Serialized Form
-
Package com.compomics.software.dialogs
-
Class com.compomics.software.dialogs.JavaHomeDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
browseButton
JButton browseButton
-
cancelButton
JButton cancelButton
-
javaHomeHelpJButton
JButton javaHomeHelpJButton
-
javaHomeLabel
JLabel javaHomeLabel
-
javaHomeOrMemoryDialogParent
JavaHomeOrMemoryDialogParent javaHomeOrMemoryDialogParent
Reference to the JavaHomeOrMemoryDialogParent. -
javaHomeTxt
JTextField javaHomeTxt
-
jSeparator1
JSeparator jSeparator1
-
okButton
JButton okButton
-
toolName
String toolName
The name of the tool, e.g., PeptideShaker. -
welcomeDialog
JDialog welcomeDialog
A reference to the Welcome Dialog.
-
-
-
Class com.compomics.software.dialogs.JavaMemoryDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
javaHomeOrMemoryDialogParent
JavaHomeOrMemoryDialogParent javaHomeOrMemoryDialogParent
Reference to the JavaHomeOrMemoryDialogParent. -
javaOptionsHelpJButton
JButton javaOptionsHelpJButton
-
jSeparator1
JSeparator jSeparator1
-
mbLabel
JLabel mbLabel
-
memoryLimitLabel
JLabel memoryLimitLabel
-
memoryTxt
JTextField memoryTxt
-
okButton
JButton okButton
-
toolName
String toolName
The name of the tool, e.g., PeptideShaker. -
welcomeDialog
JDialog welcomeDialog
A reference to the Welcome Dialog.
-
-
-
Class com.compomics.software.dialogs.JavaParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundsPanel
JPanel backgroundsPanel
-
bitLabel
JLabel bitLabel
-
bitPanel
JPanel bitPanel
-
bitRecommendationLabel
JLabel bitRecommendationLabel
-
frameParent
JFrame frameParent
The frame parent. -
javaHelpJLabel
JLabel javaHelpJLabel
-
javaHomeLabel
JLabel javaHomeLabel
-
javaHomeOrMemoryDialogParent
JavaHomeOrMemoryDialogParent javaHomeOrMemoryDialogParent
Reference to the JavaHomeOrMemoryDialogParent. -
javaHomePanel
JPanel javaHomePanel
-
memoryLabel
JLabel memoryLabel
-
memoryPanel
JPanel memoryPanel
-
memoryRecommendationLabel
JLabel memoryRecommendationLabel
-
okButton
JButton okButton
-
toolName
String toolName
The name of the tool, e.g., PeptideShaker. -
versionLabel
JLabel versionLabel
-
versionPanel
JPanel versionPanel
-
versionRecommendationLabel1
JLabel versionRecommendationLabel1
-
versionRecommendationLabel2
JLabel versionRecommendationLabel2
-
welcomeDialog
JDialog welcomeDialog
A reference to the Welcome Dialog.
-
-
-
Class com.compomics.software.dialogs.PeptideShakerSetupDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
browseButton
JButton browseButton
-
cancelButton
JButton cancelButton
-
dialogCanceled
boolean dialogCanceled
Set to true if the dialog was canceled. -
jLabel2
JLabel jLabel2
-
lastSelectedFolder
String lastSelectedFolder
The selected folder. -
okButton
JButton okButton
-
parentDialog
JDialog parentDialog
The parent dialog. Can be null. -
parentFrame
JFrame parentFrame
The parent frame. Can be null. -
peptideShakerButton
JButton peptideShakerButton
-
peptideShakerDownloadLinkLabel
JLabel peptideShakerDownloadLinkLabel
-
peptideShakerDownloadPanel
JPanel peptideShakerDownloadPanel
-
peptideShakerInfoLabel
JLabel peptideShakerInfoLabel
-
peptideShakerInstallationPanel
JPanel peptideShakerInstallationPanel
-
peptideShakerJarFileHelpLabel
JLabel peptideShakerJarFileHelpLabel
-
peptideShakernstallationJTextField
JTextField peptideShakernstallationJTextField
-
progressDialog
ProgressDialogX progressDialog
The progress dialog. -
utilitiesUserParameters
UtilitiesUserParameters utilitiesUserParameters
The utilities preferences.
-
-
-
Class com.compomics.software.dialogs.ProteoWizardSetupDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
browseButton
JButton browseButton
-
cancelButton
JButton cancelButton
-
dialogCanceled
boolean dialogCanceled
Set to true if the dialog was canceled. -
downloadLinkLabel
JLabel downloadLinkLabel
-
downloadPanel
JPanel downloadPanel
-
folderHelpLabel
JLabel folderHelpLabel
-
iconButton
JButton iconButton
-
infoLabel
JLabel infoLabel
-
installationJTextField
JTextField installationJTextField
-
installationPanel
JPanel installationPanel
-
jLabel2
JLabel jLabel2
-
lastSelectedFolder
String lastSelectedFolder
The selected folder. -
okButton
JButton okButton
-
utilitiesUserParameters
UtilitiesUserParameters utilitiesUserParameters
The utilities preferences.
-
-
-
Class com.compomics.software.dialogs.ReporterSetupDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
browseButton
JButton browseButton
-
cancelButton
JButton cancelButton
-
dialogCanceled
boolean dialogCanceled
Set to true if the dialog was canceled. -
jLabel2
JLabel jLabel2
-
lastSelectedFolder
String lastSelectedFolder
The selected folder. -
okButton
JButton okButton
-
reporterButton
JButton reporterButton
-
reporterDownloadLinkLabel
JLabel reporterDownloadLinkLabel
-
reporterDownloadPanel
JPanel reporterDownloadPanel
-
reporterInfoLabel
JLabel reporterInfoLabel
-
reporterInstallationJTextField
JTextField reporterInstallationJTextField
-
reporterInstallationPanel
JPanel reporterInstallationPanel
-
reporterJarFileHelpLabel
JLabel reporterJarFileHelpLabel
-
utilitiesUserParameters
UtilitiesUserParameters utilitiesUserParameters
The utilities preferences.
