Serialized Form (computational omics utilities 3.21.11 API)

Package com.compomics.software.dialogs

Class com.compomics.software.dialogs.JavaOptionsDialog extends javax.swing.JDialog implements Serializable
- Serialized Fields
  - javaOptionsDialogParent
```
JavaOptionsDialogParent javaOptionsDialogParent
```
    The main instance of the GUI.
  - welcomeDialog
```
javax.swing.JDialog welcomeDialog
```
    A reference to the Welcome Dialog.
  - toolName
```
java.lang.String toolName
```
    The name of the tool, e.g., PeptideShaker.
  - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
  - cancelButton
```
javax.swing.JButton cancelButton
```
  - javaOptionsHelpJButton
```
javax.swing.JButton javaOptionsHelpJButton
```
  - mbLabel
```
javax.swing.JLabel mbLabel
```
  - memoryLimitLabel
```
javax.swing.JLabel memoryLimitLabel
```
  - memoryTxt
```
javax.swing.JTextField memoryTxt
```
  - okButton
```
javax.swing.JButton okButton
```
  - settingsPanel
```
javax.swing.JPanel settingsPanel
```

Class com.compomics.software.dialogs.LowMemoryDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

javaOptionsDialogParent
```
JavaOptionsDialogParent javaOptionsDialogParent
```
The main instance of the GUI.
frameParent
```
javax.swing.JFrame frameParent
```
The frame parent.
toolName
```
java.lang.String toolName
```
The name of the tool, e.g., PeptideShaker.
welcomeDialog
```
javax.swing.JDialog welcomeDialog
```
A reference to the Welcome Dialog.
backgroundsPanel
```
javax.swing.JPanel backgroundsPanel
```
bitLabel
```
javax.swing.JLabel bitLabel
```
bitPanel
```
javax.swing.JPanel bitPanel
```

bitRecommendationLabel

javax.swing.JLabel bitRecommendationLabel

editMemoryJLabel
```
javax.swing.JLabel editMemoryJLabel
```
javaHelpJLabel
```
javax.swing.JLabel javaHelpJLabel
```
javaHomeLabel
```
javax.swing.JLabel javaHomeLabel
```
javaHomePanel
```
javax.swing.JPanel javaHomePanel
```
memoryLabel
```
javax.swing.JLabel memoryLabel
```
memoryPanel
```
javax.swing.JPanel memoryPanel
```

memoryRecommendationLabel

javax.swing.JLabel memoryRecommendationLabel

okButton
```
javax.swing.JButton okButton
```

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

Serialized Fields

utilitiesUserPreferences

UtilitiesUserPreferences utilitiesUserPreferences

The utilities preferences.

lastSelectedFolder
```
java.lang.String lastSelectedFolder
```
The selected folder.
dialogCanceled
```
boolean dialogCanceled
```
Set to true if the dialog was canceled.
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
browseButton
```
javax.swing.JButton browseButton
```
cancelButton
```
javax.swing.JButton cancelButton
```
jLabel2
```
javax.swing.JLabel jLabel2
```
okButton
```
javax.swing.JButton okButton
```
peptideShakerButton
```
javax.swing.JButton peptideShakerButton
```

peptideShakerDownloadLinkLabel

javax.swing.JLabel peptideShakerDownloadLinkLabel

peptideShakerDownloadPanel

javax.swing.JPanel peptideShakerDownloadPanel

peptideShakerInfoLabel

javax.swing.JLabel peptideShakerInfoLabel

peptideShakerInstallationPanel

javax.swing.JPanel peptideShakerInstallationPanel

peptideShakerJarFileHelpLabel

javax.swing.JLabel peptideShakerJarFileHelpLabel

peptideShakernstallationJTextField

javax.swing.JTextField peptideShakernstallationJTextField

Class com.compomics.software.dialogs.RelimsSetupDialog extends javax.swing.JDialog implements Serializable
- Serialized Fields
  - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
    Deprecated.
    
    The utilities preferences.
  - lastSelectedFolder
```
java.lang.String lastSelectedFolder
```
    Deprecated.
    
    The selected folder.
  - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
    Deprecated.
  - browseButton
```
javax.swing.JButton browseButton
```
    Deprecated.
  - cancelButton
```
javax.swing.JButton cancelButton
```
    Deprecated.
  - jLabel2
```
javax.swing.JLabel jLabel2
```
    Deprecated.
  - okButton
```
javax.swing.JButton okButton
```
    Deprecated.
  - relimsButton
```
javax.swing.JButton relimsButton
```
    Deprecated.
  - relimsDownloadLinkLabel
```
javax.swing.JLabel relimsDownloadLinkLabel
```
    Deprecated.
  - relimsDownloadPanel
```
javax.swing.JPanel relimsDownloadPanel
```
    Deprecated.
  - relimsInfoLabel
```
javax.swing.JLabel relimsInfoLabel
```
    Deprecated.
  - relimsInstallationJTextField
```
javax.swing.JTextField relimsInstallationJTextField
```
    Deprecated.
  - relimsInstallationPanel
```
javax.swing.JPanel relimsInstallationPanel
```
    Deprecated.
  - relimsJarFileHelpLabel
```
javax.swing.JLabel relimsJarFileHelpLabel
```
    Deprecated.

Class com.compomics.software.dialogs.ReporterSetupDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

utilitiesUserPreferences

UtilitiesUserPreferences utilitiesUserPreferences

The utilities preferences.

lastSelectedFolder
```
java.lang.String lastSelectedFolder
```
The selected folder.
dialogCanceled
```
boolean dialogCanceled
```
Set to true if the dialog was canceled.
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
browseButton
```
javax.swing.JButton browseButton
```
cancelButton
```
javax.swing.JButton cancelButton
```
jLabel2
```
javax.swing.JLabel jLabel2
```
okButton
```
javax.swing.JButton okButton
```
reporterButton
```
javax.swing.JButton reporterButton
```

reporterDownloadLinkLabel

javax.swing.JLabel reporterDownloadLinkLabel

reporterDownloadPanel

javax.swing.JPanel reporterDownloadPanel

reporterInfoLabel
```
javax.swing.JLabel reporterInfoLabel
```

reporterInstallationJTextField

javax.swing.JTextField reporterInstallationJTextField

reporterInstallationPanel

javax.swing.JPanel reporterInstallationPanel

reporterJarFileHelpLabel

javax.swing.JLabel reporterJarFileHelpLabel

Class com.compomics.software.dialogs.SearchGuiSetupDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

utilitiesUserPreferences

UtilitiesUserPreferences utilitiesUserPreferences

The utilities preferences.

lastSelectedFolder
```
java.lang.String lastSelectedFolder
```
The selected folder.
dialogCanceled
```
boolean dialogCanceled
```
Set to true if the dialog was canceled.
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
browseButton
```
javax.swing.JButton browseButton
```
cancelButton
```
javax.swing.JButton cancelButton
```
jLabel2
```
javax.swing.JLabel jLabel2
```
okButton
```
javax.swing.JButton okButton
```
searchGuiButton
```
javax.swing.JButton searchGuiButton
```

searchGuiDownloadLinkLabel

javax.swing.JLabel searchGuiDownloadLinkLabel

searchGuiDownloadPanel

javax.swing.JPanel searchGuiDownloadPanel

searchGuiInfoLabel
```
javax.swing.JLabel searchGuiInfoLabel
```

searchGuiInstallationJTextField

javax.swing.JTextField searchGuiInstallationJTextField

searchGuiInstallationPanel

javax.swing.JPanel searchGuiInstallationPanel

searchGuiJarFileHelpLabel

javax.swing.JLabel searchGuiJarFileHelpLabel

Package com.compomics.util
- Class com.compomics.util.AlternateRowColoursJTable extends javax.swing.JTable implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iEvenRowColor
```
java.awt.Color iEvenRowColor
```
      The background colour for the even rows. A value of 'null' means use the default background colour for JTable.
    - iUnevenRowColor
```
java.awt.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 javax.swing.table.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
```
java.lang.String[] iColNames
```
      The column names in this resultset.
    - iData
```
java.lang.Object[][] iData
```
      The data.
- Class com.compomics.util.db.GeneratorException extends java.lang.Exception implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iNested
```
java.lang.Exception iNested
```
      The nested exception.
- Class com.compomics.util.db.ObjectsDB extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -8595805180622832745L
  - Serialized Fields
    - dbName
```
java.lang.String dbName
```
      The name of the database.
    - dbConnection
```
java.sql.Connection dbConnection
```
      The connection, shall not be accessed outside this class. Don't be lazy, implement the dedicated methods here.
    - longKeys
```
java.util.ArrayList<E> longKeys
```
      Deprecated. use longTableNames instead
      
      List of keys too long to create a table.
    - longTableNames
```
java.util.ArrayList<E> longTableNames
```
      List of keys too long to create a table.
    - longKeysMap
```
java.util.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
```
java.io.BufferedWriter debugSpeedWriter
```
      The writer used to send the output to file.
    - debugContentWriter
```
java.io.BufferedWriter debugContentWriter
```
      The writer used to send the output to file.
    - debugFolder
```
java.io.File debugFolder
```
      The debug folder.
    - busy
```
boolean busy
```
      A boolean indicating whether the database is being queried.
    - tableQueueUpdating
```
java.lang.String tableQueueUpdating
```
      The name of the table currently updating in the queue.
    - tableQueue
```
java.util.ArrayList<E> tableQueue
```
      A queue of entire tables to load.
    - contentQueue
```
java.util.HashMap<K,V> contentQueue
```
      A queue of table components to load.
    - contentTableQueue
```
java.util.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 javax.swing.JFrame implements Serializable
- Serialized Fields
  - closeJButton
```
javax.swing.JButton closeJButton
```
  - textEditorScrollPane
```
javax.swing.JScrollPane textEditorScrollPane
```
  - textJEditorPane
```
javax.swing.JEditorPane textJEditorPane
```
Class com.compomics.util.examples.MirroredSpectraTestDialog extends javax.swing.JDialog implements Serializable
- Serialized Fields
  - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```

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

Serialized Fields

peffAnnotationsColorMap
```
java.util.HashMap<K,V> peffAnnotationsColorMap
```
The PEFF annotations color map.
peffAnnotationsTooltipMap
```
java.util.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
```
java.util.TreeMap<K,V> keyValuePairs
```
The map of the PEFF key value pairs.
currentSequenceFile
```
java.io.File currentSequenceFile
```
The current PEFF (or FASTA) sequence file.
currentPeffBufferedReader
```
java.io.BufferedReader currentPeffBufferedReader
```
The current PEFF (or FASTA) buffered reader.
currentSequence
```
java.lang.String currentSequence
```
The current PEFF (or FASTA) sequence.
currentSequenceLine
```
java.lang.String currentSequenceLine
```
The current PEFF (or FASTA) sequence line.
linkedSpectrumPanels
```
java.util.HashMap<K,V> linkedSpectrumPanels
```
A hashmap of both the linked spectra.
allAnnotations
```
java.util.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
```
java.lang.String cleanProteinSequence
```
Used for the in silico digestion example.
selectedAnnotationTypes
```
java.util.HashMap<K,V> selectedAnnotationTypes
```
The tag colors for PEFF formatting.
sequenceAnnotationColumnHeaderTooltips
```
java.util.ArrayList<E> sequenceAnnotationColumnHeaderTooltips
```
Sequence annotation column header tooltips.
sparklineColor
```
java.awt.Color sparklineColor
```
The color used for the sparkline bar chart plots.
H2OIonsJCheckBox
```
javax.swing.JCheckBox H2OIonsJCheckBox
```
NH3IonsJCheckBox
```
javax.swing.JCheckBox NH3IonsJCheckBox
```
aIonsJCheckBox
```
javax.swing.JCheckBox aIonsJCheckBox
```
allPeaksJCheckBox
```
javax.swing.JCheckBox allPeaksJCheckBox
```
bIonsJCheckBox
```
javax.swing.JCheckBox bIonsJCheckBox
```
browseJButton
```
javax.swing.JButton browseJButton
```
cIonsJCheckBox
```
javax.swing.JCheckBox cIonsJCheckBox
```

chargeOneJCheckBox

javax.swing.JCheckBox chargeOneJCheckBox

chargeOverTwoJCheckBox

javax.swing.JCheckBox chargeOverTwoJCheckBox

chargePeptideAJSpinner

javax.swing.JSpinner chargePeptideAJSpinner

chargePeptideBJSpinner

javax.swing.JSpinner chargePeptideBJSpinner

chargeTwoJCheckBox

javax.swing.JCheckBox chargeTwoJCheckBox

chromatogramAJPanel
```
javax.swing.JPanel chromatogramAJPanel
```
chromatogramJPanel
```
javax.swing.JPanel chromatogramJPanel
```

chromatogramPanelHelpJLabel

javax.swing.JLabel chromatogramPanelHelpJLabel

chromatogramPanelInfoJLabel

javax.swing.JLabel chromatogramPanelInfoJLabel

enzymesJComboBox

javax.swing.JComboBox<E> enzymesJComboBox

exportJButton
```
javax.swing.JButton exportJButton
```

inSilicoDigestionHelpJLabel

javax.swing.JLabel inSilicoDigestionHelpJLabel

informationJEditorPane

javax.swing.JEditorPane informationJEditorPane

informationJPanel
```
javax.swing.JPanel informationJPanel
```

informationJScrollPane

javax.swing.JScrollPane informationJScrollPane

inhibitorsJTextField

javax.swing.JTextField inhibitorsJTextField

ionSelectionJPanel
```
javax.swing.JPanel ionSelectionJPanel
```

isotopicDistributionAJPanel

javax.swing.JPanel isotopicDistributionAJPanel

isotopicDistributionCalculatorHelpJLabel

javax.swing.JLabel isotopicDistributionCalculatorHelpJLabel

isotopicDistributionCalculatorInfoJLabel

javax.swing.JLabel isotopicDistributionCalculatorInfoJLabel

isotopicDistributionJPanel

javax.swing.JPanel isotopicDistributionJPanel

jLabel1
```
javax.swing.JLabel jLabel1
```
jLabel10
```
javax.swing.JLabel jLabel10
```
jLabel11
```
javax.swing.JLabel jLabel11
```
jLabel12
```
javax.swing.JLabel jLabel12
```
jLabel13
```
javax.swing.JLabel jLabel13
```
jLabel14
```
javax.swing.JLabel jLabel14
```
jLabel15
```
javax.swing.JLabel jLabel15
```
jLabel16
```
javax.swing.JLabel jLabel16
```
jLabel17
```
javax.swing.JLabel jLabel17
```
jLabel18
```
javax.swing.JLabel jLabel18
```
jLabel19
```
javax.swing.JLabel jLabel19
```
jLabel2
```
javax.swing.JLabel jLabel2
```
jLabel20
```
javax.swing.JLabel jLabel20
```
jLabel21
```
javax.swing.JLabel jLabel21
```
jLabel24
```
javax.swing.JLabel jLabel24
```
jLabel3
```
javax.swing.JLabel jLabel3
```
jLabel4
```
javax.swing.JLabel jLabel4
```
jLabel5
```
javax.swing.JLabel jLabel5
```
jLabel6
```
javax.swing.JLabel jLabel6
```
jLabel7
```
javax.swing.JLabel jLabel7
```
jLabel8
```
javax.swing.JLabel jLabel8
```
jLabel9
```
javax.swing.JLabel jLabel9
```
jPanel1
```
javax.swing.JPanel jPanel1
```
jPanel10
```
javax.swing.JPanel jPanel10
```
jPanel11
```
javax.swing.JPanel jPanel11
```
jPanel12
```
javax.swing.JPanel jPanel12
```
jPanel2
```
javax.swing.JPanel jPanel2
```
jPanel3
```
javax.swing.JPanel jPanel3
```
jPanel4
```
javax.swing.JPanel jPanel4
```
jPanel5
```
javax.swing.JPanel jPanel5
```
jPanel6
```
javax.swing.JPanel jPanel6
```
jPanel7
```
javax.swing.JPanel jPanel7
```
jPanel8
```
javax.swing.JPanel jPanel8
```
jPanel9
```
javax.swing.JPanel jPanel9
```
jRadioButton1
```
javax.swing.JRadioButton jRadioButton1
```
jScrollPane1
```
javax.swing.JScrollPane jScrollPane1
```
jScrollPane2
```
javax.swing.JScrollPane jScrollPane2
```
jScrollPane3
```
javax.swing.JScrollPane jScrollPane3
```
jSeparator1
```
javax.swing.JSeparator jSeparator1
```
jSeparator2
```
javax.swing.JSeparator jSeparator2
```
jSeparator3
```
javax.swing.JSeparator jSeparator3
```
jSeparator4
```
javax.swing.JSeparator jSeparator4
```
jSeparator5
```
javax.swing.JSeparator jSeparator5
```
jSeparator6
```
javax.swing.JSeparator jSeparator6
```
jSeparator9
```
javax.swing.JSeparator jSeparator9
```
jTabbedPane
```
javax.swing.JTabbedPane jTabbedPane
```

linkedSpectraJCheckBox

javax.swing.JCheckBox linkedSpectraJCheckBox

lowerMassJSpinner
```
javax.swing.JSpinner lowerMassJSpinner
```

missedCleavagesJSpinner

javax.swing.JSpinner missedCleavagesJSpinner

nextJButton
```
javax.swing.JButton nextJButton
```

otherIonsJCheckBox

javax.swing.JCheckBox otherIonsJCheckBox

peffAnnotationsJTable

javax.swing.JTable peffAnnotationsJTable

peffHeaderJTable
```
javax.swing.JTable peffHeaderJTable
```
peptideAColorJPanel
```
javax.swing.JPanel peptideAColorJPanel
```

peptideACompositionJTextField

javax.swing.JTextField peptideACompositionJTextField

peptideAJScrollPane

javax.swing.JScrollPane peptideAJScrollPane

peptideAJXTable

org.jdesktop.swingx.JXTable peptideAJXTable

peptideAMzJTextField

javax.swing.JTextField peptideAMzJTextField

peptideBColorJPanel
```
javax.swing.JPanel peptideBColorJPanel
```

peptideBCompositionJTextField

javax.swing.JTextField peptideBCompositionJTextField

peptideBJScrollPane

javax.swing.JScrollPane peptideBJScrollPane

peptideBJXTable

org.jdesktop.swingx.JXTable peptideBJXTable

peptideBMzJTextField

javax.swing.JTextField peptideBMzJTextField

peptideSequenceAJTextField

javax.swing.JTextField peptideSequenceAJTextField

peptideSequenceBJTextField

javax.swing.JTextField peptideSequenceBJTextField

peptidesJPanel
```
javax.swing.JPanel peptidesJPanel
```
peptidesJTable
```
javax.swing.JTable peptidesJTable
```

peptidesScrollPane

javax.swing.JScrollPane peptidesScrollPane

positionJTextField

javax.swing.JTextField positionJTextField

profileSpectrumJCheckBox

javax.swing.JCheckBox profileSpectrumJCheckBox

proteinCoverageJScrollPane

javax.swing.JScrollPane proteinCoverageJScrollPane

proteinDigestionJLabel

javax.swing.JLabel proteinDigestionJLabel

proteinDigestionJPanel

javax.swing.JPanel proteinDigestionJPanel

proteinHeaderJTable
```
javax.swing.JTable proteinHeaderJTable
```

proteinSequenceCoverageJEditorPane

javax.swing.JEditorPane proteinSequenceCoverageJEditorPane

sequenceCoverageJPanel

javax.swing.JPanel sequenceCoverageJPanel

sequenceFileJTextField

javax.swing.JTextField sequenceFileJTextField

sequenceJTabbedPane

javax.swing.JTabbedPane sequenceJTabbedPane

silacLabelPeptideAJComboBox

javax.swing.JComboBox<E> silacLabelPeptideAJComboBox

silacLabelPeptideBJComboBox

javax.swing.JComboBox<E> silacLabelPeptideBJComboBox

siteJTextField
```
javax.swing.JTextField siteJTextField
```
spectraJPanel
```
javax.swing.JPanel spectraJPanel
```
spectrumAJPanel
```
javax.swing.JPanel spectrumAJPanel
```
spectrumBJPanel
```
javax.swing.JPanel spectrumBJPanel
```
spectrumJPanel
```
javax.swing.JPanel spectrumJPanel
```

spectrumPanelHelpJLabel

javax.swing.JLabel spectrumPanelHelpJLabel

spectrumPanelInfoJLabel

javax.swing.JLabel spectrumPanelInfoJLabel

upperMassJSpinner
```
javax.swing.JSpinner upperMassJSpinner
```
xIonsJCheckBox
```
javax.swing.JCheckBox xIonsJCheckBox
```
yIonsJCheckBox
```
javax.swing.JCheckBox yIonsJCheckBox
```
zIonsJCheckBox
```
javax.swing.JCheckBox zIonsJCheckBox
```

Package com.compomics.util.experiment
- Class com.compomics.util.experiment.MsExperiment extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  4330394623824512352L
  - Serialized Fields
    - reference
```
java.lang.String reference
```
      Reference of the experiment.
    - samples
```
java.util.HashMap<K,V> samples
```
      The samples analyzed.
    - analysis
```
java.util.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
```
java.util.HashMap<K,V> quantification
```
      Quantification results indexed by the method used
    - identification
```
java.util.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
```
java.util.HashMap<K,V> analysis
```
      The various analysis indexed by replicates indexes
Package com.compomics.util.experiment.biology
- Class com.compomics.util.experiment.biology.AminoAcid extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -3158896310928354857L
  - Serialized Fields
    - singleLetterCode
```
java.lang.String singleLetterCode
```
      Single letter code of the amino acid.
    - threeLetterCode
```
java.lang.String threeLetterCode
```
      Three letter code of the amino acid.
    - name
```
java.lang.String name
```
      Name of the amino acid.
    - averageMass
```
double averageMass
```
      Average mass of the amino acid.
    - monoisotopicMass
```
double monoisotopicMass
```
      Monoisotopic mass of the amino acid.
- Class com.compomics.util.experiment.biology.AminoAcidPattern extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -2823716418631089876L
  - Serialized Fields
    - target
```
java.lang.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.
    - aaTargeted
```
java.util.HashMap<K,V> aaTargeted
```
      The list of targeted amino acids at a given index. For trypsin: 0 -> {R, K} 1 -> {}
    - aaExcluded
```
java.util.HashMap<K,V> aaExcluded
```
      The list of excluded amino acids at a given index For trypsin: 0 -> {} 1 -> {P}
    - targetModifications
```
java.util.HashMap<K,V> targetModifications
```
      The modifications carried by the amino acid sequence at target amino acids.
- Class com.compomics.util.experiment.biology.Atom extends ExperimentObject implements Serializable
  - Serialized Fields
    - mass
```
double mass
```
    - name
```
java.lang.String name
```
    - letter
```
java.lang.String letter
```
- Class com.compomics.util.experiment.biology.Enzyme extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -1852087173903613377L
  - Serialized Fields
    - id
```
int id
```
    - name
```
java.lang.String name
```
    - aminoAcidBefore
```
java.util.ArrayList<E> aminoAcidBefore
```
    - aminoAcidAfter
```
java.util.ArrayList<E> aminoAcidAfter
```
    - restrictionBefore
```
java.util.ArrayList<E> restrictionBefore
```
    - restrictionAfter
```
java.util.ArrayList<E> restrictionAfter
```
    - isSemiSpecific
```
java.lang.Boolean isSemiSpecific
```
      If true, the enzyme is considered as semi-specific, meaning that only one end of the resulting peptide has to be enzymatic.
- Class com.compomics.util.experiment.biology.Ion extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -1505719074403886934L
  - Serialized Fields
    - type
```
Ion.IonType type
```
      Type of ion.
    - theoreticMass
```
double theoreticMass
```
- Class com.compomics.util.experiment.biology.NeutralLoss extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  5540846193082177391L
  - Serialized Fields
    - mass
```
double mass
```
      The mass lost.
    - name
```
java.lang.String name
```
      The name of the neutral loss.
    - fixed
```
java.lang.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
```
java.lang.String sequence
```
      The peptide sequence.
    - mass
```
java.lang.Double mass
```
      The peptide mass.
    - parentProteins
```
java.util.ArrayList<E> parentProteins
```
      The parent proteins.
    - modifications
```
java.util.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
```
java.lang.String accession
```
      The protein accession.
    - decoy
```
boolean decoy
```
      Boolean indicating if the protein is not existing (decoy protein for instance).
    - sequence
```
java.lang.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.
    - residuesArray
```
java.util.ArrayList<E> residuesArray
```
      Deprecated. use amino acid pattern instead
      
      The residues affected by this modification. '[' denotes N-term and ']' C-term.
    - name
```
java.lang.String name
```
      Name of the modification.
    - shortName
```
java.lang.String shortName
```
      Short name of the modification.
    - mass
```
double mass
```
      Mass difference produced by this modification.
    - neutralLosses
```
java.util.ArrayList<E> neutralLosses
```
      List of known neutral losses for this modification.
    - reporterIons
```
java.util.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).
- Class com.compomics.util.experiment.biology.PTMFactory extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  7935264190312934466L
  - Serialized Fields
    - ptmMap
```
java.util.HashMap<K,V> ptmMap
```
      A map linking indexes with modifications.
    - defaultMods
```
java.util.ArrayList<E> defaultMods
```
      List of the indexes of default modifications.
    - userMods
```
java.util.ArrayList<E> userMods
```
      List of the indexes of user modifications.
    - userColors
```
java.util.HashMap<K,V> userColors
```
      Mapping of the expected modification names to the color used.
    - shortNames
```
java.util.HashMap<K,V> shortNames
```
      Map of the short names.
    - defaultOmssaIndexes
```
java.util.HashMap<K,V> defaultOmssaIndexes
```
      Map of OMSSA indexes for default modifications.
    - 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
```
java.lang.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.Hydrogen 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.Sulfur extends Atom implements Serializable
Package com.compomics.util.experiment.biology.ions
- Class com.compomics.util.experiment.biology.ions.ElementaryIon extends Ion implements Serializable
  
  serialVersionUID:
  
  -1578136397635015592L
  - Serialized Fields
    - name
```
java.lang.String name
```
      The name of the ion.
    - subType
```
int subType
```
      The subtype identifier.
- Class com.compomics.util.experiment.biology.ions.Glycon extends Ion implements Serializable
  
  serialVersionUID:
  
  -2278483206647518565L
  - Serialized Fields
    - theoreticMasses
```
java.util.HashMap<K,V> theoreticMasses
```
      Masses of this glycon.
    - name
```
java.lang.String name
```
      The glycon short name which can be displayed on a spectrum.
    - longName
```
java.lang.String longName
```
      The glycon 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
```
java.util.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
```
java.util.ArrayList<E> neutralLosses
```
      the neutral losses found on the ion.
- Class com.compomics.util.experiment.biology.ions.ReporterIon extends Ion implements Serializable
  
