorMass
```
Double minPrecursorMass
```
      The minimum precursor mass considered.
    - maxPrecursorMass
```
Double maxPrecursorMass
```
      The maximum precursor mass considered.
    - useSmartPlusThreeModel
```
Boolean useSmartPlusThreeModel
```
      If true, the UseSmartPlusThreeModel us to be used.
    - computeXCorr
```
Boolean computeXCorr
```
      If true, a Sequest-like cross correlation (xcorr) score will be calculated for the top ranking hits in each spectrum’s result set.
    - numIntensityClasses
```
Integer numIntensityClasses
```
      The number of intensity classes.
    - classSizeMultiplier
```
Integer classSizeMultiplier
```
      The multiplier controlling the size of each intensity class relative to the class above it.
    - numberOfBatches
```
Integer numberOfBatches
```
      The number of batches per node to strive for when using the MPI-based parallelization features.
    - lowerIsotopeCorrection
```
Integer lowerIsotopeCorrection
```
      Deprecated. now general search setting
      
      The lower isotope correction range.
    - upperIsotopeCorrection
```
Integer upperIsotopeCorrection
```
      Deprecated. now general search setting
      
      The upper isotope correction range.
    - fragmentationRule
```
String fragmentationRule
```
      The fragmentation rules. CID (b, y), ETD (c, z*) or manual (user-defined (a comma-separated list of [abcxyz] or z* (z+1), e.g. manual:b,y,z)
    - maxPeakCount
```
Integer maxPeakCount
```
      The max number of peaks to use.
    - outputFormat
```
String outputFormat
```
      The output format.
- Class com.compomics.util.experiment.identification.identification_parameters.tool_specific.NovorParameters extends Object implements Serializable
  
  serialVersionUID:
  
  -1685402448885208852L
  - Serialized Fields
    - fragmentationMethod
```
String fragmentationMethod
```
      The fragmentation method.
    - massAnalyzer
```
String massAnalyzer
```
      The mass analyzer.
    - novorPtmMap
```
HashMap<K,V> novorPtmMap
```
      A map from the Novor PTM short name to the utilities PTM names. Novor PTM short name > utilities PTM name.
- Class com.compomics.util.experiment.identification.identification_parameters.tool_specific.OmssaParameters extends Object implements Serializable
  
  serialVersionUID:
  
  -6704164074092668637L
  - Serialized Fields
    - maxEValue
```
Double maxEValue
```
      Maximal e-value cut-off.
    - hitListLength
```
Integer hitListLength
```
      The maximal hit list length.
    - minimalChargeForMultipleChargedFragments
```
Charge minimalChargeForMultipleChargedFragments
```
      The minimal charge to be considered for multiple fragment charges.
    - minPeptideLength
```
Integer minPeptideLength
```
      The minimum peptide length (for semi and non tryptic searches).
    - maxPeptideLength
```
Integer maxPeptideLength
```
      The maximal peptide length (for semi and non tryptic searches).
    - removePrecursor
```
Boolean removePrecursor
```
      Indicates whether the precursor removal option is used.
    - scalePrecursor
```
Boolean scalePrecursor
```
      Indicates whether the precursor scaling option is used.
    - estimateCharge
```
Boolean estimateCharge
```
      Indicates whether the precursor charge estimation option.
    - selectedOutput
```
String selectedOutput
```
      The selected output type (see omssaOutputTypes).
    - memoryMappedSequenceLibraries
```
Boolean memoryMappedSequenceLibraries
```
      Map sequence in libraries in memory
    - numberOfItotopicPeaks
```
Integer numberOfItotopicPeaks
```
      Deprecated. now part of the general search parameters
      
      Number of isotopic peaks to consider.
    - neutronThreshold
```
Double neutronThreshold
```
      Mass after which a the exact mass of a neutron should be considered.
    - lowIntensityCutOff
```
Double lowIntensityCutOff
```
      Low intensity cut-off as percentage of the most intense peak.
    - highIntensityCutOff
```
Double highIntensityCutOff
```
      High intensity cut-off as percentage of the most intense peak.
    - intensityCutOffIncrement
```
Double intensityCutOffIncrement
```
      Intensity cut-off increment.
    - singleChargeWindow
```
Integer singleChargeWindow
```
      Window width for singly charged fragments.
    - doubleChargeWindow
```
Integer doubleChargeWindow
```
      Window width for doubly charged fragments.
    - nPeaksInSingleChargeWindow
```
Integer nPeaksInSingleChargeWindow
```
      Number of peaks allowed in a singly charged window.
    - nPeaksInDoubleChargeWindow
```
Integer nPeaksInDoubleChargeWindow
```
      Number of peaks allowed in a doubly charged window.
    - maxHitsPerSpectrumPerCharge
```
Integer maxHitsPerSpectrumPerCharge
```
      Maximum number of hits searched per spectrum and per charge.
    - nAnnotatedMostIntensePeaks
```
Integer nAnnotatedMostIntensePeaks
```
      Number of annotated most intense peaks required per spectrum.
    - minAnnotatedPeaks
```
Integer minAnnotatedPeaks
```
      Minimal number of annotated peaks required per spectrum.
    - minPeaks
```
Integer minPeaks
```
      Minimal number of peaks per spectrum.
    - cleaveNtermMethionine
```
Boolean cleaveNtermMethionine
```
      Cleave the N-term methionines.
    - maxMzLadders
```
Integer maxMzLadders
```
      Maximum length of m/z ladders.
    - maxFragmentCharge
```
Integer maxFragmentCharge
```
      Maximum fragment charge.
    - fractionOfPeaksForChargeEstimation
```
Double fractionOfPeaksForChargeEstimation
```
      Fraction of peaks below the precursor to estimate charge >1.
    - determineChargePlusOneAlgorithmically
```
Boolean determineChargePlusOneAlgorithmically
```
      Determine charge plus one algorithmically.
    - searchPositiveIons
```
Boolean searchPositiveIons
```
      Search positive ions (if false, negative ions).
    - minPrecPerSpectrum
```
Integer minPrecPerSpectrum
```
      Minimal precursor per spectrum.
    - searchForwardFragmentFirst
```
Boolean searchForwardFragmentFirst
```
      Search forward ions (b1) first.
    - searchRewindFragments
```
Boolean searchRewindFragments
```
      Search c-terminal ions.
    - maxFragmentPerSeries
```
Integer maxFragmentPerSeries
```
      Maximal number of fragment per series.
    - useCorrelationCorrectionScore
```
Boolean useCorrelationCorrectionScore
```
      Use correlation correction score.
    - consecutiveIonProbability
```
Double consecutiveIonProbability
```
      Probability of consecutive ions.
    - iterativeSequenceEvalue
```
Double iterativeSequenceEvalue
```
      E-value threshold to include a sequence in the iterative search (0 means all).
    - iterativeReplaceEvalue
```
Double iterativeReplaceEvalue
```
      E-value threshold to replace a hit in the iterative search (0 means replace if better).
    - iterativeSpectrumEvalue
```
Double iterativeSpectrumEvalue
```
      E-value threshold to include a spectrum in the iterative search (0 means all).
    - noProlineRuleSeries
```
ArrayList<E> noProlineRuleSeries
```
      ID numbers of ion series to apply no product ions at proline rule at. NOTE: not implemented for now.
    - ptmIndexes
```
HashMap<K,V> ptmIndexes
```
      Map of the OMSSA indexes used for user modifications in this search.
- Class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PepnovoParameters extends Object implements Serializable
  
  serialVersionUID:
  
  -8056507693211793829L
  - Serialized Fields
    - hitListLength
```
Integer hitListLength
```
      The maximal hit list length for PepNovo+. Max is 20.
    - estimateCharge
```
Boolean estimateCharge
```
      Indicates whether the precursor charge estimation option.
    - correctPrecursorMass
```
Boolean correctPrecursorMass
```
      Indicates whether the precursor mass shall be corrected.
    - discardLowQualitySpectra
```
Boolean discardLowQualitySpectra
```
      Indicates whether the low quality spectra shall be discarded.
    - fragmentationModel
```
String fragmentationModel
```
      PepNovo fragmentation model.
    - generateQuery
```
Boolean generateQuery
```
      Indicates whether a blast query shall be generated.
    - pepNovoPtmMap
```
Map<K,V> pepNovoPtmMap
```
      A map from the PepNovo PTM symbols to the utilities PTM names.
- Class com.compomics.util.experiment.identification.identification_parameters.tool_specific.PNovoParameters extends Object implements Serializable
  
  serialVersionUID:
  
  7525455518683797145L
  - Serialized Fields
    - numberOfPeptides
```
int numberOfPeptides
```
      The number of peptides reported.
    - lowerPrecursorMass
```
int lowerPrecursorMass
```
      The minimum precursor mass.
    - upperPrecursorMass
```
int upperPrecursorMass
```
      The maximum precursor mass.
    - acticationType
```
String acticationType
```
      The activation type (HCD, CID or ETD).
    - pNovoPtmMap
```
HashMap<K,V> pNovoPtmMap
```
      A map from the pNovo PTM character to the utilities PTM names. pNovo PTM character > utilities PTM name.
    - pNovoResidueMap
```
HashMap<K,V> pNovoResidueMap
```
      A map from the pNovo character to the original amino acids residue. pNovo PTM character > original amino acids residue.
- Class com.compomics.util.experiment.identification.identification_parameters.tool_specific.TideParameters extends Object implements Serializable
  
  serialVersionUID:
  
  1049197890002802776L
  - Serialized Fields
    - fastIndexFolderName
```
String fastIndexFolderName
```
      The name of the FASTA index folder.
    - maxVariablePtmsPerPeptide
```
Integer maxVariablePtmsPerPeptide
```
      The maximum number of variable modifications allowed on a single peptide. The default is no limit (set to null).
    - maxVariablePtmsPerTypePerPeptide
```
Integer maxVariablePtmsPerTypePerPeptide
```
      The maximum number of variable modifications of each type allowed on a single peptide.
    - minPeptideLength
```
Integer minPeptideLength
```
      The minimum peptide length.
    - maxPeptideLength
```
Integer maxPeptideLength
```
      The maximal peptide length.
    - minPrecursorMass
```
Double minPrecursorMass
```
      The minimum precursor mass considered.
    - maxPrecursorMass
```
Double maxPrecursorMass
```
      The maximum precursor mass considered.
    - decoyFormat
```
String decoyFormat
```
      The decoy format.
    - keepTerminalAminoAcids
```
String keepTerminalAminoAcids
```
      Keep terminal amino acids when creating decoys.
    - decoySeed
```
Integer decoySeed
```
      The seeed of the random number generator with the given unsigned integer when generating the decoy decoys. When given the string "time," the seed is set with the system time.
    - outputFolderName
```
String outputFolderName
```
      The name of the output folder (relative to the Tide working folder).
    - printPeptides
```
Boolean printPeptides
```
      If true, a list of all the peptides will be printed to the output folder.
    - verbosity
```
Integer verbosity
```
      The verbosity of the progress output: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info.
    - monoisotopicPrecursor
```
Boolean monoisotopicPrecursor
```
      If true, a monoisotopic precursor mass is used, false uses average.
    - clipNtermMethionine
```
Boolean clipNtermMethionine
```
      If true, starting methionine peptides will be included both with and without the starting M.
    - digestionType
```
String digestionType
```
      The enzyme digestion type: full-digest or partial-digest.
    - computeSpScore
```
Boolean computeSpScore
```
      If true, the SP score will be computed.
    - numberOfSpectrumMatches
```
Integer numberOfSpectrumMatches
```
      The maximum number of spectrum matches per peptide.
    - computeExactPValues
```
Boolean computeExactPValues
```
      If true, the exact p-values will be computed.
    - minSpectrumMz
```
Double minSpectrumMz
```
      The minimum spectrum m/z to search for.
    - maxSpectrumMz
```
Double maxSpectrumMz
```
      The maximum spectrum m/z to search for. Null if not maximum.
    - minSpectrumPeaks
```
Integer minSpectrumPeaks
```
      The minimum number of peaks in a spectrum for it to be searched.
    - spectrumCharges
```
String spectrumCharges
```
      The spectrum charges to search for: 1,2,3 or all. With 'all' every spectrum will be searched and spectra with multiple charge states will be searched once at each charge state. With 1, 2, or 3 only spectra with that charge will be searched.
    - removePrecursor
```
Boolean removePrecursor
```
      If true, the precursor peak will be removed. The range removed is specified by
    - removePrecursorTolerance
```
Double removePrecursorTolerance
```
      The tolerance in (Th) used when removing the precursor using removePrecursor.
    - printProgressIndicatorSize
```
Integer printProgressIndicatorSize
```
      Show search progress by printing every n spectra searched. Set to 0 to show no search progress.
    - useFlankingPeaks
```
Boolean useFlankingPeaks
```
      If true, the search includes flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak.
    - useNeutralLossPeaks
```
Boolean useNeutralLossPeaks
```
      Controls whether neutral loss ions are considered in the search. Two types of neutral losses are included and are applied only to singly charged b- and y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each neutral loss peak has intensity 1/5 of the primary peak.
    - mzBinWidth
```
Double mzBinWidth
```
      Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended.
    - mzBinOffset
```
Double mzBinOffset
```
      In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). The parameter must lie in the range 0 ≤ mz-bin-offset ≤ 1.
    - concatenateTargetDecoy
```
Boolean concatenateTargetDecoy
```
      If true, target and decoy search results are reported in a single file named "tide-search.txt," and only the top-scoring N matches (as specified via --top-match) are reported for each spectrum, irrespective of whether the matches involve target or decoy peptides.
    - storeSpectraFileName
```
String storeSpectraFileName
```
      Specify the name of the file where the binarized fragmentation spectra will be stored. Subsequent runs of crux tide-search will execute more quickly if provided with the spectra in binary format. The filename is specified relative to the current working directory, not the Crux output directory (as specified by --output-dir).
    - textOutput
```
Boolean textOutput
```
      If true, tab delimited text file output is generated.
    - sqtOutput
```
Boolean sqtOutput
```
      If true, SQT output is generated.
    - pepXmlOutput
```
Boolean pepXmlOutput
```
      If true, pepxml output is generated.
    - mzidOutput
```
Boolean mzidOutput
```
      If true, mzid output is generated.
    - pinOutput
```
Boolean pinOutput
```
      If true, Percolator input file is generated.
    - removeTempFolders
```
Boolean removeTempFolders
```
      If true, the tide output and index folders are removed when the search has completed.
- Class com.compomics.util.experiment.identification.identification_parameters.tool_specific.XtandemParameters extends Object implements Serializable
  
  serialVersionUID:
  
  -5898951075262732261L
  - Serialized Fields
    - maxEValue
```
Double maxEValue
```
      Maximal e-value cut-off.
    - outputResults
```
String outputResults
```
      The output results filter: all, valid or stochastic.
    - dynamicRange
```
Double dynamicRange
```
      The dynamic range for spectrum filtering. When the highest peak is given the dynamic range value peaks smaller than one are ignored. e.g. for 100 peaks with an intensity <1% of the highest peak are ignored.
    - nPeaks
```
Integer nPeaks
```
      The number of most intense peaks to consider.
    - minPrecursorMass
```
Double minPrecursorMass
```
      The minimum precursor mass.
    - minFragmentMz
```
Double minFragmentMz
```
      The minimum fragment mass.
    - minPeaksPerSpectrum
```
Integer minPeaksPerSpectrum
```
      The minimum number of peaks per spectrum.
    - proteinQuickAcetyl
```
Boolean proteinQuickAcetyl
```
      Indicates whether the protein quick acetylation option should be triggered.
    - quickPyrolidone
```
Boolean quickPyrolidone
```
      Indicates whether the quick pyrolidone option should be triggered.
    - refine
```
Boolean refine
```
      Triggers the refinement process.
    - refineSemi
```
Boolean refineSemi
```
      Sets whether semi enzymatic peptides should be search for during the refinement process.
    - refinePointMutations
```
Boolean refinePointMutations
```
      Sets whether point mutations should be search for during the refinement process.
    - refineSpectrumSynthesis
```
Boolean refineSpectrumSynthesis
```
      Sets whether the spectrum synthesis option should be used during the refinement process.
    - refineUnanticipatedCleavages
```
Boolean refineUnanticipatedCleavages
```
      Sets whether unexpected cleavages should be search for during the refinement process.
    - refineSnaps
```
Boolean refineSnaps
```
      Indicates whether snAPs should be used during the refinement process.
    - maximumExpectationValueRefinement
```
Double maximumExpectationValueRefinement
```
      The maximum expectation value for a hit to be considered during the refinement process.
    - potentialModificationsForFullRefinment
```
Boolean potentialModificationsForFullRefinment
```
      Sets the modifications to be used during the refinement process.
    - skylinePath
```
String skylinePath
```
      The skyline path.
    - outputProteins
```
Boolean outputProteins
```
      If true protein details will be exported to the to the result file.
    - outputSequences
```
boolean outputSequences
```
      If true protein sequences will be added to the protein details to the result file.
    - outputSpectra
```
Boolean outputSpectra
```
      If true spectra will be exported to the result file.
    - outputHistograms
```
Boolean outputHistograms
```
      If true histograms will be exported to the result file.
    - stpBias
```
Boolean stpBias
```
      Indicates whether the phospho stp bias option should be triggered.
    - useNoiseSuppression
```
Boolean useNoiseSuppression
```
      Triggers the noise suppression function. Note: ignored in X!Tandem VENGEANCE (2015.12.15) and newer.
    - proteinPtmComplexity
```
Double proteinPtmComplexity
```
      The value of the command "protein, ptm complexity" (C, a floating point number 0.0–12.0) sets the maximum number of variable modification alternatives that will be tested for a particular peptide. The number of alternatives is 2.0C. If this number is not specified, the default value C = 6.0 will be used.
Package com.compomics.util.experiment.identification.identifications
- Class com.compomics.util.experiment.identification.identifications.Ms2Identification extends Identification implements Serializable
  
  serialVersionUID:
  
  -7242302146506873391L
Package com.compomics.util.experiment.identification.matches
- Class com.compomics.util.experiment.identification.matches.IonMatch extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  5753142782728884464L
  - Serialized Fields
    - peak
```
Peak peak
```
      The matched peak.
    - ion
```
Ion ion
```
      The matching ion.
    - charge
```
Charge charge
```
      The supposed charge of the ion.
- Class com.compomics.util.experiment.identification.matches.ModificationMatch extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  7129515983284796207L
  - Serialized Fields
    - theoreticPtm
```
String theoreticPtm
```
      The theoretic modification name. The modification can be accessed via the PTM factory.
    - variable
```
boolean variable
```
      Is the modification variable?
    - modifiedSite
```
int modifiedSite
```
      The location in the sequence, 1 is the first residue.
    - confident
```
boolean confident
```
      A boolean indicating whether the modification is confidently localized onto the sequence. Not applicable to fixed or terminal modifications.
    - inferred
```
boolean inferred
```
      A boolean indicating whether the modification is inferred from another peptide. Not applicable to fixed or terminal modifications.
- Class com.compomics.util.experiment.identification.matches.PeptideMatch extends IdentificationMatch implements Serializable
  
  serialVersionUID:
  
  7195830246336841081L
  - Serialized Fields
    - theoreticPeptide
```
Peptide theoreticPeptide
```
      The theoretic peptide match.
    - matchKey
```
String matchKey
```
      The key of the match.
    - spectrumMatchesKeys
```
ArrayList<E> spectrumMatchesKeys
```
      All spectrum matches indexed by spectrum id. See Spectrum class.
    - isDecoy
```
Boolean isDecoy
```
      Is the peptide match a decoy hit?
- Class com.compomics.util.experiment.identification.matches.ProteinMatch extends IdentificationMatch implements Serializable
  
  serialVersionUID:
  
  -6061842447053092696L
  - Serialized Fields
    - theoreticProtein
```
ArrayList<E> theoreticProtein
```
      The matching protein(s) accessions.
    - mainMatch
```
String mainMatch
```
      The accession of the retained protein after protein inference resolution.
    - peptideMatchesKeys
```
ArrayList<E> peptideMatchesKeys
```
      The corresponding peptide match keys.
- Class com.compomics.util.experiment.identification.matches.SpectrumMatch extends IdentificationMatch implements Serializable
  
  serialVersionUID:
  
  3227760855215444318L
  - Serialized Fields
    - spectrumKey
```
String spectrumKey
```
      The index of the matched spectrum.
    - assumptionsMap
```
HashMap<K,V> assumptionsMap
```
      Map of the identification algorithm assumption: advocate number > score > assumptions.
    - tagAssumptionsMap
```
HashMap<K,V> tagAssumptionsMap
```
      A tag assumptions map. advocate number > assumptions.
    - tagAssumptionsMapKeySize
```
int tagAssumptionsMapKeySize
```
      The size of the keys used for the tag assumptions map.
    - bestPeptideAssumption
```
PeptideAssumption bestPeptideAssumption
```
      The best peptide assumption.
    - bestTagAsssumption
```
TagAssumption bestTagAsssumption
```
      The best tag assumption.
    - spectrumNumber
```
Integer spectrumNumber
```
      The spectrum number in the mgf file. Will be used in case the spectrum title does not match
Package com.compomics.util.experiment.identification.protein_inference.proteintree
- Class com.compomics.util.experiment.identification.protein_inference.proteintree.Node extends Object implements Serializable
  
  serialVersionUID:
  
  8936868785405252371L
  - Serialized Fields
    - depth
```
int depth
```
      The depth of the node in the tree.
    - accessions
```
HashMap<K,V> accessions
```
      List of accessions contained in this node.
    - termini
```
HashMap<K,V> termini
```
      In case of splitting, the terminal mappings are put here.
    - subtree
```
HashMap<K,V> subtree
```
      Subtree starting from this node.
    - listening
```
boolean listening
```
      Indicates whether the main thread is listening or preparing to wait.
Package com.compomics.util.experiment.identification.protein_sequences
- Class com.compomics.util.experiment.identification.protein_sequences.FastaIndex extends ExperimentObject implements Serializable
  - Serialized Fields
    - indexes
```
HashMap<K,V> indexes
```
      The indexes of the inspected FASTA file.
    - decoyAccessions
```
HashSet<E> decoyAccessions
```
      The decoy accessions.
    - fileName
```
String fileName
```
      The FASTA file name.
    - name
```
String name
```
      The name of the database.
    - lastModified
```
Long lastModified
```
      The last time the indexed file was modified.
    - isDefaultReversed
```
boolean isDefaultReversed
```
      In case decoy hits are found, check whether these are reversed versions of the target with default accession suffix.
    - nTarget
```
int nTarget
```
      Number of target sequences found in the database.
    - mainDatabaseType
```
Header.DatabaseType mainDatabaseType
```
      The main database type.
    - databaseTypes
```
HashMap<K,V> databaseTypes
```
      A map of all the database types and how often they occur.
    - version
```
String version
```
      The version of the database.
    - description
```
String description
```
      Description of the database.
    - accessionParsingRule
```
String accessionParsingRule
```
      The accession parsing rule.
    - concatenatedTargetDecoy
```
boolean concatenatedTargetDecoy
```
      Indicates whether the database is a concatenated target/decoy.
    - decoyTag
```
String decoyTag
```
      The tag used for decoy sequences.
    - speciesOccurrence
```
HashMap<K,V> speciesOccurrence
```
      The species occurrence in the database.
Package com.compomics.util.experiment.identification.spectrum_annotation
- Class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings extends Object implements Serializable
  
  serialVersionUID:
  
  -3739182405876385430L
  - Serialized Fields
    - yAxisZoomExcludesBackgroundPeaks
```
boolean yAxisZoomExcludesBackgroundPeaks
```
      If true, the automatic y-axis zoom excludes background peaks. False includes all peaks in the auto zoom.
    - showAllPeaks
```
boolean showAllPeaks
```
      If true, all peaks are shown, false displays the annotated peaks, and the non-annotated in the background.
    - intensityLimit
```
double intensityLimit
```
      The intensity percentile to consider for annotation. e.g. 0.75 means that the 25% most intense peaks will be annotated.
    - automaticAnnotation
```
boolean automaticAnnotation
```
      Shall automatic annotation be used.
    - selectedIonsMap
```
HashMap<K,V> selectedIonsMap
```
      The types of ions to annotate.
    - neutralLossesList
```
ArrayList<E> neutralLossesList
```
      List of neutral losses to annotate.
    - neutralLossesAuto
```
Boolean neutralLossesAuto
```
      If true neutral losses will be automatically deduced from the spectrum identification assumption.
    - reporterIons
```
Boolean reporterIons
```
      If true reporter ions will be annotated by default.
    - relatedIons
```
Boolean relatedIons
```
      If true related ions will be annotated by default.
    - fragmentIonAccuracy
```
double fragmentIonAccuracy
```
      Fragment ion accuracy used for peak matching.
    - fragmentIonPpm
```
Boolean fragmentIonPpm
```
      Indicates whether the fragment ion accuracy is in ppm.
    - showForwardIonDeNovoTags
```
boolean showForwardIonDeNovoTags
```
      If true, the automatic forward ion de novo tags are shown.
    - showRewindIonDeNovoTags
```
boolean showRewindIonDeNovoTags
```
      If true, the automatic rewind ion de novo tags are shown.
    - deNovoCharge
```
int deNovoCharge
```
      The charge for the fragment ions in the de novo sequencing.
    - highResolutionAnnotation
```
Boolean highResolutionAnnotation
```
      If there are more than one matching peak for a given annotation setting this value to true results in the most accurate peak being annotated, while setting this to false annotates the most intense peak.
- Class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap extends Object implements Serializable
  
  serialVersionUID:
  
  -4690159937753713106L
  - Serialized Fields
    - bBoundaries
```
HashMap<K,V> bBoundaries
```
      Deprecated. use String indexes instead
      
      Map indicating for each neutral loss when they should start being accounted for the forward ions (b ions for instance).
    - yBoundaries
```
HashMap<K,V> yBoundaries
```
      Deprecated. use String indexes instead
      
      Map indicating for each neutral loss when they should start being accounted for the reverse ions (y ions for instance).
    - forwardBoundaries
```
HashMap<K,V> forwardBoundaries
```
      Map indicating for each neutral loss when they should start being accounted for the forward ions (b ions for instance).
    - rewindBoundaries
```
HashMap<K,V> rewindBoundaries
```
      Map indicating for each neutral loss when they should start being accounted for the reverse ions (y ions for instance).
Package com.compomics.util.experiment.identification.spectrum_assumptions
- Class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption extends SpectrumIdentificationAssumption implements Serializable
  
  serialVersionUID:
  
  3606509518581203063L
  - Serialized Fields
    - peptide
```
Peptide peptide
```
      The theoretic peptide.
- Class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption extends SpectrumIdentificationAssumption implements Serializable
  
  serialVersionUID:
  