-
-
-
Class com.compomics.software.dialogs.SearchGuiSetupDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
browseButton
JButton browseButton
-
cancelButton
JButton cancelButton
-
dialogCanceled
boolean dialogCanceled
Set to true if the dialog was canceled. -
jLabel2
JLabel jLabel2
-
lastSelectedFolder
String lastSelectedFolder
The selected folder. -
okButton
JButton okButton
-
parentDialog
JDialog parentDialog
The parent dialog. Can be null. -
parentFrame
JFrame parentFrame
The parent frame. Can be null. -
progressDialog
ProgressDialogX progressDialog
The progress dialog. -
searchGuiButton
JButton searchGuiButton
-
searchGuiDownloadLinkLabel
JLabel searchGuiDownloadLinkLabel
-
searchGuiDownloadPanel
JPanel searchGuiDownloadPanel
-
searchGuiInfoLabel
JLabel searchGuiInfoLabel
-
searchGuiInstallationJTextField
JTextField searchGuiInstallationJTextField
-
searchGuiInstallationPanel
JPanel searchGuiInstallationPanel
-
searchGuiJarFileHelpLabel
JLabel searchGuiJarFileHelpLabel
-
utilitiesUserParameters
UtilitiesUserParameters utilitiesUserParameters
The utilities preferences.
-
-
-
-
Package com.compomics.software.settings.gui
-
Class com.compomics.software.settings.gui.PathParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the process was canceled by the user. -
editPathMenuItem
JMenuItem editPathMenuItem
-
helpLabel
JLabel helpLabel
-
informationPanel
JPanel informationPanel
-
informationScrollPane
JScrollPane informationScrollPane
-
informationTxt
JTextArea informationTxt
-
keyList
ArrayList<PathKey> keyList
List of paths. -
keyToPathMap
HashMap<PathKey,String> keyToPathMap
Map of the paths to set. -
nameToKey
HashMap<String,PathKey> nameToKey
Name to key map. -
okButton
JButton okButton
-
originalKeyToPathMap
HashMap<PathKey,String> originalKeyToPathMap
Original map of the paths to set. -
pathSettingsJPanel
JPanel pathSettingsJPanel
-
pathSettingsPopupMenu
JPopupMenu pathSettingsPopupMenu
-
pathsToolTips
ArrayList<String> pathsToolTips
Tooltips for the paths. -
pathTable
JTable pathTable
-
pathTableScrollPane
JScrollPane pathTableScrollPane
-
pathTableToolTips
ArrayList<String> pathTableToolTips
The path table column header tooltips. -
setDefaultPath
JMenuItem setDefaultPath
-
tablePanel
JPanel tablePanel
-
toolName
String toolName
The tool name.
-
-
-
-
Package com.compomics.util
-
Class com.compomics.util.AlternateRowColoursJTable extends JTable implements Serializable
-
Serialized Fields
-
iEvenRowColor
Color iEvenRowColor
The background colour for the even rows. A value of 'null' means use the default background colour for JTable. -
iUnevenRowColor
Color iUnevenRowColor
The background colour for the uneven rows. A value of 'null' (default here) means use the default background colour for JTable. -
logger
org.apache.log4j.Logger logger
-
-
-
-
Package com.compomics.util.db
-
Class com.compomics.util.db.DBResultSet extends AbstractTableModel implements Serializable
-
Class com.compomics.util.db.GeneratorException extends Exception implements Serializable
-
Serialized Fields
-
iNested
Exception iNested
The nested exception. -
logger
org.apache.log4j.Logger logger
-
-
-
-
Package com.compomics.util.db.object.objects
-
Class com.compomics.util.db.object.objects.BlobObject extends ExperimentObject implements Serializable
-
Serialized Fields
-
blob
byte[] blob
Byte representation of the blob. -
getBlob
Object getBlob
Object representation of the blob.
-
-
-
-
Package com.compomics.util.examples
-
Class com.compomics.util.examples.HelpWindow extends JFrame implements Serializable
-
Serialized Fields
-
closeJButton
JButton closeJButton
-
textEditorScrollPane
JScrollPane textEditorScrollPane
-
textJEditorPane
JEditorPane textJEditorPane
-
-
-
Class com.compomics.util.examples.MirroredSpectraTestDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
-
-
Class com.compomics.util.examples.UtilitiesDemo extends JFrame implements Serializable
-
Serialized Fields
-
aIonsJCheckBox
JCheckBox aIonsJCheckBox
-
allAnnotations
HashMap<Integer,Vector<SpectrumAnnotation>> allAnnotations
A hashmap of all spectrum panel annotations. -
allPeaksJCheckBox
JCheckBox allPeaksJCheckBox
-
backgroundPanel
JPanel backgroundPanel
-
bIonsJCheckBox
JCheckBox bIonsJCheckBox
-
browseJButton
JButton browseJButton
-
chargeOneJCheckBox
JCheckBox chargeOneJCheckBox
-
chargeOverTwoJCheckBox
JCheckBox chargeOverTwoJCheckBox
-
chargePeptideAJSpinner
JSpinner chargePeptideAJSpinner
-
chargePeptideBJSpinner
JSpinner chargePeptideBJSpinner
-
chargeTwoJCheckBox
JCheckBox chargeTwoJCheckBox
-
chromatogramAJPanel
JPanel chromatogramAJPanel
-
chromatogramJPanel
JPanel chromatogramJPanel
-
chromatogramPanelHelpJLabel
JLabel chromatogramPanelHelpJLabel
-
chromatogramPanelInfoJLabel
JLabel chromatogramPanelInfoJLabel
-
chromatogramPanelMaxPadding
int chromatogramPanelMaxPadding
The maximum padding allowed in the chromatogram panels. Increase if font size on the y-axis becomes too small. -
cIonsJCheckBox
JCheckBox cIonsJCheckBox
-
cleanProteinSequence
String cleanProteinSequence
Used for the in silico digestion example. -
currentPeffBufferedReader
BufferedReader currentPeffBufferedReader
The current PEFF (or FASTA) buffered reader. -
currentSequence
String currentSequence
The current PEFF (or FASTA) sequence. -
currentSequenceFile
File currentSequenceFile
The current PEFF (or FASTA) sequence file. -
currentSequenceLine
String currentSequenceLine
The current PEFF (or FASTA) sequence line. -
enzymesJComboBox
JComboBox enzymesJComboBox
-
exportJButton
JButton exportJButton
-
H2OIonsJCheckBox
JCheckBox H2OIonsJCheckBox
-
informationJEditorPane
JEditorPane informationJEditorPane
-
informationJPanel
JPanel informationJPanel
-
informationJScrollPane
JScrollPane informationJScrollPane
-
inhibitorsJTextField