  serialVersionUID:
  
  1109011048958734120L
  - Serialized Fields
    - name
```
java.lang.String name
```
      Ion name for user defined ions.
    - subtype
```
int subtype
```
      The ion subtype.
- Class com.compomics.util.experiment.biology.ions.TagFragmentIon extends Ion implements Serializable
  - Serialized Fields
    - neutralLosses
```
java.util.ArrayList<E> neutralLosses
```
      The neutral losses found on the ion.
    - number
```
int number
```
      Position of the ion in the tag in amino acids considering gaps as an amino acid.
    - subNumber
```
int subNumber
```
      Position of the ion in the current sequence of amino acids.
    - subType
```
int subType
```
      The type of fragment.
    - massGap
```
double massGap
```
      Mass gap before this ion.
Package com.compomics.util.experiment.identification
- Class com.compomics.util.experiment.identification.FastaIndex extends ExperimentObject implements Serializable
  - Serialized Fields
    - indexes
```
java.util.HashMap<K,V> indexes
```
      The indexes of the inspected FASTA file.
    - decoyAccessions
```
java.util.HashSet<E> decoyAccessions
```
      The decoy accessions.
    - fileName
```
java.lang.String fileName
```
      The FASTA file name.
    - name
```
java.lang.String name
```
      The name of the database.
    - lastModified
```
java.lang.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.
    - databaseType
```
Header.DatabaseType databaseType
```
      The database type.
    - version
```
java.lang.String version
```
      The version of the database.
    - concatenatedTargetDecoy
```
boolean concatenatedTargetDecoy
```
      Indicates whether the database is a concatenated target/decoy.
    - decoyTag
```
java.lang.String decoyTag
```
      The tag used for decoy sequences.
- Class com.compomics.util.experiment.identification.Identification extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  -2551700699384242554L
  - Serialized Fields
    - proteinIdentification
```
java.util.ArrayList<E> proteinIdentification
```
      List of the keys of all imported proteins.
    - peptideIdentification
```
java.util.ArrayList<E> peptideIdentification
```
      List of the keys of all imported peptides.
    - spectrumIdentificationMap
```
java.util.HashMap<K,V> spectrumIdentificationMap
```
      List of all imported PSMs indexed by mgf file name.
    - spectrumIdentification
```
java.util.ArrayList<E> spectrumIdentification
```
      Deprecated. use file specific mapping instead
      
      List of the keys of all imported PSMs.
    - proteinMap
```
java.util.HashMap<K,V> proteinMap
```
      A map linking protein accessions to all their protein matches keys.
    - methodUsed
```
int methodUsed
```
      The method used.
    - serializationDirectory
```
java.lang.String serializationDirectory
```
      The directory where matches will be serialized/the database stored.
    - urParameters
```
java.util.HashMap<K,V> urParameters
```
      Deprecated. use the database instead
      
      Map of the user's parameters.
    - longKeys
```
java.util.ArrayList<E> longKeys
```
      Deprecated. use the database instead
      
      Map of long keys (>100 characters) which will be referenced by their index for file creation/database storage.
    - isDB
```
java.lang.Boolean isDB
```
      Boolean indicating whether the matches should be stored in a database (default) or in serialized files.
    - identificationDB
```
IdentificationDB identificationDB
```
      The identificationDB object interacting with the database.
    - reference
```
java.lang.String reference
```
      The reference of the identification.
    - orderedSpectrumFileNames
```
java.util.ArrayList<E> orderedSpectrumFileNames
```
      The ordered list of spectrum file names.
- Class com.compomics.util.experiment.identification.IdentificationDB extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  691986038787590646L
  - Serialized Fields
    - dbName
```
java.lang.String dbName
```
      The name which will be used for the database.
    - proteinTableName
```
java.lang.String proteinTableName
```
      The name of the protein table.
    - proteinParametersTableSuffix
```
java.lang.String proteinParametersTableSuffix
```
      The suffix for protein parameters tables.
    - peptideTableName
```
java.lang.String peptideTableName
```
      The name of the peptide table.
    - peptideParametersTableSuffix
```
java.lang.String peptideParametersTableSuffix
```
      The suffix for a peptide parameters table.
    - psmTableSuffix
```
java.lang.String psmTableSuffix
```
      The suffix for a PSM table.
    - psmParametersTableSuffix
```
java.lang.String psmParametersTableSuffix
```
      The suffix for a PSM parameters table.
    - parametersSuffix
```
java.lang.String parametersSuffix
```
      Deprecated. use match specific mapping instead
      
      The suffix for a generic parameter table.
    - psmTables
```
java.util.ArrayList<E> psmTables
```
      List of all psms tables.
    - psmParametersTables
```
java.util.ArrayList<E> psmParametersTables
```
      List of all psm parameters tables.
    - peptideParametersTables
```
java.util.ArrayList<E> peptideParametersTables
```
      List of all peptide parameters tables.
    - proteinParametersTables
```
java.util.ArrayList<E> proteinParametersTables
```
      List of all proteins parameters tables.
    - matchParametersTables
```
java.util.ArrayList<E> matchParametersTables
```
      Deprecated. use match specific mapping instead
      
      List of all match 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.NeutralLossesMap extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -4690159937753713106L
  - Serialized Fields
    - bBoundaries
```
java.util.HashMap<K,V> bBoundaries
```
      Map indicating for each neutral loss when they should start being accounted for the forward ions (b ions for instance).
    - yBoundaries
```
java.util.HashMap<K,V> yBoundaries
```
      Map indicating for each neutral loss when they should start being accounted for the reverse ions (y ions for instance).
- Class com.compomics.util.experiment.identification.PeptideAssumption extends SpectrumIdentificationAssumption implements Serializable
  
  serialVersionUID:
  
  3606509518581203063L
  - Serialized Fields
    - peptide
```
Peptide peptide
```
      The theoretic peptide.
    - advocate
```
int advocate
```
      Deprecated. use the SpectrumIdentificationAssumption attribute
      
      The advocate supporting this assumption.
    - identificationCharge
```
Charge identificationCharge
```
      Deprecated. use the SpectrumIdentificationAssumption attribute
      
      The charge used for identification.
    - rank
```
int rank
```
      Deprecated. use the SpectrumIdentificationAssumption attribute
      
      The rank of the peptide assumption for the concerned spectrum.
    - eValue
```
double eValue
```
      Deprecated. use the SpectrumIdentificationAssumption attribute
      
      The score, the lower the better. Ought to be renamed but kept for backward compatibility.
    - file
```
java.lang.String file
```
      Deprecated. use the SpectrumIdentificationAssumption attribute
      
      The corresponding identification file.
- Class com.compomics.util.experiment.identification.SearchParameters extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -2773993307168773763L
  - Serialized Fields
    - precursorAccuracyType
```
SearchParameters.MassAccuracyType precursorAccuracyType
```
      The precursor accuracy type. Default is ppm.
    - fragmentAccuracyType
```
SearchParameters.MassAccuracyType fragmentAccuracyType
```
      The fragment accuracy type. Default is Da.
    - precursorTolerance
```
java.lang.Double precursorTolerance
```
      The precursor mass tolerance.
    - precursorToleranceDalton
```
java.lang.Double precursorToleranceDalton
```
      The precursor mass tolerance in Dalton (for de novo searches).
    - fragmentIonMZTolerance
```
java.lang.Double fragmentIonMZTolerance
```
      The MS2 ion tolerance.
    - utilitiesModificationProfile
```
ModificationProfile utilitiesModificationProfile
```
      The expected modifications. Modified peptides will be grouped and displayed according to this classification.
    - enzyme
```
Enzyme enzyme
```
      The enzyme used for digestion.
    - nMissedCleavages
```
java.lang.Integer nMissedCleavages
```
      The allowed number of missed cleavages.
    - fastaFile
```
java.io.File fastaFile
```
      The sequence database file used for identification.
    - parametersFile
```
java.io.File parametersFile
```
      The corresponding searchGUI file.
    - fractionMolecularWeights
```
java.util.HashMap<K,V> fractionMolecularWeights
```
      Deprecated. use fractionMolecularWeightRanges instead
      
      The list of fraction molecular weights. The key is the fraction file path.
    - fractionMolecularWeightRanges
```
java.util.HashMap<K,V> fractionMolecularWeightRanges
```
      The list of fraction molecular weights. The key is the fraction file path.
    - forwardIon
```
java.lang.Integer forwardIon
```
      The first kind of ions searched for (typically a, b or c).
    - rewindIon
```
java.lang.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).
    - algorithmParameters
```
java.util.HashMap<K,V> algorithmParameters
```
      The algorithm specific parameters.
    - currentPrecursorAccuracyType
```
SearchParameters.PrecursorAccuracyType currentPrecursorAccuracyType
```
      Deprecated. use precursorAccuracyType
      