  8514376202742537298L
  - Serialized Fields
    - tag
```
Tag tag
```
      List of mass gaps.
Package com.compomics.util.experiment.io.identifications
- Class com.compomics.util.experiment.io.identifications.MzIdentMLIdfileSearchParametersConverter extends ExperimentObject implements Serializable
Package com.compomics.util.experiment.io.identifications.idfilereaders
- Class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader extends ExperimentObject implements Serializable
  - Serialized Fields
    - resultsFile
```
File resultsFile
```
      The Andromeda result file to parse.
    - fileName
```
String fileName
```
      The name of the Andromeda result file.
- Class com.compomics.util.experiment.io.identifications.idfilereaders.DirecTagIdfileReader extends ExperimentObject implements Serializable
  - Serialized Fields
    - tagsGenerator
```
String tagsGenerator
```
      The name of the tags generator used to create the file.
    - tagsGeneratorVersion
```
String tagsGeneratorVersion
```
      The version of the tags generator.
    - copyRight
```
String copyRight
```
      The copyright.
    - license
```
String license
```
      The license.
    - timeStart
```
String timeStart
```
      The time of sequencing start.
    - timeEnd
```
String timeEnd
```
      The time of sequencing end.
    - taggingTimeSeconds
```
Double taggingTimeSeconds
```
      The tagging time.
    - nProcessingNode
```
Integer nProcessingNode
```
      The number of processing nodes.
    - inputFile
```
String inputFile
```
      The file used as input.
    - tagsParameters
```
HashMap<K,V> tagsParameters
```
      The tags parameters in a map.
    - spectrumLineContent
```
HashMap<K,V> spectrumLineContent
```
      Returns the content of the columns for a spectrum line. Name > index in the column.
    - tagLineContent
```
HashMap<K,V> tagLineContent
```
      Returns the content of the columns for a tag line. Name > index in the column.
    - spectrumIndexes
```
HashMap<K,V> spectrumIndexes
```
      The indexes at which are the spectra. Spectrum ID > index.
    - tagIndexes
```
HashMap<K,V> tagIndexes
```
      The indexes at which are the tags. Spectrum ID > indexes.
    - bufferedRandomAccessFile
```
uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile
```
      The random access file used.
    - tagFile
```
File tagFile
```
      The file inspected.
    - spectrumFactory
```
SpectrumFactory spectrumFactory
```
      The spectrum factory used to retrieve spectrum titles.
    - cTermCorrection
```
double cTermCorrection
```
      The mass to add to the C-terminal gap so that is corresponds to a peptide fragment.
    - nTermCorrection
```
double nTermCorrection
```
      The mass to add to the N-terminal gap so that is corresponds to a peptide fragment.
    - tagsMap
```
HashMap<K,V> tagsMap
```
      Map of the tags found indexed by amino acid sequence.
    - direcTagParameters
```
DirecTagParameters direcTagParameters
```
      The DirecTag parameters.
    - dynamicModsResidues
```
HashMap<K,V> dynamicModsResidues
```
      The residues modified by the different PTMs in the DynamicMods tag. Indexed on the symbol used to represent the PTM.
- Class com.compomics.util.experiment.io.identifications.idfilereaders.MsAmandaIdfileReader extends ExperimentObject implements Serializable
  - Serialized Fields
    - softwareName
```
String softwareName
```
      The software name.
    - softwareVersion
```
String softwareVersion
```
      The softwareVersion.
    - msAmandaCsvFile
```
File msAmandaCsvFile
```
      The MS Amanda csv file.
- Class com.compomics.util.experiment.io.identifications.idfilereaders.MzIdentMLIdfileReader extends ExperimentObject implements Serializable
  - Serialized Fields
    - tempSoftwareVersions
```
HashMap<K,V> tempSoftwareVersions
```
      List of software used to create this file according to the file.
    - softwareVersions
```
HashMap<K,V> softwareVersions
```
      The list of software according to the scores found.
    - mzIdentMLFile
```
File mzIdentMLFile
```
      The mzIdentML file.
    - mzIdentMLFileName
```
String mzIdentMLFileName
```
      The name of the mzIdentML file.
    - unmarshaller
```
uk.ac.ebi.jmzidml.xml.io.MzIdentMLUnmarshaller unmarshaller
```
      The mzIdentML unmarshaller.
    - fixedModifications
```
ArrayList<E> fixedModifications
```
      The names of the fixed modifications.
    - tempPeptideMap
```
HashMap<K,V> tempPeptideMap
```
      A temporary peptide map used by the custom parser only. Key: peptide id/ref, element: the peptide object.
    - spectrumFileNameMap
```
HashMap<K,V> spectrumFileNameMap
```
      A map of the spectrum file names. Key: spectrum id/ref, element: spectrum file name.
    - fixedModificationsCustomParser
```
ArrayList<E> fixedModificationsCustomParser
```
      The list of fixed modifications extracted by the custom parser.
    - sequenceMatchingPreferences
```
SequenceMatchingPreferences sequenceMatchingPreferences
```
      The sequence matching parameters.
    - expandAaCombinations
```
boolean expandAaCombinations
```
      Set if the amino acid combinations are to be expanded. For example replacing X's.
    - useCustomParser
```
boolean useCustomParser
```
      Set if the custom parser are to be used. If false, the jmzidentml parser is used.
    - hasDenovoTags
```
boolean hasDenovoTags
```
      Boolean indicating whether the mzId file contains de novo tags.
- Class com.compomics.util.experiment.io.identifications.idfilereaders.NovorIdfileReader extends ExperimentObject implements Serializable
  - Serialized Fields
    - softwareName
```
String softwareName
```
      The software name.
    - softwareVersion
```
String softwareVersion
```
      The softwareVersion.
    - novorCsvFile
```
File novorCsvFile
```
      The Novor csv file.
    - tagsMap
```
HashMap<K,V> tagsMap
```
      Map of the tags found indexed by amino acid sequence.
    - spectrumFactory
```
SpectrumFactory spectrumFactory
```
      The spectrum factory used to retrieve spectrum titles.
- Class com.compomics.util.experiment.io.identifications.idfilereaders.PepNovoIdfileReader extends ExperimentObject implements Serializable
  - Serialized Fields
    - index
```
HashMap<K,V> index
```
      A map of all spectrum titles and the associated index in the random access file.
    - bufferedRandomAccessFile
```
uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile
```
      The result file in random access.
    - fileName
```
String fileName
```
      The name of the result file.
    - cTermCorrection
```
double cTermCorrection
```
      The mass to add to the C-terminal gap so that is corresponds to a peptide fragment.
    - nTermCorrection
```
double nTermCorrection
```
      The mass to add to the N-terminal gap so that is corresponds to a peptide fragment.
    - tagsMap
```
HashMap<K,V> tagsMap
```
      Map of the tags found indexed by amino acid sequence.
- Class com.compomics.util.experiment.io.identifications.idfilereaders.PNovoIdfileReader extends ExperimentObject implements Serializable
  - Serialized Fields
    - index
```
HashMap<K,V> index
```
      A map of all spectrum titles and the associated index in the random access file.
    - bufferedRandomAccessFile
```
uk.ac.ebi.pride.tools.braf.BufferedRandomAccessFile bufferedRandomAccessFile
```
      The result file in random access.
    - fileName
```
String fileName
```
      The name of the result file.
    - tagsMap
```
HashMap<K,V> tagsMap
```
      Map of the tags found indexed by amino acid sequence.
- Class com.compomics.util.experiment.io.identifications.idfilereaders.TideIdfileReader extends ExperimentObject implements Serializable
  - Serialized Fields
    - softwareName
```
String softwareName
```
      The software name.
    - softwareVersion
```
String softwareVersion
```
      The softwareVersion.
    - tideTsvFile
```
File tideTsvFile
```
      The Tide tsv file.
    - spectrumFactory
```
SpectrumFactory spectrumFactory
```
      The spectrum factory used to retrieve spectrum titles.
Package com.compomics.util.experiment.io.massspectrometry
- Class com.compomics.util.experiment.io.massspectrometry.MgfIndex extends ExperimentObject implements Serializable
  - Serialized Fields
    - indexMap
```
HashMap<K,V> indexMap
```
      The map of all indexes: spectrum title > index in the file.
    - spectrumNumberIndexMap
```
HashMap<K,V> spectrumNumberIndexMap
```
      A map of all the spectrum titles and which rank they have in the file, i.e., the first spectrum has rank 0, the second rank 1, etc.
    - spectrumTitles
```
ArrayList<E> spectrumTitles
```
      List of spectrum titles.
    - duplicatedSpectrumTitles
```
HashMap<K,V> duplicatedSpectrumTitles
```
      Map of duplicated spectrum titles and how often they are duplicated.
    - precursorMzMap
```
HashMap<K,V> precursorMzMap
```
      Map of the precursor mz values.
    - fileName
```
String fileName
```
      The name of the indexed file.
    - lastModified
```
Long lastModified
```
      The last time the indexed file was modified.
    - maxRT
```
Double maxRT
```
      The maximum RT found in the spectra.
    - minRT
```
Double minRT
```
      The minimum RT found in the spectra.
    - maxMz
```
Double maxMz
```
      The maximal m/z in all precursors of the file.
    - maxIntensity
```
Double maxIntensity
```
      The maximal precursor intensity of the file.
    - maxCharge
```
Integer maxCharge
```
      The maximal charge.
    - maxPeakCount
```
Integer maxPeakCount
```
      The maximal peak count.
    - peakPicked
```
Boolean peakPicked
```
      Indicates if the spectra seem to be peak picked or not. A null value indicated that the check for peak picking was not performed.
    - spectrumCount
```
Integer spectrumCount
```
      Returns the number of spectra in the file as counted by the begin ions tags. Null if not set.
    - precursorChargesMissing
```
Boolean precursorChargesMissing
```
      Indicates if there are spectra where the precursor charge is missing. A null value indicated that the check was not performed.
Package com.compomics.util.experiment.massspectrometry
- Class com.compomics.util.experiment.massspectrometry.Charge extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -7119215126058492261L
  - Serialized Fields
    - sign
```
int sign
```
      Sign of the charge according to the static fields.
    - value
```
int value
```
      Value of the charge.
- Class com.compomics.util.experiment.massspectrometry.MS1Spectrum extends Spectrum implements Serializable
  
  serialVersionUID:
  
  -7328539274222920271L
- Class com.compomics.util.experiment.massspectrometry.MSnSpectrum extends Spectrum implements Serializable
  
  serialVersionUID:
  
  -7144961253807359274L
  - Serialized Fields
    - precursor
```
Precursor precursor
```
      The precursor.
- Class com.compomics.util.experiment.massspectrometry.Peak extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -7425947046833405676L
  - Serialized Fields
    - mz
```
double mz
```
      The mass over charge ratio of the peak.
    - rt
```
double rt
```
      The retention time when the peak was recorded.
    - intensity
```
double intensity
```
      The intensity of the peak.
- Class com.compomics.util.experiment.massspectrometry.Precursor extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -2711244157697138296L
  - Serialized Fields
    - rt
```
double rt
```
      The retention time when the precursor was isolated.
    - rtMin
```
Double rtMin
```
      In case an retention time window is given, the minimum.
    - rtMax
```
Double rtMax
```
      In case an retention time window is given, the maximum.
    - mz
```
double mz
```
      The measured m/z of the precursor.
    - intensity
```
double intensity
```
      The measured intensity of the precursor.
    - possibleCharges
```
ArrayList<E> possibleCharges
```
      The charge of the precursor.
- Class com.compomics.util.experiment.massspectrometry.Spectrum extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  7152424141470431489L
  - Serialized Fields
    - spectrumTitle
```
String spectrumTitle
```
      Spectrum title.
    - fileName
```
String fileName
```
      Spectrum file name.
    - level
```
int level
```
      The MS level.
    - peakList
```
HashMap<K,V> peakList
```
      mz indexed Peak list.
    - intensityPeakMap
```
HashMap<K,V> intensityPeakMap
```
      Intensity indexed Peak map.
    - scanNumber
```
String scanNumber
```
      Scan number or range.
    - scanStartTime
```
double scanStartTime
```
      The time point when the spectrum was recorded (scan start time in mzML files).
    - jFreePeakList
```
double[][] jFreePeakList
```
      The peak list as an array directly plottable by JFreeChart.
    - mzValuesAsArray
```
double[] mzValuesAsArray
```
      The mz values as array. Null until set by the getter.
    - mzOrdered
```
Boolean mzOrdered
```
      Boolean indicating whether the mzValuesAsArray is sorted.
    - intensityValuesAsArray
```
double[] intensityValuesAsArray
```
      The intensity values as array. Null until set by the getter.
    - intensityValuesNormaizedAsArray
```
double[] intensityValuesNormaizedAsArray
```
      The intensity values as array normalized against the most intense peak. Null until set by the getter.
    - mzAndIntensityAsArray
```
double[][] mzAndIntensityAsArray
```
      The mz and intensity values as array. Null until set by the getter.
    - totalIntensity
```
Double totalIntensity
```
      The total intensity.
    - maxIntensity
```
Double maxIntensity
```
      The maximal intensity.
    - maxMz
```
Double maxMz
```
      The maximal m/z.
    - minMz
```
Double minMz
```
      The minimal m/z.
Package com.compomics.util.experiment.massspectrometry.proteowizard.gui
- Class com.compomics.util.experiment.massspectrometry.proteowizard.gui.MsConvertParametersDialog extends JDialog implements Serializable
  - Serialized Fields
    - canceled
```
boolean canceled
```
      Boolean indicating whether the editing was canceled.
    - filters
```
HashMap<K,V> filters
```
      Map of the filters to use.
    - filterIndexes
```
ArrayList<E> filterIndexes
```
      List of the indexes of the filters to use.
    - lastSelectedFolder
```
String lastSelectedFolder
```
      The selected folder.
    - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
      The utilities preferences.
    - addFilterMenu
```
JMenu addFilterMenu
```
    - backgourdPanel
```
JPanel backgourdPanel
```
    - browseButton
```
JButton browseButton
```
    - cancelButton
```
JButton cancelButton
```
    - filterHelpLabel
```
JLabel filterHelpLabel
```
    - filtersLbl
```
JLabel filtersLbl
```
    - filtersPopupMenu
```
JPopupMenu filtersPopupMenu
```
    - filtersTable
```
JTable filtersTable
```
    - filtersTableScrollPane
```
JScrollPane filtersTableScrollPane
```
    - folderHelpLabel
```
JLabel folderHelpLabel
```
    - installationJTextField
```
JTextField installationJTextField
```
    - installationPanel
```
JPanel installationPanel
```
    - msconvertParameters
```
JPanel msconvertParameters
```
    - okButton
```
JButton okButton
```
    - outputFormatCmb
```
JComboBox<E> outputFormatCmb
```
    - outputFormatLbl
```
JLabel outputFormatLbl
```
    - removeFilterMenuItem
```
JMenuItem removeFilterMenuItem
```
Package com.compomics.util.experiment.normalization
- Class com.compomics.util.experiment.normalization.NormalizationFactors extends Object implements Serializable
  - Serialized Fields
    - proteinNormalizationFactors
```
HashMap<K,V> proteinNormalizationFactors
```
      List of protein level normalization factors. The key should be the same as for the sample assignment.
    - proteinUniqueNormalizationFactors
```
HashMap<K,V> proteinUniqueNormalizationFactors
```
      List of unique protein level normalization factors. The key should be the same as for the sample assignment.
    - proteinSharedNormalizationFactors
```
HashMap<K,V> proteinSharedNormalizationFactors
```
      List of shared protein level normalization factors. The key should be the same as for the sample assignment.
    - peptideNormalizationFactors
```
HashMap<K,V> peptideNormalizationFactors
```
      List of peptide level normalization factors. The key should be the same as for the sample assignment.
    - psmNormalizationFactors
```
HashMap<K,V> psmNormalizationFactors
```
      List of PSM level normalization factors. The key should be the same as for the sample assignment.
Package com.compomics.util.experiment.personalization
- Class com.compomics.util.experiment.personalization.ExperimentObject extends Object implements Serializable
  
  serialVersionUID:
  
  1929697552061121072L
  - Serialized Fields
    - urParams
```
HashMap<K,V> urParams
```
      Map containing user refinement parameters.
Package com.compomics.util.experiment.quantification
- Class com.compomics.util.experiment.quantification.Quantification extends ExperimentObject implements Serializable
  - Serialized Fields
    - methodUsed
```
Quantification.QuantificationMethod methodUsed
```
      The quantification method used
Package com.compomics.util.experiment.quantification.reporterion
- Class com.compomics.util.experiment.quantification.reporterion.Reagent extends Object implements Serializable
  - Serialized Fields
    - name
```
String name
```
      The name of the reagent.
    - reporterIon
```
ReporterIon reporterIon
```
      The reporter ion to look for in the spectrum.
    - minus2
```
double minus2
```
      The isotopic correction factor at -2Da.
    - minus1
```
double minus1
```
      . The isotopic correction factor at -1Da.
    - ref
```
double ref
```
      The monoisotopic correction factor.
    - plus1
```
double plus1
```
      The isotopic correction factor at +1Da.
    - plus2
```
double plus2
```
      The isotopic correction factor at +2Da.
- Class com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification extends Quantification implements Serializable
  - Serialized Fields
    - sampleAssignement
```
HashMap<K,V> sampleAssignement
```
      The sample assignment to the various reporter ions indexed by their name.
    - controlSamples
```
ArrayList<E> controlSamples
```
      List of control samples. The index should be the same as for the sample assignment.
    - reporterMethod
```
ReporterMethod reporterMethod
```
      The reporter method.
    - normalizationFactors
```
NormalizationFactors normalizationFactors
```
      The normalization factors.
- Class com.compomics.util.experiment.quantification.reporterion.ReporterMethod extends Object implements Serializable
  - Serialized Fields
    - reagents
```
HashMap<K,V> reagents
```
      Map of the reagents. Reagent name > reagent
    - name
```
String name
```
      The name of the method.
    - reporterIonsMap
```
HashMap<K,V> reporterIonsMap
```
      The names of the reporter ions in this method
- Class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory extends ExperimentObject implements Serializable
  - Serialized Fields
    - methodsNames
```
ArrayList<E> methodsNames
```
      The reporter methods names.
    - methods
```
HashMap<K,V> methods
```
      The reporter methods.
Package com.compomics.util.experiment.refinementparameters
- Class com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails extends Object implements Serializable
  - Serialized Fields
    - rankScore
```
double rankScore
```
      The PepNovo rank score.
    - mH
```
double mH
```
      The PepNovo M+H.
Package com.compomics.util.experiment.units
- Class com.compomics.util.experiment.units.UnitOfMeasurement extends Object implements Serializable
  
  serialVersionUID:
  