JTextField inhibitorsJTextField
-
inSilicoDigestionHelpJLabel
JLabel inSilicoDigestionHelpJLabel
-
ionSelectionJPanel
JPanel ionSelectionJPanel
-
isotopicDistributionAJPanel
JPanel isotopicDistributionAJPanel
-
isotopicDistributionCalculatorHelpJLabel
JLabel isotopicDistributionCalculatorHelpJLabel
-
isotopicDistributionCalculatorInfoJLabel
JLabel isotopicDistributionCalculatorInfoJLabel
-
isotopicDistributionJPanel
JPanel isotopicDistributionJPanel
-
jLabel1
JLabel jLabel1
-
jLabel10
JLabel jLabel10
-
jLabel11
JLabel jLabel11
-
jLabel12
JLabel jLabel12
-
jLabel13
JLabel jLabel13
-
jLabel14
JLabel jLabel14
-
jLabel15
JLabel jLabel15
-
jLabel16
JLabel jLabel16
-
jLabel17
JLabel jLabel17
-
jLabel18
JLabel jLabel18
-
jLabel19
JLabel jLabel19
-
jLabel2
JLabel jLabel2
-
jLabel20
JLabel jLabel20
-
jLabel21
JLabel jLabel21
-
jLabel24
JLabel jLabel24
-
jLabel3
JLabel jLabel3
-
jLabel4
JLabel jLabel4
-
jLabel5
JLabel jLabel5
-
jLabel6
JLabel jLabel6
-
jLabel7
JLabel jLabel7
-
jLabel8
JLabel jLabel8
-
jLabel9
JLabel jLabel9
-
jPanel1
JPanel jPanel1
-
jPanel10
JPanel jPanel10
-
jPanel11
JPanel jPanel11
-
jPanel12
JPanel jPanel12
-
jPanel2
JPanel jPanel2
-
jPanel3
JPanel jPanel3
-
jPanel4
JPanel jPanel4
-
jPanel5
JPanel jPanel5
-
jPanel6
JPanel jPanel6
-
jPanel7
JPanel jPanel7
-
jPanel8
JPanel jPanel8
-
jRadioButton1
JRadioButton jRadioButton1
-
jSeparator1
JSeparator jSeparator1
-
jSeparator2
JSeparator jSeparator2
-
jSeparator3
JSeparator jSeparator3
-
jSeparator4
JSeparator jSeparator4
-
jSeparator5
JSeparator jSeparator5
-
jSeparator6
JSeparator jSeparator6
-
jSeparator9
JSeparator jSeparator9
-
jTabbedPane
JTabbedPane jTabbedPane
-
keyValuePairs
TreeMap<String,String> keyValuePairs
The map of the PEFF key value pairs. -
linkedSpectraJCheckBox
JCheckBox linkedSpectraJCheckBox
-
linkedSpectrumPanels
HashMap<Integer,SpectrumPanel> linkedSpectrumPanels
A hashmap of both the linked spectra. -
lowerMassJSpinner
JSpinner lowerMassJSpinner
-
mascotEnzymeReader
MascotEnzymeReader mascotEnzymeReader
Used to read the enzyme details from file. -
missedCleavagesJSpinner
JSpinner missedCleavagesJSpinner
-
nextJButton
JButton nextJButton
-
NH3IonsJCheckBox
JCheckBox NH3IonsJCheckBox
-
otherIonsJCheckBox
JCheckBox otherIonsJCheckBox
-
peffAnnotationPanel
JPanel peffAnnotationPanel
-
peffAnnotationsColorMap
HashMap<Integer,Color> peffAnnotationsColorMap
The PEFF annotations color map. -
peffAnnotationsJTable
JTable peffAnnotationsJTable
-
peffAnnotationsScrollPane
JScrollPane peffAnnotationsScrollPane
-
peffAnnotationsTooltipMap
HashMap<Integer,String> peffAnnotationsTooltipMap
The PEFF annotations tooltip map. -
peffFormat
boolean peffFormat
If true, the format shown is PEFF, if false FASTA is assumed. -
peffHeaderJTable
JTable peffHeaderJTable
-
peffHeaderScrollPane
JScrollPane peffHeaderScrollPane
-
peptideAColorJPanel
JPanel peptideAColorJPanel
-
peptideACompositionJTextField
JTextField peptideACompositionJTextField
-
peptideAJScrollPane
JScrollPane peptideAJScrollPane
-
peptideAJTable
JTable peptideAJTable
-
peptideAMzJTextField
JTextField peptideAMzJTextField
-
peptideBColorJPanel
JPanel peptideBColorJPanel
-
peptideBCompositionJTextField
JTextField peptideBCompositionJTextField
-
peptideBJScrollPane
JScrollPane peptideBJScrollPane
-
peptideBJTable
JTable peptideBJTable
-
peptideBMzJTextField
JTextField peptideBMzJTextField
-
peptideSequenceAJTextField
JTextField peptideSequenceAJTextField
-
peptideSequenceBJTextField
JTextField peptideSequenceBJTextField
-
peptidesJPanel
JPanel peptidesJPanel
-
peptidesJTable
JTable peptidesJTable
-
peptidesScrollPane
JScrollPane peptidesScrollPane
-
positionJTextField
JTextField positionJTextField
-
profileSpectrumJCheckBox
JCheckBox profileSpectrumJCheckBox
-
proteinCoverageJScrollPane
JScrollPane proteinCoverageJScrollPane
-
proteinDetailsScrollPane
JScrollPane proteinDetailsScrollPane
-
proteinDigestionJLabel
JLabel proteinDigestionJLabel
-
proteinDigestionJPanel
JPanel proteinDigestionJPanel
-
proteinHeaderJTable
JTable proteinHeaderJTable
-
proteinSequenceCoverageJEditorPane
JEditorPane proteinSequenceCoverageJEditorPane
-
selectedAnnotationTypes
HashMap<String,Color> selectedAnnotationTypes
The tag colors for PEFF formatting. -
sequenceAnnotationColumnHeaderTooltips
ArrayList<String> sequenceAnnotationColumnHeaderTooltips
Sequence annotation column header tooltips. -
sequenceCoverageJPanel
JPanel sequenceCoverageJPanel
-
sequenceFileJTextField
JTextField sequenceFileJTextField
-
sequenceJTabbedPane
JTabbedPane sequenceJTabbedPane
-
silacLabelPeptideAJComboBox
JComboBox silacLabelPeptideAJComboBox
-
silacLabelPeptideBJComboBox
JComboBox silacLabelPeptideBJComboBox
-
siteJTextField
JTextField siteJTextField
-
sparklineColor
Color sparklineColor
The color used for the sparkline bar chart plots. -
spectraJPanel
JPanel spectraJPanel
-
spectrumAJPanel
JPanel spectrumAJPanel
-
spectrumAPanel
SpectrumPanel spectrumAPanel
The first spectrum panel. -
spectrumBJPanel
JPanel spectrumBJPanel
-
spectrumBPanel
SpectrumPanel spectrumBPanel
The second spectrum panel -
spectrumJPanel
JPanel spectrumJPanel
-
spectrumPanelHelpJLabel
JLabel spectrumPanelHelpJLabel
-
spectrumPanelInfoJLabel
JLabel spectrumPanelInfoJLabel
-
spectrumPanelMaxPadding
int spectrumPanelMaxPadding
The maximum padding allowed in the spectrum panels. Increase if font size on the y-axis becomes too small. -
upperMassJSpinner
JSpinner upperMassJSpinner
-
xIonsJCheckBox
JCheckBox xIonsJCheckBox
-
yIonsJCheckBox
JCheckBox yIonsJCheckBox
-
zIonsJCheckBox
JCheckBox zIonsJCheckBox
-
-
-
-
Package com.compomics.util.experiment
-
Class com.compomics.util.experiment.ProjectParameters extends ExperimentObject implements Serializable
-
-
Package com.compomics.util.experiment.biology.aminoacids