      The precursor accuracy type. Default is ppm.
    - maxEValue
```
java.lang.Double maxEValue
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      Maximal e-value cut-off. (OMSSA and X!Tandem only.)
    - hitListLength
```
java.lang.Integer hitListLength
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      The maximal hit list length (OMSSA setting only).
    - hitListLengthDeNovo
```
java.lang.Integer hitListLengthDeNovo
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      The maximal hit list length for PepNovo+.
    - minimalChargeForMultipleChargedFragments
```
Charge minimalChargeForMultipleChargedFragments
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      The minimal charge to be considered for multiple fragment charges for OMSSA.
    - minPeptideLength
```
java.lang.Integer minPeptideLength
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      The minimum peptide length (for semi and non tryptic searches with OMSSA).
    - maxPeptideLength
```
java.lang.Integer maxPeptideLength
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      The maximal peptide length (for semi and non tryptic searches with OMSSA).
    - removePrecursor
```
java.lang.Boolean removePrecursor
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      Indicates whether the precursor removal option of OMSSA is used.
    - scalePrecursor
```
java.lang.Boolean scalePrecursor
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      Indicates whether the precursor scaling option of OMSSA is used.
    - estimateCharge
```
java.lang.Boolean estimateCharge
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      Indicates whether the precursor charge estimation option (OMSSA and DeNovoGUI).
    - correctPrecursorMass
```
java.lang.Boolean correctPrecursorMass
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      Indicates whether the precursor mass shall be corrected (DeNovoGUI setting).
    - discardLowQualitySpectra
```
java.lang.Boolean discardLowQualitySpectra
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      Indicates whether the low quality spectra shall be discarded (DeNovoGUI setting).
    - fragmentationModel
```
java.lang.String fragmentationModel
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      DeNovoGUI fragmentation model.
    - generateQuery
```
java.lang.Boolean generateQuery
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      Indicates whether a blast query shall be generated (DeNovoGUI setting).
    - pepNovoPtmMap
```
java.util.Map<K,V> pepNovoPtmMap
```
      Deprecated. use the appropriated IdentificationAlgorithmParameters instead
      
      A map from the PepNovo PTM symbols to the utilities PTM names.
- Class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption extends ExperimentObject implements Serializable
  - 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
```
java.lang.String identificationFile
```
      The identification file.
- Class com.compomics.util.experiment.identification.TagAssumption extends SpectrumIdentificationAssumption implements Serializable
  - Serialized Fields
    - tag
```
Tag tag
```
      List of mass gaps.
Package com.compomics.util.experiment.identification.identification_parameters
- Class com.compomics.util.experiment.identification.identification_parameters.OmssaParameters extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -6704164074092668637L
  - Serialized Fields
    - maxEValue
```
java.lang.Double maxEValue
```
      Maximal e-value cut-off.
    - hitListLength
```
java.lang.Integer hitListLength
```
      The maximal hit list length.
    - minimalChargeForMultipleChargedFragments
```
Charge minimalChargeForMultipleChargedFragments
```
      The minimal charge to be considered for multiple fragment charges.
    - minPeptideLength
```
java.lang.Integer minPeptideLength
```
      The minimum peptide length (for semi and non tryptic searches).
    - maxPeptideLength
```
java.lang.Integer maxPeptideLength
```
      The maximal peptide length (for semi and non tryptic searches).
    - removePrecursor
```
java.lang.Boolean removePrecursor
```
      Indicates whether the precursor removal option is used.
    - scalePrecursor
```
java.lang.Boolean scalePrecursor
```
      Indicates whether the precursor scaling option is used.
    - estimateCharge
```
java.lang.Boolean estimateCharge
```
      Indicates whether the precursor charge estimation option.
    - selectedOutput
```
java.lang.String selectedOutput
```
      The selected output type (see omssaOutputTypes).
    - memoryMappedSequenceLibraries
```
java.lang.Boolean memoryMappedSequenceLibraries
```
      Map sequence in libraries in memory
    - numberOfItotopicPeaks
```
java.lang.Integer numberOfItotopicPeaks
```
      Number of isotopic peaks to consider.
    - neutronThreshold
```
java.lang.Double neutronThreshold
```
      Mass after which a the exact mass of a neutron should be considered.
    - lowIntensityCutOff
```
java.lang.Double lowIntensityCutOff
```
      Low intensity cut-off as percentage of the most intense peak.
    - highIntensityCutOff
```
java.lang.Double highIntensityCutOff
```
      High intensity cut-off as percentage of the most intense peak.
    - intensityCutOffIncrement
```
java.lang.Double intensityCutOffIncrement
```
      Intensity cut-off increment.
    - singleChargeWindow
```
java.lang.Integer singleChargeWindow
```
      Window width for singly charged fragments.
    - doubleChargeWindow
```
java.lang.Integer doubleChargeWindow
```
      Window width for doubly charged fragments.
    - nPeaksInSingleChargeWindow
```
java.lang.Integer nPeaksInSingleChargeWindow
```
      Number of peaks allowed in a singly charged window.
    - nPeaksInDoubleChargeWindow
```
java.lang.Integer nPeaksInDoubleChargeWindow
```
      Number of peaks allowed in a doubly charged window.
    - maxHitsPerSpectrumPerCharge
```
java.lang.Integer maxHitsPerSpectrumPerCharge
```
      Maximum number of hits searched per spectrum and per charge.
    - nAnnotatedMostIntensePeaks
```
java.lang.Integer nAnnotatedMostIntensePeaks
```
      Number of annotated most intense peaks required per spectrum.
    - minAnnotatedPeaks
```
java.lang.Integer minAnnotatedPeaks
```
      Minimal number of annotated peaks required per spectrum.
    - minPeaks
```
java.lang.Integer minPeaks
```
      Minimal number of peaks per spectrum.
    - cleaveNtermMethionine
```
java.lang.Boolean cleaveNtermMethionine
```
      Cleave the N-term methionines.
    - maxMzLadders
```
java.lang.Integer maxMzLadders
```
      Maximum length of m/z ladders.
    - maxFragmentCharge
```
java.lang.Integer maxFragmentCharge
```
      Maximum fragment charge.
    - fractionOfPeaksForChargeEstimation
```
java.lang.Double fractionOfPeaksForChargeEstimation
```
      Fraction of peaks below the precursor to estimate charge >1.
    - determineChargePlusOneAlgorithmically
```
java.lang.Boolean determineChargePlusOneAlgorithmically
```
      Determine charge plus one algorithmically.
    - searchPositiveIons
```
java.lang.Boolean searchPositiveIons
```
      Search positive ions (if false, negative ions).
    - minPrecPerSpectrum
```
java.lang.Integer minPrecPerSpectrum
```
      Minimal precursor per spectrum.
    - searchForwardFragmentFirst
```
java.lang.Boolean searchForwardFragmentFirst
```
      Search forward ions (b1) first.
    - searchRewindFragments
```
java.lang.Boolean searchRewindFragments
```
      Search c-terminal ions.
    - maxFragmentPerSeries
```
java.lang.Integer maxFragmentPerSeries
```
      Maximal number of fragment per series.
    - useCorrelationCorrectionScore
```
java.lang.Boolean useCorrelationCorrectionScore
```
      Use correlation correction score.
    - consecutiveIonProbability
```
java.lang.Double consecutiveIonProbability
```
      Probability of consecutive ions.
    - iterativeSequenceEvalue
```
java.lang.Double iterativeSequenceEvalue
```
      E-value threshold to include a sequence in the iterative search (0 means all).
    - iterativeReplaceEvalue
```
java.lang.Double iterativeReplaceEvalue
```
      E-value threshold to replace a hit in the iterative search (0 means replace if better).
    - iterativeSpectrumEvalue
```
java.lang.Double iterativeSpectrumEvalue
```
      E-value threshold to include a spectrum in the iterative search (0 means all).
    - noProlineRuleSeries
```
java.util.ArrayList<E> noProlineRuleSeries
```
      ID numbers of ion series to apply no product ions at proline rule at. NOTE: not implemented for now.
- Class com.compomics.util.experiment.identification.identification_parameters.PepnovoParameters extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -8056507693211793829L
  - Serialized Fields
    - hitListLength
```
java.lang.Integer hitListLength
```
      The maximal hit list length for PepNovo+. max is 20.
    - estimateCharge
```
java.lang.Boolean estimateCharge
```
      Indicates whether the precursor charge estimation option.
    - correctPrecursorMass
```
java.lang.Boolean correctPrecursorMass
```
      Indicates whether the precursor mass shall be corrected.
    - discardLowQualitySpectra
```
java.lang.Boolean discardLowQualitySpectra
```
      Indicates whether the low quality spectra shall be discarded.
    - fragmentationModel
```
java.lang.String fragmentationModel
```
      PepNovo fragmentation model.
    - generateQuery
```
java.lang.Boolean generateQuery
```
      Indicates whether a blast query shall be generated.
    - pepNovoPtmMap
```
java.util.Map<K,V> pepNovoPtmMap
```
      A map from the PepNovo PTM symbols to the utilities PTM names.
- Class com.compomics.util.experiment.identification.identification_parameters.XtandemParameters extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -5898951075262732261L
  - Serialized Fields
    - maxEValue
```
java.lang.Double maxEValue
```
      Maximal e-value cut-off.
    - dynamicRange
```
java.lang.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
```
java.lang.Integer nPeaks
```
      The number of most intense peaks to consider.
    - minPrecursorMass
```
java.lang.Double minPrecursorMass
```
      The minimum precursor mass.
    - minFragmentMz
```
java.lang.Double minFragmentMz
```
      The minimum fragment mass.
    - minPeaksPerSpectrum
```
java.lang.Integer minPeaksPerSpectrum
```
      The minimum number of peaks per spectrum.
    - proteinQuickAcetyl
```
java.lang.Boolean proteinQuickAcetyl
```
      Indicates whether the protein quick acetylation option should be triggered.
    - quickPyrolidone
```
java.lang.Boolean quickPyrolidone
```
      indicates whether the quick pyrolidone option should be triggered.
    - refine
```
java.lang.Boolean refine
```
      Triggers the refinement process.
    - refineSemi
```
java.lang.Boolean refineSemi
```
      Sets whether semi enzymatic peptides should be search for during the refinement process.
    - refinePointMutations
```
java.lang.Boolean refinePointMutations
```
      Sets whether point mutations should be search for during the refinement process.
    - refineSpectrumSynthesis
```
java.lang.Boolean refineSpectrumSynthesis
```
      Sets whether the spectrum synthesis option should be used during the refinement process.
    - refineUnanticipatedCleavages
```
java.lang.Boolean refineUnanticipatedCleavages
```
      Sets whether unexpected cleavages should be search for during the refinement process.
    - refineSnaps
```
java.lang.Boolean refineSnaps
```
      Indicates whether snAPs should be used during the refinement process.
    - maximumExpectationValueRefinement
```
java.lang.Double maximumExpectationValueRefinement
```
      The maximum expectation value for a hit to be considered during the refinement process.
    - potentialModificationsForFullRefinment
```
java.lang.Boolean potentialModificationsForFullRefinment
```
      Sets the modifications to be used during the refinement process.
    - skylinePath
```
java.lang.String skylinePath
```
      The skyline path.
    - outputProteins
```
java.lang.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
```
java.lang.Boolean outputSpectra
```
      If true spectra will be exported to the result file.
    - outputHistograms
```
java.lang.Boolean outputHistograms
```
      If true histograms will be exported to the result file.
    - stpBias
```
java.lang.Boolean stpBias
```
      Indicates whether the phospho stp bias option should be triggered.
    - useNoiseSuppression
```
java.lang.Boolean useNoiseSuppression
```
      Triggers the noise suppression function.
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
```
java.lang.String theoreticPtm
```
      The theoretic modiffication 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
```
java.lang.String matchKey
```
      The key of the match.
    - mainMatchKey
```
java.lang.String mainMatchKey
```
      The key of the main match, typically of the highest score.
    - spectrumMatches
```
java.util.ArrayList<E> spectrumMatches
```
      All spectrum matches indexed by spectrum id. See Spectrum class.
    - isDecoy
```
java.lang.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
```
java.util.ArrayList<E> theoreticProtein
```
      The matching protein(s) accessions.
    - mainMatch
```
java.lang.String mainMatch
```
      The accession of the retained protein after protein inference resolution.
    - peptideMatches
```
java.util.ArrayList<E> peptideMatches
```
      The corresponding peptide match keys.
- Class com.compomics.util.experiment.identification.matches.SpectrumMatch extends IdentificationMatch implements Serializable
  
  serialVersionUID:
  
  3227760855215444318L
  - Serialized Fields
    - spectrumKey
```
java.lang.String spectrumKey
```
      The index of the matched spectrum.
    - assumptions
```
java.util.HashMap<K,V> assumptions
```
      Deprecated. use the assumptionsMap instead
      
      The corresponding peptide assumptions indexed by search engine and e-value.
    - assumptionsMap
```
java.util.HashMap<K,V> assumptionsMap
```
      Map of the identification algorithm assumption: advocate number -> score -> assumptions
    - firstHits
```
java.util.HashMap<K,V> firstHits
```
      Deprecated. use the firstHitsMap instead
      
      Map containing the first hits indexed by the Advocate index.
    - firstHitsMap
```
java.util.HashMap<K,V> firstHitsMap
```
      Map containing the first hits indexed by the Advocate index.
    - bestAssumption
```
PeptideAssumption bestAssumption
```
      The best peptide assumption.
    - advocates
```
java.util.ArrayList<E> advocates
```
      All advocates used.
    - spectrumNumber
```
java.lang.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 java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8936868785405252371L
  - Serialized Fields
    - depth
```
int depth
```
      The depth of the node in the tree.
    - accessions
```
java.util.HashMap<K,V> accessions
```
      List of accessions contained in this node.
    - termini
```
java.util.HashMap<K,V> termini
```
      In case of splitting, the terminal mappings are put here.
    - subtree
```
java.util.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.tags
- Class com.compomics.util.experiment.identification.tags.Tag extends ExperimentObject implements Serializable
  - Serialized Fields
    - content
```
java.util.ArrayList<E> content
```
      The content of the tag.
Package com.compomics.util.experiment.identification.tags.tagcomponents
- Class com.compomics.util.experiment.identification.tags.tagcomponents.MassGap extends ExperimentObject implements Serializable
  - Serialized Fields
    - value
```
double value
```
      The value of the mass gap.
Package com.compomics.util.experiment.io.identifications.idfilereaders
- Class com.compomics.util.experiment.io.identifications.idfilereaders.AndromedaIdfileReader extends ExperimentObject implements Serializable
  - Serialized Fields
    - index
```
java.util.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
```
      Andromeda result file in random access.
    - fileName
```
java.lang.String fileName
```
      The name of the Andromeda result file.
Package com.compomics.util.experiment.io.massspectrometry
- Class com.compomics.util.experiment.io.massspectrometry.MgfIndex extends ExperimentObject implements Serializable
  - Serialized Fields
    - indexMap
```
java.util.HashMap<K,V> indexMap
```
      The map of all indexes: spectrum title -> index in the file.
    - spectrumTitles
```
java.util.ArrayList<E> spectrumTitles
```
      List of spectrum titles.
    - duplicatedSpectrumTitles
```
java.util.HashMap<K,V> duplicatedSpectrumTitles
```
      Map of duplicated spectrum titles and how often they are duplicated.
    - fileName
```
java.lang.String fileName
```
      The name of the indexed file.
    - lastModified
```
java.lang.Long lastModified
```
      The last time the indexed file was modified.
    - maxRT
```
java.lang.Double maxRT
```
      The maximum RT found in the spectra.
    - minRT
```
java.lang.Double minRT
```
      The minimum RT found in the spectra.
    - maxMz
```
java.lang.Double maxMz
```
      The maximal m/z in all precursors of the file.
    - maxIntensity
```
java.lang.Double maxIntensity
```
      The maximal precursor intensity of the file.
    - maxCharge
```
java.lang.Integer maxCharge
```
      The maximal charge.
    - maxPeakCount
```
java.lang.Integer maxPeakCount
```
      The maximal peak count.
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
```
java.lang.Double rtMin
```
      In case an rt window is given, the minimum.
    - rtMax
```
java.lang.Double rtMax
```
      In case an rt 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
```
java.util.ArrayList<E> possibleCharges
```
      The charge of the precursor.
- Class com.compomics.util.experiment.massspectrometry.Spectrum extends ExperimentObject implements Serializable
  
  serialVersionUID:
  