  607774099178502699L
  - Serialized Fields
    - fullName
```
String fullName
```
      The full name of the unit.
    - abbreviation
```
String abbreviation
```
      The abbreviated name of the unit.
    - metricsPrefix
```
MetricsPrefix metricsPrefix
```
      The metrics prefix.
Package com.compomics.util.general
- Class com.compomics.util.general.UnknownElementMassException extends Exception implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - element
```
String element
```
      The element symbol that was not recognized.
Package com.compomics.util.general.servlet
- Class com.compomics.util.general.servlet.MassCalcServlet extends javax.servlet.http.HttpServlet implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
Package com.compomics.util.gui
- Class com.compomics.util.gui.AaMass extends JDialog implements Serializable
  - Serialized Fields
    - daLbl
```
JLabel daLbl
```
    - massLbl
```
JLabel massLbl
```
    - massTxt
```
JTextField massTxt
```
    - sequenceLbl
```
JLabel sequenceLbl
```
    - sequenceTxt
```
JTextField sequenceTxt
```
- Class com.compomics.util.gui.AminoAcidPatternDialog extends JDialog implements Serializable
  - Serialized Fields
    - pattern
```
AminoAcidPattern pattern
```
      The pattern displayed.
    - editable
```
boolean editable
```
      A boolean indicating whether the pattern can be edited.
    - cancel
```
boolean cancel
```
      A boolean indicating whether the used clicked the cancel button.
    - patternDesignTableToolTips
```
ArrayList<E> patternDesignTableToolTips
```
      The pattern design table column header tooltips.
    - exampleSequence
```
String exampleSequence
```
      The example sequence.
    - addJMenuItem
```
JMenuItem addJMenuItem
```
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - deleteSelectedRowJMenuItem
```
JMenuItem deleteSelectedRowJMenuItem
```
    - exampleLabel
```
JLabel exampleLabel
```
    - jSeparator3
```
JSeparator jSeparator3
```
    - jSeparator4
```
JSeparator jSeparator4
```
    - moveDownJMenuItem
```
JMenuItem moveDownJMenuItem
```
    - moveUpJMenuItem
```
JMenuItem moveUpJMenuItem
```
    - okButton
```
JButton okButton
```
    - patternDesignPanel
```
JPanel patternDesignPanel
```
    - patternDesignScrollPane
```
JScrollPane patternDesignScrollPane
```
    - patternDesignTable
```
JTable patternDesignTable
```
    - patternTestEditorPane
```
JEditorPane patternTestEditorPane
```
    - patternTestJScrollPane
```
JScrollPane patternTestJScrollPane
```
    - popupJMenu
```
JPopupMenu popupJMenu
```
    - rightClickHelpLabel
```
JLabel rightClickHelpLabel
```
    - testPanel
```
JPanel testPanel
```
- Class com.compomics.util.gui.DummyFrame extends JFrame implements Serializable
- Class com.compomics.util.gui.ExportFormatSelectionDialog extends JDialog implements Serializable
  - Serialized Fields
    - canceled
```
boolean canceled
```
      True if the user canceled the dialog.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - buttonGroup
```
ButtonGroup buttonGroup
```
    - cancelJButton
```
JButton cancelJButton
```
    - excelJRadioButton
```
JRadioButton excelJRadioButton
```
    - exportJButton
```
JButton exportJButton
```
    - formatTypeJPanel
```
JPanel formatTypeJPanel
```
    - textJRadioButton
```
JRadioButton textJRadioButton
```
- Class com.compomics.util.gui.FlamableJFrame extends JFrame implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
- Class com.compomics.util.gui.JExceptionDialog extends JDialog implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iMessages
```
String[] iMessages
```
    - iThrowable
```
Throwable iThrowable
```
- Class com.compomics.util.gui.JFrameForBytes extends JFrame implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iData
```
byte[] iData
```
      This byte[] is the data that will be shown.
    - txtData
```
JTextArea txtData
```
    - btnUnzip
```
JButton btnUnzip
```
    - btnSave
```
JButton btnSave
```
- Class com.compomics.util.gui.JLabelAndComponentPanel extends JPanel implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
- Class com.compomics.util.gui.JTableForDB extends AlternateRowColoursJTable implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iDateTimeFormat
```
String iDateTimeFormat
```
      This String contains the date and time format.
    - iFrames
```
Vector<E> iFrames
```
      This Vector holds the references to all the tables that have been created during the life cycle.
- Class com.compomics.util.gui.PrivacySettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    - normalIcon
```
Image normalIcon
```
      The normal dialog icon.
    - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
      The user preferences.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - confidentialLabel
```
JLabel confidentialLabel
```
    - okButton
```
JButton okButton
```
    - openDialogHelpJButton
```
JButton openDialogHelpJButton
```
    - settingsPanel
```
JPanel settingsPanel
```
    - toolStartCheck
```
JCheckBox toolStartCheck
```
    - updatesCheck
```
JCheckBox updatesCheck
```
- Class com.compomics.util.gui.SampleSelection extends JDialog implements Serializable
  - Serialized Fields
    - samples
```
String[] samples
```
      The samples found.
    - choice
```
String choice
```
      The choice of the user.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - comboBox
```
JComboBox<E> comboBox
```
    - jLabel1
```
JLabel jLabel1
```
    - jLabel2
```
JLabel jLabel2
```
    - okButton
```
JButton okButton
```
    - titleLbl
```
JLabel titleLbl
```
- Class com.compomics.util.gui.VennDiagramDialog extends JDialog implements Serializable
  - Serialized Fields
    - dialogParent
```
Frame dialogParent
```
      The dialog parent.
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      The last selected folder.
    - normalIcon
```
Image normalIcon
```
      The normal icon for the parent dialog.
    - waitingIcon
```
Image waitingIcon
```
      The icon to use when busy.
    - vennDiagramPanel
```
VennDiagramPanel vennDiagramPanel
```
      The Venn diagram panel.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - contextMenuPlotBackgroundPanel
```
JPanel contextMenuPlotBackgroundPanel
```
    - dataPanel
```
JPanel dataPanel
```
    - datasetAColorJPanel
```
JPanel datasetAColorJPanel
```
    - datasetAScrollPane
```
JScrollPane datasetAScrollPane
```
    - datasetATextArea
```
JTextArea datasetATextArea
```
    - datasetATextField
```
JTextField datasetATextField
```
    - datasetBColorJPanel
```
JPanel datasetBColorJPanel
```
    - datasetBScrollPane
```
JScrollPane datasetBScrollPane
```
    - datasetBTextArea
```
JTextArea datasetBTextArea
```
    - datasetBTextField
```
JTextField datasetBTextField
```
    - datasetCColorJPanel
```
JPanel datasetCColorJPanel
```
    - datasetCScrollPane
```
JScrollPane datasetCScrollPane
```
    - datasetCTextArea
```
JTextArea datasetCTextArea
```
    - datasetCTextField
```
JTextField datasetCTextField
```
    - datasetDColorJPanel
```
JPanel datasetDColorJPanel
```
    - datasetDScrollPane
```
JScrollPane datasetDScrollPane
```
    - datasetDTextArea
```
JTextArea datasetDTextArea
```
    - datasetDTextField
```
JTextField datasetDTextField
```
    - exportPlotMenuItem
```
JMenuItem exportPlotMenuItem
```
    - fontSizeMenu
```
JMenu fontSizeMenu
```
    - jSeparator1
```
JPopupMenu.Separator jSeparator1
```
    - jSeparator2
```
JPopupMenu.Separator jSeparator2
```
    - legendCheckBoxMenuItem
```
JCheckBoxMenuItem legendCheckBoxMenuItem
```
    - legendFontSizeMenuItem
```
JMenuItem legendFontSizeMenuItem
```
    - legendLocationMenuItem
```
JMenuItem legendLocationMenuItem
```
    - plotHelpJButton
```
JButton plotHelpJButton
```
    - plotLayeredPane
```
JLayeredPane plotLayeredPane
```
    - plotOptionsJButton
```
JButton plotOptionsJButton
```
    - plotPopupMenu
```
JPopupMenu plotPopupMenu
```
    - valueFontSizeMenuItem
```
JMenuItem valueFontSizeMenuItem
```
    - xyPlotPanel
```
JPanel xyPlotPanel
```
- Class com.compomics.util.gui.VennDiagramLegendLocationDialog extends JDialog implements Serializable
  - Serialized Fields
    - vennDiagramDialog
```
VennDiagramDialog vennDiagramDialog
```
      The VennDiagramDialog parent.
    - legendShiftSize
```
double legendShiftSize
```
      Legend shift size.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - datasetALabel
```
JLabel datasetALabel
```
    - datasetBLabel
```
JLabel datasetBLabel
```
    - datasetCLabel
```
JLabel datasetCLabel
```
    - datasetDLabel
```
JLabel datasetDLabel
```
    - downDatasetAButton
```
JButton downDatasetAButton
```
    - downDatasetBButton
```
JButton downDatasetBButton
```
    - downDatasetCButton
```
JButton downDatasetCButton
```
    - downDatasetDButton
```
JButton downDatasetDButton
```
    - leftDatasetAButton
```
JButton leftDatasetAButton
```
    - leftDatasetBButton
```
JButton leftDatasetBButton
```
    - leftDatasetCButton
```
JButton leftDatasetCButton
```
    - leftDatasetDButton
```
JButton leftDatasetDButton
```
    - legendLocationPanel
```
JPanel legendLocationPanel
```
    - okButton
```
JButton okButton
```
    - rightDatasetAButton
```
JButton rightDatasetAButton
```
    - rightDatasetBButton
```
JButton rightDatasetBButton
```
    - rightDatasetCButton
```
JButton rightDatasetCButton
```
    - rightDatasetDButton
```
JButton rightDatasetDButton
```
    - shiftSizeLabel
```
JLabel shiftSizeLabel
```
    - shiftSizeSpinner
```
JSpinner shiftSizeSpinner
```
    - upDatasetAButton
```
JButton upDatasetAButton
```
    - upDatasetBButton
```
JButton upDatasetBButton
```
    - upDatasetCButton
```
JButton upDatasetCButton
```
    - upDatasetDButton
```
JButton upDatasetDButton
```
- Class com.compomics.util.gui.VennDiagramPanel extends JPanel implements Serializable
  - Serialized Fields
    - tooltipToDatasetMap
```
HashMap<K,V> tooltipToDatasetMap
```
      Map each dataset tooltip back to the given dataset.
    - currentVennDiagramType
```
VennDiagramPanel.VennDiagramType currentVennDiagramType
```
      The current Venn diagram type.
    - vennDiagramResults
```
HashMap<K,V> vennDiagramResults
```
      The current Venn diagram results/data.
    - groupNames
```
HashMap<K,V> groupNames
```
      The current Venn diagram group names.
    - chartPanel
```
org.jfree.chart.ChartPanel chartPanel
```
      The chart panel.
    - fontSizeValues
```
int fontSizeValues
```
      The font size to use for the values.
    - fontSizeLegend
```
int fontSizeLegend
```
      The font size to use for the legend.
    - showLegend
```
boolean showLegend
```
      If true, the legend is shown.
    - legendDatasetAThreeWay
```
no.uib.jsparklines.data.XYDataPoint legendDatasetAThreeWay
```
      The legend location of Dataset A in a one to three way Venn diagram.
    - legendDatasetBThreeWay
```
no.uib.jsparklines.data.XYDataPoint legendDatasetBThreeWay
```
      The legend location of Dataset B in a one to three way Venn diagram.
    - legendDatasetCThreeWay
```
no.uib.jsparklines.data.XYDataPoint legendDatasetCThreeWay
```
      The legend location of Dataset C in a one to three way Venn diagram.
    - legendDatasetAFourWay
```
no.uib.jsparklines.data.XYDataPoint legendDatasetAFourWay
```
      The legend location of Dataset A in a four-way Venn diagram.
    - legendDatasetBFourWay
```
no.uib.jsparklines.data.XYDataPoint legendDatasetBFourWay
```
      The legend location of Dataset B in a four-way Venn diagram.
    - legendDatasetCFourWay
```
no.uib.jsparklines.data.XYDataPoint legendDatasetCFourWay
```
      The legend location of Dataset C in a four-way Venn diagram.
    - legendDatasetDFourWay
```
no.uib.jsparklines.data.XYDataPoint legendDatasetDFourWay
```
      The legend location of Dataset D in a four-way Venn diagram.
    - datasetAColor
```
Color datasetAColor
```
      The color for dataset A.
    - datasetBColor
```
Color datasetBColor
```
      The color for dataset B.
    - datasetCColor
```
Color datasetCColor
```
      The color for dataset C.
    - datasetDColor
```
Color datasetDColor
```
      The color for dataset D.
    - plotPanel
```
JPanel plotPanel
```
- Class com.compomics.util.gui.VisibleTableColumnsDialog extends JDialog implements Serializable
  - Serialized Fields
    - visibleTableColumnsDialogParent
```
VisibleTableColumnsDialogParent visibleTableColumnsDialogParent
```
      The VisibleTableColumnsDialogParent.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - deselectAllMenuItem
```
JMenuItem deselectAllMenuItem
```
    - okButton
```
JButton okButton
```
    - selectAllMenuItem
```
JMenuItem selectAllMenuItem
```
    - selectJPopupMenu
```
JPopupMenu selectJPopupMenu
```
    - selectedColumnsTable
```
JTable selectedColumnsTable
```
    - selectedValuesTableScrollPane
```
JScrollPane selectedValuesTableScrollPane
```
- Class com.compomics.util.gui.XYPlotFiltersDialog extends JDialog implements Serializable
  - Serialized Fields
    - xyPlottingDialog
```
XYPlottingDialog xyPlottingDialog
```
      The XYPlottingDialog parent.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - filterTypesLabel
```
JLabel filterTypesLabel
```
    - filtersScrollPane
```
JScrollPane filtersScrollPane
```
    - filtersTable
```
JTable filtersTable
```
    - okButton
```
JButton okButton
```
- Class com.compomics.util.gui.XYPlottingDialog extends JDialog implements Serializable
  - Serialized Fields
    - progressDialog
```
ProgressDialogX progressDialog
```
      The progress dialog.
    - tableModel
```
TableModel tableModel
```
      The table model.
    - chartPanel
```
org.jfree.chart.ChartPanel chartPanel
```
      The chart panel.
    - bubbleSize
```
double bubbleSize
```
      The bubble size.
    - bubbleScalingFactor
```
double bubbleScalingFactor
```
      The bubble scaling factor in percent. 1.0 means no scaling.
    - numberOfBins
```
int numberOfBins
```
      The number if bins for the histograms.
    - userDefinedBinSize
```
boolean userDefinedBinSize
```
      If true, the user defined bin size will be used instead of the automatic one.
    - dialogParent
```
Frame dialogParent
```
      The dialog parent.
    - isPlotting
```
boolean isPlotting
```
      If true, the plot is currently being updated.
    - mouseDragged
```
boolean mouseDragged
```
      If true, the mouse is currently being dragged.
    - dragStart
```
Point dragStart
```
      The starting location of the mouse dragging.
    - dragEnd
```
Point dragEnd
```
      The ending location of the mouse dragging.
    - selectedDataPoints
```
HashMap<K,V> selectedDataPoints
```
      The currently selected data points. The keys are the series keys, while the elements are the lists of data indexes.
    - selectionActive
```
boolean selectionActive
```
      If true, selection is currently being performed.
    - dataPointToRowNumber
```
HashMap<K,V> dataPointToRowNumber
```
      The data point to model row number map.
    - selectedModelRows
```
ArrayList<E> selectedModelRows
```
      The index of the selected rows.
    - cellRenderers
```
HashMap<K,V> cellRenderers
```
      The cell renderers for the table.
    - maxColumnWidths
```
HashMap<K,V> maxColumnWidths
```
      The maximum column widths for the table.
    - minColumnWidths
```
HashMap<K,V> minColumnWidths
```
      The minimum column widths for the table.
    - tableToolTips
```
ArrayList<E> tableToolTips
```
      The table column header tool tips.
    - colorGradient
```
no.uib.jsparklines.renderers.util.GradientColorCoding.ColorGradient colorGradient
```
      The color gradient to use.
    - histogramColor
```
Color histogramColor
```
      The color used for the bars in the histograms.
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      The last selected folder.
    - normalIcon
```
Image normalIcon
```
      The normal icon for the parent dialog.
    - waitingIcon
```
Image waitingIcon
```
      The icon to use when busy.
    - allTableColumns
```
ArrayList<E> allTableColumns
```
      The table columns.
    - visibleColumns
```
HashMap<K,V> visibleColumns
```
      Boolean indicators of which columns to show.
    - useGradientColorCoding
```
boolean useGradientColorCoding
```
      If true, gradient color coding is used.
    - showRegressionLine
```
boolean showRegressionLine
```
      If true, the regression line is shown.
    - filters
```
HashMap<K,V> filters
```
      The data filters.
    - colummnNames
```
Vector<E> colummnNames
```
      The column names.
    - rowsAfterDataFiltering
```
ArrayList<E> rowsAfterDataFiltering
```
      The rows remaining after applying the data filters.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - binSizeSpinner
```
JSpinner binSizeSpinner
```
    - binsLabel
```
JLabel binsLabel
```
    - bubbleSizeComboBox
```
JComboBox<E> bubbleSizeComboBox
```
    - bubbleSizeLabel
```
JLabel bubbleSizeLabel
```
    - colorLabel
```
JLabel colorLabel
```
    - colorsComboBox
```
JComboBox<E> colorsComboBox
```
    - contextMenuPlotBackgroundPanel
```
JPanel contextMenuPlotBackgroundPanel
```
    - contextMenuSelectedValuesTableBackgroundPanel
```
JPanel contextMenuSelectedValuesTableBackgroundPanel
```
    - densityPlotRadioButton
```
JRadioButton densityPlotRadioButton
```
    - dragButtonGroup
```
ButtonGroup dragButtonGroup
```
    - dragSettingsPanel
```
JPanel dragSettingsPanel
```
    - dragToSelectRadioButton
```
JRadioButton dragToSelectRadioButton
```
    - dragToZoomRadioButton
```
JRadioButton dragToZoomRadioButton
```
    - editFiltersButton
```
JButton editFiltersButton
```
    - exportPlotMenuItem
```
JMenuItem exportPlotMenuItem
```
    - exportSelectedValuesMenuItem
```
JMenuItem exportSelectedValuesMenuItem
```
    - filterPanel
```
JPanel filterPanel
```
    - hideColumnsMenuItem
```
JMenuItem hideColumnsMenuItem
```
    - histogramRadioButton
```
JRadioButton histogramRadioButton
```
    - logAcisPanel
```
JPanel logAcisPanel
```
    - plotHelpJButton
```
JButton plotHelpJButton
```
    - plotLayeredPane
```
JLayeredPane plotLayeredPane
```
    - plotOptionsJButton
```
JButton plotOptionsJButton
```
    - plotPanel
```
JPanel plotPanel
```
    - plotPopupMenu
```
JPopupMenu plotPopupMenu
```
    - plotTypeButtonGroup
```
ButtonGroup plotTypeButtonGroup
```
    - plotTypePanel
```
JPanel plotTypePanel
```
    - regressionLineCheckBoxMenuItem
```
JCheckBoxMenuItem regressionLineCheckBoxMenuItem
```
    - selectedValuesLayeredPane
```
JLayeredPane selectedValuesLayeredPane
```
    - selectedValuesPanel
```
JPanel selectedValuesPanel
```
    - selectedValuesScrollPane
```
JScrollPane selectedValuesScrollPane
```
    - selectedValuesTable
```
JTable selectedValuesTable
```
    - selectedValuesTableHelpJButton
```
JButton selectedValuesTableHelpJButton
```
    - selectedValuesTableOptionsJButton
```
JButton selectedValuesTableOptionsJButton
```
    - selectedValuesTablePopupMenu
```
JPopupMenu selectedValuesTablePopupMenu
```
    - sizeLogCheckBox
```
JCheckBox sizeLogCheckBox
```
    - xAxisComboBox
```
JComboBox<E> xAxisComboBox
```
    - xAxisLabel
```
JLabel xAxisLabel
```
    - xAxisLogCheckBox
```
JCheckBox xAxisLogCheckBox
```
    - xAxisPanel
```
JPanel xAxisPanel
```
    - xyPlotPanel
```
JPanel xyPlotPanel
```
    - xyPlotRadioButton
```
JRadioButton xyPlotRadioButton
```
    - yAxisComboBox
```
JComboBox<E> yAxisComboBox
```
    - yAxisLabel
```
JLabel yAxisLabel
```
    - yAxisLogCheckBox
```
JCheckBox yAxisLogCheckBox
```
Package com.compomics.util.gui.atoms
- Class com.compomics.util.gui.atoms.AtomChainDialog extends JDialog implements Serializable
  - Serialized Fields
    - atomChainAdded
```
AtomChain atomChainAdded
```
      The added atom chain edited by the user.
    - atomChainRemoved
```
AtomChain atomChainRemoved
```
      The removed atom chain edited by the user.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the input.
    - atomPanelIndex
```
int atomPanelIndex
```
      The atom panel index.
    - settingUpGUI
```
boolean settingUpGUI
```
      True of the GUI is currently being set up.
    - addOnly
```
boolean addOnly
```
      If true, then only adding atoms is allowed.
    - MassLbl
```
JLabel MassLbl
```
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - compositionLbl
```
JLabel compositionLbl
```
    - compositionPanel
```
JPanel compositionPanel
```
    - compositionTxt
```
JTextField compositionTxt
```
    - editPanel
```
JPanel editPanel
```
    - elementsPanel
```
JPanel elementsPanel
```
    - elementsScrollPane
```
JScrollPane elementsScrollPane
```
    - helpJButton
```
JButton helpJButton
```
    - massTxt
```
JTextField massTxt
```
    - okButton
```
JButton okButton
```
- Class com.compomics.util.gui.atoms.AtomPanel extends JPanel implements Serializable
  - Serialized Fields
    - isotopesMap
```
HashMap<K,V> isotopesMap
```
      Map of the isotopes as displayed: displayed string | isotope number.
    - atomChainDialog
```
AtomChainDialog atomChainDialog
```
      The parent dialog.
    - panelIndex
```
int panelIndex
```
      The panel index.
    - addLabel
```
JLabel addLabel
```
    - atomCmb
```
JComboBox<E> atomCmb
```
    - isotopeCmb
```
JComboBox<E> isotopeCmb
```
    - occurenceSpinner
```
JSpinner occurenceSpinner
```
    - removeLabel
```
JLabel removeLabel
```
Package com.compomics.util.gui.error_handlers
- Class com.compomics.util.gui.error_handlers.BugReport extends JDialog implements Serializable
  - Serialized Fields
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      The folder to open in the file selection dialog.
    - toolName
```
String toolName
```
      The name of the tool to get the bug report for, e.g., "PeptideShaker".
    - gitHubProjectName
```
String gitHubProjectName
```
      The GitHub name of the tool, e.g., "peptide-shaker".
    - toolVersion
```
String toolVersion
```
      The version number of the tool the log files belongs to.
    - googleGroup
```
String googleGroup
```
      The name of the Google Group.
    - googleGroupName
```
String googleGroupName
```
      The human readable name of the the Google Group.
    - logFile
```
File logFile
```
      The log file to display.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - clearJButton
```
JButton clearJButton
```
    - exitButton
```
JButton exitButton
```
    - infoJEditorPane
```
JEditorPane infoJEditorPane
```
    - infoJPanel
```
JPanel infoJPanel
```
    - infoJScrollPane
```
JScrollPane infoJScrollPane
```
    - logJPanel
```
JPanel logJPanel
```
    - logJScrollPane
```
JScrollPane logJScrollPane
```
    - logTxt
```
JTextArea logTxt
```
    - saveJButton
```
JButton saveJButton
```
- Class com.compomics.util.gui.error_handlers.HelpDialog extends JDialog implements Serializable
  - Serialized Fields
    - frameParent
```
Frame frameParent
```
      The parent of the parent is a Frame.
    - dialogParent
```
JDialog dialogParent
```
      The parent of the parent is a JDialog.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - closeJButton
```
JButton closeJButton
```
    - jScrollPane1
```
JScrollPane jScrollPane1
```
    - textJEditorPane
```
JEditorPane textJEditorPane
```
Package com.compomics.util.gui.error_handlers.notification
- Class com.compomics.util.gui.error_handlers.notification.NotesDialog extends JDialog implements Serializable
  - Serialized Fields
    - backgroundPanel
```
JPanel backgroundPanel
```
    - notesEditorPane
```
JEditorPane notesEditorPane
```
    - notesScrollPane
```
JScrollPane notesScrollPane
```
    - okButton
```
JButton okButton
```
- Class com.compomics.util.gui.error_handlers.notification.NotificationDialog extends JDialog implements Serializable
  - Serialized Fields
    - notificationDialogParent
```
NotificationDialogParent notificationDialogParent
```
      The notification dialog parent.
    - notificationType
```
String notificationType
```
      The notification type.
    - notificationLabel
```
JLabel notificationLabel
```
    - notificationPanel
```
JPanel notificationPanel
```
Package com.compomics.util.gui.export.graphics
- Class com.compomics.util.gui.export.graphics.ExportGraphicsDialog extends JDialog implements Serializable
  - Serialized Fields
    - chartPanel
```
org.jfree.chart.ChartPanel chartPanel
```
      The chart panel to export.
    - graphicsPanel
```
Component graphicsPanel
```
      The panel to export.
    - progressDialog
```
ProgressDialogX progressDialog
```
      The progress dialog.
    - frame
```
JFrame frame
```
      The parent frame.
    - normalIcon
```
Image normalIcon
```
      The normal icon.
    - waitingIcon
```
Image waitingIcon
```
      The waiting icon.
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      The last selected folder.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - buttonGroup
```
ButtonGroup buttonGroup
```
    - cancelJButton
```
JButton cancelJButton
```
    - exportJButton
```
JButton exportJButton
```
    - pdfJRadioButton
```
JRadioButton pdfJRadioButton
```
    - plottingTypeJPanel
```
JPanel plottingTypeJPanel
```
    - pngJRadioButton
```
JRadioButton pngJRadioButton
```
    - svgJRadioButton
```
JRadioButton svgJRadioButton
```
    - tiffJRadioButton
```
JRadioButton tiffJRadioButton
```

Package com.compomics.util.gui.export.report

Class com.compomics.util.gui.export.report.ReportEditor extends JDialog implements Serializable

Serialized Fields

exportFactory
```
ExportFactory exportFactory
```
The export factory.
oldName
```
String oldName
```
The original name of the report.
editable
```
boolean editable
```
A boolean indicating whether the report can be edited.
selection
```
HashMap<K,V> selection
```
The original selection.
sectionName
```
String sectionName
```
The selected section name.
featuresList
```
ArrayList<E> featuresList
```
The list of implemented features for the selected section.
advancedFeaturesCheck
```
JCheckBox advancedFeaturesCheck
```
backgroundPanel
```
JPanel backgroundPanel
```
cancelButton
```
JButton cancelButton
```
columnDelimiterLabel
```
JLabel columnDelimiterLabel
```
commaRadioButton
```
JRadioButton commaRadioButton
```
decoysCheck
```
JCheckBox decoysCheck
```
delimiterButtonGroup
```
ButtonGroup delimiterButtonGroup
```
featuresScrollPane
```
JScrollPane featuresScrollPane
```
featuresTable
```
JTable featuresTable
```
headerCheckBox
```
JCheckBox headerCheckBox
```
lineNumberCheckBox
```
JCheckBox lineNumberCheckBox
```
mainTitleTxt
```
JTextField mainTitleTxt
```
maintTitleCheckBox
```
JCheckBox maintTitleCheckBox
```
matchesLbl
```
JLabel matchesLbl
```
nameTxt
```
JTextField nameTxt
```
numberOfSeparationLinesLabel
```
JLabel numberOfSeparationLinesLabel
```
okButton
```
JButton okButton
```
reportTitleLabel
```
JLabel reportTitleLabel
```
reporterSettingsPanel
```
JPanel reporterSettingsPanel
```
reporterTypePanel
```
JPanel reporterTypePanel
```
rowDelimiterLabel
```
JLabel rowDelimiterLabel
```
sectionContentPanel
```
JPanel sectionContentPanel
```
sectionTitleCheckBox
```
JCheckBox sectionTitleCheckBox
```
sectionsPanel
```
JPanel sectionsPanel
```
sectionsScrollPane
```
JScrollPane sectionsScrollPane
```
sectionsTable
```
JTable sectionsTable
```
semicolonRadioButton
```
JRadioButton semicolonRadioButton
```
separationLinesSpinner
```
JSpinner separationLinesSpinner
```
spaceRadioButton
```
JRadioButton spaceRadioButton
```
structureLabel
```
JLabel structureLabel
```
subFeaturesCheck
```
JCheckBox subFeaturesCheck
```
tabRadioButton
```
JRadioButton tabRadioButton
```
validatedCheck
```
JCheckBox validatedCheck
```

Package com.compomics.util.gui.filehandling
- Class com.compomics.util.gui.filehandling.FileDisplayDialog extends JDialog implements Serializable
  - Serialized Fields
    - files
```
ArrayList<E> files
```
      The list of files.
    - canceled
```
boolean canceled
```
      True if the dialog was canceled by the user.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - okButton
```
JButton okButton
```
    - selectedFilesEditorPane
```
JEditorPane selectedFilesEditorPane
```
    - selectedFilesScrollPane
```
JScrollPane selectedFilesScrollPane
```
- Class com.compomics.util.gui.filehandling.FileSelectionDialog extends JDialog implements Serializable
  - Serialized Fields
    - fileMap
```
HashMap<K,V> fileMap
```
      A map of the parameter files indexed by their name.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the dialog.
    - cancelButton
```
JButton cancelButton
```
    - fileList
```
JList<E> fileList
```
    - fileListScrollPane
```
JScrollPane fileListScrollPane
```
    - helpLabel
```
JLabel helpLabel
```
    - okButton
```
JButton okButton
```
Package com.compomics.util.gui.genes
- Class com.compomics.util.gui.genes.GeneDetailsDialog extends JDialog implements Serializable
  - Serialized Fields
    - geneMaps
```
GeneMaps geneMaps
```
      The Gene maps.
    - proteinAccessions
```
ArrayList<E> proteinAccessions
```
      The protein accessions of this match.
    - proteinAccessionColumn
```
ArrayList<E> proteinAccessionColumn
```
      The protein accession column in the table. Only used if more than one accession.
    - goTermDescriptions
```
ArrayList<E> goTermDescriptions
```
      The GO term descriptions attached to this protein match.
    - selectedRowHtmlTagFontColor
```
String selectedRowHtmlTagFontColor
```
      The color to use for the HTML tags for the selected rows, in HTML color code.
    - notSelectedRowHtmlTagFontColor
```
String notSelectedRowHtmlTagFontColor
```
      The color to use for the HTML tags for the rows that are not selected, in HTML color code.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - chromosomeLabel
```
JLabel chromosomeLabel
```
    - chromosomeNameTxt
```
JTextField chromosomeNameTxt
```
    - detailsPanel
```
JPanel detailsPanel
```
    - ensemlbIdLabel
```
JLabel ensemlbIdLabel
```
    - geneIdTxt
```
JTextField geneIdTxt
```
    - geneNameLabel
```
JLabel geneNameLabel
```
    - geneNameTxt
```
JTextField geneNameTxt
```
    - goAnnotationLabel
```
JLabel goAnnotationLabel
```
    - goTable
```
JTable goTable
```
    - goTableScrollPane
```
JScrollPane goTableScrollPane
```
    - okButton
```
JButton okButton
```
- Class com.compomics.util.gui.genes.SpeciesDialog extends JDialog implements Serializable
  - Serialized Fields
    - parentFrame
```
Frame parentFrame
```
      Deprecated.
      
      The frame parent, if any.
    - canceled
```
boolean canceled
```
      Deprecated.
      
      Boolean indicating whether the user canceled the editing.
    - geneFactory
```
GeneFactory geneFactory
```
      Deprecated.
      
      The gene factory.
    - speciesFactory
```
SpeciesFactory speciesFactory
```
      Deprecated.
      
      The species factory
    - progressDialog
```
ProgressDialogX progressDialog
```
      Deprecated.
      
      The progress dialog.
    - dialogParent
```
JDialog dialogParent
```
      Deprecated.
      
      The dialog parent, if any.
    - waitingImage
```
Image waitingImage
```
      Deprecated.
      
      The icon to display when waiting.
    - normalImage
```
Image normalImage
```
      Deprecated.
      
      The icon to display when processing is finished.
    - speciesToTaxonMap
```
HashMap<K,V> speciesToTaxonMap
```
      Deprecated.
      
      A species name to taxon map.
    - selectedSpeciesList
```
ArrayList<E> selectedSpeciesList
```
      Deprecated.
      
      The selected species.
    - backgroundPanel
```
JPanel backgroundPanel
```
      Deprecated.
    - cancelButton
```
JButton cancelButton
```
      Deprecated.
    - chickenLabel
```
JLabel chickenLabel
```
      Deprecated.
    - comma1Label
```
JLabel comma1Label
```
      Deprecated.
    - comma2Label
```
JLabel comma2Label
```
      Deprecated.
    - comma3Label
```
JLabel comma3Label
```
      Deprecated.
    - comma4Label
```
JLabel comma4Label
```
      Deprecated.
    - ensemblCategoryJComboBox
```
JComboBox<E> ensemblCategoryJComboBox
```
      Deprecated.
    - ensemblVersionLabel
```
JLabel ensemblVersionLabel
```
      Deprecated.
    - humanLabel
```
JLabel humanLabel
```
      Deprecated.
    - mouseLabel
```
JLabel mouseLabel
```
      Deprecated.
    - okButton
```
JButton okButton
```
      Deprecated.
    - popularSpeciesLabel
```
JLabel popularSpeciesLabel
```
      Deprecated.
    - ratLabel
```
JLabel ratLabel
```
      Deprecated.
    - speciesJComboBox
```
JComboBox<E> speciesJComboBox
```
      Deprecated.
    - speciesPanel
```
JPanel speciesPanel
```
      Deprecated.
    - unknownSpeciesLabel
```
JLabel unknownSpeciesLabel
```
      Deprecated.
    - updateMappingsButton
```
JButton updateMappingsButton
```
      Deprecated.
    - zebrafishLabel
```
JLabel zebrafishLabel
```
      Deprecated.
Package com.compomics.util.gui.isotopic_calculator
- Class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui extends JFrame implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - txtSequence
```
JTextArea txtSequence
```
    - lblComp
```
JLabel lblComp
```
    - lblMass
```
JLabel lblMass
```
    - calculateButton
```
JButton calculateButton
```
    - table1
```
AlternateRowColoursJTable table1
```
    - jpanContent
```
JPanel jpanContent
```
    - headerTable
```
JPanel headerTable
```
    - spectrumPanel
```
JPanel spectrumPanel
```
    - spinCharge
```
JSpinner spinCharge
```
    - lblPeptide
```
JLabel lblPeptide
```
    - iSequence
```
AASequenceImpl iSequence
```
      The amino acid sequence
    - iElements
```
HashMap<K,V> iElements
```
      HashMap with the molecular formula for all the aminoacids
    - iCharge
```
double iCharge
```
      The charge
Package com.compomics.util.gui.parameters
- Class com.compomics.util.gui.parameters.IdentificationParametersEditionDialog extends JDialog implements Serializable
  - Serialized Fields
    - parentFrame
```
Frame parentFrame
```
      The parent frame.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the editing.
    - normalIcon
```
Image normalIcon
```
      The normal icon.
    - waitingIcon
```
Image waitingIcon
```
      The waiting icon.
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      The last selected folder
    - editable
```
boolean editable
```
      Boolean indicating whether the parameters can be edited.
    - configurationFile
```
ConfigurationFile configurationFile
```
      The configuration file containing the modification use.
    - annotationSettings
```
AnnotationSettings annotationSettings
```
      The peak annotation settings.
    - searchParameters
```
SearchParameters searchParameters
```
      The parameters used for the spectrum matching.
    - sequenceMatchingPreferences
```
SequenceMatchingPreferences sequenceMatchingPreferences
```
      The peptide to protein matching preferences.
    - genePreferences
```
GenePreferences genePreferences
```
      The gene preferences.
    - psmScoringPreferences
```
PsmScoringPreferences psmScoringPreferences
```
      The PSM scores to use.
    - peptideAssumptionFilter
```
PeptideAssumptionFilter peptideAssumptionFilter
```
      The PSM filter.
    - ptmScoringPreferences
```
PTMScoringPreferences ptmScoringPreferences
```
      The PTM localization scoring preferences.
    - proteinInferencePreferences
```
ProteinInferencePreferences proteinInferencePreferences
```
      The protein inference preferences.
    - idValidationPreferences
```
IdMatchValidationPreferences idValidationPreferences
```
      The identification validation preferences.
    - fractionSettings
```
FractionSettings fractionSettings
```
      The fraction settings.
    - validationQCPreferencesDialogParent
```
ValidationQCPreferencesDialogParent validationQCPreferencesDialogParent
```
      A parent handling the edition of QC filters.
    - showAdvancedSettings
```
boolean showAdvancedSettings
```
      If yes, the advanced settings are shown.
    - identificationParametersFactory
```
IdentificationParametersFactory identificationParametersFactory
```
      The identification parameters factory.
    - oldIdentificationParameters
```
IdentificationParameters oldIdentificationParameters
```
      The old identification settings.
    - advancedSettingsLabel
```
JLabel advancedSettingsLabel
```
    - attributesPanel
```
JPanel attributesPanel
```
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - exportLabel
```
JLabel exportLabel
```
    - fractionsButton
```
JButton fractionsButton
```
    - geneMappingButton
```
JButton geneMappingButton
```
    - importLabel
```
JLabel importLabel
```
    - matchesFiltersButton
```
JButton matchesFiltersButton
```
    - nameLabel
```
JLabel nameLabel
```
    - nameTxt
```
JTextField nameTxt
```
    - proteinInferenceButton
```
JButton proteinInferenceButton
```
    - psmScoringButton
```
JButton psmScoringButton
```
    - ptmLocalizationButton
```
JButton ptmLocalizationButton
```
    - qualityControlButton
```
JButton qualityControlButton
```
    - saveButton
```
JButton saveButton
```
    - scrollPane
```
JScrollPane scrollPane
```
    - sequenceMatchingButton
```
JButton sequenceMatchingButton
```
    - settingsOuterPanel
```
JPanel settingsOuterPanel
```
    - settingsPanel
```
JPanel settingsPanel
```
    - spectrumAnnotationButton
```
JButton spectrumAnnotationButton
```
    - spectrumMatchingButton
```
JButton spectrumMatchingButton
```
    - validationButton
```
JButton validationButton
```
- Class com.compomics.util.gui.parameters.IdentificationParametersOverviewDialog extends JDialog implements Serializable
  - Serialized Fields
    - identificationParametersFactory
```
IdentificationParametersFactory identificationParametersFactory
```
      The identification parameters factory.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - helpLbl
```
JLabel helpLbl
```
    - okButton
```
JButton okButton
```
    - parametersPopupMenu
```
JPopupMenu parametersPopupMenu
```
    - removeMenuItem
```
JMenuItem removeMenuItem
```
    - settingsTable
```
JTable settingsTable
```
    - settingsTableScrollPane
```
JScrollPane settingsTableScrollPane
```
    - tablePanel
```
JPanel tablePanel
```
- Class com.compomics.util.gui.parameters.IdentificationParametersSelectionDialog extends JDialog implements Serializable
  - Serialized Fields
    - parentFrame
```
Frame parentFrame
```
      Deprecated.
      