-
Class com.compomics.util.experiment.biology.aminoacids.AminoAcid extends ExperimentObject implements Serializable
-
Serialized Fields
-
aminoAcidCombinations
char[] aminoAcidCombinations
The amino acid combinations. -
monoisotopicAtomChain
AtomChain monoisotopicAtomChain
The monoisotopic atom chain. -
name
String name
Name of the amino acid. -
singleLetterCode
String singleLetterCode
Single letter code of the amino acid. -
standardGeneticCode
String[] standardGeneticCode
The standard genetic code. -
subAminoAcidsWithCombination
char[] subAminoAcidsWithCombination
The sub amino acids with combination. -
subAminoAcidsWithoutCombination
char[] subAminoAcidsWithoutCombination
The sub amino acids without combination. -
threeLetterCode
String threeLetterCode
Three letter code of the amino acid.
-
-
-
-
Package com.compomics.util.experiment.biology.aminoacids.impl
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Alanine extends AminoAcid implements Serializable
- serialVersionUID:
- 2553535668713619525L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Arginine extends AminoAcid implements Serializable
- serialVersionUID:
- -5308475190007072857L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Asparagine extends AminoAcid implements Serializable
- serialVersionUID:
- 5951975489690885808L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.AsparticAcid extends AminoAcid implements Serializable
- serialVersionUID:
- -8410332876209882538L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.B extends AminoAcid implements Serializable
- serialVersionUID:
- -584166511231722270L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Cysteine extends AminoAcid implements Serializable
- serialVersionUID:
- 9171494537928740228L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.GlutamicAcid extends AminoAcid implements Serializable
- serialVersionUID:
- 6850534412637609745L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Glutamine extends AminoAcid implements Serializable
- serialVersionUID:
- -1552736259723394861L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Glycine extends AminoAcid implements Serializable
- serialVersionUID:
- 2128316713069027803L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Histidine extends AminoAcid implements Serializable
- serialVersionUID:
- -669587024023052011L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Isoleucine extends AminoAcid implements Serializable
- serialVersionUID:
- -514676021245212886L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.J extends AminoAcid implements Serializable
- serialVersionUID:
- 1963175809911841522L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Leucine extends AminoAcid implements Serializable
- serialVersionUID:
- -656824121858821632L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Lysine extends AminoAcid implements Serializable
- serialVersionUID:
- 3427548228986235710L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Methionine extends AminoAcid implements Serializable
- serialVersionUID:
- 1841628592146093511L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Phenylalanine extends AminoAcid implements Serializable
- serialVersionUID:
- -939609662176974248L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Proline extends AminoAcid implements Serializable
- serialVersionUID:
- 3754407258673679661L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Pyrrolysine extends AminoAcid implements Serializable
- serialVersionUID:
- 8680204019988094523L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Selenocysteine extends AminoAcid implements Serializable
- serialVersionUID:
- -2123392615229813870L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Serine extends AminoAcid implements Serializable
- serialVersionUID:
- -2201410868329421240L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Threonine extends AminoAcid implements Serializable
- serialVersionUID:
- 172831874616867727L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Tryptophan extends AminoAcid implements Serializable
- serialVersionUID:
- -6773437038176247799L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Tyrosine extends AminoAcid implements Serializable
- serialVersionUID:
- 7542892886050340088L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Valine extends AminoAcid implements Serializable
- serialVersionUID:
- -5155418025636472676L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.X extends AminoAcid implements Serializable
- serialVersionUID:
- -2618109862080991929L
-
Class com.compomics.util.experiment.biology.aminoacids.impl.Z extends AminoAcid implements Serializable
- serialVersionUID:
- -7714841171012071337L
-
-
Package com.compomics.util.experiment.biology.aminoacids.sequence
-
Class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidPattern extends ExperimentObject implements Serializable
- serialVersionUID:
- -2823716418631089876L
-
Serialized Fields
-
aaAtTarget
HashSet<Character> aaAtTarget
Cache for the amino acids at target. -
length
int length
The length of the pattern, -1 if not set. -
residueTargeted
HashMap<Integer,ArrayList<Character>> residueTargeted
The list of targeted amino acids at a given index represented by their single letter code. For trypsin: 0 > {R, K} 1 > {all but P}
-
-
Class com.compomics.util.experiment.biology.aminoacids.sequence.AminoAcidSequence extends ExperimentObject implements Serializable
-
Serialized Fields
-
sequence
String sequence
The sequence as string. -
sequenceStringBuilder
StringBuilder sequenceStringBuilder
The sequence as string builder. -
variableModifications
ModificationMatch[] variableModifications
The variable modifications carried by the amino acid sequence at target amino acids. 1 is the first amino acid.