  7152424141470431489L
  - Serialized Fields
    - spectrumTitle
```
java.lang.String spectrumTitle
```
      Spectrum title.
    - fileName
```
java.lang.String fileName
```
      Spectrum file name.
    - level
```
int level
```
      The MS level.
    - peakList
```
java.util.HashMap<K,V> peakList
```
      Peak list.
    - scanNumber
```
java.lang.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
```
java.lang.Boolean mzOrdered
```
      Boolean indicating whether the mzValuesAsArray is sorted.
    - intensityValuesAsArray
```
double[] intensityValuesAsArray
```
      The intensity values as array. Null until set by the getter.
    - mzAndIntensityAsArray
```
double[][] mzAndIntensityAsArray
```
      The mz and intensity values as array. Null until set by the getter.
    - totalIntensity
```
java.lang.Double totalIntensity
```
      The total intensity.
    - maxIntensity
```
java.lang.Double maxIntensity
```
      The maximal intensity.
    - maxMz
```
java.lang.Double maxMz
```
      The maximal m/z.
    - minMz
```
java.lang.Double minMz
```
      The minimal m/z.
Package com.compomics.util.experiment.personalization
- Class com.compomics.util.experiment.personalization.ExperimentObject extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1929697552061121072L
  - Serialized Fields
    - urParams
```
java.util.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.ReporterIonQuantification extends Quantification implements Serializable
  - Serialized Fields
    - sampleAssignement
```
java.util.HashMap<K,V> sampleAssignement
```
      The sample assignment to the various ions indexed by their index.
    - controlSamples
```
java.util.ArrayList<E> controlSamples
```
      List of control samples. The index should be the same as for the sample assignment.
    - normalisationFactors
```
java.util.HashMap<K,V> normalisationFactors
```
      List of normalisation factors. The index should be the same as for the sample assignment.
    - reporterMethod
```
ReporterMethod reporterMethod
```
      The reporter method.
- Class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory extends ExperimentObject implements Serializable
Package com.compomics.util.experiment.refinementparameters
- Class com.compomics.util.experiment.refinementparameters.MascotScore extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  1781298332459022056L
  - Serialized Fields
    - score
```
double score
```
      The Mascot score.
- Class com.compomics.util.experiment.refinementparameters.PepnovoAssumptionDetails extends java.lang.Object implements Serializable
  - Serialized Fields
    - rankScore
```
double rankScore
```
      The PepNovo rank score.
    - mH
```
double mH
```
      The PepNovo M+H.
Package com.compomics.util.general
- Class com.compomics.util.general.UnknownElementMassException extends java.lang.Exception implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - element
```
java.lang.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.AminoAcidPatternDialog extends javax.swing.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
```
java.util.ArrayList<E> patternDesignTableToolTips
```
The pattern design table column header tooltips.
exampleSequence
```
java.lang.String exampleSequence
```
The example sequence.
addJMenuItem
```
javax.swing.JMenuItem addJMenuItem
```
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
cancelButton
```
javax.swing.JButton cancelButton
```

deleteSelectedRowJMenuItem

javax.swing.JMenuItem deleteSelectedRowJMenuItem

exampleLabel
```
javax.swing.JLabel exampleLabel
```
jSeparator3
```
javax.swing.JSeparator jSeparator3
```
jSeparator4
```
javax.swing.JSeparator jSeparator4
```
moveDownJMenuItem
```
javax.swing.JMenuItem moveDownJMenuItem
```
moveUpJMenuItem
```
javax.swing.JMenuItem moveUpJMenuItem
```
okButton
```
javax.swing.JButton okButton
```
patternDesignPanel
```
javax.swing.JPanel patternDesignPanel
```

patternDesignScrollPane

javax.swing.JScrollPane patternDesignScrollPane

patternDesignTable
```
javax.swing.JTable patternDesignTable
```

patternTestEditorPane

javax.swing.JEditorPane patternTestEditorPane

patternTestJScrollPane

javax.swing.JScrollPane patternTestJScrollPane

popupJMenu
```
javax.swing.JPopupMenu popupJMenu
```
rightClickHelpLabel
```
javax.swing.JLabel rightClickHelpLabel
```
testPanel
```
javax.swing.JPanel testPanel
```

Class com.compomics.util.gui.DummyFrame extends javax.swing.JFrame implements Serializable
Class com.compomics.util.gui.FlamableJFrame extends javax.swing.JFrame implements Serializable
- Serialized Fields
  - logger
```
org.apache.log4j.Logger logger
```
Class com.compomics.util.gui.GeneDetailsDialog extends javax.swing.JDialog implements Serializable
- Serialized Fields
  - goFactory
```
GOFactory goFactory
```
    The GO terms factory.
  - geneFactory
```
GeneFactory geneFactory
```
    The Gene factory.
  - proteinAccessions
```
java.util.ArrayList<E> proteinAccessions
```
    the protein accessions of this match.
  - goTermDescriptions
```
java.util.ArrayList<E> goTermDescriptions
```
    The GO term descriptions attached to this protein match.
  - selectedRowHtmlTagFontColor
```
java.lang.String selectedRowHtmlTagFontColor
```
    The color to use for the HTML tags for the selected rows, in HTML color code.
  - notSelectedRowHtmlTagFontColor
```
java.lang.String notSelectedRowHtmlTagFontColor
```
    The color to use for the HTML tags for the rows that are not selected, in HTML color code.
  - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
  - chromosomeLabel
```
javax.swing.JLabel chromosomeLabel
```
  - chromosomeNameTxt
```
javax.swing.JTextField chromosomeNameTxt
```
  - detailsPanel
```
javax.swing.JPanel detailsPanel
```
  - ensemlbIdLabel
```
javax.swing.JLabel ensemlbIdLabel
```
  - geneIdTxt
```
javax.swing.JTextField geneIdTxt
```
  - geneNameLabel
```
javax.swing.JLabel geneNameLabel
```
  - geneNameTxt
```
javax.swing.JTextField geneNameTxt
```
  - goAnnotationLabel
```
javax.swing.JLabel goAnnotationLabel
```
  - goTable
```
javax.swing.JTable goTable
```
  - goTableScrollPane
```
javax.swing.JScrollPane goTableScrollPane
```
  - okButton
```
javax.swing.JButton okButton
```
Class com.compomics.util.gui.JExceptionDialog extends javax.swing.JDialog implements Serializable
- Serialized Fields
  - logger
```
org.apache.log4j.Logger logger
```
  - iMessages
```
java.lang.String[] iMessages
```
  - iThrowable
```
java.lang.Throwable iThrowable
```
Class com.compomics.util.gui.JFrameForBytes extends javax.swing.JFrame implements Serializable
- Serialized Fields
  - logger
```
org.apache.log4j.Logger logger
```
  - iData
```
byte[] iData
```
    This byte[] is the data that will be shown.
  - txtData
```
javax.swing.JTextArea txtData
```
  - btnUnzip
```
javax.swing.JButton btnUnzip
```
  - btnSave
```
javax.swing.JButton btnSave
```
Class com.compomics.util.gui.JLabelAndComponentPanel extends javax.swing.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
```
java.lang.String iDateTimeFormat
```
    This String contains the date and time format.
  - iFrames
```
java.util.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.SampleSelection extends javax.swing.JDialog implements Serializable

Serialized Fields

samples
```
java.lang.String[] samples
```
The samples found.
choice
```
java.lang.String choice
```
The choice of the user.
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
comboBox
```
javax.swing.JComboBox<E> comboBox
```
jLabel1
```
javax.swing.JLabel jLabel1
```
jLabel2
```
javax.swing.JLabel jLabel2
```
okButton
```
javax.swing.JButton okButton
```
titleLbl
```
javax.swing.JLabel titleLbl
```

Class com.compomics.util.gui.VennDiagramDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

currentVennDiagramType

VennDiagramDialog.VennDiagramType currentVennDiagramType

The current Venn diagram type.

tooltipToDatasetMap
```
java.util.HashMap<K,V> tooltipToDatasetMap
```
Map each dataset tooltip back to the given dataset.
vennDiagramResults
```
java.util.HashMap<K,V> vennDiagramResults
```
The current Venn diagram results/data.
groupNames
```
java.util.HashMap<K,V> groupNames
```
The current Venn diagram group names.
chartPanel
```
org.jfree.chart.ChartPanel chartPanel
```
The chart panel.
dialogParent
```
java.awt.Frame dialogParent
```
The dialog parent.
lastSelectedFolder
```
java.lang.String lastSelectedFolder
```
The last selected folder.
normalIcon
```
java.awt.Image normalIcon
```
The normal icon for the parent dialog.
waitingIcon
```
java.awt.Image waitingIcon
```
The icon to use when busy.
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.
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```

contextMenuPlotBackgroundPanel

javax.swing.JPanel contextMenuPlotBackgroundPanel

dataPanel
```
javax.swing.JPanel dataPanel
```
datasetAColorJPanel
```
javax.swing.JPanel datasetAColorJPanel
```

datasetAScrollPane

javax.swing.JScrollPane datasetAScrollPane

datasetATextArea
```
javax.swing.JTextArea datasetATextArea
```

datasetATextField

javax.swing.JTextField datasetATextField

datasetBColorJPanel
```
javax.swing.JPanel datasetBColorJPanel
```

datasetBScrollPane

javax.swing.JScrollPane datasetBScrollPane

datasetBTextArea
```
javax.swing.JTextArea datasetBTextArea
```

datasetBTextField

javax.swing.JTextField datasetBTextField

datasetCColorJPanel
```
javax.swing.JPanel datasetCColorJPanel
```

datasetCScrollPane

javax.swing.JScrollPane datasetCScrollPane

datasetCTextArea
```
javax.swing.JTextArea datasetCTextArea
```

datasetCTextField

javax.swing.JTextField datasetCTextField

datasetDColorJPanel
```
javax.swing.JPanel datasetDColorJPanel
```

datasetDScrollPane

javax.swing.JScrollPane datasetDScrollPane

datasetDTextArea
```
javax.swing.JTextArea datasetDTextArea
```

datasetDTextField

javax.swing.JTextField datasetDTextField

exportPlotMenuItem

javax.swing.JMenuItem exportPlotMenuItem

fontSizeMenu
```
javax.swing.JMenu fontSizeMenu
```

jSeparator1

javax.swing.JPopupMenu.Separator jSeparator1

jSeparator2

javax.swing.JPopupMenu.Separator jSeparator2

legendCheckBoxMenuItem

javax.swing.JCheckBoxMenuItem legendCheckBoxMenuItem

legendFontSizeMenuItem

javax.swing.JMenuItem legendFontSizeMenuItem

legendLocationMenuItem

javax.swing.JMenuItem legendLocationMenuItem

plotHelpJButton
```
javax.swing.JButton plotHelpJButton
```

plotLayeredPane

javax.swing.JLayeredPane plotLayeredPane

plotOptionsJButton
```
javax.swing.JButton plotOptionsJButton
```
plotPanel
```
javax.swing.JPanel plotPanel
```
plotPopupMenu
```
javax.swing.JPopupMenu plotPopupMenu
```

valueFontSizeMenuItem

javax.swing.JMenuItem valueFontSizeMenuItem

xyPlotPanel
```
javax.swing.JPanel xyPlotPanel
```

Class com.compomics.util.gui.VennDiagramLegendLocationDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

vennDiagramDialog
```
VennDiagramDialog vennDiagramDialog
```
The VennDiagramDialog parent.
legendShiftSize
```
double legendShiftSize
```
Legend shift size.
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
datasetALabel
```
javax.swing.JLabel datasetALabel
```
datasetBLabel
```
javax.swing.JLabel datasetBLabel
```
datasetCLabel
```
javax.swing.JLabel datasetCLabel
```
datasetDLabel
```
javax.swing.JLabel datasetDLabel
```
downDatasetAButton
```
javax.swing.JButton downDatasetAButton
```
downDatasetBButton
```
javax.swing.JButton downDatasetBButton
```
downDatasetCButton
```
javax.swing.JButton downDatasetCButton
```
downDatasetDButton
```
javax.swing.JButton downDatasetDButton
```
leftDatasetAButton
```
javax.swing.JButton leftDatasetAButton
```
leftDatasetBButton
```
javax.swing.JButton leftDatasetBButton
```
leftDatasetCButton
```
javax.swing.JButton leftDatasetCButton
```
leftDatasetDButton
```
javax.swing.JButton leftDatasetDButton
```
legendLocationPanel
```
javax.swing.JPanel legendLocationPanel
```
okButton
```
javax.swing.JButton okButton
```
rightDatasetAButton
```
javax.swing.JButton rightDatasetAButton
```
rightDatasetBButton
```
javax.swing.JButton rightDatasetBButton
```
rightDatasetCButton
```
javax.swing.JButton rightDatasetCButton
```
rightDatasetDButton
```
javax.swing.JButton rightDatasetDButton
```
shiftSizeLabel
```
javax.swing.JLabel shiftSizeLabel
```
shiftSizeSpinner
```
javax.swing.JSpinner shiftSizeSpinner
```
upDatasetAButton
```
javax.swing.JButton upDatasetAButton
```
upDatasetBButton
```
javax.swing.JButton upDatasetBButton
```
upDatasetCButton
```
javax.swing.JButton upDatasetCButton
```
upDatasetDButton
```
javax.swing.JButton upDatasetDButton
```

Class com.compomics.util.gui.VisibleTableColumnsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

visibleTableColumnsDialogParent
```
VisibleTableColumnsDialogParent visibleTableColumnsDialogParent
```
The VisibleTableColumnsDialogParent.
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```

deselectAllMenuItem

javax.swing.JMenuItem deselectAllMenuItem

okButton
```
javax.swing.JButton okButton
```
selectAllMenuItem
```
javax.swing.JMenuItem selectAllMenuItem
```
selectJPopupMenu
```
javax.swing.JPopupMenu selectJPopupMenu
```
selectedColumnsTable
```
javax.swing.JTable selectedColumnsTable
```

selectedValuesTableScrollPane

javax.swing.JScrollPane selectedValuesTableScrollPane

Class com.compomics.util.gui.XYPlotFiltersDialog extends javax.swing.JDialog implements Serializable
- Serialized Fields
  - xyPlottingDialog
```
XYPlottingDialog xyPlottingDialog
```
    The XYPlottingDialog parent.
  - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
  - cancelButton
```
javax.swing.JButton cancelButton
```
  - filterTypesLabel
```
javax.swing.JLabel filterTypesLabel
```
  - filtersScrollPane
```
javax.swing.JScrollPane filtersScrollPane
```
  - filtersTable
```
javax.swing.JTable filtersTable
```
  - okButton
```
javax.swing.JButton okButton
```

Class com.compomics.util.gui.XYPlottingDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

progressDialog
```
ProgressDialogX progressDialog
```
The progress dialog.
tableModel
```
javax.swing.table.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
```
java.awt.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
```
java.awt.Point dragStart
```
The starting location of the mouse dragging.
dragEnd
```
java.awt.Point dragEnd
```
The ending location of the mouse dragging.
selectedDataPoints
```
java.util.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
```
java.util.HashMap<K,V> dataPointToRowNumber
```
The data point to model row number map.
selectedModelRows
```
java.util.ArrayList<E> selectedModelRows
```
The index of the selected rows.
cellRenderers
```
java.util.HashMap<K,V> cellRenderers
```
The cell renderers for the table.
maxColumnWidths
```
java.util.HashMap<K,V> maxColumnWidths
```
The maximum column widths for the table.
minColumnWidths
```
java.util.HashMap<K,V> minColumnWidths
```
The minimum column widths for the table.
tableToolTips
```
java.util.ArrayList<E> tableToolTips
```
The table column header tool tips.

colorGradient

no.uib.jsparklines.renderers.util.GradientColorCoding.ColorGradient colorGradient

The color gradient to use.

histogramColor
```
java.awt.Color histogramColor
```
The color used for the bars in the histograms.
lastSelectedFolder
```
java.lang.String lastSelectedFolder
```
The last selected folder.
normalIcon
```
java.awt.Image normalIcon
```
The normal icon for the parent dialog.
waitingIcon
```
java.awt.Image waitingIcon
```
The icon to use when busy.
allTableColumns
```
java.util.ArrayList<E> allTableColumns
```
The table columns.
visibleColumns
```
java.util.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
```
java.util.HashMap<K,V> filters
```
The data filters.
colummnNames
```
java.util.Vector<E> colummnNames
```
The column names.
rowsAfterDataFiltering
```
java.util.ArrayList<E> rowsAfterDataFiltering
```
The rows remaining after applying the data filters.
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
binSizeSpinner
```
javax.swing.JSpinner binSizeSpinner
```
binsLabel
```
javax.swing.JLabel binsLabel
```

bubbleSizeComboBox

javax.swing.JComboBox<E> bubbleSizeComboBox

bubbleSizeLabel
```
javax.swing.JLabel bubbleSizeLabel
```
colorLabel
```
javax.swing.JLabel colorLabel
```
colorsComboBox
```
javax.swing.JComboBox<E> colorsComboBox
```

contextMenuPlotBackgroundPanel

javax.swing.JPanel contextMenuPlotBackgroundPanel

contextMenuSelectedValuesTableBackgroundPanel

javax.swing.JPanel contextMenuSelectedValuesTableBackgroundPanel

densityPlotRadioButton

javax.swing.JRadioButton densityPlotRadioButton

dragButtonGroup
```
javax.swing.ButtonGroup dragButtonGroup
```
dragSettingsPanel
```
javax.swing.JPanel dragSettingsPanel
```

dragToSelectRadioButton

javax.swing.JRadioButton dragToSelectRadioButton

dragToZoomRadioButton

javax.swing.JRadioButton dragToZoomRadioButton

editFiltersButton
```
javax.swing.JButton editFiltersButton
```

exportPlotMenuItem

javax.swing.JMenuItem exportPlotMenuItem

exportSelectedValuesMenuItem

javax.swing.JMenuItem exportSelectedValuesMenuItem

filterPanel
```
javax.swing.JPanel filterPanel
```

hideColumnsMenuItem

javax.swing.JMenuItem hideColumnsMenuItem

histogramRadioButton

javax.swing.JRadioButton histogramRadioButton

logAcisPanel
```
javax.swing.JPanel logAcisPanel
```
plotHelpJButton
```
javax.swing.JButton plotHelpJButton
```

plotLayeredPane

javax.swing.JLayeredPane plotLayeredPane

plotOptionsJButton
```
javax.swing.JButton plotOptionsJButton
```
plotPanel
```
javax.swing.JPanel plotPanel
```
plotPopupMenu
```
javax.swing.JPopupMenu plotPopupMenu
```

plotTypeButtonGroup

javax.swing.ButtonGroup plotTypeButtonGroup

plotTypePanel
```
javax.swing.JPanel plotTypePanel
```

regressionLineCheckBoxMenuItem

javax.swing.JCheckBoxMenuItem regressionLineCheckBoxMenuItem

selectedValuesLayeredPane

javax.swing.JLayeredPane selectedValuesLayeredPane

selectedValuesPanel
```
javax.swing.JPanel selectedValuesPanel
```

selectedValuesScrollPane

javax.swing.JScrollPane selectedValuesScrollPane

selectedValuesTable
```
javax.swing.JTable selectedValuesTable
```

selectedValuesTableHelpJButton

javax.swing.JButton selectedValuesTableHelpJButton

selectedValuesTableOptionsJButton

javax.swing.JButton selectedValuesTableOptionsJButton

selectedValuesTablePopupMenu

javax.swing.JPopupMenu selectedValuesTablePopupMenu

sizeLogCheckBox
```
javax.swing.JCheckBox sizeLogCheckBox
```
xAxisComboBox
```
javax.swing.JComboBox<E> xAxisComboBox
```
xAxisLabel
```
javax.swing.JLabel xAxisLabel
```
xAxisLogCheckBox
```
javax.swing.JCheckBox xAxisLogCheckBox
```
xAxisPanel
```
javax.swing.JPanel xAxisPanel
```
xyPlotPanel
```
javax.swing.JPanel xyPlotPanel
```

xyPlotRadioButton

javax.swing.JRadioButton xyPlotRadioButton

yAxisComboBox
```
javax.swing.JComboBox<E> yAxisComboBox
```
yAxisLabel
```
javax.swing.JLabel yAxisLabel
```
yAxisLogCheckBox
```
javax.swing.JCheckBox yAxisLogCheckBox
```