      The parent frame.
    - canceled
```
boolean canceled
```
      Deprecated.
      
      Boolean indicating whether the user canceled the editing.
    - normalIcon
```
Image normalIcon
```
      Deprecated.
      
      The normal icon.
    - waitingIcon
```
Image waitingIcon
```
      Deprecated.
      
      The waiting icon.
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      Deprecated.
      
      The last selected folder.
    - editable
```
boolean editable
```
      Deprecated.
      
      Boolean indicating whether the parameters can be edited.
    - configurationFile
```
ConfigurationFile configurationFile
```
      Deprecated.
      
      The configuration file containing the modification use.
    - validationQCPreferencesDialogParent
```
ValidationQCPreferencesDialogParent validationQCPreferencesDialogParent
```
      Deprecated.
      
      A parent handling the edition of QC filters.
    - identificationParametersFactory
```
IdentificationParametersFactory identificationParametersFactory
```
      Deprecated.
      
      The identification parameters factory.
    - addDetailsMenuItem
```
JMenuItem addDetailsMenuItem
```
      Deprecated.
    - addFile
```
JMenuItem addFile
```
      Deprecated.
    - addMenu
```
JMenu addMenu
```
      Deprecated.
    - addProtocolMenuItem
```
JMenuItem addProtocolMenuItem
```
      Deprecated.
    - addSearchSettingsMenuItem
```
JMenuItem addSearchSettingsMenuItem
```
      Deprecated.
    - backgroundPanel
```
JPanel backgroundPanel
```
      Deprecated.
    - cancelButton
```
JButton cancelButton
```
      Deprecated.
    - editDetailsMenuItem
```
JMenuItem editDetailsMenuItem
```
      Deprecated.
    - editMenu
```
JMenu editMenu
```
      Deprecated.
    - editProtocolMenuItem
```
JMenuItem editProtocolMenuItem
```
      Deprecated.
    - editSearchSettingsMenuItem
```
JMenuItem editSearchSettingsMenuItem
```
      Deprecated.
    - helpLbl
```
JLabel helpLbl
```
      Deprecated.
    - okButton
```
JButton okButton
```
      Deprecated.
    - parametersPopupMenu
```
JPopupMenu parametersPopupMenu
```
      Deprecated.
    - removeMenuItem
```
JMenuItem removeMenuItem
```
      Deprecated.
    - renameMenuItem
```
JMenuItem renameMenuItem
```
      Deprecated.
    - saveAsMenuItem
```
JMenuItem saveAsMenuItem
```
      Deprecated.
    - settingsTable
```
JTable settingsTable
```
      Deprecated.
    - settingsTableScrollPane
```
JScrollPane settingsTableScrollPane
```
      Deprecated.
    - tablePanel
```
JPanel tablePanel
```
      Deprecated.
- Class com.compomics.util.gui.parameters.OldProcessingPreferencesDialog extends JDialog implements Serializable
  - Serialized Fields
    - processingPreferences
```
PSProcessingPreferences processingPreferences
```
      The processing preferences.
    - identificationParameters
```
IdentificationParameters identificationParameters
```
      The identification parameters
    - editable
```
boolean editable
```
      Boolean indicating whether the processing and identification parameters should be edited upon clicking on OK.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the cancel button was pressed.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - fractionsPanel
```
JPanel fractionsPanel
```
    - helpJButton
```
JButton helpJButton
```
    - neutralLossesCmb
```
JComboBox<E> neutralLossesCmb
```
    - neutralLossesCmb2
```
JComboBox<E> neutralLossesCmb2
```
    - neutralLossesLabel
```
JLabel neutralLossesLabel
```
    - neutralLossesLabel2
```
JLabel neutralLossesLabel2
```
    - okButton
```
JButton okButton
```
    - peptideFdrLabel
```
JLabel peptideFdrLabel
```
    - peptideFdrTxt
```
JTextField peptideFdrTxt
```
    - percentLabel
```
JLabel percentLabel
```
    - percentLabel2
```
JLabel percentLabel2
```
    - percentLabel3
```
JLabel percentLabel3
```
    - percentLabel4
```
JLabel percentLabel4
```
    - processingParamsPanel
```
JPanel processingParamsPanel
```
    - proteinConfidenceMwTxt
```
JTextField proteinConfidenceMwTxt
```
    - proteinFdrLabel
```
JLabel proteinFdrLabel
```
    - proteinFdrTxt
```
JTextField proteinFdrTxt
```
    - proteinMwLabel
```
JLabel proteinMwLabel
```
    - psmFdrLabel
```
JLabel psmFdrLabel
```
    - psmFdrTxt
```
JTextField psmFdrTxt
```
    - ptmScoringPanel
```
JPanel ptmScoringPanel
```
    - scoreCmb
```
JComboBox<E> scoreCmb
```
    - scoreTypeLabel
```
JLabel scoreTypeLabel
```
    - thresholdAutpoCmb
```
JComboBox<E> thresholdAutpoCmb
```
    - thresholdAutpoLabel
```
JLabel thresholdAutpoLabel
```
    - thresholdLabel
```
JLabel thresholdLabel
```
    - thresholdTxt
```
JTextField thresholdTxt
```
- Class com.compomics.util.gui.parameters.ProcessingPreferencesDialog extends JDialog implements Serializable
  - Serialized Fields
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the editing.
    - editable
```
boolean editable
```
      Boolean indicating whether the processing and identification parameters should be edited upon clicking on OK.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - nThreadsSpinner
```
JSpinner nThreadsSpinner
```
    - okButton
```
JButton okButton
```
    - performanceLbl
```
JLabel performanceLbl
```
    - performancePanel
```
JPanel performancePanel
```
    - processingTypeCmb
```
JComboBox<E> processingTypeCmb
```
    - processingTypeLbl
```
JLabel processingTypeLbl
```
    - processingTypePanel
```
JPanel processingTypePanel
```
Package com.compomics.util.gui.parameters.identification_parameters
- Class com.compomics.util.gui.parameters.identification_parameters.AnnotationSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    - parentFrame
```
Frame parentFrame
```
      The parent frame.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the editing.
    - reporterIons
```
ArrayList<E> reporterIons
```
      List of possible reporter ions.
    - neutralLossesMap
```
HashMap<K,V> neutralLossesMap
```
      Map of the neutral losses selection.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - maxFragmentIonAccuracy
```
double maxFragmentIonAccuracy
```
      The fragment ion accuracy used for the search.
    - aBox
```
JCheckBox aBox
```
    - accuracySpinner
```
JSpinner accuracySpinner
```
    - annotationLevelLabel
```
JLabel annotationLevelLabel
```
    - annotationLevelPercentLabel
```
JLabel annotationLevelPercentLabel
```
    - annotationPreferencesHelpJButton
```
JButton annotationPreferencesHelpJButton
```
    - bBox
```
JCheckBox bBox
```
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cBox
```
JCheckBox cBox
```
    - cancelButton
```
JButton cancelButton
```
    - fragmentIonAccuracyLabel
```
JLabel fragmentIonAccuracyLabel
```
    - fragmentIonAccuracyTypeLabel
```
JLabel fragmentIonAccuracyTypeLabel
```
    - highResolutionBox
```
JCheckBox highResolutionBox
```
    - immoniumBox
```
JCheckBox immoniumBox
```
    - intensitySpinner
```
JSpinner intensitySpinner
```
    - ionsPanel
```
JPanel ionsPanel
```
    - neutralLossPanel
```
JPanel neutralLossPanel
```
    - neutralLossScrollPane
```
JScrollPane neutralLossScrollPane
```
    - neutralLossesTable
```
JTable neutralLossesTable
```
    - okButton
```
JButton okButton
```
    - peakMatchingPanel
```
JPanel peakMatchingPanel
```
    - precursorBox
```
JCheckBox precursorBox
```
    - relatedBox
```
JCheckBox relatedBox
```
    - reporterBox
```
JCheckBox reporterBox
```
    - xBox
```
JCheckBox xBox
```
    - yBox
```
JCheckBox yBox
```
    - zBox
```
JCheckBox zBox
```
- Class com.compomics.util.gui.parameters.identification_parameters.EnzymeSelectionDialog extends JDialog implements Serializable
  - Serialized Fields
    - enzymeFactory
```
EnzymeFactory enzymeFactory
```
      The enzyme factory.
    - selectionCanceled
```
boolean selectionCanceled
```
      True of the enzyme selection was canceled by the user.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - enzymeLabel
```
JLabel enzymeLabel
```
    - enzymesCmb
```
JComboBox<E> enzymesCmb
```
    - mappingPanel
```
JPanel mappingPanel
```
    - okButton
```
JButton okButton
```
    - prideEnzymeNameLabel
```
JLabel prideEnzymeNameLabel
```
    - prideEnzymeNameTextField
```
JTextField prideEnzymeNameTextField
```
- Class com.compomics.util.gui.parameters.identification_parameters.FractionSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the editing.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - backgrounPanel
```
JPanel backgrounPanel
```
    - cancelButton
```
JButton cancelButton
```
    - fractionsPanel
```
JPanel fractionsPanel
```
    - okButton
```
JButton okButton
```
    - proteinMwLabel
```
JLabel proteinMwLabel
```
    - proteinMwSpinner
```
JSpinner proteinMwSpinner
```
- Class com.compomics.util.gui.parameters.identification_parameters.GenePreferencesDialog extends JDialog implements Serializable
  - Serialized Fields
    - canceled
```
boolean canceled
```
      True of the dialog was canceled by the user.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - genePreferences
```
GenePreferences genePreferences
```
      The gene preferences.
    - searchParameters
```
SearchParameters searchParameters
```
      The search parameters.
    - speciesFactory
```
SpeciesFactory speciesFactory
```
      The species factory.
    - speciesMap
```
HashMap<K,V> speciesMap
```
      A map from the species names used in the drop down menu to the taxon.
    - autoUpdateCmb
```
JComboBox<E> autoUpdateCmb
```
    - autoUpdateLabel
```
JLabel autoUpdateLabel
```
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - mappingPanel
```
JPanel mappingPanel
```
    - okButton
```
JButton okButton
```
    - speciesCmb
```
JComboBox<E> speciesCmb
```
    - speciesLabel
```
JLabel speciesLabel
```
    - useMappingCmb
```
JComboBox<E> useMappingCmb
```
    - useMappingLabel
```
JLabel useMappingLabel
```
- Class com.compomics.util.gui.parameters.identification_parameters.IdentificationParametersNameDialog extends JDialog implements Serializable
  - Serialized Fields
    - parentFrame
```
Frame parentFrame
```
      The parent frame.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the editing.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - originalDescription
```
String originalDescription
```
      The original description.
    - attributesPanel
```
JPanel attributesPanel
```
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - decriptionLbl
```
JLabel decriptionLbl
```
    - descriptionTxt
```
JTextArea descriptionTxt
```
    - jScrollPane1
```
JScrollPane jScrollPane1
```
    - nameLbl
```
JLabel nameLbl
```
    - nameTxt
```
JTextField nameTxt
```
    - okButton
```
JButton okButton
```
- Class com.compomics.util.gui.parameters.identification_parameters.MatchesImportFiltersDialog extends JDialog implements Serializable
  - Serialized Fields
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the editing.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - filterPanel
```
JPanel filterPanel
```
    - helpJButton
```
JButton helpJButton
```
    - isotopesLbl
```
JLabel isotopesLbl
```
    - isotopesRangeLabel
```
JLabel isotopesRangeLabel
```
    - maxIsotopesTxt
```
JTextField maxIsotopesTxt
```
    - maxMissedCleavagesTxt
```
JTextField maxMissedCleavagesTxt
```
    - minIsotopesTxt
```
JTextField minIsotopesTxt
```
    - minMissedCleavagesTxt
```
JTextField minMissedCleavagesTxt
```
    - missedCleavagesLabel
```
JLabel missedCleavagesLabel
```
    - missedCleavagesRangeLabel
```
JLabel missedCleavagesRangeLabel
```
    - nAAmaxTxt
```
JTextField nAAmaxTxt
```
    - nAAminTxt
```
JTextField nAAminTxt
```
    - okButton
```
JButton okButton
```
    - peptideLengthLabel
```
JLabel peptideLengthLabel
```
    - peptideLengthRangeLabel
```
JLabel peptideLengthRangeLabel
```
    - precDevTxt
```
JTextField precDevTxt
```
    - precursorAccuracyLabel
```
JLabel precursorAccuracyLabel
```
    - ptmsCheck
```
JCheckBox ptmsCheck
```
    - unitCmb
```
JComboBox<E> unitCmb
```
- Class com.compomics.util.gui.parameters.identification_parameters.ProteinInferenceSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    - parentFrame
```
Frame parentFrame
```
      The parent frame.
    - normalIcon
```
Image normalIcon
```
      The normal dialog icon.
    - waitingIcon
```
Image waitingIcon
```
      The waiting dialog icon.
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      The last selected folder to use.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the editing.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - dataBasePanelSettings
```
JPanel dataBasePanelSettings
```
    - databaseSettingsLbl
```
JLabel databaseSettingsLbl
```
    - databaseSettingsTxt
```
JTextField databaseSettingsTxt
```
    - editDatabaseDetailsButton
```
JButton editDatabaseDetailsButton
```
    - okButton
```
JButton okButton
```
- Class com.compomics.util.gui.parameters.identification_parameters.PsmScoringSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the editing.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - okButton
```
JButton okButton
```
- Class com.compomics.util.gui.parameters.identification_parameters.PTMLocalizationParametersDialog extends JDialog implements Serializable
  - Serialized Fields
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the editing.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - jSeparator1
```
JSeparator jSeparator1
```
    - neutralLossesCmb
```
JComboBox<E> neutralLossesCmb
```
    - neutralLossesLabel
```
JLabel neutralLossesLabel
```
    - okButton
```
JButton okButton
```
    - ptmScoringPanel
```
JPanel ptmScoringPanel
```
    - scoreCmb
```
JComboBox<E> scoreCmb
```
    - scoreTypeLabel
```
JLabel scoreTypeLabel
```
    - thresholdAutpoCmb
```
JComboBox<E> thresholdAutpoCmb
```
    - thresholdAutpoLabel
```
JLabel thresholdAutpoLabel
```
    - thresholdLabel
```
JLabel thresholdLabel
```
    - thresholdTxt
```
JTextField thresholdTxt
```
- Class com.compomics.util.gui.parameters.identification_parameters.SearchSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    - sequenceFactory
```
SequenceFactory sequenceFactory
```
      The sequence factory.
    - enzymeFactory
```
EnzymeFactory enzymeFactory
```
      The enzyme factory.
    - forwardIons
```
String[] forwardIons
```
      Convenience array for forward ion type selection.
    - rewindIons
```
String[] rewindIons
```
      Convenience array for rewind ion type selection.
    - ptmFactory
```
PTMFactory ptmFactory
```
      The post translational modifications factory.
    - searchParameters
```
SearchParameters searchParameters
```
    - modificationTableToolTips
```
ArrayList<E> modificationTableToolTips
```
      The modification table column header tooltips.
    - parentFrame
```
Frame parentFrame
```
      The dialog parent frame.
    - normalIcon
```
Image normalIcon
```
      The normal dialog icon.
    - waitingIcon
```
Image waitingIcon
```
      The waiting dialog icon.
    - keyPressedCounter
```
int keyPressedCounter
```
      Counts the number of times the users has pressed a key on the keyboard in the search field.
    - currentPtmSearchString
```
String currentPtmSearchString
```
      The current PTM search string.
    - waitingTime
```
int waitingTime
```
      The time to wait between keys typed before updating the search.
    - configurationFile
```
ConfigurationFile configurationFile
```
      The configuration file containing the modification use.
    - modificationUse
```
ArrayList<E> modificationUse
```
      The list of the default modifications.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the cancel button was pressed.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      The last selected folder to use.
    - refMass
```
Double refMass
```
      Reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.
    - addFixedModification
```
JButton addFixedModification
```
    - addVariableModification
```
JButton addVariableModification
```
    - availableModsPanel
```
JPanel availableModsPanel
```
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - dataBasePanelSettings
```
JPanel dataBasePanelSettings
```
    - databaseSettingsLbl
```
JLabel databaseSettingsLbl
```
    - databaseSettingsTxt
```
JTextField databaseSettingsTxt
```
    - editDatabaseDetailsButton
```
JButton editDatabaseDetailsButton
```
    - enzymeLabel
```
JLabel enzymeLabel
```
    - enzymesCmb
```
JComboBox<E> enzymesCmb
```
    - fixedModificationsLabel
```
JLabel fixedModificationsLabel
```
    - fixedModsJScrollPane
```
JScrollPane fixedModsJScrollPane
```
    - fixedModsPanel
```
JPanel fixedModsPanel
```
    - fixedModsTable
```
JTable fixedModsTable
```
    - fragmentIon1Cmb
```
JComboBox<E> fragmentIon1Cmb
```
    - fragmentIon2Cmb
```
JComboBox<E> fragmentIon2Cmb
```
    - fragmentIonAccuracyTxt
```
JTextField fragmentIonAccuracyTxt
```
    - fragmentIonLbl
```
JLabel fragmentIonLbl
```
    - fragmentIonType1Lbl
```
JLabel fragmentIonType1Lbl
```
    - fragmentIonUnit
```
JComboBox<E> fragmentIonUnit
```
    - isotopeMaxTxt
```
JTextField isotopeMaxTxt
```
    - isotopeMinTxt
```
JTextField isotopeMinTxt
```
    - isotopesLbl
```
JLabel isotopesLbl
```
    - maxMissedCleavagesLabel
```
JLabel maxMissedCleavagesLabel
```
    - maxMissedCleavagesTxt
```
JTextField maxMissedCleavagesTxt
```
    - maxPrecursorChargeTxt
```
JTextField maxPrecursorChargeTxt
```
    - minPrecursorChargeTxt
```
JTextField minPrecursorChargeTxt
```
    - modificationTypesSplitPane
```
JSplitPane modificationTypesSplitPane
```
    - modificationsJScrollPane
```
JScrollPane modificationsJScrollPane
```
    - modificationsLayeredPane
```
JLayeredPane modificationsLayeredPane
```
    - modificationsListCombo
```
JComboBox<E> modificationsListCombo
```
    - modificationsPanel
```
JPanel modificationsPanel
```
    - modificationsTable
```
JTable modificationsTable
```
    - okButton
```
JButton okButton
```
    - openDialogHelpJButton1
```
JButton openDialogHelpJButton1
```
    - openModificationSettingsJButton
```
JButton openModificationSettingsJButton
```
    - precursorChargeLbl
```
JLabel precursorChargeLbl
```
    - precursorChargeRangeLabel
```
JLabel precursorChargeRangeLabel
```
    - precursorChargeRangeLabel1
```
JLabel precursorChargeRangeLabel1
```
    - precursorIonAccuracyTxt
```
JTextField precursorIonAccuracyTxt
```
    - precursorIonLbl
```
JLabel precursorIonLbl
```
    - precursorIonUnit
```
JComboBox<E> precursorIonUnit
```
    - proteaseAndFragmentationPanel
```
JPanel proteaseAndFragmentationPanel
```
    - removeFixedModification
```
JButton removeFixedModification
```
    - removeVariableModification
```
JButton removeVariableModification
```
    - variableModificationsLabel
```
JLabel variableModificationsLabel
```
    - variableModsJScrollPane
```
JScrollPane variableModsJScrollPane
```
    - variableModsPanel
```
JPanel variableModsPanel
```
    - variableModsTable
```
JTable variableModsTable
```
- Class com.compomics.util.gui.parameters.identification_parameters.SequenceMatchingSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the editing.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - matchingCmb
```
JComboBox<E> matchingCmb
```
    - matchingMethodLbl
```
JLabel matchingMethodLbl
```
    - okButton
```
JButton okButton
```
    - sequenceMatchingPanel
```
JPanel sequenceMatchingPanel
```
    - xLbl
```
JLabel xLbl
```
    - xSpinner
```
JSpinner xSpinner
```
- Class com.compomics.util.gui.parameters.identification_parameters.SpectrumMatchingSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    - parentFrame
```
Frame parentFrame
```
      The parent frame.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the editing.
    - normalIcon
```
Image normalIcon
```
      The normal dialog icon.
    - waitingIcon
```
Image waitingIcon
```
      The waiting dialog icon.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      The last selected folder to use.
    - configurationFile
```
ConfigurationFile configurationFile
```
      The configuration file containing the modification use.
    - searchParameters
```
SearchParameters searchParameters
```
      The current search parameters.
    - algorithmParameters
```
HashMap<K,V> algorithmParameters
```
      The algorithm specific parameters.
    - advocates
```
ArrayList<E> advocates
```
      List of identification algorithms indexes.
    - algorithmPanel
```
JPanel algorithmPanel
```
    - algorithmSettingsTable
```
JTable algorithmSettingsTable
```
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - editButton
```
JButton editButton
```
    - generalPanel
```
JPanel generalPanel
```
    - jScrollPane1
```
JScrollPane jScrollPane1
```
    - okButton
```
JButton okButton
```
    - settingsLbl
```
JLabel settingsLbl
```
    - settingsTxt
```
JTextField settingsTxt
```
- Class com.compomics.util.gui.parameters.identification_parameters.ValidationQCPreferencesDialog extends JDialog implements Serializable
  - Serialized Fields
    - validationQCPreferencesDialogParent
```
ValidationQCPreferencesDialogParent validationQCPreferencesDialogParent
```
      A parent handling the edition of filters.
    - psmFilters
```
ArrayList<E> psmFilters
```
      List of the PSM quality filters.
    - peptideFilters
```
ArrayList<E> peptideFilters
```
      List of the peptide quality filters.
    - proteinFilters
```
ArrayList<E> proteinFilters
```
      List of the protein quality filters.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the dialog was canceled.
    - filtersChanged
```
boolean filtersChanged
```
      Boolean indicating whether the filters have been changed.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - addPeptideFilterMenuItem
```
JMenuItem addPeptideFilterMenuItem
```
    - addProteinFilterMenuItem
```
JMenuItem addProteinFilterMenuItem
```
    - addPsmFilterMenuItem
```
JMenuItem addPsmFilterMenuItem
```
    - cancelButton
```
JButton cancelButton
```
    - confidenceCheck
```
JCheckBox confidenceCheck
```
    - dbCheck
```
JCheckBox dbCheck
```
    - editPeptideFilterMenuItem
```
JMenuItem editPeptideFilterMenuItem
```
    - editProteinFilterMenuItem
```
JMenuItem editProteinFilterMenuItem
```
    - editPsmFilterMenuItem
```
JMenuItem editPsmFilterMenuItem
```
    - generalSettingsPanel
```
JPanel generalSettingsPanel
```
    - helpLbl
```
JLabel helpLbl
```
    - markDoubtfulLabel
```
JLabel markDoubtfulLabel
```
    - nTargetCheck
```
JCheckBox nTargetCheck
```
    - okButton
```
JButton okButton
```
    - peptideFiltersPanel
```
JPanel peptideFiltersPanel
```
    - peptidePopupMenu
```
JPopupMenu peptidePopupMenu
```
    - peptideScrollPane
```
JScrollPane peptideScrollPane
```
    - peptideTable
```
JTable peptideTable
```
    - proteinFiltersPanel
```
JPanel proteinFiltersPanel
```
    - proteinPopupMenu
```
JPopupMenu proteinPopupMenu
```
    - proteinScrollPane
```
JScrollPane proteinScrollPane
```
    - proteinTable
```
JTable proteinTable
```
    - psmFiltersPanel
```
JPanel psmFiltersPanel
```
    - psmPopupMenu
```
JPopupMenu psmPopupMenu
```
    - psmScrollPane
```
JScrollPane psmScrollPane
```
    - psmTable
```
JTable psmTable
```
    - removePeptideFilterMenuItem
```
JMenuItem removePeptideFilterMenuItem
```
    - removeProteinFilterMenuItem
```
JMenuItem removeProteinFilterMenuItem
```
    - removePsmFilterMenuItem
```
JMenuItem removePsmFilterMenuItem
```
    - validationQCPreferencesDialogPanel
```
JPanel validationQCPreferencesDialogPanel
```
- Class com.compomics.util.gui.parameters.identification_parameters.ValidationSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user canceled the editing.
    - editable
```
boolean editable
```
      Boolean indicating whether the settings can be edited by the user.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - groupsComboBox
```
JComboBox<E> groupsComboBox
```
    - groupsLabel
```
JLabel groupsLabel
```
    - groupsPanel
```
JPanel groupsPanel
```
    - okButton
```
JButton okButton
```
    - peptideFdrLabel
```
JLabel peptideFdrLabel
```
    - peptideFdrTxt
```
JTextField peptideFdrTxt
```
    - processingParamsPanel
```
JPanel processingParamsPanel
```
    - proteinFdrLabel
```
JLabel proteinFdrLabel
```
    - proteinFdrTxt
```
JTextField proteinFdrTxt
```
    - psmFdrLabel
```
JLabel psmFdrLabel
```
    - psmFdrTxt
```
JTextField psmFdrTxt
```

Package com.compomics.util.gui.parameters.identification_parameters.algorithm_settings

Class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.AndromedaSettingsDialog extends JDialog implements Serializable

Serialized Fields

cancelled
```
boolean cancelled
```
Boolean indicating whether the used canceled the editing.
editable
```
boolean editable
```
Boolean indicating whether the settings can be edited by the user.
advancedSettingsWarningLabel
```
JLabel advancedSettingsWarningLabel
```
ammoniaLossCmb
```
JComboBox<E> ammoniaLossCmb
```
ammoniaLossLabel
```
JLabel ammoniaLossLabel
```
backgroundPanel
```
JPanel backgroundPanel
```
closeButton
```
JButton closeButton
```
empiricalCorrectionCombo
```
JComboBox<E> empiricalCorrectionCombo
```
empiricalCorrectionLabel
```
JLabel empiricalCorrectionLabel
```
equalILCombo
```
JComboBox<E> equalILCombo
```
equalILLabel
```
JLabel equalILLabel
```
fragMethodCmb
```
JComboBox<E> fragMethodCmb
```
fragMethodLabel
```
JLabel fragMethodLabel
```
fragmentAllCmb
```
JComboBox<E> fragmentAllCmb
```
fragmentAllLabel
```
JLabel fragmentAllLabel
```
higherChargeCombo
```
JComboBox<E> higherChargeCombo
```
higherChargeLabel
```
JLabel higherChargeLabel
```
maxCombinationsLabel
```
JLabel maxCombinationsLabel
```
maxCombinationsTxt
```
JTextField maxCombinationsTxt
```
maxPepLengthNoEnzymeTxt
```
JTextField maxPepLengthNoEnzymeTxt
```
maxPeptideMassLabel
```
JLabel maxPeptideMassLabel
```
maxPeptideMassTxt
```
JTextField maxPeptideMassTxt
```
maxPtmsLabel
```
JLabel maxPtmsLabel
```
maxPtmsTxt
```
JTextField maxPtmsTxt
```
minPepLengthNoEnzymeTxt
```
JTextField minPepLengthNoEnzymeTxt
```
neutralLossesCmb
```
JComboBox<E> neutralLossesCmb
```
neutralLossesLabel
```
JLabel neutralLossesLabel
```
numberMatchesLabel
```
JLabel numberMatchesLabel
```
numberMatchesTxt
```
JTextField numberMatchesTxt
```
okButton
```
JButton okButton
```
openDialogHelpJButton
```
JButton openDialogHelpJButton
```

peptideLengthNoEnzymeDividerLabel

JLabel peptideLengthNoEnzymeDividerLabel

peptideLengthNoEnzymeLabel
```
JLabel peptideLengthNoEnzymeLabel
```
settingsInnerPanel
```
JPanel settingsInnerPanel
```
settingsPanel
```
JPanel settingsPanel
```
settingsScrollPane
```
JScrollPane settingsScrollPane
```
topPeaksLabel
```
JLabel topPeaksLabel
```
topPeaksTxt
```
JTextField topPeaksTxt
```
topPeaksWindowLabel
```
JLabel topPeaksWindowLabel
```
topPeaksWindowTxt
```
JTextField topPeaksWindowTxt
```
waterLossCombo
```
JComboBox<E> waterLossCombo
```
waterLossLabel
```
JLabel waterLossLabel
```