-
-
-
-
Package com.compomics.util.experiment.biology.atoms
-
Class com.compomics.util.experiment.biology.atoms.Atom extends ExperimentObject implements Serializable
- serialVersionUID:
- 1059024301538472131L
-
Serialized Fields
-
isotopeMap
HashMap<Integer,Double> isotopeMap
Map of the isotope masses relative to the monoisotopic peak (+1 for carbon 13). -
letter
String letter
The symbol for the atom. -
monoisotopicMass
double monoisotopicMass
The monoisotopic mass. Access is faster then querying the isotope map. -
name
String name
The name of the atom. -
representativeComposition
HashMap<Integer,Double> representativeComposition
Map of the isotope representative composition of the stable isotopes.
-
-
Class com.compomics.util.experiment.biology.atoms.AtomChain extends ExperimentObject implements Serializable
- serialVersionUID:
- 2222259572093523514L
-
Class com.compomics.util.experiment.biology.atoms.AtomImpl extends ExperimentObject implements Serializable
- serialVersionUID:
- 3269643086590455656L
-
Class com.compomics.util.experiment.biology.atoms.ElementaryElement extends ExperimentObject implements Serializable
-
Serialized Fields
-
name
String name
The name of the element. -
theoreticMass
double theoreticMass
-
-
-
-
Package com.compomics.util.experiment.biology.atoms.impl
-
Class com.compomics.util.experiment.biology.atoms.impl.Calcium extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Carbon extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Copper extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Fluorine extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Helium extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Hydrogen extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Iodine extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Iron extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Lithium extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Magnesium extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Nitrogen extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Oxygen extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Phosphorus extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Potassium extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Selenium extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Sodium extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Sulfur extends Atom implements Serializable
-
Class com.compomics.util.experiment.biology.atoms.impl.Zinc extends Atom implements Serializable
-
-
Package com.compomics.util.experiment.biology.enzymes
-
Class com.compomics.util.experiment.biology.enzymes.Enzyme extends ExperimentObject implements Serializable
-
Serialized Fields
-
-
-
Package com.compomics.util.experiment.biology.genes
-
Class com.compomics.util.experiment.biology.genes.GeneMaps extends ExperimentObject implements Serializable
-
Serialized Fields
-
ensemblVersionsMap
HashMap<String,String> ensemblVersionsMap
The Ensembl versions for each species. -
geneNameToChromosomeMap
HashMap<String,String> geneNameToChromosomeMap
Gene name to chromosome name map. -
geneNameToEnsemblIdMap
HashMap<String,String> geneNameToEnsemblIdMap
Gene name to EnsemblId map. -
goAccessionToProteinMap
HashMap<String,HashSet<String>> goAccessionToProteinMap
GO term to protein accession map. -
goNamesMap
HashMap<String,String> goNamesMap
GO term accession to name map. -
proteinToGoMap
HashMap<String,HashSet<String>> proteinToGoMap
Protein accession to GO terms map.
-
-
-
-
Package com.compomics.util.experiment.biology.ions
-
Class com.compomics.util.experiment.biology.ions.Ion extends ExperimentObject implements Serializable
- serialVersionUID:
- -1505719074403886934L
-
Serialized Fields
-
atomChain
AtomChain atomChain
The atomic composition of the ion. -
neutralLossesAsString
String neutralLossesAsString
Cache for the neutral losses as string. -
theoreticMass
Double theoreticMass
Deprecated.use the double value instead.The theoretic mass. -
theoreticMass1
double theoreticMass1
The theoretic mass. -
type
Ion.IonType type
Type of ion.
-
-
Class com.compomics.util.experiment.biology.ions.NeutralLoss extends ExperimentObject implements Serializable
- serialVersionUID:
- 5540846193082177391L
-
Serialized Fields
-
aminoAcids
char[] aminoAcids
Amino acids that are likely to induce this loss. Null if not a loss originating from amino acids. -
composition
AtomChain composition
The composition of the ion. -
fixed
boolean fixed
Boolean indicating whether the neutral loss will always be accounted for. -
name
String name
The name of the neutral loss. -
psiCvTerm
CvTerm psiCvTerm
The PSI MS CV term of the neutral loss, null if not set.
-
-
-
Package com.compomics.util.experiment.biology.ions.impl
-
Class com.compomics.util.experiment.biology.ions.impl.ElementaryIon extends Ion implements Serializable
- serialVersionUID:
- -1578136397635015592L
-
Serialized Fields
-
name
String name
The name of the ion. -
subType
int subType
The subtype identifier.
-
-
Class com.compomics.util.experiment.biology.ions.impl.Glycan extends Ion implements Serializable
- serialVersionUID:
- -2278483206647518565L
-
Class com.compomics.util.experiment.biology.ions.impl.ImmoniumIon extends Ion implements Serializable
- serialVersionUID:
- -3403620196563864756L
-
Serialized Fields
-
aa
char aa
The amino acid that can generate this ion as single letter code. -
subType
int subType
Subtype of immonium ion.
-
-
Class com.compomics.util.experiment.biology.ions.impl.PeptideFragmentIon extends Ion implements Serializable
- serialVersionUID:
- 8283809283803740651L
-
Serialized Fields
-
cvTerm
CvTerm cvTerm
The CV term of the reporter ion, null if not set. -
neutralLosses
NeutralLoss[] neutralLosses
The neutral losses found on the ion. -
number
int number
Position of the ion in the peptide for peptide ions. -
psiCvTerm
CvTerm psiCvTerm
The PSI MS CV term of the reporter ion, null if not set. -
subType
int subType
The type of fragment.
-
-
Class com.compomics.util.experiment.biology.ions.impl.PrecursorIon extends Ion implements Serializable
- serialVersionUID:
- -2630586959372309153L
-
Serialized Fields
-
cvTerm
CvTerm cvTerm
The CV term of the reporter ion, null if not set. -
neutralLosses
NeutralLoss[] neutralLosses
The neutral losses found on the ion. -
psiCvTerm
CvTerm psiCvTerm
The PSI MS CV term of the reporter ion, null if not set.
-
-
Class com.compomics.util.experiment.biology.ions.impl.RelatedIon extends Ion implements Serializable
- serialVersionUID:
- -4605345486425465764L
-
Serialized Fields
-
aminoAcidTarget
AminoAcid aminoAcidTarget
The amino acid target. -
subType
int subType
The sub type.