Package com.compomics.util.gui.error_handlers
- Class com.compomics.util.gui.error_handlers.BugReport extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - selectionFolder
```
java.lang.String selectionFolder
```
      The folder to open in the file selection dialog.
    - toolName
```
java.lang.String toolName
```
      The name of the tool to get the bug report for, e.g., "PeptideShaker"
    - googleCodeToolName
```
java.lang.String googleCodeToolName
```
      The google code name of the tool, e.g., "peptide-shaker"
    - toolVersion
```
java.lang.String toolVersion
```
      The version number of the tool the log files belongs to.
    - logFile
```
java.io.File logFile
```
      The log file to display.
    - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
    - clearJButton
```
javax.swing.JButton clearJButton
```
    - exitButton
```
javax.swing.JButton exitButton
```
    - infoJEditorPane
```
javax.swing.JEditorPane infoJEditorPane
```
    - infoJPanel
```
javax.swing.JPanel infoJPanel
```
    - infoJScrollPane
```
javax.swing.JScrollPane infoJScrollPane
```
    - logJPanel
```
javax.swing.JPanel logJPanel
```
    - logJScrollPane
```
javax.swing.JScrollPane logJScrollPane
```
    - logTxt
```
javax.swing.JTextArea logTxt
```
    - saveJButton
```
javax.swing.JButton saveJButton
```
- Class com.compomics.util.gui.error_handlers.HelpDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - frameParent
```
java.awt.Frame frameParent
```
      The parent of the parent is a Frame.
    - dialogParent
```
javax.swing.JDialog dialogParent
```
      The parent of the parent is a JDialog.
    - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
    - closeJButton
```
javax.swing.JButton closeJButton
```
    - jScrollPane1
```
javax.swing.JScrollPane jScrollPane1
```
    - textJEditorPane
```
javax.swing.JEditorPane textJEditorPane
```
Package com.compomics.util.gui.error_handlers.notification
- Class com.compomics.util.gui.error_handlers.notification.NotesDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
    - notesEditorPane
```
javax.swing.JEditorPane notesEditorPane
```
    - notesScrollPane
```
javax.swing.JScrollPane notesScrollPane
```
    - okButton
```
javax.swing.JButton okButton
```
- Class com.compomics.util.gui.error_handlers.notification.NotificationDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - notificationDialogParent
```
NotificationDialogParent notificationDialogParent
```
      The notification dialog parent.
    - notificationType
```
java.lang.String notificationType
```
      The notification type.
    - notificationLabel
```
javax.swing.JLabel notificationLabel
```
    - notificationPanel
```
javax.swing.JPanel notificationPanel
```

Package com.compomics.util.gui.export_graphics

Class com.compomics.util.gui.export_graphics.ExportGraphicsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

chartPanel
```
org.jfree.chart.ChartPanel chartPanel
```
The chart panel to export.
graphicsPanel
```
java.awt.Component graphicsPanel
```
The panel to export.
progressDialog
```
ProgressDialogX progressDialog
```
The progress dialog.
exportGraphicsDialogParent
```
ExportGraphicsDialogParent exportGraphicsDialogParent
```
The export graphics dialog parent.
frame
```
javax.swing.JFrame frame
```
The parent frame.
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
buttonGroup
```
javax.swing.ButtonGroup buttonGroup
```
cancelJButton
```
javax.swing.JButton cancelJButton
```
exportJButton
```
javax.swing.JButton exportJButton
```

pdfJRadioButton

javax.swing.JRadioButton pdfJRadioButton

plottingTypeJPanel
```
javax.swing.JPanel plottingTypeJPanel
```

pngJRadioButton

javax.swing.JRadioButton pngJRadioButton

svgJRadioButton

javax.swing.JRadioButton svgJRadioButton

tiffJRadioButton

javax.swing.JRadioButton tiffJRadioButton

Package com.compomics.util.gui.filehandling
- Class com.compomics.util.gui.filehandling.FileDisplayDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - files
```
java.util.ArrayList<E> files
```
      The list of files.
    - canceled
```
boolean canceled
```
      True if the dialog was canceled by the user.
    - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
    - okButton
```
javax.swing.JButton okButton
```
    - selectedFilesEditorPane
```
javax.swing.JEditorPane selectedFilesEditorPane
```
    - selectedFilesScrollPane
```
javax.swing.JScrollPane selectedFilesScrollPane
```
- Class com.compomics.util.gui.filehandling.FileSelectionDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - fileMap
```
java.util.HashMap<K,V> fileMap
```
      A map of the parameter files indexed by their name.
    - canceled
```
boolean canceled
```
      Boolean indicating whether the user pushed the cancel button.
    - cancelButton
```
javax.swing.JButton cancelButton
```
    - fileList
```
javax.swing.JList<E> fileList
```
    - fileListScrollPane
```
javax.swing.JScrollPane fileListScrollPane
```
    - helpLabel
```
javax.swing.JLabel helpLabel
```
    - okButton
```
javax.swing.JButton okButton
```
Package com.compomics.util.gui.gene_mapping
- Class com.compomics.util.gui.gene_mapping.SpeciesDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - goFactory
```
GOFactory goFactory
```
      The GO factory.
    - geneFactory
```
GeneFactory geneFactory
```
      The gene factory.
    - progressDialog
```
ProgressDialogX progressDialog
```
      The progress dialog.
    - frameParent
```
javax.swing.JFrame frameParent
```
      The frame parent, if any.
    - dialogParent
```
javax.swing.JDialog dialogParent
```
      The dialog parent, if any.
    - waitingImage
```
java.awt.Image waitingImage
```
      The icon to display when waiting
    - normalImage
```
java.awt.Image normalImage
```
      The icon to display when processing is finished
    - genePreferences
```
GenePreferences genePreferences
```
      The gene preferences
    - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
    - ensemblCategoryJComboBox
```
javax.swing.JComboBox<E> ensemblCategoryJComboBox
```
    - ensemblVersionLabel
```
javax.swing.JLabel ensemblVersionLabel
```
    - jPanel1
```
javax.swing.JPanel jPanel1
```
    - okButton
```
javax.swing.JButton okButton
```
    - speciesJComboBox
```
javax.swing.JComboBox<E> speciesJComboBox
```
    - unknownSpeciesLabel
```
javax.swing.JLabel unknownSpeciesLabel
```
    - updateMappingsButton
```
javax.swing.JButton updateMappingsButton
```
Package com.compomics.util.gui.isotopic_calculator
- Class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui extends javax.swing.JFrame implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - txtSequence
```
javax.swing.JTextArea txtSequence
```
    - lblComp
```
javax.swing.JLabel lblComp
```
    - lblMass
```
javax.swing.JLabel lblMass
```
    - calculateButton
```
javax.swing.JButton calculateButton
```
    - table1
```
AlternateRowColoursJTable table1
```
    - jpanContent
```
javax.swing.JPanel jpanContent
```
    - headerTable
```
javax.swing.JPanel headerTable
```
    - spectrumPanel
```
javax.swing.JPanel spectrumPanel
```
    - spinCharge
```
javax.swing.JSpinner spinCharge
```
    - lblPeptide
```
javax.swing.JLabel lblPeptide
```
    - iSequence
```
AASequenceImpl iSequence
```
      The amino acid sequence
    - iElements
```
java.util.HashMap<K,V> iElements
```
      HashMap with the molecular formula for all the aminoacids
    - iCharge
```
double iCharge
```
      The charge
Package com.compomics.util.gui.protein
- Class com.compomics.util.gui.protein.AdvancedProteinDatabaseDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - dbFolder
```
java.io.File dbFolder
```
      The database folder.
    - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
    - browseDatabaseFolderButton
```
javax.swing.JButton browseDatabaseFolderButton
```
    - cancelButton
```
javax.swing.JButton cancelButton
```
    - clearDatabaseFolderButton
```
javax.swing.JButton clearDatabaseFolderButton
```
    - databasesFolderTxt
```
javax.swing.JTextField databasesFolderTxt
```
    - folderPanel
```
javax.swing.JPanel folderPanel
```
    - okButton
```
javax.swing.JButton okButton
```
- Class com.compomics.util.gui.protein.SequenceDbDetailsDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - sequenceFactory
```
SequenceFactory sequenceFactory
```
      The sequence factory.
    - lastSelectedFolder
```
java.lang.String lastSelectedFolder
```
      The last selected folder.
    - dbEditable
```
boolean dbEditable
```
      boolean indicating whether the db can be changed.
    - waitingImage
```
java.awt.Image waitingImage
```
      The icon to display when waiting.
    - normalImange
```
java.awt.Image normalImange
```
      The normal icon.
    - parentFrame
```
java.awt.Frame parentFrame
```
      The parent frame.
    - utilitiesUserPreferences
```
UtilitiesUserPreferences utilitiesUserPreferences
```
      The utilities user preferences.
    - accessionsSpinner
```
javax.swing.JSpinner accessionsSpinner
```
    - advancedButton
```
javax.swing.JButton advancedButton
```
    - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
    - browseButton
```
javax.swing.JButton browseButton
```
    - cancelButton
```
javax.swing.JButton cancelButton
```
    - databaseHelpSettingsJLabel
```
javax.swing.JLabel databaseHelpSettingsJLabel
```
    - databaseInformationPanel
```
javax.swing.JPanel databaseInformationPanel
```
    - dbNameTxt
```
javax.swing.JTextField dbNameTxt
```
    - decoyButton
```
javax.swing.JButton decoyButton
```
    - decoyFlagTxt
```
javax.swing.JTextField decoyFlagTxt
```
    - decoyTagLabel
```
javax.swing.JLabel decoyTagLabel
```
    - fileLabel
```
javax.swing.JLabel fileLabel
```
    - fileTxt
```
javax.swing.JTextField fileTxt
```
    - lastModifiedLabel
```
javax.swing.JLabel lastModifiedLabel
```
    - lastModifiedTxt
```
javax.swing.JTextField lastModifiedTxt
```
    - nameLabel
```
javax.swing.JLabel nameLabel
```
    - okButton
```
javax.swing.JButton okButton
```
    - previewPanel
```
javax.swing.JPanel previewPanel
```
    - proteinLabel
```
javax.swing.JLabel proteinLabel
```
    - proteinTxt
```
javax.swing.JTextArea proteinTxt
```
    - proteinYxtScrollPane
```
javax.swing.JScrollPane proteinYxtScrollPane
```
    - sizeLabel
```
javax.swing.JLabel sizeLabel
```
    - sizeTxt
```
javax.swing.JTextField sizeTxt
```
    - targetDecoyTxt
```
javax.swing.JLabel targetDecoyTxt
```
    - typeCmb
```
javax.swing.JComboBox<E> typeCmb
```
    - typeLabel
```
javax.swing.JLabel typeLabel
```
    - versionLabel
```
javax.swing.JLabel versionLabel
```
    - versionTxt
```
javax.swing.JTextField versionTxt
```
- Class com.compomics.util.gui.protein.SequenceModificationPanel extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - fragmentIonRectangles
```
java.util.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
```
java.lang.String[] iSequenceComponents
```
      Elementary data for composing the Panel.
    - profiles
```
java.util.ArrayList<E> profiles
```
      The list of modification profiles.
    - iBaseFont
```
java.awt.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-KENNY-COOH
    - score1Name
```
java.lang.String score1Name
```
      The name of the score above of the sequence.
    - score2Name
```
java.lang.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 javax.swing.JDialog implements Serializable

Serialized Fields

ptmFactory
```
PTMFactory ptmFactory
```
The post translational modifications factory.
ptmDialogParent
```
PtmDialogParent ptmDialogParent
```
The dialog parent.
ptmToPrideMap
```
PtmToPrideMap ptmToPrideMap
```
The PSI-MOD mappings.
sparklineColor
```
java.awt.Color sparklineColor
```
The color used for the sparkline bar chart plots.
selectedRowHtmlTagFontColor
```
java.lang.String selectedRowHtmlTagFontColor
```
The color to use for the HTML tags for the selected rows, in HTML color code.
notSelectedRowHtmlTagFontColor
```
java.lang.String notSelectedRowHtmlTagFontColor
```
The color to use for the HTML tags for the rows that are not selected, in HTML color code.
defaultModsTableToolTips
```
java.util.ArrayList<E> defaultModsTableToolTips
```
The default mods table column header tooltips.
userModsTableToolTips
```
java.util.ArrayList<E> userModsTableToolTips
```
The user mods table column header tooltips.
searchPossibilities
```
java.util.ArrayList<E> searchPossibilities
```
The lines of the PTMs concerned by the search.
searchCurrentSelection
```
int searchCurrentSelection
```
The search current selection.
searchWelcomeText
```
java.lang.String searchWelcomeText
```
The search text to display by default.
addUserPTM
```
javax.swing.JButton addUserPTM
```

defaultModificationsTable

javax.swing.JTable defaultModificationsTable

defaultModsPanel
```
javax.swing.JPanel defaultModsPanel
```

defaultModsScrollPane

javax.swing.JScrollPane defaultModsScrollPane

defaultPtmPopupMenu

javax.swing.JPopupMenu defaultPtmPopupMenu

deleteUserPTM
```
javax.swing.JButton deleteUserPTM
```

editDefaultPtmJMenuItem

javax.swing.JMenuItem editDefaultPtmJMenuItem

editUserPTM
```
javax.swing.JButton editUserPTM
```

editUserPtmJMenuItem

javax.swing.JMenuItem editUserPtmJMenuItem

findJLabel
```
javax.swing.JLabel findJLabel
```

modificationsEditorPanel

javax.swing.JPanel modificationsEditorPanel

modificationsHelpJButton

javax.swing.JButton modificationsHelpJButton

modificationsSplitPane

javax.swing.JSplitPane modificationsSplitPane

okButton
```
javax.swing.JButton okButton
```
searchIndexLabel
```
javax.swing.JLabel searchIndexLabel
```
searchInputTxt
```
javax.swing.JTextField searchInputTxt
```
searchNextButton
```
javax.swing.JButton searchNextButton
```

searchPreviousButton

javax.swing.JButton searchPreviousButton

userModificationsTable

javax.swing.JTable userModificationsTable

userModsPanel
```
javax.swing.JPanel userModsPanel
```

userModsScrollPane

javax.swing.JScrollPane userModsScrollPane

userPtmPopupMenu
```
javax.swing.JPopupMenu userPtmPopupMenu
```

Class com.compomics.util.gui.ptm.PtmChooser extends javax.swing.JDialog implements Serializable
- Serialized Fields
  - canceled
```
boolean canceled
```
    Boolean indicating whether the cancel button has been pressed.
  - ptmFactory
```
PTMFactory ptmFactory
```
    The post translational modifications factory.
  - ptmList
```
java.util.ArrayList<E> ptmList
```
    List of PTMs to display.
  - modificationTableToolTips
```
java.util.ArrayList<E> modificationTableToolTips
```
    The modification table column header tooltips.
  - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
  - cancelButton
```
javax.swing.JButton cancelButton
```
  - okButton
```
javax.swing.JButton okButton
```
  - ptmSelectionPanel
```
javax.swing.JPanel ptmSelectionPanel
```
  - ptmTable
```
javax.swing.JTable ptmTable
```
  - ptmTableScrollPane
```
javax.swing.JScrollPane ptmTableScrollPane
```

Class com.compomics.util.gui.ptm.PtmDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

ptmDialogParent
```
PtmDialogParent ptmDialogParent
```
The PtmDialog parent.
ptmFactory
```
PTMFactory ptmFactory
```
The post translational modifications factory.
currentPtm
```
PTM currentPtm
```
The edited PTM.
neutralLosses
```
java.util.ArrayList<E> neutralLosses
```
The neutral losses.
reporterIons
```
java.util.ArrayList<E> reporterIons
```
The reporter ions.
ptmToPrideMap
```
PtmToPrideMap ptmToPrideMap
```
The PTM to PRIDE map.
cvTerm
```
CvTerm cvTerm
```
The modification CV term.
editable
```
boolean editable
```
Boolean indicating whether the user can edit the PTM or not.
pattern
```
AminoAcidPattern pattern
```
The amino acid pattern of the modification
reporterIonTableToolTips
```
java.util.ArrayList<E> reporterIonTableToolTips
```
The reporter ion table column header tooltips.
neutralLossesTableToolTips
```
java.util.ArrayList<E> neutralLossesTableToolTips
```
The neutral losses table column header tooltips.
addNeutralLoss
```
javax.swing.JButton addNeutralLoss
```
addReporterIon
```
javax.swing.JButton addReporterIon
```
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
cancelButton
```
javax.swing.JButton cancelButton
```
detailsPanel
```
javax.swing.JPanel detailsPanel
```
helpJButton
```
javax.swing.JButton helpJButton
```
jLabel1
```
javax.swing.JLabel jLabel1
```
jPanel1
```
javax.swing.JPanel jPanel1
```
massLabel
```
javax.swing.JLabel massLabel
```
massTxt
```
javax.swing.JTextField massTxt
```
nameLabel
```
javax.swing.JLabel nameLabel
```
nameShortLabel
```
javax.swing.JLabel nameShortLabel
```
nameShortTxt
```
javax.swing.JTextField nameShortTxt
```
nameTxt
```
javax.swing.JTextField nameTxt
```

neutralLossesAndReporterIonsPanel

javax.swing.JPanel neutralLossesAndReporterIonsPanel

neutralLossesJScrollPane

javax.swing.JScrollPane neutralLossesJScrollPane

neutralLossesTable
```
javax.swing.JTable neutralLossesTable
```
okButton
```
javax.swing.JButton okButton
```
olsJButton
```
javax.swing.JButton olsJButton
```
patternLabel
```
javax.swing.JLabel patternLabel
```

psiModMappingJTextField

javax.swing.JTextField psiModMappingJTextField

psiModMappingPanel
```
javax.swing.JPanel psiModMappingPanel
```
removeNeutralLoss
```
javax.swing.JButton removeNeutralLoss
```
removerReporterIon
```
javax.swing.JButton removerReporterIon
```

reporterIonsJScrollPane

javax.swing.JScrollPane reporterIonsJScrollPane

reporterIonsTable
```
javax.swing.JTable reporterIonsTable
```
residuesTxt
```
javax.swing.JTextField residuesTxt
```
typeCmb
```
javax.swing.JComboBox<E> typeCmb
```

Package com.compomics.util.gui.renderers
- Class com.compomics.util.gui.renderers.AlignedListCellRenderer extends javax.swing.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 javax.swing.table.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 javax.swing.JLabel implements Serializable
  - Serialized Fields
    - minXAxisValue
```
double minXAxisValue
```
      The minimum x-axis value.
    - maxXAxisValue
```
double maxXAxisValue
```
      The maxium x-axis value.
    - delegate
```
javax.swing.table.TableCellRenderer delegate
```
      A reference to a standard table cell renderer.
- Class com.compomics.util.gui.renderers.TimestampRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
- Class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer extends javax.swing.plaf.basic.BasicComboBoxRenderer implements Serializable
  - Serialized Fields
    - tooltips
```
java.util.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.