Class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.CometSettingsDialog extends JDialog implements Serializable

Serialized Fields

cancelled
```
boolean cancelled
```
Boolean indicating whether the used canceled the editing.
editable
```
boolean editable
```
Boolean indicating whether the settings can be edited by the user.
advancedSettingsWarningLabel
```
JLabel advancedSettingsWarningLabel
```
backgroundPanel
```
JPanel backgroundPanel
```
batchSizeLabel
```
JLabel batchSizeLabel
```
batchSizeTxt
```
JTextField batchSizeTxt
```
clearMzRangeDividerLabel
```
JLabel clearMzRangeDividerLabel
```
clearMzRangeLabel
```
JLabel clearMzRangeLabel
```
clearMzRangeLowerTxt
```
JTextField clearMzRangeLowerTxt
```
clearMzRangeUpperTxt
```
JTextField clearMzRangeUpperTxt
```
closeButton
```
JButton closeButton
```
correlationScoreTypeCmb
```
JComboBox<E> correlationScoreTypeCmb
```
correlationScoreTypeLabel
```
JLabel correlationScoreTypeLabel
```
enzymeTypeCmb
```
JComboBox<E> enzymeTypeCmb
```
enzymeTypeLabel
```
JLabel enzymeTypeLabel
```
fragmentBinOffsetLabel
```
JLabel fragmentBinOffsetLabel
```
fragmentBinOffsetTxt
```
JTextField fragmentBinOffsetTxt
```
fragmentIonsPanel
```
JPanel fragmentIonsPanel
```
isotopeCorrectionCmb
```
JComboBox<E> isotopeCorrectionCmb
```
isotopeCorrectionLabel
```
JLabel isotopeCorrectionLabel
```
maxFragmentChargeLabel
```
JLabel maxFragmentChargeLabel
```
maxFragmentChargeTxt
```
JTextField maxFragmentChargeTxt
```
maxPrecursorMassTxt
```
JTextField maxPrecursorMassTxt
```
maxPtmsLabel
```
JLabel maxPtmsLabel
```
maxPtmsTxt
```
JTextField maxPtmsTxt
```
minPeakIntensityLbl
```
JLabel minPeakIntensityLbl
```
minPeakIntensityTxt
```
JTextField minPeakIntensityTxt
```
minPeaksLbl
```
JLabel minPeaksLbl
```
minPeaksTxt
```
JTextField minPeaksTxt
```
minPrecursorMassTxt
```
JTextField minPrecursorMassTxt
```
numberMatchesLabel
```
JLabel numberMatchesLabel
```
numberMatchesTxt
```
JTextField numberMatchesTxt
```
okButton
```
JButton okButton
```
openDialogHelpJButton
```
JButton openDialogHelpJButton
```
outputFormatCmb
```
JComboBox<E> outputFormatCmb
```
outputPanel
```
JPanel outputPanel
```
outputPepXmlLabel
```
JLabel outputPepXmlLabel
```
precursorMassDividerLabel
```
JLabel precursorMassDividerLabel
```
precursorMassLabel
```
JLabel precursorMassLabel
```
printExpecScoreLabel
```
JLabel printExpecScoreLabel
```
printExpectScoreCmb
```
JComboBox<E> printExpectScoreCmb
```
removeMethionineCmb
```
JComboBox<E> removeMethionineCmb
```
removeMethionineLabel
```
JLabel removeMethionineLabel
```
removePrecursorPeakCombo
```
JComboBox<E> removePrecursorPeakCombo
```
removePrecursorPeakLabel
```
JLabel removePrecursorPeakLabel
```
removePrecursorPeakToleranceLbl
```
JLabel removePrecursorPeakToleranceLbl
```

removePrecursorPeakToleranceTxt

JTextField removePrecursorPeakToleranceTxt

requireVariablePtmCmb
```
JComboBox<E> requireVariablePtmCmb
```
requireVariablePtmLabel
```
JLabel requireVariablePtmLabel
```
searchSettingsPanel
```
JPanel searchSettingsPanel
```
spectrumProcessingPanel
```
JPanel spectrumProcessingPanel
```
tabbedPane
```
JTabbedPane tabbedPane
```

Class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.DirecTagSettingsDialog extends JDialog implements Serializable

Serialized Fields

searchParameters
```
SearchParameters searchParameters
```
The search parameters
canceled
```
boolean canceled
```
True if the dialog was canceled by the user.
editable
```
boolean editable
```
Boolean indicating whether the settings can be edited by the user.
backgroundPanel
```
JPanel backgroundPanel
```
cancelButton
```
JButton cancelButton
```
complementScoreWeightLabel
```
JLabel complementScoreWeightLabel
```

complementScoreWeightTextField

JTextField complementScoreWeightTextField

complementToleranceLabel
```
JLabel complementToleranceLabel
```
complementToleranceTextField
```
JTextField complementToleranceTextField
```
deisotopingModeLabel
```
JLabel deisotopingModeLabel
```
deisptopingModeTextField
```
JTextField deisptopingModeTextField
```
directTagPanel
```
JPanel directTagPanel
```
duplicateSpectraLabel
```
JLabel duplicateSpectraLabel
```

duplicateSpectraPerChargeCmb

JComboBox<E> duplicateSpectraPerChargeCmb

intensityScoreWeightLabel
```
JLabel intensityScoreWeightLabel
```

intensityScoreWeightTextField

JTextField intensityScoreWeightTextField

isotopeToleranceLabel
```
JLabel isotopeToleranceLabel
```
isotopeToleranceTextField
```
JTextField isotopeToleranceTextField
```
maxPeakCountLabel
```
JLabel maxPeakCountLabel
```
maxPeakCountTextField
```
JTextField maxPeakCountTextField
```
maxPrecursorAdjustmentLabel
```
JLabel maxPrecursorAdjustmentLabel
```

maxPrecursorAdjustmentTextField

JTextField maxPrecursorAdjustmentTextField

minPrecursorAdjustmentLabel
```
JLabel minPrecursorAdjustmentLabel
```

minPrecursorAdjustmentTextField

JTextField minPrecursorAdjustmentTextField

mzFidelityScoreWeightLabel
```
JLabel mzFidelityScoreWeightLabel
```

mzFidelityScoreWeightTextField

JTextField mzFidelityScoreWeightTextField

numVariableModsLabel
```
JLabel numVariableModsLabel
```
numVariableModsTextField
```
JTextField numVariableModsTextField
```
numberOfChargeStatesLabel
```
JLabel numberOfChargeStatesLabel
```

numberOfChargeStatesTextField

JTextField numberOfChargeStatesTextField

numberOfIntensityClassesLabel
```
JLabel numberOfIntensityClassesLabel
```

numberOfIntensityClassesTextField

JTextField numberOfIntensityClassesTextField

okButton
```
JButton okButton
```
openDialogHelpJButton
```
JButton openDialogHelpJButton
```
outputSuffixLabel
```
JLabel outputSuffixLabel
```
outputSuffixTextField
```
JTextField outputSuffixTextField
```
precursorAdjustmentStepLabel
```
JLabel precursorAdjustmentStepLabel
```

precursorAdjustmentStepTextField

JTextField precursorAdjustmentStepTextField

tagLengthLabel
```
JLabel tagLengthLabel
```
tagLengthTextField
```
JTextField tagLengthTextField
```
ticCutoffLabel
```
JLabel ticCutoffLabel
```
ticCutoffTextField
```
JTextField ticCutoffTextField
```

Class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsAmandaSettingsDialog extends JDialog implements Serializable
- Serialized Fields
  - cancelled
```
boolean cancelled
```
    Boolean indicating whether the used canceled the editing.
  - editable
```
boolean editable
```
    Boolean indicating whether the settings can be edited by the user.
  - advancedSearchSettingsPanel
```
JPanel advancedSearchSettingsPanel
```
  - advancedSettingsWarningLabel
```
JLabel advancedSettingsWarningLabel
```
  - backgroundPanel
```
JPanel backgroundPanel
```
  - closeButton
```
JButton closeButton
```
  - decoyDatabaseCmb
```
JComboBox<E> decoyDatabaseCmb
```
  - decoyDatabaseLabel
```
JLabel decoyDatabaseLabel
```
  - instrumentCmb
```
JComboBox<E> instrumentCmb
```
  - instrumentLabel
```
JLabel instrumentLabel
```
  - lowMemoryModeCmb
```
JComboBox<E> lowMemoryModeCmb
```
  - lowMemoryModeLabel
```
JLabel lowMemoryModeLabel
```
  - maxRankLabel
```
JLabel maxRankLabel
```
  - maxRankTxt
```
JTextField maxRankTxt
```
  - monoIsotopicCmb
```
JComboBox<E> monoIsotopicCmb
```
  - monoIsotopicLabel
```
JLabel monoIsotopicLabel
```
  - okButton
```
JButton okButton
```
  - openDialogHelpJButton
```
JButton openDialogHelpJButton
```
Class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MsgfSettingsDialog extends JDialog implements Serializable
- Serialized Fields
  - cancelled
```
boolean cancelled
```
    Boolean indicating whether the used canceled the editing.
  - editable
```
boolean editable
```
    Boolean indicating whether the settings can be edited by the user.
  - additionalOutputCmb
```
JComboBox<E> additionalOutputCmb
```
  - additionalOutputLabel
```
JLabel additionalOutputLabel
```
  - advancedSearchSettingsPanel
```
JPanel advancedSearchSettingsPanel
```
  - advancedSettingsWarningLabel
```
JLabel advancedSettingsWarningLabel
```
  - backgroundPanel
```
JPanel backgroundPanel
```
  - closeButton
```
JButton closeButton
```
  - decoyDatabaseCmb
```
JComboBox<E> decoyDatabaseCmb
```
  - decoyDatabaseLabel
```
JLabel decoyDatabaseLabel
```
  - fragmentationMethodCmb
```
JComboBox<E> fragmentationMethodCmb
```
  - fragmentationMethodLabel
```
JLabel fragmentationMethodLabel
```
  - instrumentCmb
```
JComboBox<E> instrumentCmb
```
  - instrumentLabel
```
JLabel instrumentLabel
```
  - maxPepLengthTxt
```
JTextField maxPepLengthTxt
```
  - maxPtmsLabel
```
JLabel maxPtmsLabel
```
  - maxPtmsTxt
```
JTextField maxPtmsTxt
```
  - minPepLengthTxt
```
JTextField minPepLengthTxt
```
  - numberMatchesLabel
```
JLabel numberMatchesLabel
```
  - numberMatchesTxt
```
JTextField numberMatchesTxt
```
  - numberTerminiLabel
```
JLabel numberTerminiLabel
```
  - okButton
```
JButton okButton
```
  - openDialogHelpJButton
```
JButton openDialogHelpJButton
```
  - peptideLengthDividerLabel
```
JLabel peptideLengthDividerLabel
```
  - peptideLengthLabel
```
JLabel peptideLengthLabel
```
  - protocolCmb
```
JComboBox<E> protocolCmb
```
  - protocolLabel
```
JLabel protocolLabel
```
  - terminiCmb
```
JComboBox<E> terminiCmb
```

Class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.MyriMatchSettingsDialog extends JDialog implements Serializable

Serialized Fields

cancelled
```
boolean cancelled
```
Boolean indicating whether the used canceled the editing.
editable
```
boolean editable
```
Boolean indicating whether the settings can be edited by the user.
advancedSearchSettingsPanel
```
JPanel advancedSearchSettingsPanel
```
advancedSettingsPanel
```
JPanel advancedSettingsPanel
```
advancedSettingsWarningLabel
```
JLabel advancedSettingsWarningLabel
```
backgroundPanel
```
JPanel backgroundPanel
```
classSizeMultiplierLabel
```
JLabel classSizeMultiplierLabel
```
classSizeMultiplierTxt
```
JTextField classSizeMultiplierTxt
```
closeButton
```
JButton closeButton
```
computeXCorrCmb
```
JComboBox<E> computeXCorrCmb
```
computeXCorrlLabel
```
JLabel computeXCorrlLabel
```
fragmentationMethodCmb
```
JComboBox<E> fragmentationMethodCmb
```
fragmentationMethodLabel
```
JLabel fragmentationMethodLabel
```
maxPeakCountLabel
```
JLabel maxPeakCountLabel
```
maxPeakCountTxt
```
JTextField maxPeakCountTxt
```
maxPepLengthTxt
```
JTextField maxPepLengthTxt
```
maxPrecursorMassTxt
```
JTextField maxPrecursorMassTxt
```
maxPtmsLabel
```
JLabel maxPtmsLabel
```
maxPtmsTxt
```
JTextField maxPtmsTxt
```
minPepLengthTxt
```
JTextField minPepLengthTxt
```
minPrecursorMassTxt
```
JTextField minPrecursorMassTxt
```
numIntensityClassesLabel
```
JLabel numIntensityClassesLabel
```
numIntensityClassesTxt
```
JTextField numIntensityClassesTxt
```
numbBatchesLabel
```
JLabel numbBatchesLabel
```
numbBatchesTxt
```
JTextField numbBatchesTxt
```
numberMatchesLabel
```
JLabel numberMatchesLabel
```
numberMatchesTxt
```
JTextField numberMatchesTxt
```
numberTerminiLabel
```
JLabel numberTerminiLabel
```
okButton
```
JButton okButton
```
openDialogHelpJButton
```
JButton openDialogHelpJButton
```
outputFormatCmb
```
JComboBox<E> outputFormatCmb
```
outputFormatLabel
```
JLabel outputFormatLabel
```
peptideLengthDividerLabel
```
JLabel peptideLengthDividerLabel
```
peptideLengthLabel
```
JLabel peptideLengthLabel
```
precursorMassDividerLabel
```
JLabel precursorMassDividerLabel
```
precursorMassLabel
```
JLabel precursorMassLabel
```
scrollPane
```
JScrollPane scrollPane
```
terminiCmb
```
JComboBox<E> terminiCmb
```
ticCutoffPercentageLabel
```
JLabel ticCutoffPercentageLabel
```
ticCutoffPercentageTxt
```
JTextField ticCutoffPercentageTxt
```
useSmartPlusThreeModelCmb
```
JComboBox<E> useSmartPlusThreeModelCmb
```
useSmartPlusThreeModelLabel
```
JLabel useSmartPlusThreeModelLabel
```

Class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.NovorSettingsDialog extends JDialog implements Serializable
- Serialized Fields
  - searchParameters
```
SearchParameters searchParameters
```
    The search parameters.
  - canceled
```
boolean canceled
```
    True if the dialog was canceled by the user.
  - editable
```
boolean editable
```
    Boolean indicating whether the settings can be edited by the user.
  - backgroundPanel
```
JPanel backgroundPanel
```
  - cancelButton
```
JButton cancelButton
```
  - fragmentationMethodCmb
```
JComboBox<E> fragmentationMethodCmb
```
  - fragmentationMethodLabel
```
JLabel fragmentationMethodLabel
```
  - massAnalyzerCmb
```
JComboBox<E> massAnalyzerCmb
```
  - massAnalyzerLabel
```
JLabel massAnalyzerLabel
```
  - novorPanel
```
JPanel novorPanel
```
  - okButton
```
JButton okButton
```
  - openDialogHelpJButton
```
JButton openDialogHelpJButton
```

Class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.OmssaSettingsDialog extends JDialog implements Serializable

Serialized Fields

cancelled
```
boolean cancelled
```
Boolean indicating whether the used canceled the editing.
editable
```
boolean editable
```
Boolean indicating whether the settings can be edited by the user.
advancedSearchSettingsPanel
```
JPanel advancedSearchSettingsPanel
```
advancedSettingsWarningLabel
```
JLabel advancedSettingsWarningLabel
```
backgroundPanel
```
JPanel backgroundPanel
```
cTermIonsCmb
```
JComboBox<E> cTermIonsCmb
```
cTermIonsLbl
```
JLabel cTermIonsLbl
```
chargeEstimationCombo
```
JComboBox<E> chargeEstimationCombo
```
chargeReductionLabel
```
JLabel chargeReductionLabel
```

cleaveNterminalMethionineCmb

JComboBox<E> cleaveNterminalMethionineCmb

cleaveNterminalMethionineLbl
```
JLabel cleaveNterminalMethionineLbl
```
closeButton
```
JButton closeButton
```
consecutiveIonProbabilityLbl
```
JLabel consecutiveIonProbabilityLbl
```
consecutiveIonProbabilityTxt
```
JTextField consecutiveIonProbabilityTxt
```

correlationCorrectionScoreCmb

JComboBox<E> correlationCorrectionScoreCmb

correlationCorrectionScoreLbl
```
JLabel correlationCorrectionScoreLbl
```
databaseProcessingPanel
```
JPanel databaseProcessingPanel
```
doublyChargedNPeaksLbl
```
JLabel doublyChargedNPeaksLbl
```
doublyChargedNpeaksTxt
```
JTextField doublyChargedNpeaksTxt
```
doublyChargedWindowWidthLbl
```
JLabel doublyChargedWindowWidthLbl
```
doublyChargedWindowWidthTxt
```
JTextField doublyChargedWindowWidthTxt
```
eValueLbl
```
JLabel eValueLbl
```
eliminatePrecursorCombo
```
JComboBox<E> eliminatePrecursorCombo
```
forwardIonsFirstCmb
```
JComboBox<E> forwardIonsFirstCmb
```
forwardIonsFirstLbl
```
JLabel forwardIonsFirstLbl
```
fractionChargeLbl
```
JLabel fractionChargeLbl
```
fractionChargeTxt
```
JTextField fractionChargeTxt
```
highIntensityLbl
```
JLabel highIntensityLbl
```
highIntensityTxt
```
JTextField highIntensityTxt
```
hitListLbl
```
JLabel hitListLbl
```
hitlistTxt
```
JTextField hitlistTxt
```
intensityIncrementLbl
```
JLabel intensityIncrementLbl
```
intensityIncrementTxt
```
JTextField intensityIncrementTxt
```
iterativeReplaceEvalueLbl
```
JLabel iterativeReplaceEvalueLbl
```
iterativeReplaceEvalueTxt
```
JTextField iterativeReplaceEvalueTxt
```
iterativeSearchSettingsPanel
```
JPanel iterativeSearchSettingsPanel
```
iterativeSequenceEvalueLbl
```
JLabel iterativeSequenceEvalueLbl
```
iterativeSequenceEvalueTxt
```
JTextField iterativeSequenceEvalueTxt
```
iterativeSpectraEvalueLbl
```
JLabel iterativeSpectraEvalueLbl
```
iterativeSpectraEvalueTxt
```
JTextField iterativeSpectraEvalueTxt
```
jSeparator1
```
JSeparator jSeparator1
```
lowIntensityLbl
```
JLabel lowIntensityLbl
```
lowIntensityTxt
```
JTextField lowIntensityTxt
```
maxEvalueTxt
```
JTextField maxEvalueTxt
```
maxFragmentChargeLbl
```
JLabel maxFragmentChargeLbl
```
maxFragmentChargeTxt
```
JTextField maxFragmentChargeTxt
```
maxFragmentsPerSeriesLbl
```
JLabel maxFragmentsPerSeriesLbl
```
maxFragmentsPerSeriesTxt
```
JTextField maxFragmentsPerSeriesTxt
```
maxLaddersLbl
```
JLabel maxLaddersLbl
```
maxLaddersTxt
```
JTextField maxLaddersTxt
```
maxPepLengthTxt
```
JTextField maxPepLengthTxt
```
minAnnotatedMostIntensePeaksLbl
```
JLabel minAnnotatedMostIntensePeaksLbl
```

minAnnotatedMostIntensePeaksTxt

JTextField minAnnotatedMostIntensePeaksTxt

minAnnotatedPeaksLbl
```
JLabel minAnnotatedPeaksLbl
```
minAnnotatedPeaksTxt
```
JTextField minAnnotatedPeaksTxt
```
minPepLengthTxt
```
JTextField minPepLengthTxt
```

minPrecChargeMultipleChargedFragmentsTxt

JTextField minPrecChargeMultipleChargedFragmentsTxt

minPrecPerSpectrumLbl
```
JLabel minPrecPerSpectrumLbl
```
minPrecPerSpectrumTxt
```
JTextField minPrecPerSpectrumTxt
```

minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel

JLabel minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel

nHitsPerSpectrumPerChargeLbl
```
JLabel nHitsPerSpectrumPerChargeLbl
```
nHitsPerSpectrumPerChargeTxt
```
JTextField nHitsPerSpectrumPerChargeTxt
```
nPeaksLbl
```
JLabel nPeaksLbl
```
nPeaksTxt
```
JTextField nPeaksTxt
```
neutronLbl
```
JLabel neutronLbl
```
neutronTxt
```
JTextField neutronTxt
```
okButton
```
JButton okButton
```
omssaOutputFormatComboBox
```
JComboBox<E> omssaOutputFormatComboBox
```
omssaOutputFormatLabel
```
JLabel omssaOutputFormatLabel
```
openDialogHelpJButton
```
JButton openDialogHelpJButton
```
outputParametersPanel
```
JPanel outputParametersPanel
```
peptideLengthDividerLabel1
```
JLabel peptideLengthDividerLabel1
```
peptideLengthJLabel
```
JLabel peptideLengthJLabel
```
plusOneChargeAutomaticLbl
```
JLabel plusOneChargeAutomaticLbl
```
plusOneChargeCmb
```
JComboBox<E> plusOneChargeCmb
```
precursorChargeEstimationLabel
```
JLabel precursorChargeEstimationLabel
```
precursorMassScalingLabel
```
JLabel precursorMassScalingLabel
```
precursorScalingCombo
```
JComboBox<E> precursorScalingCombo
```
searchPositiveIonsCmb
```
JComboBox<E> searchPositiveIonsCmb
```
searchPositiveIonsLbl
```
JLabel searchPositiveIonsLbl
```
searchSettingsPanel
```
JPanel searchSettingsPanel
```
searchSettingsScrollPane
```
JScrollPane searchSettingsScrollPane
```
semiEnzymaticParametersPanel
```
JPanel semiEnzymaticParametersPanel
```
sequenceMappingCmb
```
JComboBox<E> sequenceMappingCmb
```
sequenceMappingLbl
```
JLabel sequenceMappingLbl
```
singlyChargedNPeaksLbl
```
JLabel singlyChargedNPeaksLbl
```
singlyChargedNpeaksTxt
```
JTextField singlyChargedNpeaksTxt
```
singlyChargedWindowWidthLbl
```
JLabel singlyChargedWindowWidthLbl
```
singlyChargedWindowWidthTxt
```
JTextField singlyChargedWindowWidthTxt
```
spectrumProcessingPanel
```
JPanel spectrumProcessingPanel
```
tabbedPane
```
JTabbedPane tabbedPane
```

Class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.PNovoSettingsDialog extends JDialog implements Serializable
- Serialized Fields
  - searchParameters
```
SearchParameters searchParameters
```
    The search parameters.
  - canceled
```
boolean canceled
```
    True if the dialog was canceled by the user.
  - editable
```
boolean editable
```
    Boolean indicating whether the settings can be edited by the user.
  - activationTypeCmb
```
JComboBox<E> activationTypeCmb
```
  - activationTypeLabel
```
JLabel activationTypeLabel
```
  - backgroundPanel
```
JPanel backgroundPanel
```
  - cancelButton
```
JButton cancelButton
```
  - maxPrecursorMassLabel
```
JLabel maxPrecursorMassLabel
```
  - maxPrecursorMassTextField
```
JTextField maxPrecursorMassTextField
```
  - minPrecursorMassLabel
```
JLabel minPrecursorMassLabel
```
  - minPrecursorMassTextField
```
JTextField minPrecursorMassTextField
```
  - okButton
```
JButton okButton
```
  - openDialogHelpJButton
```
JButton openDialogHelpJButton
```
  - pNovoPanel
```
JPanel pNovoPanel
```

Class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.TideSettingsDialog extends JDialog implements Serializable

Serialized Fields

cancelled
```
boolean cancelled
```
Boolean indicating whether the used canceled the editing.
editable
```
boolean editable
```
Boolean indicating whether the settings can be edited by the user.
advancedSettingsWarningLabel
```
JLabel advancedSettingsWarningLabel
```
backgroundPanel
```
JPanel backgroundPanel
```
chargesCombo
```
JComboBox<E> chargesCombo
```
chargesLabel
```
JLabel chargesLabel
```
closeButton
```
JButton closeButton
```
decoyFormatCombo
```
JComboBox<E> decoyFormatCombo
```
decoySeedLabel
```
JLabel decoySeedLabel
```
decoySeedTxt
```
JTextField decoySeedTxt
```
decoyformatLabel
```
JLabel decoyformatLabel
```
enzymeTypeCmb
```
JComboBox<E> enzymeTypeCmb
```
enzymeTypeLabel
```
JLabel enzymeTypeLabel
```
exactPvalueCombo
```
JComboBox<E> exactPvalueCombo
```
exactPvalueLabel
```
JLabel exactPvalueLabel
```
indexPanel
```
JPanel indexPanel
```
keepTerminalAaCombo
```
JComboBox<E> keepTerminalAaCombo
```
keepTerminalAaLabel
```
JLabel keepTerminalAaLabel
```
maxPepLengthTxt
```
JTextField maxPepLengthTxt
```
maxPrecursorMassTxt
```
JTextField maxPrecursorMassTxt
```
maxPtmsLabel
```
JLabel maxPtmsLabel
```
maxPtmsTxt
```
JTextField maxPtmsTxt
```
maxSpectrumMzTxt
```
JTextField maxSpectrumMzTxt
```
maxVariablePtmsPerTypeLabel
```
JLabel maxVariablePtmsPerTypeLabel
```
maxVariablePtmsPerTypeTxt
```
JTextField maxVariablePtmsPerTypeTxt
```
minPeaksLbl
```
JLabel minPeaksLbl
```
minPeaksTxt
```
JTextField minPeaksTxt
```
minPepLengthTxt
```
JTextField minPepLengthTxt
```
minPrecursorMassTxt
```
JTextField minPrecursorMassTxt
```
minSpectrumMzTxt
```
JTextField minSpectrumMzTxt
```
monoPrecursorCmb
```
JComboBox<E> monoPrecursorCmb
```
monoPrecursorLabel
```
JLabel monoPrecursorLabel
```
mzBinOffsetLabel
```
JLabel mzBinOffsetLabel
```
mzBinOffsetTxt
```
JTextField mzBinOffsetTxt
```
mzBinWidthLabel
```
JLabel mzBinWidthLabel
```
mzBinWidthTxt
```
JTextField mzBinWidthTxt
```
numberMatchesLabel
```
JLabel numberMatchesLabel
```
numberMatchesTxt
```
JTextField numberMatchesTxt
```
okButton
```
JButton okButton
```
openDialogHelpJButton
```
JButton openDialogHelpJButton
```
outputFormatCombo
```
JComboBox<E> outputFormatCombo
```
outputFormatLabel
```
JLabel outputFormatLabel
```
peptideLengthDividerLabel
```
JLabel peptideLengthDividerLabel
```
peptideLengthLabel
```
JLabel peptideLengthLabel
```
peptideListCmb
```
JComboBox<E> peptideListCmb
```
peptideListLabel
```
JLabel peptideListLabel
```
precursorMassDividerLabel
```
JLabel precursorMassDividerLabel
```
precursorMassLabel
```
JLabel precursorMassLabel
```
removeMethionineCmb
```
JComboBox<E> removeMethionineCmb
```
removeMethionineLabel
```
JLabel removeMethionineLabel
```
removePrecursorPeakCombo
```
JComboBox<E> removePrecursorPeakCombo
```
removePrecursorPeakLabel
```
JLabel removePrecursorPeakLabel
```
removePrecursorPeakToleranceLbl
```
JLabel removePrecursorPeakToleranceLbl
```

removePrecursorPeakToleranceTxt

JTextField removePrecursorPeakToleranceTxt

removeTempFoldersCmb
```
JComboBox<E> removeTempFoldersCmb
```
removeTempFoldersLabel
```
JLabel removeTempFoldersLabel
```
searchPanel
```
JPanel searchPanel
```
spScoreCombo
```
JComboBox<E> spScoreCombo
```
spScoreLabel
```
JLabel spScoreLabel
```
spectrumMzDividerLabel
```
JLabel spectrumMzDividerLabel
```
spectrumMzLabel
```
JLabel spectrumMzLabel
```
tabbedPane
```
JTabbedPane tabbedPane
```
useFlankingCmb
```
JComboBox<E> useFlankingCmb
```
useFlankingLabel
```
JLabel useFlankingLabel
```
useNeutralLossCmb
```
JComboBox<E> useNeutralLossCmb
```
useNeutralLossLabel
```
JLabel useNeutralLossLabel
```