-
-
Class com.compomics.util.experiment.biology.ions.impl.ReporterIon extends Ion implements Serializable
- serialVersionUID:
- 1109011048958734120L
-
Class com.compomics.util.experiment.biology.ions.impl.TagFragmentIon extends Ion implements Serializable
-
Serialized Fields
-
cvTerm
CvTerm cvTerm
The CV term of the reporter ion, null if not set. -
massGap
double massGap
Mass gap before this ion. -
neutralLosses
NeutralLoss[] neutralLosses
The neutral losses found on the ion. -
number
int number
Position of the ion in the tag of amino acids considering gaps as an amino acid. 0 based. -
psiCvTerm
CvTerm psiCvTerm
The PSI MS CV term of the reporter ion, null if not set. -
subNumber
int subNumber
Position of the ion in the current sequence of amino acids. 0 based. -
subType
int subType
The type of fragment.
-
-
-
-
Package com.compomics.util.experiment.biology.modifications
-
Class com.compomics.util.experiment.biology.modifications.Modification extends ExperimentObject implements Serializable
- serialVersionUID:
- -545472596243822505L
-
Serialized Fields
-
ambiguityKey
String ambiguityKey
The ambiguity key for ambiguous modifications. -
atomChainAdded
AtomChain atomChainAdded
The composition of the molecule added. Null if not set. -
atomChainRemoved
AtomChain atomChainRemoved
The composition of the molecule removed. Null if not set. -
category
ModificationCategory category
The category for the modification. Null if not set. -
mass
Double mass
Mass difference produced by this modification. Null if not set. -
modificationType
ModificationType modificationType
The modification type. -
name
String name
Name of the modification. -
neutralLosses
ArrayList<NeutralLoss> neutralLosses
List of known neutral losses for this modification. -
pattern
AminoAcidPattern pattern
The amino acid pattern targeted by this modification (can be set using the AminoAcidPatternDialog). Null if not set. -
psiModCvTerm
CvTerm psiModCvTerm
The PSI-MOD CV term associated with this modification. Null if not set. -
reporterIons
ArrayList<ReporterIon> reporterIons
List of known reporter ions for this modification. -
shortName
String shortName
Short name of the modification. -
unimodCvTerm
CvTerm unimodCvTerm
The Unimod CV term associated with this modification. Null if not set.
-
-
-
Package com.compomics.util.experiment.biology.proteins
-
Class com.compomics.util.experiment.biology.proteins.Peptide extends ExperimentObject implements Serializable
-
Serialized Fields
-
key
long key
The peptide key. -
keySet
boolean keySet
Boolean indicating whether the matching key is set. -
mass
double mass
The peptide mass. -
matchingKey
long matchingKey
The peptide matching key. -
proteinMapping
TreeMap<String,int[]> proteinMapping
The mapping of this peptide on proteins as a map, accession to position. Position on protein sequences is 0 based. -
sequence
String sequence
The peptide sequence. -
variableModifications
ModificationMatch[] variableModifications
The variable modifications carried by the peptide. -
variantMatches
HashMap<String,HashMap<Integer,PeptideVariantMatches>> variantMatches
The variants observed when mapping this peptide to the database. Peptide variant matches are indexed by protein and by peptide start.
-
-
-
Class com.compomics.util.experiment.biology.proteins.Protein extends ExperimentObject implements Serializable
- serialVersionUID:
- 1987224639519365761L
-
-
Package com.compomics.util.experiment.biology.variants
-
Class com.compomics.util.experiment.biology.variants.AaSubstitutionMatrix extends ExperimentObject implements Serializable
-
Serialized Fields
-
description
String description
The description of the substitution matrix. -
name
String name
The name of this substitution matrix. -
reverseMap
HashMap<Character,HashSet<Character>> reverseMap
Reverse map of the possible amino acid substitution: substituted aa > original aa. -
substitutions
HashMap<Character,HashSet<Character>> substitutions
Map of the possible amino acid substitutions: original aa > substituted aa.
-
-
-
-
Package com.compomics.util.experiment.identification
-
Class com.compomics.util.experiment.identification.Advocate extends ExperimentObject implements Serializable
-
Serialized Fields
-
color
Color color
The color of the advocate. Defaults to light gray. -
index
int index
The index of the advocate. -
name
String name
The name of the advocate. -
type
Advocate.AdvocateType type
The type of advocate
-
-
-
Class com.compomics.util.experiment.identification.Identification extends ExperimentObject implements Serializable
-
Serialized Fields
-
dbDirectory
String dbDirectory
The directory where the database stored. -
identificationKeys
IdentificationKeys identificationKeys
The keys of the objects in the identification. -
objectsDB
ObjectsDB objectsDB
The database which will contain the objects.
-
-
-
Class com.compomics.util.experiment.identification.IdentificationKeys extends ExperimentObject implements Serializable
-
Serialized Fields
-
fractions
ArrayList<String> fractions
The names of the spectrum files (without extensions) that were used for the PSMs. -
peptideIdentification
HashSet<Long> peptideIdentification
List of the keys of all imported peptides. -
proteinIdentification
HashSet<Long> proteinIdentification
List of the keys of all imported proteins. -
proteinMap
HashMap<String,HashSet<Long>> proteinMap
A map linking protein accessions to all their protein matches keys. -
spectrumIdentification
HashMap<String,HashSet<Long>> spectrumIdentification
Map mapping spectra per file.
-
-
-
Class com.compomics.util.experiment.identification.IdentificationMatch extends ExperimentObject implements Serializable
- serialVersionUID:
- -9132138792119651421L
-
Class com.compomics.util.experiment.identification.IdentificationMethod extends ExperimentObject implements Serializable
- serialVersionUID:
- 4601179275244591663L
-
Serialized Fields
-
index
int index
index of the method
-
-
Class com.compomics.util.experiment.identification.SpectrumIdentificationAssumption extends ExperimentObject implements Serializable
-
Serialized Fields
-
advocate
int advocate
The advocate supporting this assumption. -
aminoAcidScores
ArrayList<double[]> aminoAcidScores
The individual amino acid scores. Null if not set. -
identificationCharge
int identificationCharge
The charge used for identification. -
identificationFile
String identificationFile
The identification file. -
rank
int rank
The rank of the peptide assumption for the concerned spectrum. -
rawScore
double rawScore
The raw score as provided by the identification algorithm. -
score
double score
The (advocate specific) score used to rank this assumption.
-
-
-
-
Package com.compomics.util.experiment.identification.amino_acid_tags
-
Class com.compomics.util.experiment.identification.amino_acid_tags.MassGap extends ExperimentObject implements Serializable
-
Serialized Fields
-
sequence
String sequence
The value as sequence. -
value
double value
The value of the mass gap.