Package com.compomics.util.gui.searchsettings

Class com.compomics.util.gui.searchsettings.EnzymeSelectionDialog extends javax.swing.JDialog implements Serializable
- Serialized Fields
  - enzymeFactory
```
EnzymeFactory enzymeFactory
```
    The enzyme factory.
  - selectionCanceled
```
boolean selectionCanceled
```
    True of the enzyme selection was canceled by the user.
  - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
  - cancelButton
```
javax.swing.JButton cancelButton
```
  - enzymeLabel
```
javax.swing.JLabel enzymeLabel
```
  - enzymesCmb
```
javax.swing.JComboBox<E> enzymesCmb
```
  - mappingPanel
```
javax.swing.JPanel mappingPanel
```
  - okButton
```
javax.swing.JButton okButton
```
  - prideEnzymeNameLabel
```
javax.swing.JLabel prideEnzymeNameLabel
```
  - prideEnzymeNameTextField
```
javax.swing.JTextField prideEnzymeNameTextField
```

Class com.compomics.util.gui.searchsettings.SearchSettingsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

sequenceFactory
```
SequenceFactory sequenceFactory
```
The sequence factory.
enzymeFactory
```
EnzymeFactory enzymeFactory
```
The enzyme factory.
forwardIons
```
java.lang.String[] forwardIons
```
Convenience array for forward ion type selection.
rewindIons
```
java.lang.String[] rewindIons
```
Convenience array for rewind ion type selection.
ptmFactory
```
PTMFactory ptmFactory
```
The post translational modifications factory.
parametersFile
```
java.io.File parametersFile
```
The parameter file.
searchSettingsDialogParent
```
SearchSettingsDialogParent searchSettingsDialogParent
```
The SearchSettingsDialogParent.
searchParameters
```
SearchParameters searchParameters
```
modificationTableToolTips
```
java.util.ArrayList<E> modificationTableToolTips
```
The modification table column header tooltips.
parentFrame
```
javax.swing.JFrame parentFrame
```
The dialog parent frame.
normalIcon
```
java.awt.Image normalIcon
```
The normal dialog icon.
waitingIcon
```
java.awt.Image waitingIcon
```
The waiting dialog icon.

addFixedModification

javax.swing.JButton addFixedModification

addVariableModification

javax.swing.JButton addVariableModification

availableModsPanel
```
javax.swing.JPanel availableModsPanel
```
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
cancelButton
```
javax.swing.JButton cancelButton
```

dataBasePanelSettings

javax.swing.JPanel dataBasePanelSettings

databaseSettingsLbl
```
javax.swing.JLabel databaseSettingsLbl
```

databaseSettingsTxt

javax.swing.JTextField databaseSettingsTxt

editDatabaseSettings

javax.swing.JButton editDatabaseSettings

enzymeLabel
```
javax.swing.JLabel enzymeLabel
```
enzymesCmb
```
javax.swing.JComboBox<E> enzymesCmb
```

fixedModificationsLabel

javax.swing.JLabel fixedModificationsLabel

fixedModsJScrollPane

javax.swing.JScrollPane fixedModsJScrollPane

fixedModsTable
```
javax.swing.JTable fixedModsTable
```

fragmentIon1Cmb

javax.swing.JComboBox<E> fragmentIon1Cmb

fragmentIon2Cmb

javax.swing.JComboBox<E> fragmentIon2Cmb

fragmentIonAccuracyTxt

javax.swing.JTextField fragmentIonAccuracyTxt

fragmentIonLbl
```
javax.swing.JLabel fragmentIonLbl
```
fragmentIonType1Lbl
```
javax.swing.JLabel fragmentIonType1Lbl
```
jPanel8
```
javax.swing.JPanel jPanel8
```
jPanel9
```
javax.swing.JPanel jPanel9
```

maxMissedCleavagesLabel

javax.swing.JLabel maxMissedCleavagesLabel

maxPrecursorChargeTxt

javax.swing.JTextField maxPrecursorChargeTxt

minPrecursorChargeTxt

javax.swing.JTextField minPrecursorChargeTxt

missedCleavagesTxt

javax.swing.JTextField missedCleavagesTxt

modificationTypesSplitPane

javax.swing.JSplitPane modificationTypesSplitPane

modificationsJScrollPane

javax.swing.JScrollPane modificationsJScrollPane

modificationsLayeredPane

javax.swing.JLayeredPane modificationsLayeredPane

modificationsListCombo

javax.swing.JComboBox<E> modificationsListCombo

modificationsPanel
```
javax.swing.JPanel modificationsPanel
```
modificationsTable
```
javax.swing.JTable modificationsTable
```
okButton
```
javax.swing.JButton okButton
```

openDialogHelpJButton1

javax.swing.JButton openDialogHelpJButton1

openModificationSettingsJButton

javax.swing.JButton openModificationSettingsJButton

precursorChargeLbl
```
javax.swing.JLabel precursorChargeLbl
```

precursorChargeRangeLabel

javax.swing.JLabel precursorChargeRangeLabel

precursorIonAccuracyTxt

javax.swing.JTextField precursorIonAccuracyTxt

precursorIonLbl
```
javax.swing.JLabel precursorIonLbl
```

precursorIonUnit

javax.swing.JComboBox<E> precursorIonUnit

proteaseAndFragmentationPanel

javax.swing.JPanel proteaseAndFragmentationPanel

removeFixedModification

javax.swing.JButton removeFixedModification

removeVariableModification

javax.swing.JButton removeVariableModification

variableModificationsLabel

javax.swing.JLabel variableModificationsLabel

variableModsJScrollPane

javax.swing.JScrollPane variableModsJScrollPane

variableModsTable
```
javax.swing.JTable variableModsTable
```

Package com.compomics.util.gui.searchsettings.algorithm_settings

Class com.compomics.util.gui.searchsettings.algorithm_settings.OmssaSettingsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

omssaParameters
```
OmssaParameters omssaParameters
```
The OMSSA parameters class containing the information to display.
cancelled
```
boolean cancelled
```
Boolean indicating whether the used canceled the editing.

advancedSearchSettingsPanel

javax.swing.JPanel advancedSearchSettingsPanel

advancedSettingsWarningLabel

javax.swing.JLabel advancedSettingsWarningLabel

backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
cTermIonsCmb
```
javax.swing.JComboBox<E> cTermIonsCmb
```
cTermIonsLbl
```
javax.swing.JLabel cTermIonsLbl
```

chargeEstimationCombo

javax.swing.JComboBox<E> chargeEstimationCombo

chargeReductionLabel
```
javax.swing.JLabel chargeReductionLabel
```

cleaveNterminalMethionineCmb

javax.swing.JComboBox<E> cleaveNterminalMethionineCmb

cleaveNterminalMethionineLbl

javax.swing.JLabel cleaveNterminalMethionineLbl

closeButton
```
javax.swing.JButton closeButton
```

consecutiveIonProbabilityLbl

javax.swing.JLabel consecutiveIonProbabilityLbl

consecutiveIonProbabilityTxt

javax.swing.JTextField consecutiveIonProbabilityTxt

correlationCorrectionScoreCmb

javax.swing.JComboBox<E> correlationCorrectionScoreCmb

correlationCorrectionScoreLbl

javax.swing.JLabel correlationCorrectionScoreLbl

databaseProcessingPanel

javax.swing.JPanel databaseProcessingPanel

doublyChargedNPeaksLbl

javax.swing.JLabel doublyChargedNPeaksLbl

doublyChargedNpeaksTxt

javax.swing.JTextField doublyChargedNpeaksTxt

doublyChargedWindowWidthLbl

javax.swing.JLabel doublyChargedWindowWidthLbl

doublyChargedWindowWidthTxt

javax.swing.JTextField doublyChargedWindowWidthTxt

eValueLbl
```
javax.swing.JLabel eValueLbl
```

eliminatePrecursorCombo

javax.swing.JComboBox<E> eliminatePrecursorCombo

forwardIonsFirstCmb

javax.swing.JComboBox<E> forwardIonsFirstCmb

forwardIonsFirstLbl
```
javax.swing.JLabel forwardIonsFirstLbl
```
fractionChargeLbl
```
javax.swing.JLabel fractionChargeLbl
```

fractionChargeTxt

javax.swing.JTextField fractionChargeTxt

highIntensityLbl
```
javax.swing.JLabel highIntensityLbl
```
highIntensityTxt
```
javax.swing.JTextField highIntensityTxt
```
hitListLbl
```
javax.swing.JLabel hitListLbl
```
hitlistTxt
```
javax.swing.JTextField hitlistTxt
```

intensityIncrementLbl

javax.swing.JLabel intensityIncrementLbl

intensityIncrementTxt

javax.swing.JTextField intensityIncrementTxt

iterativeReplaceEvalueLbl

javax.swing.JLabel iterativeReplaceEvalueLbl

iterativeReplaceEvalueTxt

javax.swing.JTextField iterativeReplaceEvalueTxt

iterativeSearchSettingsPanel

javax.swing.JPanel iterativeSearchSettingsPanel

iterativeSequenceEvalueLbl

javax.swing.JLabel iterativeSequenceEvalueLbl

iterativeSequenceEvalueTxt

javax.swing.JTextField iterativeSequenceEvalueTxt

iterativeSpectraEvalueLbl

javax.swing.JLabel iterativeSpectraEvalueLbl

iterativeSpectraEvalueTxt

javax.swing.JTextField iterativeSpectraEvalueTxt

jSeparator1
```
javax.swing.JSeparator jSeparator1
```
lowIntensityLbl
```
javax.swing.JLabel lowIntensityLbl
```
lowIntensityTxt
```
javax.swing.JTextField lowIntensityTxt
```
maxEvalueTxt
```
javax.swing.JTextField maxEvalueTxt
```
maxFragmentChargeLbl
```
javax.swing.JLabel maxFragmentChargeLbl
```

maxFragmentChargeTxt

javax.swing.JTextField maxFragmentChargeTxt

maxFragmentsPerSeriesLbl

javax.swing.JLabel maxFragmentsPerSeriesLbl

maxFragmentsPerSeriesTxt

javax.swing.JTextField maxFragmentsPerSeriesTxt

maxLaddersLbl
```
javax.swing.JLabel maxLaddersLbl
```
maxLaddersTxt
```
javax.swing.JTextField maxLaddersTxt
```
maxPepLengthTxt
```
javax.swing.JTextField maxPepLengthTxt
```

minAnnotatedMostIntensePeaksLbl

javax.swing.JLabel minAnnotatedMostIntensePeaksLbl

minAnnotatedMostIntensePeaksTxt

javax.swing.JTextField minAnnotatedMostIntensePeaksTxt

minAnnotatedPeaksLbl
```
javax.swing.JLabel minAnnotatedPeaksLbl
```

minAnnotatedPeaksTxt

javax.swing.JTextField minAnnotatedPeaksTxt

minPepLengthTxt
```
javax.swing.JTextField minPepLengthTxt
```

minPrecChargeMultipleChargedFragmentsTxt

javax.swing.JTextField minPrecChargeMultipleChargedFragmentsTxt

minPrecPerSpectrumLbl

javax.swing.JLabel minPrecPerSpectrumLbl

minPrecPerSpectrumTxt

javax.swing.JTextField minPrecPerSpectrumTxt

minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel

javax.swing.JLabel minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel

nHitsPerSpectrumPerChargeLbl

javax.swing.JLabel nHitsPerSpectrumPerChargeLbl

nHitsPerSpectrumPerChargeTxt

javax.swing.JTextField nHitsPerSpectrumPerChargeTxt

nIsotopesLbl
```
javax.swing.JLabel nIsotopesLbl
```
nIsotopesTxt
```
javax.swing.JTextField nIsotopesTxt
```
nPeaksLbl
```
javax.swing.JLabel nPeaksLbl
```
nPeaksTxt
```
javax.swing.JTextField nPeaksTxt
```
neutronLbl
```
javax.swing.JLabel neutronLbl
```
neutronTxt
```
javax.swing.JTextField neutronTxt
```
okButton
```
javax.swing.JButton okButton
```

omssaOutputFormatComboBox

javax.swing.JComboBox<E> omssaOutputFormatComboBox

omssaOutputFormatLabel

javax.swing.JLabel omssaOutputFormatLabel

openDialogHelpJButton

javax.swing.JButton openDialogHelpJButton

outputParametersPanel

javax.swing.JPanel outputParametersPanel

peptideLengthDividerLabel1

javax.swing.JLabel peptideLengthDividerLabel1

peptideLengthJLabel
```
javax.swing.JLabel peptideLengthJLabel
```

plusOneChargeAutomaticLbl

javax.swing.JLabel plusOneChargeAutomaticLbl

plusOneChargeCmb

javax.swing.JComboBox<E> plusOneChargeCmb

precursorChargeEstimationLabel

javax.swing.JLabel precursorChargeEstimationLabel

precursorMassScalingLabel

javax.swing.JLabel precursorMassScalingLabel

precursorScalingCombo

javax.swing.JComboBox<E> precursorScalingCombo

searchPositiveIonsCmb

javax.swing.JComboBox<E> searchPositiveIonsCmb

searchPositiveIonsLbl

javax.swing.JLabel searchPositiveIonsLbl

semiEnzymaticParametersPanel

javax.swing.JPanel semiEnzymaticParametersPanel

sequenceMappingCmb

javax.swing.JComboBox<E> sequenceMappingCmb

sequenceMappingLbl
```
javax.swing.JLabel sequenceMappingLbl
```

singlyChargedNPeaksLbl

javax.swing.JLabel singlyChargedNPeaksLbl

singlyChargedNpeaksTxt

javax.swing.JTextField singlyChargedNpeaksTxt

singlyChargedWindowWidthLbl

javax.swing.JLabel singlyChargedWindowWidthLbl

singlyChargedWindowWidthTxt

javax.swing.JTextField singlyChargedWindowWidthTxt

spectrumProcessingPanel

javax.swing.JPanel spectrumProcessingPanel

tabbedPane
```
javax.swing.JTabbedPane tabbedPane
```

Class com.compomics.util.gui.searchsettings.algorithm_settings.XTandemSettingsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

xtandemParameters
```
XtandemParameters xtandemParameters
```
The X!Tandem parameters class containing the information to display.
modificationProfile
```
ModificationProfile modificationProfile
```
The modification profile used for the search.
fragmentIonMassAccuracy
```
double fragmentIonMassAccuracy
```
The fragment ion mass accuracy.
cancelled
```
boolean cancelled
```
Boolean indicating whether the used canceled the editing.
modificationTableToolTips
```
java.util.ArrayList<E> modificationTableToolTips
```
The modification table column header tooltips.
ptmFactory
```
PTMFactory ptmFactory
```
The post translational modifications factory.