Class com.compomics.util.gui.parameters.identification_parameters.algorithm_settings.XTandemSettingsDialog extends JDialog implements Serializable

Serialized Fields

modificationProfile
```
PtmSettings modificationProfile
```
The modification profile used for the search.
fragmentIonMassAccuracyInDa
```
double fragmentIonMassAccuracyInDa
```
The fragment ion mass accuracy.
cancelled
```
boolean cancelled
```
Boolean indicating whether the used canceled the editing.
modificationTableToolTips
```
ArrayList<E> modificationTableToolTips
```
The modification table column header tooltips.
ptmFactory
```
PTMFactory ptmFactory
```
The post translational modifications factory.
modProfileChanged
```
boolean modProfileChanged
```
Boolean indicating whether the modification profile has been changed. Note that it only checks if the user has made changed to the selection, not if the end result is different or not.
editable
```
boolean editable
```
Boolean indicating whether the settings can be edited by the user.
advancedSearchSettingsPanel
```
JPanel advancedSearchSettingsPanel
```
advancedSettingsWarningLabel
```
JLabel advancedSettingsWarningLabel
```
backgroundPanel
```
JPanel backgroundPanel
```
closeButton
```
JButton closeButton
```
dynamicRangeLbl
```
JLabel dynamicRangeLbl
```
dynamicRangeTxt
```
JTextField dynamicRangeTxt
```
eValueLbl
```
JLabel eValueLbl
```
eValueTxt
```
JTextField eValueTxt
```
jSeparator1
```
JSeparator jSeparator1
```
maxEValueRefineTxt
```
JTextField maxEValueRefineTxt
```
maxEValueRefinmentLbl
```
JLabel maxEValueRefinmentLbl
```
minFragMzLbl
```
JLabel minFragMzLbl
```
minFragmentMzTxt
```
JTextField minFragmentMzTxt
```
minPeaksLbl
```
JLabel minPeaksLbl
```
minPeaksTxt
```
JTextField minPeaksTxt
```
minPrecMassLbl
```
JLabel minPrecMassLbl
```
minPrecMassTxt
```
JTextField minPrecMassTxt
```
modificationsJScrollPane
```
JScrollPane modificationsJScrollPane
```
modificationsTable
```
JTable modificationsTable
```
nPeaksLbl
```
JLabel nPeaksLbl
```
nPeaksTxt
```
JTextField nPeaksTxt
```
noiseSuppressionCmb
```
JComboBox<E> noiseSuppressionCmb
```
noiseSuppressionLabel
```
JLabel noiseSuppressionLabel
```
okButton
```
JButton okButton
```
openDialogHelpJButton
```
JButton openDialogHelpJButton
```
openModificationSettingsJButton
```
JButton openModificationSettingsJButton
```
outputHistogramsCmb
```
JComboBox<E> outputHistogramsCmb
```
outputHistogramsLabel
```
JLabel outputHistogramsLabel
```
outputProteinsCmb
```
JComboBox<E> outputProteinsCmb
```
outputProteinsLabel
```
JLabel outputProteinsLabel
```
outputResultsCmb
```
JComboBox<E> outputResultsCmb
```
outputResultsLabel
```
JLabel outputResultsLabel
```
outputSequencesCmb
```
JComboBox<E> outputSequencesCmb
```
outputSequencesLabel
```
JLabel outputSequencesLabel
```
outputSettingsPanel
```
JPanel outputSettingsPanel
```
outputSpectraCmb
```
JComboBox<E> outputSpectraCmb
```
outputSpectraLabel
```
JLabel outputSpectraLabel
```
pointMutationLabel
```
JLabel pointMutationLabel
```
pointMutationsCmb
```
JComboBox<E> pointMutationsCmb
```
potentialModificationsCmb
```
JComboBox<E> potentialModificationsCmb
```
ptmComplexityLbl
```
JLabel ptmComplexityLbl
```
ptmComplexityTxt
```
JTextField ptmComplexityTxt
```
quickAcetylCmb
```
JComboBox<E> quickAcetylCmb
```
quickAcetylLabel
```
JLabel quickAcetylLabel
```
quickPyroCmb
```
JComboBox<E> quickPyroCmb
```
quickPyroLabel
```
JLabel quickPyroLabel
```
refinementCmb
```
JComboBox<E> refinementCmb
```
refinementLabel
```
JLabel refinementLabel
```
refinementModificationsJPanel
```
JPanel refinementModificationsJPanel
```
refinementModificationsLabel
```
JLabel refinementModificationsLabel
```
refinementSettingsPanel
```
JPanel refinementSettingsPanel
```
semiEnzymaticCmb
```
JComboBox<E> semiEnzymaticCmb
```
semiEnzymaticLabel
```
JLabel semiEnzymaticLabel
```
skylinePathValueLbl
```
JLabel skylinePathValueLbl
```
skylineTxt
```
JTextField skylineTxt
```
snapsCmb
```
JComboBox<E> snapsCmb
```
snapsLabel
```
JLabel snapsLabel
```
spectrumImportSettingsPanel
```
JPanel spectrumImportSettingsPanel
```
spectrumSynthesisCmb
```
JComboBox<E> spectrumSynthesisCmb
```
spectrumSynthesisLabel
```
JLabel spectrumSynthesisLabel
```
stpBiasCmb
```
JComboBox<E> stpBiasCmb
```
stpBiasLabel
```
JLabel stpBiasLabel
```
tabbedPane
```
JTabbedPane tabbedPane
```
unanticipatedCleavageCmb
```
JComboBox<E> unanticipatedCleavageCmb
```
unanticipatedCleavageLabel
```
JLabel unanticipatedCleavageLabel
```
usePotentialModsLabel
```
JLabel usePotentialModsLabel
```

Package com.compomics.util.gui.protein
- Class com.compomics.util.gui.protein.AdvancedProteinDatabaseDialog extends JDialog implements Serializable
  - Serialized Fields
    - dbFolder
```
File dbFolder
```
      The database folder.
    - userPreferences
```
UtilitiesUserPreferences userPreferences
```
      The user preferences.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - browseDatabaseFolderButton
```
JButton browseDatabaseFolderButton
```
    - cancelButton
```
JButton cancelButton
```
    - clearDatabaseFolderButton
```
JButton clearDatabaseFolderButton
```
    - databasesFolderTxt
```
JTextField databasesFolderTxt
```
    - fastaSuffixTxt
```
JTextField fastaSuffixTxt
```
    - fileProcessingPanel
```
JPanel fileProcessingPanel
```
    - folderPanel
```
JPanel folderPanel
```
    - okButton
```
JButton okButton
```
- Class com.compomics.util.gui.protein.SequenceModificationPanel extends JPanel implements Serializable
  - Serialized Fields
    - fragmentIonRectangles
```
HashMap<K,V> fragmentIonRectangles
```
      A map of the rectangles used to draw each profile peak. This map is later used for the tooltip for each peak.
    - iSequenceComponents
```
String[] iSequenceComponents
```
      Elementary data for composing the Panel.
    - profiles
```
ArrayList<E> profiles
```
      The list of modification profiles.
    - iBaseFont
```
Font iBaseFont
```
      The font to use.
    - iMaxBarHeight
```
double iMaxBarHeight
```
      The maximum bar height.
    - iBarWidth
```
int iBarWidth
```
      The width of the bars.
    - iHorizontalSpace
```
int iHorizontalSpace
```
      The horizontal space.
    - iXStart
```
int iXStart
```
      The x-axis start position.
    - iYStart
```
int iYStart
```
      The y-axis start position.
    - isModifiedSequence
```
boolean isModifiedSequence
```
      This boolean holds whether or not the given sequence is a modified sequence or a normal peptide sequence. Normal: KENNY Modified: NH2-K<Ace>ENNY-COOH
    - score1Name
```
String score1Name
```
      The name of the score above of the sequence.
    - score2Name
```
String score2Name
```
      The name of the score under of the sequence.
Package com.compomics.util.gui.ptm
- Class com.compomics.util.gui.ptm.ModificationsDialog extends JDialog implements Serializable
  - Serialized Fields
    - ptmFactory
```
PTMFactory ptmFactory
```
      The post translational modifications factory.
    - sparklineColor
```
Color sparklineColor
```
      The color used for the sparkline bar chart plots.
    - selectedRowHtmlTagFontColor
```
String selectedRowHtmlTagFontColor
```
      The color to use for the HTML tags for the selected rows, in HTML color code.
    - notSelectedRowHtmlTagFontColor
```
String notSelectedRowHtmlTagFontColor
```
      The color to use for the HTML tags for the rows that are not selected, in HTML color code.
    - defaultModsTableToolTips
```
ArrayList<E> defaultModsTableToolTips
```
      The default mods table column header tooltips.
    - userModsTableToolTips
```
ArrayList<E> userModsTableToolTips
```
      The user mods table column header tooltips.
    - searchPossibilities
```
ArrayList<E> searchPossibilities
```
      The lines of the PTMs concerned by the search.
    - searchCurrentSelection
```
int searchCurrentSelection
```
      The search current selection.
    - searchWelcomeText
```
String searchWelcomeText
```
      The search text to display by default.
    - addUserPTM
```
JButton addUserPTM
```
    - defaultModificationsTable
```
JTable defaultModificationsTable
```
    - defaultModsPanel
```
JPanel defaultModsPanel
```
    - defaultModsScrollPane
```
JScrollPane defaultModsScrollPane
```
    - defaultPtmPopupMenu
```
JPopupMenu defaultPtmPopupMenu
```
    - deleteUserPTM
```
JButton deleteUserPTM
```
    - editUserPTM
```
JButton editUserPTM
```
    - editUserPtmJMenuItem
```
JMenuItem editUserPtmJMenuItem
```
    - findJLabel
```
JLabel findJLabel
```
    - modificationsEditorPanel
```
JPanel modificationsEditorPanel
```
    - modificationsHelpJButton
```
JButton modificationsHelpJButton
```
    - modificationsSplitPane
```
JSplitPane modificationsSplitPane
```
    - okButton
```
JButton okButton
```
    - searchIndexLabel
```
JLabel searchIndexLabel
```
    - searchInputTxt
```
JTextField searchInputTxt
```
    - searchNextButton
```
JButton searchNextButton
```
    - searchPreviousButton
```
JButton searchPreviousButton
```
    - userModificationsTable
```
JTable userModificationsTable
```
    - userModsPanel
```
JPanel userModsPanel
```
    - userModsScrollPane
```
JScrollPane userModsScrollPane
```
    - userPtmPopupMenu
```
JPopupMenu userPtmPopupMenu
```
    - viewDefaultPtmJMenuItem
```
JMenuItem viewDefaultPtmJMenuItem
```
- Class com.compomics.util.gui.ptm.PtmDialog extends JDialog implements Serializable
  - Serialized Fields
    - ptmFactory
```
PTMFactory ptmFactory
```
      The post translational modifications factory.
    - currentPtm
```
PTM currentPtm
```
      The edited PTM.
    - neutralLosses
```
ArrayList<E> neutralLosses
```
      The neutral losses.
    - reporterIons
```
ArrayList<E> reporterIons
```
      The reporter ions.
    - editable
```
boolean editable
```
      Boolean indicating whether the user can edit the PTM or not.
    - pattern
```
AminoAcidPattern pattern
```
      The amino acid pattern of the modification
    - atomChainAdded
```
AtomChain atomChainAdded
```
      The atom chain added by the modification.
    - atomChainRemoved
```
AtomChain atomChainRemoved
```
      The atom chain removed by the modification.
    - reporterIonTableToolTips
```
ArrayList<E> reporterIonTableToolTips
```
      The reporter ion table column header tooltips.
    - neutralLossesTableToolTips
```
ArrayList<E> neutralLossesTableToolTips
```
      The neutral losses table column header tooltips.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the edition has been canceled by the user.
    - addNeutralLoss
```
JButton addNeutralLoss
```
    - addReporterIon
```
JButton addReporterIon
```
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - compositionLabel
```
JLabel compositionLabel
```
    - compositionTxt
```
JTextField compositionTxt
```
    - cvExampleLabel
```
JLabel cvExampleLabel
```
    - detailsPanel
```
JPanel detailsPanel
```
    - helpJButton
```
JButton helpJButton
```
    - jLabel1
```
JLabel jLabel1
```
    - massLabel
```
JLabel massLabel
```
    - massTxt
```
JTextField massTxt
```
    - nameLabel
```
JLabel nameLabel
```
    - nameShortLabel
```
JLabel nameShortLabel
```
    - nameShortTxt
```
JTextField nameShortTxt
```
    - nameTxt
```
JTextField nameTxt
```
    - neutralLossesJScrollPane
```
JScrollPane neutralLossesJScrollPane
```
    - neutralLossesPanel
```
JPanel neutralLossesPanel
```
    - neutralLossesTable
```
JTable neutralLossesTable
```
    - okButton
```
JButton okButton
```
    - patternLabel
```
JLabel patternLabel
```
    - patternTxt
```
JTextField patternTxt
```
    - removeNeutralLoss
```
JButton removeNeutralLoss
```
    - removerReporterIon
```
JButton removerReporterIon
```
    - reporterIonsJScrollPane
```
JScrollPane reporterIonsJScrollPane
```
    - reporterIonsPanel
```
JPanel reporterIonsPanel
```
    - reporterIonsTable
```
JTable reporterIonsTable
```
    - scrollPane
```
JScrollPane scrollPane
```
    - scrollPanePanel
```
JPanel scrollPanePanel
```
    - typeCmb
```
JComboBox<E> typeCmb
```
    - unimodAccessionJTextField
```
JTextField unimodAccessionJTextField
```
    - unimodAccessionLabel
```
JLabel unimodAccessionLabel
```
    - unimodLinkLabel
```
JLabel unimodLinkLabel
```
    - unimodMappingPanel
```
JPanel unimodMappingPanel
```
    - unimodNameJTextField
```
JTextField unimodNameJTextField
```
    - unimodNameLabel
```
JLabel unimodNameLabel
```
Package com.compomics.util.gui.renderers
- Class com.compomics.util.gui.renderers.AlignedListCellRenderer extends DefaultListCellRenderer implements Serializable
  - Serialized Fields
    - align
```
int align
```
      One of the following constants defined in SwingConstants: LEFT, CENTER (the default for image-only labels), RIGHT, LEADING (the default for text-only labels) or TRAILING.
- Class com.compomics.util.gui.renderers.ByteArrayRenderer extends DefaultTableCellRenderer implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iData
```
byte[] iData
```
      This byte[] is the actual data cached by the renderer.
- Class com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer extends JLabel implements Serializable
  - Serialized Fields
    - minXAxisValue
```
double minXAxisValue
```
      The minimum x-axis value.
    - maxXAxisValue
```
double maxXAxisValue
```
      The maxium x-axis value.
    - delegate
```
TableCellRenderer delegate
```
      A reference to a standard table cell renderer.
- Class com.compomics.util.gui.renderers.TimestampRenderer extends DefaultTableCellRenderer implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
- Class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer extends BasicComboBoxRenderer implements Serializable
  - Serialized Fields
    - tooltips
```
Vector<E> tooltips
```
      The tooltips for each element in the list.
    - align
```
int align
```
      The horizontal alignment of the text.
    - MAX_TOOLTIP_WIDTH
```
int MAX_TOOLTIP_WIDTH
```
      The maximum width of a tool tip (in number of characters). Tooltips longer than the maximum will be split into multiple lines.
    - backgroundColor
```
Color backgroundColor
```
      The background color for the list. Defaults to white if not set.
Package com.compomics.util.gui.spectrum
- Class com.compomics.util.gui.spectrum.ChromatogramPanel extends GraphicsPanel implements Serializable
  - Serialized Fields
    - iChromatogramColor
```
Color iChromatogramColor
```
      Color in which the profileChromatogram polyline is rendered. Defaults to gray.
    - iChromatogramPointColor
```
Color iChromatogramPointColor
```
      Color in which the data points and peaks are rendered. Defaults to black.
- Class com.compomics.util.gui.spectrum.FragmentIonTable extends JTable implements Serializable
  - Serialized Fields
    - currentFragmentIonTypes
```
HashSet<E> currentFragmentIonTypes
```
      The list of currently selected fragment ion types.
    - neutralLosses
```
NeutralLossesMap neutralLosses
```
      The list of the currently selected neutral loss types.
    - singleCharge
```
boolean singleCharge
```
      If true, singly charge ions are included in the table.
    - twoCharges
```
boolean twoCharges
```
      If true, doubly charged ions are included in the table.
    - tooltips
```
ArrayList<E> tooltips
```
      The table tooltips.
    - currentPeptide
```
Peptide currentPeptide
```
      The current peptide.
    - peptideSequence
```
String peptideSequence
```
      The current peptide sequence.
    - allAnnotations
```
ArrayList<E> allAnnotations
```
      The spectrum annotations map.
    - allSpectra
```
ArrayList<E> allSpectra
```
      The list of spectra. Needed for intensity normalization.
- Class com.compomics.util.gui.spectrum.GraphicsPanel extends JPanel implements Serializable
  - Serialized Fields
    - peakWidth
```
float peakWidth
```
      The width used for the annotated peaks.
    - backgroundPeakWidth
```
float backgroundPeakWidth
```
      The width used for the background peaks.
    - subscriptAnnotationNumbers
```
boolean subscriptAnnotationNumbers
```
      If true, all numbers in peak annotations are subscripted.
    - peakWaterMarkColor
```
Color peakWaterMarkColor
```
      The color to use for the non-annotated peaks when only the annotated peaks are to be shown.
    - scientificXAxis
```
boolean scientificXAxis
```
      If true the x-axis will be drawn using the scientific annotation. The pattern i set in the "scientificPattern" field.
    - scientificYAxis
```
boolean scientificYAxis
```
      If true the y-axis will be drawn using the scientific annotation. The pattern i set in the "scientificPattern" field.
    - scientificPattern
```
String scientificPattern
```
      The number format pattern for scientific annotation.
    - referenceAreasXAxis
```
HashMap<K,V> referenceAreasXAxis
```
      A hashmap of the current x-axis reference areas. Key is the name of the reference area.
    - referenceAreasYAxis
```
HashMap<K,V> referenceAreasYAxis
```
      A hashmap of the current y-axis reference areas. Key is the name of the reference area.
    - miniature
```
boolean miniature
```
      If set to true, the y-axis is removed, the y- and x-axis tags are removed, and any annotations are hidden. All to make the graphics panel look better in a smaller version, e.g., when put into a table cell. When turning miniature mode one it is also recommended to reduce the max padding. Note that miniature and reduced max padding is set automatically by the GraphicsPanelTableCellRenderer.
    - yDataIsPositive
```
boolean yDataIsPositive
```
      If set to true, all y data is assumed to be positive. This adds a white polygon under the y-axis hiding any polygon data lines that crosses (slightly) below the y-axis.
    - alphaLevel
```
float alphaLevel
```
      The opacity of the spectra. 0 means completely see-through, 1 means opaque.
    - dataSetCounter
```
int dataSetCounter
```
      The number of datasets currently displayed in the panel.
    - dataSetCounterMirroredSpectra
```
int dataSetCounterMirroredSpectra
```
      The number of mirrored datasets currently displayed in the panel.
    - INTERACTIVE_STATUS
```
int INTERACTIVE_STATUS
```
      This status indicates that no annotation will be displayed, but the user will have a fully functional interface (point clicking, selecting, sequencing etc.)
    - ANNOTATED_STATUS
```
int ANNOTATED_STATUS
```
      This status indicates that annotation (if present) will be displayed, while limiting the user to zooming in/out.
    - useMassDeltaCombinations
```
boolean useMassDeltaCombinations
```
      If true, pairs of delta mass annotations are used when doing de novo sequencing. If false, only single delta masses are annotated.
    - deltaMassWindow
```
double deltaMassWindow
```
      The size of the window to use when searching for matches in the known masses list when the user hovers over a second data point after clicking a previous data point.
    - iXAxisLabel
```
String iXAxisLabel
```
      The label (and unit between brackets, if available) for the x-axis. Defaults to "m/z".
    - iYAxisLabel
```
String iYAxisLabel
```
      The label (and unit between brackets, if available) for the y-axis. Defaults to "Int".
    - iFilenameColor
```
Color iFilenameColor
```
      This is the color the filename should be presented in.
    - iDataPointAndLineColor
```
ArrayList<E> iDataPointAndLineColor
```
      Colors in which the data points and peaks are rendered. Indexed by dataset.
    - iDataPointAndLineColorMirroredSpectra
```
ArrayList<E> iDataPointAndLineColorMirroredSpectra
```
      Colors in which the data points and peaks are rendered for the mirrored spectra. Indexed by dataset.
    - iAreaUnderCurveColor
```
ArrayList<E> iAreaUnderCurveColor
```
      Colors in which the chromatogram polyline is rendered. Indexed by dataset.
    - iAreaUnderCurveColorMirroredSpectra
```
ArrayList<E> iAreaUnderCurveColorMirroredSpectra
```
      Colors in which the chromatogram polyline is rendered for the mirrored spectra. Indexed by dataset.
    - iPointSize
```
Integer iPointSize
```
      Size for the point on a polygon.
    - iFilename
```
String iFilename
```
      The spectrum or chromatogram filename.
    - iFilenameMirrorredSpectrum
```
String iFilenameMirrorredSpectrum
```
      The spectrum or chromatogram filename for the mirrored spectrum or chromatogram.
    - iSpecPanelListeners
```
ArrayList<E> iSpecPanelListeners
```
      The list of SpectrumPanelListeners.
    - iPointDetectionTolerance
```
int iPointDetectionTolerance
```
      The deviation (both left and right) allowed for point highlighting detection.
    - iStartXLoc
```
int iStartXLoc
```
      When the mouse is dragged, this represents the X-coordinate of the starting location.
    - iStartYLoc
```
int iStartYLoc
```
      When the mouse is dragged, this represents the Y-coordinate of the starting location.
    - iEndXLoc
```
int iEndXLoc
```
      When the mouse is dragged, this represents the X-coordinate of the ending location.
    - xAxisZoomRangeLowerValue
```
double xAxisZoomRangeLowerValue
```
      The lower range for the current zoom range.
    - xAxisZoomRangeUpperValue
```
double xAxisZoomRangeUpperValue
```
      The upper range for the current zoom range.
    - iDragXLoc
```
int iDragXLoc
```
      The current dragging location.
    - iXScaleUnit
```
double iXScaleUnit
```
      Scale unit for the X axis.
    - iYScaleUnit
```
double iYScaleUnit
```
      Scale unit for the Y axis.
    - iXUnit
```
int iXUnit
```
      Graphical unit for the X axis.
    - iYUnit
```
int iYUnit
```
      Graphical unit for the Y axis.
    - iXPadding
```
int iXPadding
```
      Effective distance from the x-axis to the panel border.
    - iTopPadding
```
int iTopPadding
```
      Effective distance from the panel top border to 5 pixels above the top of the highest point (or y-tick mark).
    - iXAxisStartAtZero
```
boolean iXAxisStartAtZero
```
      This boolean is set to 'true' if the x-axis should start at zero.
    - iDragged
```
boolean iDragged
```
      This boolean is set to 'true' when dragging is performed.
    - xTagCount
```
int xTagCount
```
      The number of X-axis tags.
    - yTagCount
```
int yTagCount
```
      The number of Y-axis tags.
    - padding
```
int padding
```
      The padding (distance between the axes and the border of the panel).
    - currentPadding
```
int currentPadding
```
      The current padding (distance between the axes and the border of the panel).
    - maxPadding
```
int maxPadding
```
      The maximum padding (distance between the axes and the border of the panel). Increase if font size on the y-axis becomes too small.
    - showFileName
```
boolean showFileName
```
      The boolean is set to 'true' if the file name is to be shown in the panel.
    - showPrecursorDetails
```
boolean showPrecursorDetails
```
      The boolean is set to 'true' if the precursor details is to be shown in the panel.
    - showResolution
```
boolean showResolution
```
      The boolean is set to 'true' if the resolution is to be shown in the panel.
    - iXAxisData
```
ArrayList<E> iXAxisData
```
      All the x-axis data points. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc.Should at all times be sorted from high to low.
    - iXAxisDataMirroredSpectrum
```
ArrayList<E> iXAxisDataMirroredSpectrum
```
      All the x-axis data points for the mirrored spectrum. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc.Should at all times be sorted from high to low.
    - iXAxisMin
```
double iXAxisMin
```
      The minimum x-axis value to display.
    - iXAxisMax
```
double iXAxisMax
```
      The maximum x-axis value to display.
    - iYAxisMin
```
double iYAxisMin
```
      The minimum y-axis value to display.
    - iYAxisMax
```
double iYAxisMax
```
      The maximum y-axis value to display.
    - iAnnotationYAxisThreshold
```
double iAnnotationYAxisThreshold
```
      The percent non-inclusive, minimal y-axis value (compared to the highest point in the spectrum) a point should have before being eligible for annotation. Default is '0.0'.
    - iYAxisData
```
ArrayList<E> iYAxisData
```
      All the y-axis values. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc. Y-axis values are related to the x-axis values by the table index. So the first y-axis value of the first dataset is the value for the first x-axis value in the first dataset etc.
    - iYAxisDataMirroredSpectrum
```
ArrayList<E> iYAxisDataMirroredSpectrum
```
      All the y-axis values for the mirrored spectra. Indexed by dataset (one double[] per dataset). First dataset is the first double[], second dataset is the second double[] etc. Y-axis values are related to the x-axis values by the table index. So the first y-axis value of the first dataset is the value for the first x-axis value in the first dataset etc.
    - iPrecursorMZ
```
double iPrecursorMZ
```
      This variable holds the precursor M/Z.
    - iPrecursorMZMirroredSpectrum
```
double iPrecursorMZMirroredSpectrum
```
      This variable holds the precursor M/Z for the mirrored spectrum.
    - iPrecursorCharge
```
String iPrecursorCharge
```
      This String holds the charge for the precursor.
    - iPrecursorChargeMirorredSpectrum
```
String iPrecursorChargeMirorredSpectrum
```
      This String holds the charge for the precursor for the mirrored spectrum.
    - iXAxisDataInPixels
```
ArrayList<E> iXAxisDataInPixels
```
      This array will hold the x-coordinates in pixels for all the x-axis values. Link is through index. Again indexed by dataset (one double[] per dataset).
    - iYAxisDataInPixels
```
ArrayList<E> iYAxisDataInPixels
```
      This array will hold the y-coordinates in pixels for all the y-axis values. Link is through index. Again indexed by dataset (one double[] per dataset).
    - iXAxisDataInPixelsMirroredSpectrum
```
ArrayList<E> iXAxisDataInPixelsMirroredSpectrum
```
      This array will hold the x-coordinates in pixels for all the x-axis values of the mirrored spectrum. Link is through index. Again indexed by dataset (one double[] per dataset).
    - iYAxisDataInPixelsMirroredSpectrum
```
ArrayList<E> iYAxisDataInPixelsMirroredSpectrum
```
      This array will hold the y-coordinates in pixels for all the y-axis values of the mirrored spectrum. Link is through index. Again indexed by dataset (one double[] per dataset).
    - iHighLight
```
boolean iHighLight
```
      Boolean that will be 'true' when a point needs highlighting.
    - iHighLightMirrored
```
boolean iHighLightMirrored
```
      Boolean that will be 'true' when a point needs highlighting in the mirrored spectra.
    - iHighLightIndex
```
int iHighLightIndex
```
      Index of the point that needs to be highlighted.
    - iHighLightIndexMirrored
```
int iHighLightIndexMirrored
```
      Index of the point that needs to be highlighted in the mirrored spectra.
    - iHighLightDatasetIndex
```
int iHighLightDatasetIndex
```
      Index of the dataset containing the point that needs to be highlighted.
    - iHighLightDatasetIndexMirrored
```
int iHighLightDatasetIndexMirrored
```
      Index of the dataset containing the point that needs to be highlighted in the mirrored spectra.
    - iClicked
```
boolean iClicked
```
      Boolean that indicates whether a point has been marked by clicking.
    - iClickedMirrored
```
boolean iClickedMirrored
```
      Boolean that indicates whether a point has been marked by clicking in the mirrored spectra.
    - iClickedIndex
```
int iClickedIndex
```
      Int that indicates which point was clicked.
    - iClickedIndexMirrored
```
int iClickedIndexMirrored
```
      Int that indicates which point was clicked in the mirrored spectra.
    - iClickedDataSetIndex
```
int iClickedDataSetIndex
```
      Int that indicates which dataset contains the clicked point.
    - iClickedDataSetIndexMirrored
```
int iClickedDataSetIndexMirrored
```
      Int that indicates which dataset contains the clicked point in the mirrored spectra.
    - iClickedList
```
Vector<E> iClickedList
```
      The Vector that holds all points clicked up to now.
    - iClickedListMirrored
```
Vector<E> iClickedListMirrored
```
      The Vector that holds all points clicked up to now in the mirrored spectra.
    - iClickedListDatasetIndices
```
Vector<E> iClickedListDatasetIndices
```
      The Vector that holds the dataset indices of all points clicked up to now.
    - iClickedListDatasetIndicesMirrored
```
Vector<E> iClickedListDatasetIndicesMirrored
```
      The Vector that holds the dataset indices of all points clicked up to now in the mirrored spectra.
    - iStoredSequence
```
Vector<E> iStoredSequence
```
      The Vector that holds a set of stored points from a previously established list.
    - iStoredSequenceMirrored
```
Vector<E> iStoredSequenceMirrored
```
      The Vector that holds a set of stored points from a previously established list in the mirrored spectra.
    - iStoredSequenceDatasetIndices
```
Vector<E> iStoredSequenceDatasetIndices
```
      The Vector that holds the dataset indices of stored points from a previously established list.
    - iStoredSequenceDatasetIndicesMirrored
```
Vector<E> iStoredSequenceDatasetIndicesMirrored
```
      The Vector that holds the dataset indices of stored points from a previously established list in the mirrored spectra.
    - iAnnotations
```
Vector<E> iAnnotations
```
      The Vector that holds a set of Annotation instances.
    - iAnnotationsMirroredSpectra
```
Vector<E> iAnnotationsMirroredSpectra
```
      The Vector that holds a set of Annotation instances for the mirrored spectra.
    - iMinDrag
```
int iMinDrag
```
      Minimal dragging distance in pixels.
    - iCurrentDrawStyle
```
GraphicsPanel.DrawingStyle iCurrentDrawStyle
```
      This variable holds the current drawing style.
    - iDotRadius
```
int iDotRadius
```
      This variable holds the dot radius; only used when drawing style is DOTS style.
    - iMSLevel
```
int iMSLevel
```
      The ms level of the current spectrum. O is assumed to mean no ms level given.
    - showAllPeaks
```
boolean showAllPeaks
```
      If false, only the annotated peaks will be shown. Note that this setting is ignored in profile mode!
    - yAxisZoomExcludesBackgroundPeaks
```
boolean yAxisZoomExcludesBackgroundPeaks
```
      If true, the automatic y-axis zoom excludes the background peaks. False includes all peaks in the zoom.
    - annotateHighestPeak
```
boolean annotateHighestPeak
```
      If more than one peak is within the accuracy range of an annotation setting this to true will always select the most intense of possible peaks. Setting this variable to false will instead select the most accurate peak.
    - currentGraphicsPanelType
```
GraphicsPanel.GraphicsPanelType currentGraphicsPanelType
```
      Sets the current GraphicsPanel type, default to centroid spectrum.
- Class com.compomics.util.gui.spectrum.IntensityHistogram extends JPanel implements Serializable
  - Serialized Fields
    - chartPanel
```
org.jfree.chart.ChartPanel chartPanel
```
      The chart panel for external access.
- Class com.compomics.util.gui.spectrum.IonLabelColorTableModel extends DefaultTableModel implements Serializable
  - Serialized Fields
    - ionMap
```
HashMap<K,V> ionMap
```
      The list of ions.
    - keys
```
ArrayList<E> keys
```
      The keys.
- Class com.compomics.util.gui.spectrum.IsotopicDistributionPanel extends GraphicsPanel implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - aSpectrumPeakColor
```
Color aSpectrumPeakColor
```
      The color used for the peaks. Default to red.
    - aSpectrumProfileModeLineColor
```
Color aSpectrumProfileModeLineColor
```
      The color used for the area under the curve. Defaults to pink.
    - peptideSequences
```
ArrayList<E> peptideSequences
```
      The peptide sequences to display the isotopic distribution for.
    - peptideCharges
```
ArrayList<E> peptideCharges
```
      The charges of the peptides. Indexed by dataset.
    - iElements
```
HashMap<K,V> iElements
```
      HashMap with the molecular formula for all the amino acids.
- Class com.compomics.util.gui.spectrum.MassErrorBubblePlot extends JPanel implements Serializable
  - Serialized Fields
    - useRelativeError
```
boolean useRelativeError
```
      If true the relative error (ppm) is used instead of the absolute error (Da).
    - currentlyUsedIonMatches
```
ArrayList<E> currentlyUsedIonMatches
```
      The list of currently used ions.
    - chartPanel
```
org.jfree.chart.ChartPanel chartPanel
```
      The chart panel.
    - dataSeriesfragmentIonColors
```
ArrayList<E> dataSeriesfragmentIonColors
```
      The data series fragment ion colors.
- Class com.compomics.util.gui.spectrum.MassErrorPlot extends JPanel implements Serializable
  - Serialized Fields
    - annotations
```
ArrayList<E> annotations
```
      The complete list of possible spectrum annotations.
    - chartPanel
```
org.jfree.chart.ChartPanel chartPanel
```
      The chart panel.
- Class com.compomics.util.gui.spectrum.SequenceFragmentationPanel extends JPanel implements Serializable
  - Serialized Fields
    - tooltipRectangles
```
HashMap<K,V> tooltipRectangles
```
      A map of the rectangles that have tooltips, i.e., the fragment ion peaks and the PTM highlighting.
    - iSequenceComponents
```
String[] iSequenceComponents
```
      Elementary data for composing the Panel.
    - iIonMatches
```
ArrayList<E> iIonMatches
```
      The list of fragment ion matches.
    - bIons
```
double[] bIons
```
      Double array on b-ions for the sequence components. If '0', no corresponding ions were given for the component. Otherwise, a double between [0:1] is stored in the array that is relative with the intensity of the most intense fragment ion.
    - yIons
```
double[] yIons
```
      Double array on y-ions for the sequence components. If '0', no corresponding ions were given for the component. Otherwise, a double between [0:1] is stored in the array that is relative with the intensity of the most intense fragment ion.
    - iBaseFont
```
Font iBaseFont
```
      The font to use.
    - iMaxBarHeight
```
double iMaxBarHeight
```
      The maximum bar height.
    - iBarWidth
```
int iBarWidth
```
      The width of the bars.
    - iHorizontalSpace
```
int iHorizontalSpace
```
      The horizontal space.
    - iXStart
```
int iXStart
```
      The x-axis start position.
    - isModifiedSequence
```
boolean isModifiedSequence
```
      This boolean holds whether or not the given sequence is a modified sequence or a normal peptide sequence. Normal: KENNY Modified: NH2-K<Ace>ENNY-COOH
    - iHighlightModifications
```
boolean iHighlightModifications
```
      If true the modification are highlighted with a background color.
    - modificationProfile
```
PtmSettings modificationProfile
```
      The modification profile.
    - forwardIon
```
int forwardIon
```
      the forward ion type (for instance B ion) as indexed by the PeptideFragmentIon static fields
    - rewindIon
```
int rewindIon
```
      the rewind ion type (for instance B ion) as indexed by the PeptideFragmentIon static fields
    - forwardColor
```
Color forwardColor
```
      Color for the forward ion
    - rewindColor
```
Color rewindColor
```
      Color for the rewind ion
- Class com.compomics.util.gui.spectrum.SpectrumPanel extends GraphicsPanel implements Serializable
  - Serialized Fields
    - spectrumPeakColor
```
Color spectrumPeakColor
```
      The color used for the peaks. Default to red.
    - spectrumProfileModeLineColor
```
Color spectrumProfileModeLineColor
```
      The color used for the profile mode spectra. Defaults to pink.
Package com.compomics.util.gui.tablemodels
- Class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel extends DefaultTableModel implements Serializable
  - Serialized Fields
    - rowStartLoading
```
int rowStartLoading
```
      The view start index of the rows being loaded.
    - rowEndLoading
```
int rowEndLoading
```
      The view end index of the rows being loaded.
    - selfUpdating
```
boolean selfUpdating
```
      If false, the table will not update automatically.
    - updateScheduled
```
boolean updateScheduled
```
      boolean indicating whether an update was scheduled.
    - lastLoadingRunnable
```
com.compomics.util.gui.tablemodels.SelfUpdatingTableModel.LoadingRunnable lastLoadingRunnable
```
      The last loading runnable.
    - viewIndexes
```
ArrayList<E> viewIndexes
```
      List of view indexes.
    - lastColumnSorted
```
int lastColumnSorted
```
      Indicates which column was last changed.
    - sortAscending
```
boolean sortAscending
```
      If true the current sorting is ascending.
    - unsorted
```
boolean unsorted
```
      If true the table has not yet been sorted.
    - progressDialog
```
ProgressDialogX progressDialog
```
      A progress dialog.
    - isScrolling
```
boolean isScrolling
```
      When true this indicates that the user is currently scrolling in the table and that the table should not update.
Package com.compomics.util.gui.utils
- Class com.compomics.util.gui.utils.ConnectionDialog extends JDialog implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iConnections
```
ArrayList<E> iConnections
```
      ArrayList that holds all the preconfigured connections. Note that when this list holds only 0 or 1 elements, it changes the behaviour of the GUI.
    - cmbConfigurations
```
JComboBox<E> cmbConfigurations
```
    - txtDriver
```
JTextField txtDriver
```
    - txtUrl
```
JTextField txtUrl
```
    - txtUser
```
JTextField txtUser
```
    - txtPassword
```
JPasswordField txtPassword
```
    - btnOK
```
JButton btnOK
```
    - btnCancel
```
JButton btnCancel
```
    - iTarget
```
Connectable iTarget
```
    - iPropsFile
```
String iPropsFile
```
    - iLastInitiatedConfiguration
```
String iLastInitiatedConfiguration
```
- Class com.compomics.util.gui.utils.DateChooser extends JDialog implements Serializable
  - Serialized Fields
    - iSelectedCalendar
```
Calendar iSelectedCalendar
```
    - iShownCalendar
```
Calendar iShownCalendar
```
    - iSelectedDayIndex
```
int iSelectedDayIndex
```
    - lblDayNames
```
JLabel[] lblDayNames
```
    - lblDays
```
JLabel[] lblDays
```
    - iDays
```
Integer[] iDays
```
    - lblCurrentMonthYear
```
JLabel lblCurrentMonthYear
```
Package com.compomics.util.gui.utils.user_choice
- Class com.compomics.util.gui.utils.user_choice.ListChooser extends JDialog implements Serializable
  - Serialized Fields
    - items
```
ArrayList<E> items
```
      The list of items the user will choose from.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the selection has been cancelled.
    - tableToolTips
```
ArrayList<E> tableToolTips
```
      Table column header tooltips.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - itemsLabel
```
JLabel itemsLabel
```
    - itemsPanel
```
JPanel itemsPanel
```
    - itemsTable
```
JTable itemsTable
```
    - itemsTableScrollPane
```
JScrollPane itemsTableScrollPane
```
    - okButton
```
JButton okButton
```
Package com.compomics.util.gui.utils.user_choice.list_choosers
- Class com.compomics.util.gui.utils.user_choice.list_choosers.PtmChooser extends ListChooser implements Serializable
  - Serialized Fields
    - ptmFactory
```
PTMFactory ptmFactory
```
      The post translational modifications factory.
    - ptmList
```
ArrayList<E> ptmList
```
      List of PTMs to display.
- Class com.compomics.util.gui.utils.user_choice.list_choosers.StringListChooser extends ListChooser implements Serializable
Package com.compomics.util.gui.waiting.waitinghandlers
- Class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog extends JDialog implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iProgress
```
JProgressBar iProgress
```
- Class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX extends JDialog implements Serializable
  - Serialized Fields
    - doNothingOnClose
```
boolean doNothingOnClose
```
      If set to true, trying to close the progress bar will be ignored. Use this option if the process being monitored can not be stopped.
      Note: replaced by unstoppable.
    - unstoppable
```
boolean unstoppable
```
      Set this to true of the process the progress bar is used for is not possible to stop, or not possible to stop nicely. If the user still tries to close the progress bar the a warning message is first shown were the user has to confirm that he/she still wants to close the progress bar.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the process has been canceled.
    - finished
```
boolean finished
```
      Boolean indicating whether the process has been completed.
    - displayProgress
```
boolean displayProgress
```
      Set if the waiting handler is to show the progress for the current process or not. Useful when running subprocesses that one wants to be able to cancel but do not want to show the progress for.
    - waitingIcon
```
Image waitingIcon
```
      The dialog/frame icon to use when waiting.
    - normalIcon
```
Image normalIcon
```
      The dialog/frame icon to use when done.
    - waitingHandlerParentFrame
```
Frame waitingHandlerParentFrame
```
      The waitingHandlerParent frame.
    - waitingHandlerParentDialog
```
JDialog waitingHandlerParentDialog
```
      The waitingHandlerParent dialog.
    - waitingActionListener
```
WaitingActionListener waitingActionListener
```
      The waiting action listener.
    - progressBar
```
JProgressBar progressBar
```
- Class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog extends JDialog implements Serializable
  - Serialized Fields
    - dialog
```
JDialog dialog
```
      Needed for the shaking feature.
    - naturalLocation
```
Point naturalLocation
```
      Used in the shaking feature.
    - shakeTimer
```
Timer shakeTimer
```
      Timer for the shaking feature.
    - runFinished
```
boolean runFinished
```
      Boolean indicating whether the process is finished.
    - runCanceled
```
boolean runCanceled
```
      Boolean indicating whether the process is canceled.
    - displayProgress
```
boolean displayProgress
```
      Set if the waiting handler is to show the progress for the current process or not. Useful when running subprocesses that one wants to be able to cancel but do not want to show the progress for.
    - tips
```
ArrayList<E> tips
```
      An array list of the tip of the day.
    - currentTipIndex
```
int currentTipIndex
```
      The current tip index.
    - lastSelectedFolder
```
String lastSelectedFolder
```
      The last selected folder
    - waitingIcon
```
Image waitingIcon
```
      The dialog/frame icon to use when waiting.
    - normalIcon
```
Image normalIcon
```
      The dialog/frame icon to use when done.
    - waitingHandlerParent
```
Frame waitingHandlerParent
```
      The waitingHandlerParent.
    - shakeWhenFinished
```
boolean shakeWhenFinished
```
      If true, the dialog will shake when completed. Mainly a PeptideShaker feature.
    - processName
```
String processName
```
      The name of the process we are waiting for, e.g., 'Import Data' or 'Search'.
    - toolName
```
String toolName
```
      The name of the tool using the waiting dialog. Used for the report.
    - toolVersion
```
String toolVersion
```
      The version number of the tool using the waiting dialog. Used for the report.
    - waitingActionListener
```
WaitingActionListener waitingActionListener
```
      The waiting action listener.
    - lineBreak
```
String lineBreak
```
      The line break type.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - closeDialogWhenImportCompletesCheckBox
```
JCheckBox closeDialogWhenImportCompletesCheckBox
```
    - closeJButton
```
JButton closeJButton
```
    - layeredPane
```
JLayeredPane layeredPane
```
    - nextJButton
```
JButton nextJButton
```
    - okButton
```
JButton okButton
```
    - processProgressPanel
```
JPanel processProgressPanel
```
    - progressBar
```
JProgressBar progressBar
```
    - reportScrollPane
```
JScrollPane reportScrollPane
```
    - reportTextArea
```
JTextArea reportTextArea
```
    - saveReportLabel
```
JLabel saveReportLabel
```
    - secondaryJProgressBar
```
JProgressBar secondaryJProgressBar
```
    - secondaryProgressBarSplitPane
```
JSplitPane secondaryProgressBarSplitPane
```
    - showTipOfTheDayCheckBox
```
JCheckBox showTipOfTheDayCheckBox
```
    - tempJProgressBar
```
JProgressBar tempJProgressBar
```
    - tipOfTheDayEditorPane
```
JEditorPane tipOfTheDayEditorPane
```
    - tipOfTheDayJPanel
```
JPanel tipOfTheDayJPanel
```
    - tipOfTheDayLayeredPane
```
JLayeredPane tipOfTheDayLayeredPane
```
    - tipOfTheDayScrollPane
```
JScrollPane tipOfTheDayScrollPane
```
Package com.compomics.util.io
- Class com.compomics.util.io.FtpConnectionException extends FtpProtocolException implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
- Class com.compomics.util.io.FtpLoginException extends FtpProtocolException implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
- Class com.compomics.util.io.FtpProtocolException extends IOException implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
Package com.compomics.util.io.export
- Class com.compomics.util.io.export.ExportScheme extends Object implements Serializable
  