-
-
-
Class com.compomics.util.experiment.identification.amino_acid_tags.Tag extends ExperimentObject implements Serializable
- serialVersionUID:
- 1625541843008045218L
-
Serialized Fields
-
content
ArrayList<TagComponent> content
The content of the tag.
-
-
-
Package com.compomics.util.experiment.identification.features
-
Class com.compomics.util.experiment.identification.features.IdentificationFeaturesCache extends ExperimentObject implements Serializable
-
Serialized Fields
-
currentPeptideKey
long currentPeptideKey
The current peptide key. -
currentProteinKey
long currentProteinKey
The current protein key. -
filtered
boolean filtered
Boolean indicating whether a filtering was already used. If yes, proteins might need to be unhidden. -
largeObjectsCache
HashMap<IdentificationFeaturesCache.ObjectType,HashMap<Long,Object>> largeObjectsCache
Cache for the large objects. -
largeObjectsInCache
int largeObjectsInCache
The number of large objects in cache. -
maxSpectrumCount
int maxSpectrumCount
The maximum number of PSMs across all peptides of the last selected protein. -
nValidatedPsms
int nValidatedPsms
The number of validated PSMs in the currently selected peptide. -
peptideList
long[] peptideList
The peptide list. -
proteinList
long[] proteinList
Back-up list for when proteins are hidden. -
proteinListAfterHiding
long[] proteinListAfterHiding
The protein list. -
psmList
long[] psmList
The PSM list. -
readOnly
boolean readOnly
Indicates whether the cache is read only. -
smallObjectsCache
HashMap<IdentificationFeaturesCache.ObjectType,HashMap<Long,Object>> smallObjectsCache
Cache for the small objects. -
smallObjectsInCache
int smallObjectsInCache
The number of small objects in cache. -
validatedProteinList
long[] validatedProteinList
List of the validated proteins.
-
-
-
-
Package com.compomics.util.experiment.identification.filtering
-
Class com.compomics.util.experiment.identification.filtering.AssumptionFilter extends MatchFilter implements Serializable
-
Class com.compomics.util.experiment.identification.filtering.MatchFilter extends ExperimentObject implements Serializable
-
Serialized Fields
-
active
boolean active
Boolean indicating whether the filter is active. -
comparatorsMap
HashMap<String,FilterItemComparator> comparatorsMap
Map of the comparators to use. -
condition
String condition
Description of the condition to meet to pass the filter. -
description
String description
Description of the filter. -
exceptions
HashSet<Long> exceptions
The exceptions to the rule. -
filterType
MatchFilter.FilterType filterType
The type of filter. -
manualValidation
HashSet<Long> manualValidation
The key of the manually validated matches. -
name
String name
Name of the filter. -
reportFailed
String reportFailed
Report when the filter is not passed. -
reportPassed
String reportPassed
Report when the filter is passed. -
valuesMap
HashMap<String,Object> valuesMap
Map of the values to filter on.
-
-
-
Class com.compomics.util.experiment.identification.filtering.PeptideAssumptionFilter extends ExperimentObject implements Serializable
-
Serialized Fields
-
isPpm
boolean isPpm
Boolean indicating the unit of the allowed m/z deviation (true: ppm, false: Da). -
maxIsotopes
Integer maxIsotopes
The maximum number of isotopes allowed. Null means no upper limit. -
maxMassDeviation
double maxMassDeviation
The maximal m/z deviation allowed. -
maxMissedCleavages
Integer maxMissedCleavages
The maximum number of missed cleavages allowed. Null means no upper limit. -
maxPepLength
int maxPepLength
The maximal peptide length allowed. -
minIsotopes
Integer minIsotopes
The minimum number of isotopes allowed. Null means no lower limit. -
minMissedCleavages
Integer minMissedCleavages
The minimum number of missed cleavages allowed. Null means no lower limit. -
minPepLength
int minPepLength
The minimal peptide length allowed. -
unknownModification
boolean unknownModification
Boolean indicating whether peptides presenting unknown modifications should be ignored.
-
-
-
Class com.compomics.util.experiment.identification.filtering.PeptideFilter extends MatchFilter implements Serializable
- serialVersionUID:
- 959658989341486818L
-
Class com.compomics.util.experiment.identification.filtering.ProteinFilter extends MatchFilter implements Serializable
- serialVersionUID:
- 5753850468907866679L
-
Class com.compomics.util.experiment.identification.filtering.PsmFilter extends MatchFilter implements Serializable
- serialVersionUID:
- 2930349531911042645L
-
Serialized Fields
-
assumptionFilter
AssumptionFilter assumptionFilter
The filter used to filter the best assumption.
-
-
-
Package com.compomics.util.experiment.identification.matches
-
Class com.compomics.util.experiment.identification.matches.IonMatch extends ExperimentObject implements Serializable
-
Serialized Fields
-
charge
int charge
The inferred charge of the ion. -
ion
Ion ion
The matching ion. -
peakIntensity
double peakIntensity
The matched peak intensity. -
peakMz
double peakMz
The matched peak m/z.
-
-
-
Class com.compomics.util.experiment.identification.matches.ModificationMatch extends ExperimentObject implements Serializable
-
Serialized Fields
-
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. -
modification
String modification
The modification name. The modification can be accessed via the factory. -
modifiedSite
int modifiedSite
The location in the sequence. N-term modifications are at index 0, C-term at index sequence length + 1, and other modifications at amino acid index starting from 1. An error is thrown if attempting to stack modifications.
-
-
-
Class com.compomics.util.experiment.identification.matches.PeptideMatch extends IdentificationMatch implements Serializable
-
Serialized Fields
-
key
long key
The key of the match. -
peptide
Peptide peptide
The peptide. -
spectrumMatchesKeys
long[] spectrumMatchesKeys
The keys of the spectrum matches linking to this peptide match.
-
-
-
Class com.compomics.util.experiment.identification.matches.PeptideVariantMatches extends ExperimentObject implements Serializable
-
Serialized Fields
-
-
Class com.compomics.util.experiment.identification.matches.ProteinMatch extends IdentificationMatch implements Serializable
- serialVersionUID:
- -6061842447053092696L
-
Serialized Fields
-
accessions
String[] accessions
The matching protein(s) accessions sorted in natural order. -
decoy
boolean decoy
Boolean indicating whether the protein match is decoy. -
leadingAccession
String leadingAccession
The accession of the leading protein. -
matchKey
long matchKey
The key of the match. -
p
ProteinMatch p
-
peptideMatchesKeys
long[] peptideMatchesKeys
The keys of the peptide matches associated to this protein match.