advancedSearchSettingsPanel

javax.swing.JPanel advancedSearchSettingsPanel

advancedSettingsWarningLabel

javax.swing.JLabel advancedSettingsWarningLabel

backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
closeButton
```
javax.swing.JButton closeButton
```
dynamicRangeLbl
```
javax.swing.JLabel dynamicRangeLbl
```
dynamicRangeTxt
```
javax.swing.JTextField dynamicRangeTxt
```
eValueLbl
```
javax.swing.JLabel eValueLbl
```
eValueTxt
```
javax.swing.JTextField eValueTxt
```

fixedModificationsLabel

javax.swing.JLabel fixedModificationsLabel

jPanel8
```
javax.swing.JPanel jPanel8
```

maxEValueRefineTxt

javax.swing.JTextField maxEValueRefineTxt

maxEValueRefinmentLbl

javax.swing.JLabel maxEValueRefinmentLbl

minFragMzLbl
```
javax.swing.JLabel minFragMzLbl
```
minFragmentMzTxt
```
javax.swing.JTextField minFragmentMzTxt
```
minPeaksLbl
```
javax.swing.JLabel minPeaksLbl
```
minPeaksTxt
```
javax.swing.JTextField minPeaksTxt
```
minPrecMassLbl
```
javax.swing.JLabel minPrecMassLbl
```
minPrecMassTxt
```
javax.swing.JTextField minPrecMassTxt
```

modificationsJScrollPane

javax.swing.JScrollPane modificationsJScrollPane

modificationsTable
```
javax.swing.JTable modificationsTable
```
nPeaksLbl
```
javax.swing.JLabel nPeaksLbl
```
nPeaksTxt
```
javax.swing.JTextField nPeaksTxt
```

noiseSuppressionCmb

javax.swing.JComboBox<E> noiseSuppressionCmb

noiseSuppressionLabel

javax.swing.JLabel noiseSuppressionLabel

okButton
```
javax.swing.JButton okButton
```

openDialogHelpJButton

javax.swing.JButton openDialogHelpJButton

openModificationSettingsJButton

javax.swing.JButton openModificationSettingsJButton

outputHistogramsCmb

javax.swing.JComboBox<E> outputHistogramsCmb

outputHistogramsLabel

javax.swing.JLabel outputHistogramsLabel

outputProteinsCmb

javax.swing.JComboBox<E> outputProteinsCmb

outputProteinsLabel
```
javax.swing.JLabel outputProteinsLabel
```

outputSequencesCmb

javax.swing.JComboBox<E> outputSequencesCmb

outputSequencesLabel
```
javax.swing.JLabel outputSequencesLabel
```
outputSettingsPanel
```
javax.swing.JPanel outputSettingsPanel
```

outputSpectraCmb

javax.swing.JComboBox<E> outputSpectraCmb

outputSpectraLabel
```
javax.swing.JLabel outputSpectraLabel
```
pointMutationLabel
```
javax.swing.JLabel pointMutationLabel
```

pointMutationsCmb

javax.swing.JComboBox<E> pointMutationsCmb

potentialModificationsCmb

javax.swing.JComboBox<E> potentialModificationsCmb

quickAcetylCmb
```
javax.swing.JComboBox<E> quickAcetylCmb
```
quickAcetylLabel
```
javax.swing.JLabel quickAcetylLabel
```
quickPyroCmb
```
javax.swing.JComboBox<E> quickPyroCmb
```
quickPyroLabel
```
javax.swing.JLabel quickPyroLabel
```
refinementCmb
```
javax.swing.JComboBox<E> refinementCmb
```
refinementLabel
```
javax.swing.JLabel refinementLabel
```

refinementSettingsPanel

javax.swing.JPanel refinementSettingsPanel

semiEnzymaticCmb

javax.swing.JComboBox<E> semiEnzymaticCmb

semiEnzymaticLabel
```
javax.swing.JLabel semiEnzymaticLabel
```
skylinePathValueLbl
```
javax.swing.JLabel skylinePathValueLbl
```
skylineTxt
```
javax.swing.JTextField skylineTxt
```
snapsCmb
```
javax.swing.JComboBox<E> snapsCmb
```
snapsLabel
```
javax.swing.JLabel snapsLabel
```

spectrumImportSettingsPanel

javax.swing.JPanel spectrumImportSettingsPanel

spectrumSynthesisCmb

javax.swing.JComboBox<E> spectrumSynthesisCmb

spectrumSynthesisLabel

javax.swing.JLabel spectrumSynthesisLabel

stpBiasCmb
```
javax.swing.JComboBox<E> stpBiasCmb
```
stpBiasLabel
```
javax.swing.JLabel stpBiasLabel
```

unanticipatedCleavageCmb

javax.swing.JComboBox<E> unanticipatedCleavageCmb

unanticipatedCleavageLabel

javax.swing.JLabel unanticipatedCleavageLabel

usePotentialModsLabel

javax.swing.JLabel usePotentialModsLabel

Package com.compomics.util.gui.spectrum
- Class com.compomics.util.gui.spectrum.ChromatogramPanel extends GraphicsPanel implements Serializable
  - Serialized Fields
    - iChromatogramColor
```
java.awt.Color iChromatogramColor
```
      Color in which the chromatogram polyline is rendered. Defaults to gray.
    - iChromatogramPointColor
```
java.awt.Color iChromatogramPointColor
```
      Color in which the data points and peaks are rendered. Defaults to black.
- Class com.compomics.util.gui.spectrum.FragmentIonTable extends javax.swing.JTable implements Serializable
  - Serialized Fields
    - currentFragmentIonTypes
```
java.util.ArrayList<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
```
java.util.ArrayList<E> tooltips
```
      The table tooltips.
    - currentPeptide
```
Peptide currentPeptide
```
      The current peptide.
    - peptideSequence
```
java.lang.String peptideSequence
```
      The current peptide sequence.
    - allAnnotations
```
java.util.ArrayList<E> allAnnotations
```
      The spectrum annotations map.
    - allSpectra
```
java.util.ArrayList<E> allSpectra
```
      The list of spectra. Needed for intensity normalization.
- Class com.compomics.util.gui.spectrum.GraphicsPanel extends javax.swing.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
```
java.awt.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
```
java.lang.String scientificPattern
```
      The number format pattern for scientific annotation.
    - referenceAreasXAxis
```
java.util.HashMap<K,V> referenceAreasXAxis
```
      A hashmap of the current x-axis reference areas. Key is the name of the reference area.
    - referenceAreasYAxis
```
java.util.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
```
java.lang.String iXAxisLabel
```
      The label (and unit between brackets, if available) for the x-axis. Defaults to "m/z".
    - iYAxisLabel
```
java.lang.String iYAxisLabel
```
      The label (and unit between brackets, if available) for the y-axis. Defaults to "Int".
    - iFilenameColor
```
java.awt.Color iFilenameColor
```
      This is the color the filename should be presented in.
    - iDataPointAndLineColor
```
java.util.ArrayList<E> iDataPointAndLineColor
```
      Colors in which the data points and peaks are rendered. Indexed by dataset.
    - iDataPointAndLineColorMirroredSpectra
```
java.util.ArrayList<E> iDataPointAndLineColorMirroredSpectra
```
      Colors in which the data points and peaks are rendered for the mirrored spectra. Indexed by dataset.
    - iAreaUnderCurveColor
```
java.util.ArrayList<E> iAreaUnderCurveColor
```
      Colors in which the chromatogram polyline is rendered. Indexed by dataset.
    - iAreaUnderCurveColorMirroredSpectra
```
java.util.ArrayList<E> iAreaUnderCurveColorMirroredSpectra
```
      Colors in which the chromatogram polyline is rendered for the mirrored spectra. Indexed by dataset.
    - iPointSize
```
java.lang.Integer iPointSize
```
      Size for the point on a polygon.
    - iFilename
```
java.lang.String iFilename
```
      The spectrum or chromatogram filename.
    - iFilenameMirrorredSpectrum
```
java.lang.String iFilenameMirrorredSpectrum
```
      The spectrum or chromatogram filename for the mirrored spectrum or chromatogram.
    - iSpecPanelListeners
```
java.util.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
```
java.util.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
```
java.util.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 procentual 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
```
java.util.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
```
java.util.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
```
java.lang.String iPrecursorCharge
```
      This String holds the charge for the precursor.
    - iPrecursorChargeMirorredSpectrum
```
java.lang.String iPrecursorChargeMirorredSpectrum
```
      This String holds the charge for the precursor for the mirrored spectrum.
    - iXAxisDataInPixels
```
java.util.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
```
java.util.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
```
java.util.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
```
java.util.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.
    - iHighLightIndex
```
int iHighLightIndex
```
      Index of the point that needs to be highlighted.
    - iHighLightDatasetIndex
```
int iHighLightDatasetIndex
```
      Index of the dataset containing the point that needs to be highlighted.
    - iClicked
```
boolean iClicked
```
      Boolean that indicates whether a point has been marked by clicking.
    - iClickedIndex
```
int iClickedIndex
```
      Int that indicates which point was clicked.
    - iClickedDataSetIndex
```
int iClickedDataSetIndex
```
      Int that indicates which dataset contains the clicked point.
    - iClickedList
```
java.util.Vector<E> iClickedList
```
      The Vector that holds all points clicked up to now.
    - iClickedListDatasetIndices
```
java.util.Vector<E> iClickedListDatasetIndices
```
      The Vector that holds the dataset indices of all points clicked up to now.
    - iStoredSequence
```
java.util.Vector<E> iStoredSequence
```
      The Vector that holds a set of stored points from a previously established list.
    - iStoredSequenceDatasetIndices
```
java.util.Vector<E> iStoredSequenceDatasetIndices
```
      The Vector that holds the dataset indices of stored points from a previously established list.
    - iAnnotations
```
java.util.Vector<E> iAnnotations
```
      The Vector that holds a set of Annotation instances.
    - 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.
    - currentGraphicsPanelType
```
GraphicsPanel.GraphicsPanelType currentGraphicsPanelType
```
      Sets the current GraphicsPanel type, default to centroid spectrum.
- Class com.compomics.util.gui.spectrum.IntensityHistogram extends javax.swing.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 javax.swing.table.DefaultTableModel implements Serializable
  - Serialized Fields
    - ionMap
```
java.util.HashMap<K,V> ionMap
```
      The list of ions.
    - keys
```
java.util.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
```
java.awt.Color aSpectrumPeakColor
```
      The color used for the peaks. Default to red.
    - aSpectrumProfileModeLineColor
```
java.awt.Color aSpectrumProfileModeLineColor
```
      The color used for the area under the curve. Defaults to pink.
    - peptideSequences
```
java.util.ArrayList<E> peptideSequences
```
      The peptide sequences to display the isotopic distribution for.
    - peptideCharges
```
java.util.ArrayList<E> peptideCharges
```
      The charges of the peptides. Indexed by dataset.
    - iElements
```
java.util.HashMap<K,V> iElements
```
      HashMap with the molecular formula for all the aminoacids
- Class com.compomics.util.gui.spectrum.MassErrorBubblePlot extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - useRelativeError
```
boolean useRelativeError
```
      If true the relative error (ppm) is used instead of the absolute error (Da).
    - currentlyUsedIonMatches
```
java.util.ArrayList<E> currentlyUsedIonMatches
```
      The list of currently used ions.
    - chartPanel
```
org.jfree.chart.ChartPanel chartPanel
```
      The chart panel.
    - dataSeriesfragmentIonColors
```
java.util.ArrayList<E> dataSeriesfragmentIonColors
```
      The data series fragment ion colors.
- Class com.compomics.util.gui.spectrum.MassErrorPlot extends javax.swing.JPanel implements Serializable
  - Serialized Fields
    - annotations
```
java.util.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 javax.swing.JPanel implements Serializable
  - Serialized Fields
    - tooltipRectangles
```
java.util.HashMap<K,V> tooltipRectangles
```
      A map of the rectangles that have tooltips, i.e., the fragment ion peaks and the PTM highlighting.
    - iSequenceComponents
```
java.lang.String[] iSequenceComponents
```
      Elementary data for composing the Panel.
    - iIonMatches
```
java.util.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
```
java.awt.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
```
ModificationProfile 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
```
java.awt.Color forwardColor
```
      Color for the forward ion
    - rewindColor
```
java.awt.Color rewindColor
```
      Color for the rewind ion
- Class com.compomics.util.gui.spectrum.SpectrumPanel extends GraphicsPanel implements Serializable
  - Serialized Fields
    - spectrumPeakColor
```
java.awt.Color spectrumPeakColor
```
      The color used for the peaks. Default to red.
    - spectrumProfileModeLineColor
```
java.awt.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 javax.swing.table.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
```
java.util.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.
Package com.compomics.util.gui.utils
- Class com.compomics.util.gui.utils.ConnectionDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iConnections
```
java.util.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
```
javax.swing.JComboBox<E> cmbConfigurations
```
    - txtDriver
```
javax.swing.JTextField txtDriver
```
    - txtUrl
```
javax.swing.JTextField txtUrl
```
    - txtUser
```
javax.swing.JTextField txtUser
```
    - txtPassword
```
javax.swing.JPasswordField txtPassword
```
    - btnOK
```
javax.swing.JButton btnOK
```
    - btnCancel
```
javax.swing.JButton btnCancel
```
    - iTarget
```
Connectable iTarget
```
    - iPropsFile
```
java.lang.String iPropsFile
```
    - iLastInitiatedConfiguration
```
java.lang.String iLastInitiatedConfiguration
```
- Class com.compomics.util.gui.utils.DateChooser extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - iSelectedCalendar
```
java.util.Calendar iSelectedCalendar
```
    - iShownCalendar
```
java.util.Calendar iShownCalendar
```
    - iSelectedDayIndex
```
int iSelectedDayIndex
```
    - lblDayNames
```
javax.swing.JLabel[] lblDayNames
```
    - lblDays
```
javax.swing.JLabel[] lblDays
```
    - iDays
```
java.lang.Integer[] iDays
```
    - lblCurrentMonthYear
```
javax.swing.JLabel lblCurrentMonthYear
```
Package com.compomics.util.gui.waiting.waitinghandlers
- Class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - iProgress
```
javax.swing.JProgressBar iProgress
```
- Class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX extends javax.swing.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.
    - waitingIcon
```
java.awt.Image waitingIcon
```
      The dialog/frame icon to use when waiting.
    - normalIcon
```
java.awt.Image normalIcon
```
      The dialog/frame icon to use when done.
    - waitingHandlerParentFrame
```
java.awt.Frame waitingHandlerParentFrame
```
      The waitingHandlerParent frame.
    - waitingHandlerParentDialog
```
javax.swing.JDialog waitingHandlerParentDialog
```
      The waitingHandlerParent dialog.
    - waitingActionListener
```
WaitingActionListener waitingActionListener
```
      The waiting action listener.
    - progressBar
```
javax.swing.JProgressBar progressBar
```
- Class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog extends javax.swing.JDialog implements Serializable
  - Serialized Fields
    - dialog
```
javax.swing.JDialog dialog
```
      Needed for the shaking feature.
    - naturalLocation
```
java.awt.Point naturalLocation
```
      Used in the shaking feature.
    - shakeTimer
```
javax.swing.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.
    - tips
```
java.util.ArrayList<E> tips
```
      An array list of the tip of the day.
    - currentTipIndex
```
int currentTipIndex
```
      The current tip index.
    - lastSelectedFolder
```
java.lang.String lastSelectedFolder
```
      The last selected folder
    - waitingIcon
```
java.awt.Image waitingIcon
```
      The dialog/frame icon to use when waiting.
    - normalIcon
```
java.awt.Image normalIcon
```
      The dialog/frame icon to use when done.
    - waitingHandlerParent
```
java.awt.Frame waitingHandlerParent
```
      The waitingHandlerParent.
    - shakeWhenFinished
```
boolean shakeWhenFinished
```
      If true, the dialog will shake when completed. Mainly a PeptideShaker feature.
    - processName
```
java.lang.String processName
```
      The name of the process we are waiting for, e.g., 'Import Data' or 'Search'.
    - toolName
```
java.lang.String toolName
```
      The name of the tool using the waiting dialog. Used for the report.
    - toolVersion
```
java.lang.String toolVersion
```
      The version number of the tool using the waiting dialog. Used for the report.
    - waitingActionListener
```
WaitingActionListener waitingActionListener
```
      The waiting action listener.
    - backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
    - closeDialogWhenImportCompletesCheckBox
```
javax.swing.JCheckBox closeDialogWhenImportCompletesCheckBox
```
    - closeJButton
```
javax.swing.JButton closeJButton
```
    - layeredPane
```
javax.swing.JLayeredPane layeredPane
```
    - nextJButton
```
javax.swing.JButton nextJButton
```
    - okButton
```
javax.swing.JButton okButton
```
    - processProgressPanel
```
javax.swing.JPanel processProgressPanel
```
    - progressBar
```
javax.swing.JProgressBar progressBar
```
    - reportEditorPane
```
javax.swing.JEditorPane reportEditorPane
```
    - reportPaneScrollPane
```
javax.swing.JScrollPane reportPaneScrollPane
```
    - saveReportLabel
```
javax.swing.JLabel saveReportLabel
```
    - secondaryJProgressBar
```
javax.swing.JProgressBar secondaryJProgressBar
```
    - secondaryProgressBarSplitPane
```
javax.swing.JSplitPane secondaryProgressBarSplitPane
```
    - showTipOfTheDayCheckBox
```
javax.swing.JCheckBox showTipOfTheDayCheckBox
```
    - tempJProgressBar
```
javax.swing.JProgressBar tempJProgressBar
```
    - tipOfTheDayEditorPane
```
javax.swing.JEditorPane tipOfTheDayEditorPane
```
    - tipOfTheDayJPanel
```
javax.swing.JPanel tipOfTheDayJPanel
```
    - tipOfTheDayLayeredPane
```
javax.swing.JLayeredPane tipOfTheDayLayeredPane
```
    - tipOfTheDayScrollPane
```
javax.swing.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 java.io.IOException implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
Package com.compomics.util.preferences
- Class com.compomics.util.preferences.AnnotationPreferences extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -524156803097913546L
  - Serialized Fields
    - yAxisZoomExcludesBackgroundPeaks
```
boolean yAxisZoomExcludesBackgroundPeaks
```
      If true, the automatic y-axis zoom excludes background peaks. False includes all peaks in the auto zoom.
    - intensityIonTable
```
boolean intensityIonTable
```
      If true, the ion table is shown as an intensity versionm, false displays the standard Mascot version.
    - showBars
```
boolean showBars
```
      If true, bars are shown in the bubble plot highlighting the ions.
    - 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 limit used when only the most intense peaks are to be annotated.
    - automaticAnnotation
```
boolean automaticAnnotation
```
      Shall PeptideShaker use automatic annotation.
    - selectedIons
```
java.util.HashMap<K,V> selectedIons
```
      The types of ions to annotate.
    - neutralLossesMap
```
NeutralLossesMap neutralLossesMap
```
      The neutral losses searched for.
    - neutralLossesSequenceDependant
```
boolean neutralLossesSequenceDependant
```
      Shall neutral losses be only considered for ions containing amino acids of interest?
    - selectedCharges
```
java.util.ArrayList<E> selectedCharges
```
      The maximum fragment charge to be searched for.
    - fragmentIonAccuracy
```
double fragmentIonAccuracy
```
      Fragment ion accuracy used for peak matching.
    - currentPeptide
```
Peptide currentPeptide
```
      Deprecated. use the spectrumIdentificationAssumption
      
      The currently inspected peptide.
    - spectrumIdentificationAssumption
```
SpectrumIdentificationAssumption spectrumIdentificationAssumption
```
      The currently annotated spectrumIdentificationAssumption.
    - currentPrecursorCharge
```
int currentPrecursorCharge
```
      Deprecated. use the value in spectrumIdentificationAssumption.
      