  serialVersionUID:
  
  -4712918049667194600L
  - Serialized Fields
    - name
```
String name
```
      The name of the scheme.
    - editable
```
boolean editable
```
      A boolean indicating whether the scheme can be modified.
    - mainTitle
```
String mainTitle
```
      The title of the report.
    - sectionList
```
ArrayList<E> sectionList
```
      Ordered list of the features in that scheme.
    - exportFeaturesMap
```
HashMap<K,V> exportFeaturesMap
```
      Map of the features to export indexed by feature type.
    - separator
```
String separator
```
      The separator used to separate columns.
    - indexes
```
boolean indexes
```
      Boolean indicating whether the line shall be indexed.
    - header
```
boolean header
```
      Boolean indicating whether column headers shall be included.
    - separationLines
```
int separationLines
```
      indicates how many lines shall be used to separate sections.
    - includeSectionTitles
```
boolean includeSectionTitles
```
      Indicates whether the title of every section shall be included.
    - validatedOnly
```
Boolean validatedOnly
```
      Indicates whether only validated matches should be included.
    - includeDecoy
```
Boolean includeDecoy
```
      Indicates whether decoy matches should be included.
Package com.compomics.util.math.clustering.settings
- Class com.compomics.util.math.clustering.settings.KMeansClusteringSettings extends Object implements Serializable
  - Serialized Fields
    - nClusters
```
int nClusters
```
      The number of clusters to use.
Package com.compomics.util.math.statistics
Package com.compomics.util.math.statistics.distributions
- Class com.compomics.util.math.statistics.distributions.BinomialDistribution extends Object implements Serializable
  - Serialized Fields
    - binomialDistributionImpl
```
org.apache.commons.math.distribution.BinomialDistributionImpl binomialDistributionImpl
```
      Instance of the apache distribution.
    - n
```
int n
```
      The number of trials.
    - p
```
double p
```
      The probability of success of each trial.
    - cacheSize
```
int cacheSize
```
      The maximal number of keys kept in each cache map.
    - pCache
```
HashMap<K,V> pCache
```
      A cache for the probabilities.
    - descendingCumulativePCache
```
HashMap<K,V> descendingCumulativePCache
```
      A cache for the cumulative probabilities.
- Class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution extends Object implements Serializable
  
  serialVersionUID:
  
  -5258258835569357886L
  - Serialized Fields
    - stdUp
```
double stdUp
```
      The standard deviation on the right of the distribution.
    - stdDown
```
double stdDown
```
      The standard deviation on the left of the distribution.
    - mean
```
double mean
```
      The mean.
    - distributionUp
```
NormalDistribution distributionUp
```
      Distribution equivalent to the right of the distribution.
    - distributionDown
```
NormalDistribution distributionDown
```
      Distribution equivalent to the left of the distribution.
- Class com.compomics.util.math.statistics.distributions.NormalDistribution extends Object implements Serializable
  
  serialVersionUID:
  
  -4944773548279233917L
  - Serialized Fields
    - normalDistributionImpl
```
org.apache.commons.math.distribution.NormalDistributionImpl normalDistributionImpl
```
      The apache normal distribution implementation.
    - mean
```
double mean
```
      The mean of the distribution.
    - std
```
double std
```
      The standard deviation of the distribution.
Package com.compomics.util.preferences
- Class com.compomics.util.preferences.FractionSettings extends Object implements Serializable
  
  serialVersionUID:
  
  5193356878844799148L
  - Serialized Fields
    - proteinConfidenceMwPlots
```
Double proteinConfidenceMwPlots
```
      The minimum confidence required for a protein to be included in the calculation of the average molecular weight plot in the Fractions tab of PeptideShaker.
- Class com.compomics.util.preferences.GenePreferences extends Object implements Serializable
  
  serialVersionUID:
  
  -1286840382594446279L
  - Serialized Fields
    - autoUpdate
```
Boolean autoUpdate
```
      If true the gene mappings will auto update.
    - useGeneMapping
```
Boolean useGeneMapping
```
      If true the gene mappings will be used.
    - selectedBackgroundSpecies
```
Integer selectedBackgroundSpecies
```
      The taxon of the species selected as background for the GO analysis.
    - currentSpecies
```
String currentSpecies
```
      Deprecated. use the species in the database.
      
      The current species. Used for the gene mappings.
    - currentSpeciesType
```
String currentSpeciesType
```
      Deprecated. use gene factory map.
      
      The current species type. Used for the gene mappings.
    - goDomainMap
```
HashMap<K,V> goDomainMap
```
      Deprecated. use gene factory map.
      
      The GO domain map. e.g., key: GO term: GO:0007568, element: biological_process.
    - allSpeciesMap
```
HashMap<K,V> allSpeciesMap
```
      Deprecated. use gene factory map.
      
      The species map. Main key: Ensembl type, e.g., Vertebrates or Plants. Next level: key: latin name, element: ensembl database name, e.g., key: Homo sapiens, element: hsapiens_gene_ensembl.
    - allSpecies
```
HashMap<K,V> allSpecies
```
      Deprecated. use gene factory map.
      
      Map of all the species.
- Class com.compomics.util.preferences.IdentificationParameters extends Object implements Serializable
  
  serialVersionUID:
  
  -5516259326385167746L
  - Serialized Fields
    - marshallableParameterType
```
String marshallableParameterType
```
      Name of the type of marshalled parameter.
    - name
```
String name
```
      The name of the parameters.
    - description
```
String description
```
      The description of the parameters.
    - defaultDescription
```
Boolean defaultDescription
```
      Indicates whether the description is automatically generated.
    - searchParameters
```
SearchParameters searchParameters
```
      The parameters used for the spectrum matching.
    - annotationSettings
```
AnnotationSettings annotationSettings
```
      The peak annotation preferences.
    - sequenceMatchingPreferences
```
SequenceMatchingPreferences sequenceMatchingPreferences
```
      The peptide to protein matching preferences.
    - genePreferences
```
GenePreferences genePreferences
```
      The gene preferences.
    - psmScoringPreferences
```
PsmScoringPreferences psmScoringPreferences
```
      The PSM scores to use.
    - peptideAssumptionFilter
```
PeptideAssumptionFilter peptideAssumptionFilter
```
      The PSM filter.
    - ptmScoringPreferences
```
PTMScoringPreferences ptmScoringPreferences
```
      The PTM localization scoring preferences.
    - proteinInferencePreferences
```
ProteinInferencePreferences proteinInferencePreferences
```
      The protein inference preferences.
    - idValidationPreferences
```
IdMatchValidationPreferences idValidationPreferences
```
      The identification validation preferences.
    - fractionSettings
```
FractionSettings fractionSettings
```
      The fraction settings.
- Class com.compomics.util.preferences.IdMatchValidationPreferences extends Object implements Serializable
  
  serialVersionUID:
  
  4327810348755338485L
  - Serialized Fields
    - defaultProteinFDR
```
double defaultProteinFDR
```
      The default protein FDR.
    - defaultPeptideFDR
```
double defaultPeptideFDR
```
      The default peptide FDR.
    - defaultPsmFDR
```
double defaultPsmFDR
```
      The default PSM FDR.
    - separatePeptides
```
Boolean separatePeptides
```
      Boolean indicating whether Peptides should be grouped according to their modification status.
    - separatePsms
```
Boolean separatePsms
```
      Boolean indicating whether PSMs should be grouped according to their modification status.
    - mergeSmallSubgroups
```
Boolean mergeSmallSubgroups
```
      If true, groups of matches of small size will be merged.
    - validationQCPreferences
```
ValidationQCPreferences validationQCPreferences
```
      The validation quality control preferences.
- Class com.compomics.util.preferences.LastSelectedFolder extends Object implements Serializable
  
  serialVersionUID:
  
  7612497861284156966L
  - Serialized Fields
    - lastSelectedFolder
```
HashMap<K,V> lastSelectedFolder
```
      Map of the last selected folders indexed by use cases.
- Class com.compomics.util.preferences.ProteinInferencePreferences extends Object implements Serializable
  
  serialVersionUID:
  
  447785006299636157L
  - Serialized Fields
    - proteinSequenceDatabase
```
File proteinSequenceDatabase
```
      The database to use for protein inference.
- Class com.compomics.util.preferences.PsmScoringPreferences extends Object implements Serializable
  
  serialVersionUID:
  
  4997457408322410176L
  - Serialized Fields
    - spectrumMatchingScores
```
HashMap<K,V> spectrumMatchingScores
```
      The scores used to score the spectrum matches for every advocate in a map: advocate index > list of score indexes.
- Class com.compomics.util.preferences.PSProcessingPreferences extends Object implements Serializable
  
  serialVersionUID:
  
  -5883143685674607162L
  - Serialized Fields
    - nThreads
```
int nThreads
```
      Deprecated.
      
      The number of threads to use.
    - proteinConfidenceMwPlots
```
Double proteinConfidenceMwPlots
```
      Deprecated.
      
      The minimum confidence required for a protein to be included in the calculation of the average molecular weight plot in the Fractions tab.
- Class com.compomics.util.preferences.PTMScoringPreferences extends Object implements Serializable
  
  serialVersionUID:
  
  -6656074270981104708L
  - Serialized Fields
    - flr
```
double flr
```
      The FLR threshold in percent.
    - probabilitsticScoreCalculation
```
Boolean probabilitsticScoreCalculation
```
      Boolean indicating whether a probabilistic score is to be calculated.
    - selectedProbabilisticScore
```
PtmScore selectedProbabilisticScore
```
      The probabilistic score selected.
    - estimateFlr
```
boolean estimateFlr
```
      Boolean indicating whether the threshold should be FLR based.
    - probabilisticScoreThreshold
```
double probabilisticScoreThreshold
```
      The probabilistic score threshold.
    - probabilisticScoreNeutralLosses
```
Boolean probabilisticScoreNeutralLosses
```
      Boolean indicating whether neutral losses shall be accounted for in the calculation of the probabilistic score.
    - sequenceMatchingPreferences
```
SequenceMatchingPreferences sequenceMatchingPreferences
```
      The preferences to use when matching PTMs to amino acid sequences.
- Class com.compomics.util.preferences.SequenceMatchingPreferences extends Object implements Serializable
  
  serialVersionUID:
  
  228961121369106450L
  - Serialized Fields
    - sequenceMatchingType
```
SequenceMatchingPreferences.MatchingType sequenceMatchingType
```
      The amino acid matching type.
    - limitX
```
Double limitX
```
      Limit the share of X's a match can contain, range [0.0-1.0].
    - mutationMatrix
```
MutationMatrix mutationMatrix
```
      Matrix of allowed mutations.
    - maxMutationsPerPeptide
```
Integer maxMutationsPerPeptide
```
      The maximal number of mutations allowed per peptide.
- Class com.compomics.util.preferences.UtilitiesUserPreferences extends Object implements Serializable
  
  serialVersionUID:
  
  -4343570286224891504L
  - Serialized Fields
    - spectrumAnnotatedPeakWidth
```
Float spectrumAnnotatedPeakWidth
```
      The width to use for the annotated peaks.
    - spectrumBackgroundPeakWidth
```
Float spectrumBackgroundPeakWidth
```
      The width to use for the background peaks.
    - spectrumAnnotatedPeakColor
```
Color spectrumAnnotatedPeakColor
```
      The color to use for the annotated peaks.
    - spectrumAnnotatedMirroredPeakColor
```
Color spectrumAnnotatedMirroredPeakColor
```
      The color to use for the annotated mirrored peaks.
    - spectrumBackgroundPeakColor
```
Color spectrumBackgroundPeakColor
```
      The color to use for the background peaks.
    - sparklineColorValidated
```
Color sparklineColorValidated
```
      The color used for the sparkline bar chart plots.
    - sparklineColorNonValidated
```
Color sparklineColorNonValidated
```
      The color used for the non-validated sparkline bar chart plots.
    - sparklineColorNotFound
```
Color sparklineColorNotFound
```
      The color used for the not found sparkline bar chart plots.
    - sparklineColorPossible
```
Color sparklineColorPossible
```
      The color used for the possible values sparkline bar chart plots.
    - sparklineColorDoubtful
```
Color sparklineColorDoubtful
```
      The color used for the doubtful matches in sparkline bar chart plots.
    - sparklineColorFalsePositive
```
Color sparklineColorFalsePositive
```
      The color used for the false positive in sparkline bar chart plots.
    - peptideSelected
```
Color peptideSelected
```
      The color of the selected peptide.
    - memoryPreference
```
Integer memoryPreference
```
      The memory to use.
    - javaHome
```
String javaHome
```
      The Java Home, for example, C:\Program Files\Java\jdk1.8.0_25\bin. Null if not set. Note that this setting will be ignored of a JavaHome.txt file is found.
    - proteinTreeFolder
```
File proteinTreeFolder
```
      The folder where to store the protein trees.
    - proteinTreeImportTime
```
HashMap<K,V> proteinTreeImportTime
```
      Maps saving the protein trees import time in a map: FASTA file size > import times.
    - proteoWizardPath
```
String proteoWizardPath
```
      The path to the ProteoWizard installation (if any). Set to null if no path is provided.
    - searchGuiPath
```
String searchGuiPath
```
      The path to the SearchGUI installation (if any). Makes it possible to start SearchGUI directly from PeptideShaker. Set to null if no path is provided.
    - peptideShakerPath
```
String peptideShakerPath
```
      The path to the PeptideShaker installation (if any). Set to null if no path is provided.
    - deNovoGuiPath
```
String deNovoGuiPath
```
      The path to the DeNovoGUI installation (if any). Set to null if no path is provided.
    - reporterPath
```
String reporterPath
```
      The path to the Reporter installation (if any). Set to null if no path is provided.
    - relimsPath
```
String relimsPath
```
      The path to the Relims installation (if any). Set to null if no path is provided.
    - localPrideFolder
```
String localPrideFolder
```
      The local PRIDE projects folder.
    - dbFolder
```
File dbFolder
```
      The user last used database folder.
    - proteinSequencesManagerFolder
```
File proteinSequencesManagerFolder
```
      The folder used to store fasta files.
    - favoriteDBs
```
ArrayList<E> favoriteDBs
```
      The user last used databases.
    - readTweets
```
ArrayList<E> readTweets
```
      The list of already read tweets.
    - displayedTips
```
ArrayList<E> displayedTips
```
      The list of already displayed tips.
    - autoUpdate
```
Boolean autoUpdate
```
      Indicates whether the tool should check for updates.
    - notifyStart
```
Boolean notifyStart
```
      Indicates whether the tool should notify its start.
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      The last selected folder.
    - sortPsmsOnRt
```
Boolean sortPsmsOnRt
```
      If true, the PSMs are sorted on retention time, false sorts on PSM score.
    - targetDecoyFileNameTag
```
String targetDecoyFileNameTag
```
      The tag added after adding decoy sequences to a FASTA file.
    - checkPeakPicking
```
Boolean checkPeakPicking
```
      If true, the selected spectra will be checked for peak picking.
    - checkDuplicateTitles
```
Boolean checkDuplicateTitles
```
      If true, the selected spectra will be checked for duplicate spectrum titles.
    - checkMgfSize
```
Boolean checkMgfSize
```
      If true, the mgf files will be checked for size.
    - mgfMaxSize
```
Double mgfMaxSize
```
      If an mgf file exceeds this limit, the user will be asked for a split.
    - mgfNSpectra
```
Integer mgfNSpectra
```
      Number of spectra allowed in the split file.
    - refMass
```
Double refMass
```
      Reference mass for the conversion of the fragment ion tolerance from ppm to Dalton.
    - generateProteinTree
```
Boolean generateProteinTree
```
      If true the protein tree will be created parallel to the searches.
    - outputOption
```
SearchGuiOutputOption outputOption
```
      The way output files should be exported.
    - outputData
```
Boolean outputData
```
      Indicates whether data files (mgf and FASTA) should be copied in the output.
    - includeDateInOutputName
```
Boolean includeDateInOutputName
```
      Indicates whether the date should be included in the output.
    - renameXTandemFile
```
Boolean renameXTandemFile
```
      If true the X! Tandem file will be renamed.
    - checkSpectrumCharges
```
Boolean checkSpectrumCharges
```
      If true, the spectra will be checked for missing charges.
    - minSpectrumChargeRange
```
Integer minSpectrumChargeRange
```
      The maximum charge added when the charge is missing for a given spectrum.
    - maxSpectrumChargeRange
```
Integer maxSpectrumChargeRange
```
      The minimum charge added when the charge is missing for a given spectrum.
- Class com.compomics.util.preferences.ValidationQCPreferences extends Object implements Serializable
  
  serialVersionUID:
  
  -3984640691136489708L
  - Serialized Fields
    - dbSize
```
boolean dbSize
```
      Indicates whether the database size should be checked.
    - firstDecoy
```
boolean firstDecoy
```
      Indicates whether the number of hits before the first decoy should be checked.
    - confidenceMargin
```
Double confidenceMargin
```
      The margin in number of resolution over the confidence threshold.
    - psmFilters
```
ArrayList<E> psmFilters
```
      List of QC filters for PSMs.
    - peptideFilters
```
ArrayList<E> peptideFilters
```
      List of QC filters for peptides.
    - proteinFilters
```
ArrayList<E> proteinFilters
```
      List of QC filters for proteins.
Package com.compomics.util.pride
- Class com.compomics.util.pride.CvTerm extends Object implements Serializable
  
  serialVersionUID:
  
  -2890434198335005181L
  - Serialized Fields
    - ontology
```
String ontology
```
      The ontology.
    - accession
```
String accession
```
      The accession number.
    - name
```
String name
```
      The name/term.
    - value
```
String value
```
      The value for the given term.
- Class com.compomics.util.pride.PtmToPrideMap extends Object implements Serializable
  
  serialVersionUID:
  
  2436108005958307507L
  - Serialized Fields
    - modToCvMap
```
HashMap<K,V> modToCvMap
```
      Map of the CV terms indexed by modification user name.
Package com.compomics.util.pride.prideobjects
- Class com.compomics.util.pride.prideobjects.Contact extends Object implements Serializable
  
  serialVersionUID:
  
  -9182316910747747823L
  - Serialized Fields
    - name
```
String name
```
      The contact's name.
    - eMail
```
String eMail
```
      The contact's e-mail.
    - institution
```
String institution
```
      The contact's institution.
- Class com.compomics.util.pride.prideobjects.ContactGroup extends Object implements Serializable
  
  serialVersionUID:
  
  -9182316910747747823L
  - Serialized Fields
    - contacts
```
ArrayList<E> contacts
```
      The contacts.
    - groupName
```
String groupName
```
      The contact group name.
- Class com.compomics.util.pride.prideobjects.Instrument extends Object implements Serializable
  
  serialVersionUID:
  
  -8802861658166703745L
  - Serialized Fields
    - name
```
String name
```
      The instrument name.
    - cvTerms
```
ArrayList<E> cvTerms
```
      The list of analyzer CV terms.
    - source
```
CvTerm source
```
      The instrument source.
    - detector
```
CvTerm detector
```
      The instrument detector.
- Class com.compomics.util.pride.prideobjects.Protocol extends Object implements Serializable
  
  serialVersionUID:
  
  -9045298216154032632L
  - Serialized Fields
    - name
```
String name
```
      The protocol name.
    - cvTerms
```
ArrayList<E> cvTerms
```
      The list of CV terms.
- Class com.compomics.util.pride.prideobjects.Reference extends Object implements Serializable
  
  serialVersionUID:
  
  -5449836209751629549L
  - Serialized Fields
    - reference
```
String reference
```
      The reference text.
    - pmid
```
String pmid
```
      The PubMed ID.
    - doi
```
String doi
```
      The Digital Object Identifier.
- Class com.compomics.util.pride.prideobjects.ReferenceGroup extends Object implements Serializable
  
  serialVersionUID:
  
  -9182316910747747823L
  - Serialized Fields
    - references
```
ArrayList<E> references
```
      The references.
    - groupName
```
String groupName
```
      The reference group name.
- Class com.compomics.util.pride.prideobjects.Sample extends Object implements Serializable
  
  serialVersionUID:
  
  -7142471175737857227L
  - Serialized Fields
    - name
```
String name
```
      The sample name.
    - cvTerms
```
ArrayList<E> cvTerms
```
      The list of CV terms.
Package com.compomics.util.protein
- Class com.compomics.util.protein.Header extends Object implements Serializable
  
  serialVersionUID:
  
  7665784733371863163L
  - Serialized Fields
    - iID
```
String iID
```
      The ID String corresponds to the String that is present as the first element following the opening '>'. It is most notably 'sw' for SwissProt, and 'gi' for NCBI.
      ID is the first element in the abbreviated header String.
    - iForeignID
```
String iForeignID
```
      The foreign ID is the ID of another database this entry is originally from. Most notably used for SwissProt entries in NCBI.
      The foreign ID String is an addendum to the accession String in the abbreviated header String.
    - iAccession
```
String iAccession
```
      The accession String is the unique identifier for the sequence in the respective database. Note that for NCBI, the accession number also defines a unique moment in time.
      Accession String is the second element in the abbreviated header String.
    - databaseType
```
Header.DatabaseType databaseType
```
      Extracted database name. As there are no standard database names, this is only an internally consistent naming scheme included to be able to later separate the databases. For example when linking to the online version of the database. The links themselves are not included as these might change outside the control of the compomics-utilities library. Note that the type is set to unknown by default, and is set to the correct type during the parsing of the header.
    - iForeignAccession
```
String iForeignAccession
```
      The foreign accession String is an accession String in another database of significance. Most notably used for SwissProt accessions that are kept in the NCBI database.
      The foreign accession String is an addendum to the foreign ID String in the abbreviated header String.
    - iDescription
```
String iDescription
```
      The description is a more or less elaborate description of the protein in question.
      The description is the third element (and final) in the abbreviated header String.
    - iDescriptionShort
```
String iDescriptionShort
```
      A short protein description, removing all but the protein description itself. For example: "GRP78_HUMAN 78 kDa glucose-regulated protein OS=Homo sapiens GN=HSPA5 PE=1 SV=2" becomes "78 kDa glucose-regulated protein".
    - iDescriptionProteinName
```
String iDescriptionProteinName
```
      Protein name, the protein name extracted from the protein description. For example: "GRP78_HUMAN 78 kDa glucose-regulated protein OS=Homo sapiens GN=HSPA5 PE=1 SV=2" returns "GRP78_HUMAN".
    - iGeneName
```
String iGeneName
```
      The name of the gene the protein comes from. Note that this is only available for UniProt and NextProt based databases.
    - iProteinEvidence
```
String iProteinEvidence
```
      The protein evidence for the protein. Note that this is only available for UniProt-based databases.
    - iTaxonomy
```
String iTaxonomy
```
      The name of the taxonomy the protein comes from. Note that this is only available for UniProt-based databases.
    - iForeignDescription
```
String iForeignDescription
```
      The foreign Description is a description for an entry in another DB. Most notably, the SwissProt short description for an entry that is found within NCBI.
      The foreign description is an addendum to the foreign accession String in the abbreviated header String.
    - iRest
```
String iRest
```
      This variable holds all unidentified parts for the Header. If the String was not (recognized as) a standard SwissProt or NCBI header, this variable holds the entire header.
    - iRawHeader
```
String iRawHeader
```
      This variable holds the raw complete unformatted header. Only trailing white space is removed.
    - iAddenda
```
StringBuffer iAddenda
```
      This StringBuffer holds all the addenda for this header.
    - iStart
```
int iStart
```
      This variable holds a possible start index for the associated sequence.
    - iEnd
```
int iEnd
```
      This variable holds a possible end index for the associated sequence.
- Class com.compomics.util.protein.ModificationImplementation extends Object implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iTemplate
```
ModificationTemplate iTemplate
```
      The ModificationTemplate which holds all the shared information for a modification. It is to be considered a singleton and it is immutable.
    - iLocation
```
int iLocation
```
      The location for the modification in the parent sequence.
Package com.compomics.util.protein_sequences_manager.gui
- Class com.compomics.util.protein_sequences_manager.gui.ProteinSequencesManagerGUI extends JDialog implements Serializable
  - Serialized Fields
    - parentFrame
```
Frame parentFrame
```
      The parent frame.
    - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
      The utilities user preferences.
    - proteinSequencesManager
```
ProteinSequencesManager proteinSequencesManager
```
      The protein sequences manager.
    - yesNo
```
String[] yesNo
```
      convenience array for yes or no.
    - notAvailable
```
String notAvailable
```
      String to display when an option is not available.
    - waitingImage
```
Image waitingImage
```
      The icon to display when waiting.
    - normalImange
```
Image normalImange
```
      The normal icon.
    - selectedVersion
```
HashMap<K,V> selectedVersion
```
      The selected version for every database indexed by name.
    - reviewedSelection
```
HashMap<K,V> reviewedSelection
```
      The selection for reviewed for every database indexed by name.
    - isoformsSelection
```
HashMap<K,V> isoformsSelection
```
      The selection for isoforms for every database indexed by name.
    - contaminantsSelection
```
HashMap<K,V> contaminantsSelection
```
      The selection for contaminants for every database indexed by name.
    - decoySelection
```
HashMap<K,V> decoySelection
```
      The selection for decoy for every database indexed by name.
    - aboutMenuItem
```
JMenuItem aboutMenuItem
```
    - andromedaExportMenu
```
JMenuItem andromedaExportMenu
```
    - backgroundPanel
```
JPanel backgroundPanel
```
    - bugReportMenuItem
```
JMenuItem bugReportMenuItem
```
    - cancelButton
```
JButton cancelButton
```
    - configMenuItem
```
JMenuItem configMenuItem
```
    - dbPanel
```
JPanel dbPanel
```
    - dbTable
```
JTable dbTable
```
    - dbTableScrollPane
```
JScrollPane dbTableScrollPane
```
    - editMenu
```
JMenu editMenu
```
    - exitMenuItem
```
JMenuItem exitMenuItem
```
    - exportMenu
```
JMenu exportMenu
```
    - fileMenu
```
JMenu fileMenu
```
    - fileMenuBar
```
JMenuBar fileMenuBar
```
    - helpMenu
```
JMenu helpMenu
```
    - helpMenuItem
```
JMenuItem helpMenuItem
```
    - importFromDNAMenuItem
```
JMenuItem importFromDNAMenuItem
```
    - importFromFileMenuItem
```
JMenuItem importFromFileMenuItem
```
    - importFromUnitprot
```
JMenuItem importFromUnitprot
```
    - importMenu
```
JMenu importMenu
```
    - jMenu1
```
JMenu jMenu1
```
    - jMenuItem1
```
JMenuItem jMenuItem1
```
    - jMenuItem2
```
JMenuItem jMenuItem2
```
    - jSeparator1
```
JPopupMenu.Separator jSeparator1
```
    - jSeparator2
```
JPopupMenu.Separator jSeparator2
```
    - okButton
```
JButton okButton
```
- Class com.compomics.util.protein_sequences_manager.gui.SequenceDbDetailsDialog extends JDialog implements Serializable
  - Serialized Fields
    - sequenceFactory
```
SequenceFactory sequenceFactory
```
      The sequence factory.
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      The last selected folder.
    - dbEditable
```
boolean dbEditable
```
      boolean indicating whether the db can be changed.
    - waitingImage
```
Image waitingImage
```
      The icon to display when waiting.
    - normalImange
```
Image normalImange
```
      The normal icon.
    - parentFrame
```
Frame parentFrame
```
      The parent frame.
    - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
      The utilities user preferences.
    - accessionsSpinner
```
JSpinner accessionsSpinner
```
    - advancedButton
```
JButton advancedButton
```
    - backgroundPanel
```
JPanel backgroundPanel
```
    - browseButton
```
JButton browseButton
```
    - cancelButton
```
JButton cancelButton
```
    - databaseHelpSettingsJLabel
```
JLabel databaseHelpSettingsJLabel
```
    - databaseInformationPanel
```
JPanel databaseInformationPanel
```
    - dbNameTxt
```
JTextField dbNameTxt
```
    - decoyButton
```
JButton decoyButton
```
    - decoyFlagTxt
```
JTextField decoyFlagTxt
```
    - decoyTagLabel
```
JLabel decoyTagLabel
```
    - fileLabel
```
JLabel fileLabel
```
    - fileTxt
```
JTextField fileTxt
```
    - lastModifiedLabel
```
JLabel lastModifiedLabel
```
    - lastModifiedTxt
```
JTextField lastModifiedTxt
```
    - nameLabel
```
JLabel nameLabel
```
    - okButton
```
JButton okButton
```
    - previewPanel
```
JPanel previewPanel
```
    - proteinLabel
```
JLabel proteinLabel
```
    - proteinTxt
```
JTextArea proteinTxt
```
    - proteinYxtScrollPane
```
JScrollPane proteinYxtScrollPane
```
    - sizeLabel
```
JLabel sizeLabel
```
    - sizeTxt
```
JTextField sizeTxt
```
    - speciesJTextField
```
JTextField speciesJTextField
```
    - speciesLabel
```
JLabel speciesLabel
```
    - targetDecoyTxt
```
JLabel targetDecoyTxt
```
    - typeJTextField
```
JTextField typeJTextField
```
    - typeLabel
```
JLabel typeLabel
```
    - versionLabel
```
JLabel versionLabel
```
    - versionTxt
```
JTextField versionTxt
```
Package com.compomics.util.protein_sequences_manager.gui.preferences
- Class com.compomics.util.protein_sequences_manager.gui.preferences.ProteinSequencesPreferencesDialog extends JDialog implements Serializable
  - Serialized Fields
    - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
      The utilities user preferences.
    - backgroundPanel
```
JPanel backgroundPanel
```
    - cancelButton
```
JButton cancelButton
```
    - folderTxt
```
JTextField folderTxt
```
    - jButton1
```
JButton jButton1
```
    - jButton2
```
JButton jButton2
```
    - jLabel1
```
JLabel jLabel1
```
    - okButton
```
JButton okButton
```
    - parametersPanel
```
JPanel parametersPanel
```
Package com.compomics.util.protein_sequences_manager.gui.sequences_import
- Class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromDnaDialog extends JDialog implements Serializable
  - Serialized Fields
    - canceled
```
boolean canceled
```
      Boolean indicating whether the import has been canceled by the user.
    - selectedFile
```
File selectedFile
```
      The file containing the translated protein sequences.
    - cancelButton
```
JButton cancelButton
```
    - importSequencesFromDnaPanel
```
JPanel importSequencesFromDnaPanel
```
    - okButton
```
JButton okButton
```
- Class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromFilesDialog extends JDialog implements Serializable
  - Serialized Fields
    - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
      The utilities user preferences.
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      The last selected folder.
    - selectedFile
```
File selectedFile
```
      The file selected by the user.
    - selectedFileIndex
```
FastaIndex selectedFileIndex
```
      The index of the file selected by the user.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the import has been canceled by the user.
    - parentFrame
```
Frame parentFrame
```
      The parent frame.
    - waitingImage
```
Image waitingImage
```
      The icon to display when waiting.
    - normalImange
```
Image normalImange
```
      The normal icon.
    - browseButton
```
JButton browseButton
```
    - cancelButton
```
JButton cancelButton
```
    - clearButton
```
JButton clearButton
```
    - descriptionLbl
```
JLabel descriptionLbl
```
    - descriptionScrollPane
```
JScrollPane descriptionScrollPane
```
    - descriptionTxt
```
JTextArea descriptionTxt
```
    - fastaFileLabel
```
JLabel fastaFileLabel
```
    - fastaFilesTxt
```
JTextField fastaFilesTxt
```
    - fileSelectionPanel
```
JPanel fileSelectionPanel
```
    - importSequencesFromFilesPanel
```
JPanel importSequencesFromFilesPanel
```
    - inputPanel
```
JPanel inputPanel
```
    - nameLbl
```
JLabel nameLbl
```
    - nameTxt
```
JTextField nameTxt
```
    - okButton
```
JButton okButton
```
    - parsingRuleLbl
```
JLabel parsingRuleLbl
```
    - parsingRuleTxt
```
JTextField parsingRuleTxt
```
    - typeCmb
```
JComboBox<E> typeCmb
```
    - typeLbl
```
JLabel typeLbl
```
    - versionLbl
```
JLabel versionLbl
```
    - versionTxt
```
JTextField versionTxt
```
- Class com.compomics.util.protein_sequences_manager.gui.sequences_import.ImportSequencesFromUniprotDialog extends JDialog implements Serializable
  - Serialized Fields
    - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
      The utilities user preferences.
    - lastSelectedFolder
```
LastSelectedFolder lastSelectedFolder
```
      The last selected folder.
    - downloadFile
```
File downloadFile
```
      The file selected by the user.
    - selectedFileIndex
```
FastaIndex selectedFileIndex
```
      The index of the file selected by the user.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the import has been canceled by the user.
    - parentFrame
```
Frame parentFrame
```
      The parent frame.
    - waitingImage
```
Image waitingImage
```
      The icon to display when waiting.
    - normalImange
```
Image normalImange
```
      The normal icon.
    - btnTaxonomyTree
```
JButton btnTaxonomyTree
```
    - buttonGroup1
```
ButtonGroup buttonGroup1
```
    - cancelButton
```
JButton cancelButton
```
    - cbModelOrganism
```
JComboBox<E> cbModelOrganism
```
    - cbSequenceDatabaseType
```
JComboBox<E> cbSequenceDatabaseType
```
    - descriptionLbl
```
JLabel descriptionLbl
```
    - descriptionScrollPane
```
JScrollPane descriptionScrollPane
```
    - descriptionTxt
```
JTextArea descriptionTxt
```
    - downloadButton
```
JButton downloadButton
```
    - inputPanel
```
JPanel inputPanel
```
    - lbSequenceContentType
```
JLabel lbSequenceContentType
```
    - modelOrganismLabel
```
JLabel modelOrganismLabel
```
    - nameLbl
```
JLabel nameLbl
```
    - nameTxt
```
JTextField nameTxt
```
    - okButton
```
JButton okButton
```
    - parsingRuleLbl
```
JLabel parsingRuleLbl
```
    - parsingRuleTxt
```
JTextField parsingRuleTxt
```
    - taxIdLabel
```
JLabel taxIdLabel
```
    - taxonomyPanel
```
JPanel taxonomyPanel
```
    - tfTaxonomyID
```
JTextField tfTaxonomyID
```
    - typeLabel
```
JLabel typeLabel
```
    - typeLbl
```
JLabel typeLbl
```
    - versionLbl
```
JLabel versionLbl
```
    - versionTxt
```
JTextField versionTxt
```
Package com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy
- Class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreeDialog extends JDialog implements Serializable
  - Serialized Fields
    - backgroundPanel
```
JPanel backgroundPanel
```
    - btnCancel
```
JButton btnCancel
```
    - btnConfirm
```
JButton btnConfirm
```
    - taxonomyTreePanel1
```
TaxonomyTreePanel taxonomyTreePanel1
```
- Class com.compomics.util.protein_sequences_manager.gui.sequences_import.taxonomy.TaxonomyTreePanel extends JPanel implements Serializable
  - Serialized Fields
    - query
```
UniprotTaxonomyProvider query
```
      The query.
    - btnSearch
```
JButton btnSearch
```
    - taxonomyTree
```
JTree taxonomyTree
```
    - taxonomyTreeScrollPane
```
JScrollPane taxonomyTreeScrollPane
```
    - tfSearchField
```
JTextField tfSearchField
```
Package com.compomics.util.sun
- Class com.compomics.util.sun.TableMap extends AbstractTableModel implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - model
```
TableModel model
```
- Class com.compomics.util.sun.TableSorter extends TableMap implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - indexes
```
int[] indexes
```
    - sortingColumns
```
Vector<E> sortingColumns
```
    - ascending
```
boolean ascending
```
    - compares
```
int compares
```
    - listMouseListener
```
MouseAdapter listMouseListener
```

Serialized Form

Package com.compomics.software.dialogs

Class com.compomics.software.dialogs.JavaHomeDialog extends JDialog implements Serializable

Serialized Fields

javaHomeOrMemoryDialogParent

welcomeDialog

toolName

backgroundPanel

browseButton

cancelButton

jSeparator1

javaHomeHelpJButton

javaHomeLabel

javaHomeTxt

okButton

Class com.compomics.software.dialogs.JavaMemoryDialog extends JDialog implements Serializable

Serialized Fields

javaHomeOrMemoryDialogParent

welcomeDialog

toolName

backgroundPanel

cancelButton

jSeparator1

javaOptionsHelpJButton

mbLabel

memoryLimitLabel

memoryTxt

okButton

Class com.compomics.software.dialogs.JavaSettingsDialog extends JDialog implements Serializable

Serialized Fields

javaHomeOrMemoryDialogParent

frameParent

toolName

welcomeDialog

backgroundsPanel

bitLabel

bitPanel

bitRecommendationLabel

javaHelpJLabel

javaHomeLabel

javaHomePanel

memoryLabel

memoryPanel

memoryRecommendationLabel

okButton

versionLabel

versionPanel

versionRecommendationLabel1

versionRecommendationLabel2

Class com.compomics.software.dialogs.PeptideShakerSetupDialog extends JDialog implements Serializable

Serialized Fields

utilitiesUserPreferences

lastSelectedFolder

dialogCanceled

parentFrame

parentDialog

progressDialog

backgroundPanel

browseButton

cancelButton

jLabel2

okButton

peptideShakerButton

peptideShakerDownloadLinkLabel

peptideShakerDownloadPanel

peptideShakerInfoLabel

peptideShakerInstallationPanel

peptideShakerJarFileHelpLabel

peptideShakernstallationJTextField

Class com.compomics.software.dialogs.ProteoWizardSetupDialog extends JDialog implements Serializable

Serialized Fields

utilitiesUserPreferences

lastSelectedFolder

dialogCanceled

backgroundPanel

browseButton

cancelButton

downloadLinkLabel

downloadPanel

folderHelpLabel