      The charge of the currently inspected precursor.
    - 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.
- Class com.compomics.util.preferences.GenePreferences extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -1286840382594446279L
  - Serialized Fields
    - currentSpecies
```
java.lang.String currentSpecies
```
      The current species. Used for the gene mappings.
    - currentSpeciesType
```
java.lang.String currentSpeciesType
```
      The current species type. Used for the gene mappings.
    - goDomainMap
```
java.util.HashMap<K,V> goDomainMap
```
      The GO domain map. e.g., key: GO term: GO:0007568, element: biological_process.
    - speciesMap
```
java.util.HashMap<K,V> speciesMap
```
      Deprecated. use
      
      The species map, key: latin name, element: ensembl database name, e.g., key: Homo sapiens, element: hsapiens_gene_ensembl.
    - allSpeciesMap
```
java.util.HashMap<K,V> allSpeciesMap
```
      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.
    - ensemblVersionsMap
```
java.util.HashMap<K,V> ensemblVersionsMap
```
      The Ensembl versions for the downloaded species.
    - availableSpecies
```
java.util.ArrayList<E> availableSpecies
```
      Deprecated. use allSpecies instead
      
      The list of species.
    - allSpecies
```
java.util.HashMap<K,V> allSpecies
```
      Map of all the species.
    - species
```
java.util.Vector<E> species
```
      Deprecated.
      
      Old vector of species.
- Class com.compomics.util.preferences.IdFilter extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  8416219001106063781L
  - Serialized Fields
    - minPepLength
```
int minPepLength
```
      The minimal peptide length allowed.
    - maxPepLength
```
int maxPepLength
```
      The maximal peptide length allowed.
    - mascotMaxEvalue
```
double mascotMaxEvalue
```
      Mascot maximal e-value allowed.
    - omssaMaxEvalue
```
double omssaMaxEvalue
```
      OMSSA maximal e-value allowed.
    - xtandemMaxEvalue
```
double xtandemMaxEvalue
```
      X!Tandem maximal e-value 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.
- Class com.compomics.util.preferences.ModificationProfile extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  342611308111304721L
  - Serialized Fields
    - modificationNames
```
java.util.HashMap<K,V> modificationNames
```
      Deprecated. use the expected variable modification lists.
      
      Mapping of the utilities modification names to the PeptideShaker names.
    - fixedModifications
```
java.util.ArrayList<E> fixedModifications
```
      List of the expected fixed modifications.
    - variableModifications
```
java.util.ArrayList<E> variableModifications
```
      List of the expected variable modifications.
    - refinementVariableModifications
```
java.util.ArrayList<E> refinementVariableModifications
```
      List of variable modifications searched during the second pass search.
    - refinementFixedModifications
```
java.util.ArrayList<E> refinementFixedModifications
```
      List of variable modifications searched during the second pass search.
    - refinementModifications
```
java.util.ArrayList<E> refinementModifications
```
      Deprecated. use the variable/fixed versions
      
      List of modifications searched during the second pass search.
    - omssaIndexes
```
java.util.HashMap<K,V> omssaIndexes
```
      Map of the OMSSA indexes used for user modifications in this search.
    - colors
```
java.util.HashMap<K,V> colors
```
      Mapping of the expected modification names to the color used.
    - backUp
```
java.util.HashMap<K,V> backUp
```
      Back-up mapping of the PTMs for portability.
- Class com.compomics.util.preferences.ProcessingPreferences extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -5883143685674607162L
  - Serialized Fields
    - aScore
```
boolean aScore
```
      Deprecated. use the PTM scoring preferences instead
      
      Boolean indicating whether the A-score should be estimated.
    - proteinFDR
```
double proteinFDR
```
      The default protein FDR.
    - peptideFDR
```
double peptideFDR
```
      The default peptide FDR.
    - psmFDR
```
double psmFDR
```
      The default PSM FDR.
    - proteinConfidenceMwPlots
```
java.lang.Double proteinConfidenceMwPlots
```
      The minimum confidence required for a protein to be included in the average molecular weight analysis in the Fractions tab.
- Class com.compomics.util.preferences.PTMScoringPreferences extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -6656074270981104708L
  - Serialized Fields
    - aScoreCalculation
```
boolean aScoreCalculation
```
      Deprecated. use probabilitsticScoreCalculation instead
      
      Boolean indicating whether the A-score should be calculated.
    - aScoreNeutralLosses
```
boolean aScoreNeutralLosses
```
      Deprecated. use probabilisticScoreNeutralLosses instead
      
      Boolean indicating whether neutral losses shall be accounted in the calculation of the A-score.
    - flr
```
double flr
```
      The FLR threshold in percent
    - probabilitsticScoreCalculation
```
java.lang.Boolean probabilitsticScoreCalculation
```
      Boolean indicating whether a probabilitstic 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
```
java.lang.Boolean probabilisticScoreNeutralLosses
```
      Boolean indicating whether neutral losses shall be accounted for in the calculation of the probabilistic score.
- Class com.compomics.util.preferences.UtilitiesUserPreferences extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -4343570286224891504L
  - Serialized Fields
    - spectrumAnnotatedPeakWidth
```
java.lang.Float spectrumAnnotatedPeakWidth
```
      The width to use for the annotated peaks.
    - spectrumBackgroundPeakWidth
```
java.lang.Float spectrumBackgroundPeakWidth
```
      The width to use for the background peaks.
    - spectrumAnnotatedPeakColor
```
java.awt.Color spectrumAnnotatedPeakColor
```
      The color to use for the annotated peaks.
    - spectrumBackgroundPeakColor
```
java.awt.Color spectrumBackgroundPeakColor
```
      The color to use for the background peaks.
    - sparklineColorValidated
```
java.awt.Color sparklineColorValidated
```
      The color used for the sparkline bar chart plots.
    - sparklineColorNonValidated
```
java.awt.Color sparklineColorNonValidated
```
      The color used for the non-validated sparkline bar chart plots.
    - sparklineColorNotFound
```
java.awt.Color sparklineColorNotFound
```
      The color used for the not found sparkline bar chart plots.
    - sparklineColorPossible
```
java.awt.Color sparklineColorPossible
```
      The color used for the possible values sparkline bar chart plots.
    - peptideSelected
```
java.awt.Color peptideSelected
```
      The color of the selected peptide.
    - memoryPreference
```
int memoryPreference
```
      The memory to use.
    - proteinTreeFolder
```
java.io.File proteinTreeFolder
```
      The folder where to store the protein trees. Note: for backward compatibility not initialized here.
    - proteinTreeImportTime
```
java.util.HashMap<K,V> proteinTreeImportTime
```
      Maps saving the protein trees import time in a map: fasta file size -> import times. Note: for backward compatibility not initialized here.
    - searchGuiPath
```
java.lang.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
```
java.lang.String peptideShakerPath
```
      The path to the PeptideShaker installation (if any). Set to null if no path is provided.
    - reporterPath
```
java.lang.String reporterPath
```
      The path to the Reporter installation (if any). Set to null if no path is provided.
    - relimsPath
```
java.lang.String relimsPath
```
      The path to the Relims installation (if any). Set to null if no path is provided.
    - localPrideFolder
```
java.lang.String localPrideFolder
```
      The local PRIDE projects folder.
    - dbFolder
```
java.io.File dbFolder
```
      The user last used database folder.
    - favoriteDBs
```
java.util.ArrayList<E> favoriteDBs
```
      The user last used databases.
    - readTweets
```
java.util.ArrayList<E> readTweets
```
      The list of already read tweets.
    - displayedTips
```
java.util.ArrayList<E> displayedTips
```
      The list of already displayed tips.

Package com.compomics.util.preferences.gui

Class com.compomics.util.preferences.gui.ImportSettingsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

editable
```
boolean editable
```
If true the user can edit the settings.
userFilter
```
IdFilter userFilter
```
The identification filter set by the user. Null if cancel was pressed.
originalFilter
```
IdFilter originalFilter
```
The original filter
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
cancelButton
```
javax.swing.JButton cancelButton
```
filterPanel
```
javax.swing.JPanel filterPanel
```
helpJButton
```
javax.swing.JButton helpJButton
```
mascotEValueLabel
```
javax.swing.JLabel mascotEValueLabel
```
mascotEvalueTxt
```
javax.swing.JTextField mascotEvalueTxt
```
nAAmaxTxt
```
javax.swing.JTextField nAAmaxTxt
```
nAAminTxt
```
javax.swing.JTextField nAAminTxt
```
okButton
```
javax.swing.JButton okButton
```
omssaEValueLabel
```
javax.swing.JLabel omssaEValueLabel
```
omssaEvalueTxt
```
javax.swing.JTextField omssaEvalueTxt
```
peptideLengthLabel
```
javax.swing.JLabel peptideLengthLabel
```

peptideLengthRangeLabel

javax.swing.JLabel peptideLengthRangeLabel

precDevTxt
```
javax.swing.JTextField precDevTxt
```

precursorAccuracyLabel

javax.swing.JLabel precursorAccuracyLabel

ptmsCheck
```
javax.swing.JCheckBox ptmsCheck
```
unitCmb
```
javax.swing.JComboBox<E> unitCmb
```
xtandemEValueLabel
```
javax.swing.JLabel xtandemEValueLabel
```
xtandemEvalueTxt
```
javax.swing.JTextField xtandemEvalueTxt
```

Class com.compomics.util.preferences.gui.ProcessingPreferencesDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

processingPreferences
```
ProcessingPreferences processingPreferences
```
The processing preferences.
ptmScoringPreferences
```
PTMScoringPreferences ptmScoringPreferences
```
The PTM preferences. This deserves to be modifiable after import of the files as well.
aScoreLabel
```
javax.swing.JLabel aScoreLabel
```
backgroundPanel
```
javax.swing.JPanel backgroundPanel
```
estimateAScoreLabel
```
javax.swing.JLabel estimateAScoreLabel
```
fractionsPanel
```
javax.swing.JPanel fractionsPanel
```
helpJButton
```
javax.swing.JButton helpJButton
```

neutralLossesCmb

javax.swing.JComboBox<E> neutralLossesCmb

neutralLossesCmb2

javax.swing.JComboBox<E> neutralLossesCmb2

neutralLossesLabel
```
javax.swing.JLabel neutralLossesLabel
```
neutralLossesLabel1
```
javax.swing.JLabel neutralLossesLabel1
```
neutralLossesLabel2
```
javax.swing.JLabel neutralLossesLabel2
```
neutralLossesLabel3
```
javax.swing.JLabel neutralLossesLabel3
```
okButton
```
javax.swing.JButton okButton
```
peptideFdrLabel
```
javax.swing.JLabel peptideFdrLabel
```
peptideFdrTxt
```
javax.swing.JTextField peptideFdrTxt
```
percentLabel
```
javax.swing.JLabel percentLabel
```
percentLabel2
```
javax.swing.JLabel percentLabel2
```
percentLabel3
```
javax.swing.JLabel percentLabel3
```
percentLabel4
```
javax.swing.JLabel percentLabel4
```

probabilisticScoreCmb

javax.swing.JComboBox<E> probabilisticScoreCmb

processingParamsPanel

javax.swing.JPanel processingParamsPanel

proteinConfidenceMwTxt

javax.swing.JTextField proteinConfidenceMwTxt

proteinFdrLabel
```
javax.swing.JLabel proteinFdrLabel
```
proteinFdrTxt
```
javax.swing.JTextField proteinFdrTxt
```
proteinMwLabel
```
javax.swing.JLabel proteinMwLabel
```
psmFdrLabel
```
javax.swing.JLabel psmFdrLabel
```
psmFdrTxt
```
javax.swing.JTextField psmFdrTxt
```
ptmScoringPanel
```
javax.swing.JPanel ptmScoringPanel
```
scoreCmb
```
javax.swing.JComboBox<E> scoreCmb
```
thresholdCmb
```
javax.swing.JComboBox<E> thresholdCmb
```
thresholdTxt
```
javax.swing.JTextField thresholdTxt
```

Package com.compomics.util.pride
- Class com.compomics.util.pride.CvTerm extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -2890434198335005181L
  - Serialized Fields
    - ontology
```
java.lang.String ontology
```
      The ontology.
    - accession
```
java.lang.String accession
```
      The accession number.
    - name
```
java.lang.String name
```
      The name/term.
    - value
```
java.lang.String value
```
      The value for the given term.
- Class com.compomics.util.pride.PtmToPrideMap extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  7368502853292052566L
  - Serialized Fields
    - modToCvMap
```
java.util.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 java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -9182316910747747823L
  - Serialized Fields
    - name
```
java.lang.String name
```
      The contact's name.
    - eMail
```
java.lang.String eMail
```
      The contact's e-mail.
    - institution
```
java.lang.String institution
```
      The contact's institution.
- Class com.compomics.util.pride.prideobjects.ContactGroup extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -9182316910747747823L
  - Serialized Fields
    - contacts
```
java.util.ArrayList<E> contacts
```
      The contacts.
    - groupName
```
java.lang.String groupName
```
      The contact group name.
- Class com.compomics.util.pride.prideobjects.Instrument extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -8802861658166703745L
  - Serialized Fields
    - name
```
java.lang.String name
```
      The instrument name.
    - cvTerms
```
java.util.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 java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -9045298216154032632L
  - Serialized Fields
    - name
```
java.lang.String name
```
      The protcol name.
    - cvTerms
```
java.util.ArrayList<E> cvTerms
```
      The list of CV terms.
- Class com.compomics.util.pride.prideobjects.Reference extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -5449836209751629549L
  - Serialized Fields
    - reference
```
java.lang.String reference
```
      The reference text.
    - pmid
```
java.lang.String pmid
```
      The PubMed ID.
    - doi
```
java.lang.String doi
```
      The Digital Object Identifier.
- Class com.compomics.util.pride.prideobjects.ReferenceGroup extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -9182316910747747823L
  - Serialized Fields
    - references
```
java.util.ArrayList<E> references
```
      The references.
    - groupName
```
java.lang.String groupName
```
      The reference group name.
- Class com.compomics.util.pride.prideobjects.Sample extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  -7142471175737857227L
  - Serialized Fields
    - name
```
java.lang.String name
```
      The sample name.
    - cvTerms
```
java.util.ArrayList<E> cvTerms
```
      The list of CV terms.
Package com.compomics.util.protein
- Class com.compomics.util.protein.Header extends java.lang.Object implements Serializable
  
  serialVersionUID:
  
  7665784733371863163L
  - Serialized Fields
    - iID
```
java.lang.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
```
java.lang.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
```
java.lang.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-utilties 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
```
java.lang.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
```
java.lang.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
```
java.lang.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
```
java.lang.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
```
java.lang.String iGeneName
```
      The name of the gene the protein comes from. Note that this is only available for UniProt-based databases.
    - iProteinEvidence
```
java.lang.String iProteinEvidence
```
      The protein evidence for the protein. Note that this is only available for UniProt-based databases.
    - iTaxonomy
```
java.lang.String iTaxonomy
```
      The name of the taxonomy the protein comes from. Note that this is only available for UniProt-based databases.
    - iForeignDescription
```
java.lang.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
```
java.lang.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.
    - iAddenda
```
java.lang.StringBuffer iAddenda
```
      This StringBuffer holds all the addenda for this header.
    - iStart
```
int iStart
```
      This variable holds a possible startindex for the associated sequence
    - iEnd
```
int iEnd
```
      This variable holds a possible endindex for the associated sequence
- Class com.compomics.util.protein.ModificationImplementation extends java.lang.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.sun
- Class com.compomics.util.sun.TableMap extends javax.swing.table.AbstractTableModel implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - model
```
javax.swing.table.TableModel model
```
- Class com.compomics.util.sun.TableSorter extends TableMap implements Serializable
  - Serialized Fields
    - logger
```
org.apache.log4j.Logger logger
```
    - indexes
```
int[] indexes
```
    - sortingColumns
```
java.util.Vector<E> sortingColumns
```
    - ascending
```
boolean ascending
```
    - compares
```
int compares
```
    - listMouseListener
```
java.awt.event.MouseAdapter listMouseListener
```

Serialized Form

Package com.compomics.software.dialogs

Class com.compomics.software.dialogs.JavaOptionsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

javaOptionsDialogParent

welcomeDialog

toolName

backgroundPanel

cancelButton

javaOptionsHelpJButton

mbLabel

memoryLimitLabel

memoryTxt

okButton

settingsPanel

Class com.compomics.software.dialogs.LowMemoryDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

javaOptionsDialogParent

frameParent

toolName

welcomeDialog

backgroundsPanel

bitLabel

bitPanel

bitRecommendationLabel

editMemoryJLabel

javaHelpJLabel

javaHomeLabel

javaHomePanel

memoryLabel

memoryPanel

memoryRecommendationLabel

okButton

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

Serialized Fields

utilitiesUserPreferences

lastSelectedFolder

dialogCanceled

backgroundPanel

browseButton

cancelButton

jLabel2

okButton

peptideShakerButton

peptideShakerDownloadLinkLabel

peptideShakerDownloadPanel

peptideShakerInfoLabel

peptideShakerInstallationPanel

peptideShakerJarFileHelpLabel

peptideShakernstallationJTextField

Class com.compomics.software.dialogs.RelimsSetupDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

utilitiesUserPreferences

lastSelectedFolder

backgroundPanel

browseButton

cancelButton

jLabel2

okButton

relimsButton

relimsDownloadLinkLabel

relimsDownloadPanel

relimsInfoLabel

relimsInstallationJTextField

relimsInstallationPanel

relimsJarFileHelpLabel

Class com.compomics.software.dialogs.ReporterSetupDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

utilitiesUserPreferences

lastSelectedFolder

dialogCanceled

backgroundPanel

browseButton

cancelButton

jLabel2

okButton

reporterButton

reporterDownloadLinkLabel

reporterDownloadPanel

reporterInfoLabel