-
-
Class com.compomics.util.experiment.identification.matches.SpectrumMatch extends IdentificationMatch implements Serializable
-
Serialized Fields
-
bestPeptideAssumption
PeptideAssumption bestPeptideAssumption
The best peptide assumption. -
bestTagAssumption
TagAssumption bestTagAssumption
The best tag assumption. -
key
long key
The key of the match. -
peptideAssumptionsMap
HashMap<Integer,TreeMap<Double,ArrayList<PeptideAssumption>>> peptideAssumptionsMap
Map of the identification algorithm peptide assumptions: advocate number > score > assumptions. -
spectrumFile
String spectrumFile
The name of the file (without extension) containing the spectrum. -
spectrumtitle
String spectrumtitle
The title of the spectrum. -
tagAssumptionsMap
HashMap<Integer,TreeMap<Double,ArrayList<TagAssumption>>> tagAssumptionsMap
Map of the identification algorithm tag assumptions: advocate number > score > assumptions.
-
-
-
-
Package com.compomics.util.experiment.identification.peptide_shaker
-
Class com.compomics.util.experiment.identification.peptide_shaker.Metrics extends ExperimentObject implements Serializable
-
Serialized Fields
-
foundCharges
int[] foundCharges
The charges found in all PSMs (only the best hit per spectrum). Charges are ordered. -
foundModifications
TreeSet<String> foundModifications
List of modifications found in the dataset. -
fractionPsmMatches
HashMap<String,ArrayList<Long>> fractionPsmMatches
The PSM matches for each fraction for each peptide. Key: 'fraction name'_'peptide key'. Values: arraylist of spectrum keys. -
maxMW
Double maxMW
The weight of the fattest protein in the dataset. -
maxNPeptides
Integer maxNPeptides
The maximal number of peptides among the proteins of the dataset. -
maxNPsms
Integer maxNPsms
The maximal number of PSMs among the proteins of the dataset. -
maxPrecursorErrorDa
double maxPrecursorErrorDa
The maximal peptide precursor error in Da in all PSMs (only the best peptide hit per spectrum). -
maxPrecursorErrorPpm
double maxPrecursorErrorPpm
The maximal peptide precursor error in ppm in all PSMs (only the best peptide hit per spectrum). -
maxProteinAccessionLength
Integer maxProteinAccessionLength
The max protein key length. -
maxProteinAveragePrecursorIntensity
Double maxProteinAveragePrecursorIntensity
The maximum protein average precursor intensity. -
maxProteinSummedPrecursorIntensity
Double maxProteinSummedPrecursorIntensity
The maximum protein summed precursor intensity. -
maxSpectrumCounting
Double maxSpectrumCounting
The maximal spectrum counting in the proteins of the dataset. -
maxTagPrecursorErrorDa
double maxTagPrecursorErrorDa
The maximal tag precursor error in Da in all PSMs (only the best tag hit per spectrum when no peptide is found). -
maxTagPrecursorErrorPpm
double maxTagPrecursorErrorPpm
The maximal tag precursor error in ppm in all PSMs (only the best tag hit per spectrum when no peptide is found). -
maxValidatedPeptidesPerFraction
Integer maxValidatedPeptidesPerFraction
The maximum number of peptides detected at the fraction level. -
maxValidatedSpectraPerFraction
Integer maxValidatedSpectraPerFraction
The maximum number of spectra at the fraction level. -
nConfidentProteins
Integer nConfidentProteins
Number of validated confident proteins. -
nValidatedProteins
int nValidatedProteins
Number of validated proteins. -
observedFractionalMassesAll
HashMap<String,ArrayList<Double>> observedFractionalMassesAll
The observed molecular masses in kDa for each fraction. -
peptideLengthDistribution
NonSymmetricalNormalDistribution peptideLengthDistribution
The distribution of peptide validated lengths. -
proteinKeys
long[] proteinKeys
The ordered list of protein keys as estimated during the import process. -
totalPeptidesPerFractions
HashMap<String,Integer> totalPeptidesPerFractions
The total number of peptides per fraction. -
totalSpectrumCounting
Double totalSpectrumCounting
The sum of all spectrum counting indexes. -
totalSpectrumCountingMass
Double totalSpectrumCountingMass
The sum of all spectrum counting masses. -
validatedTargetProteinKeys
long[] validatedTargetProteinKeys
The keys of the validated target protein matches.
-
-
-
Class com.compomics.util.experiment.identification.peptide_shaker.ModificationScoring extends ExperimentObject implements Serializable
- serialVersionUID:
- -3357368272501542941L
-
Serialized Fields
-
deltaScoresAtAA
HashMap<Integer,Double> deltaScoresAtAA
Amino acid specific delta score. 1 is the first amino acid. -
probabilisticScoresAtAA
HashMap<Integer,Double> probabilisticScoresAtAA
Amino acid specific probabilistic score. -
ptmLocationAtAA
HashMap<Integer,Integer> ptmLocationAtAA
The retained PTM site assignment. -
ptmName
String ptmName
The name of the modification of interest. 1 is the first amino acid.
-
-
Class com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores extends ExperimentObject implements Serializable
-
Serialized Fields
-
ambiguousModificationsByModName
HashMap<String,HashMap<Integer,HashSet<Integer>>> ambiguousModificationsByModName
A map of all ambiguous modifications in a sequence indexed by modification name. -
ambiguousModificationsByRepresentativeSite
HashMap<Integer,HashMap<Integer,HashSet<String>>> ambiguousModificationsByRepresentativeSite
A list of all ambiguous modifications in a sequence: representative site > secondary site > modification names. -
confidentModificationsByModName
HashMap<String,HashSet<Integer>> confidentModificationsByModName
A map of all confident modifications in a sequence indexed by modification name. -
mainModificationSites
HashMap<Integer,HashSet<String>> mainModificationSites
A list of all modification sites confidently localized on a sequence in a map: site > modification names. -
modificationMap
HashMap<String,ModificationScoring> modificationMap
A map containing all scores indexed by the modification of interest for a peptide or a PSM.
-
-
-
Class com.compomics.util.experiment.identification.peptide_shaker.PSParameter extends ExperimentObject implements Serializable
- serialVersionUID:
- 2846587135366515967L
-
Serialized Fields
-
algorithmDeltaPEP
double algorithmDeltaPEP
The difference in identification algorithm level PEP with the next best peptide assumption. -
deltaPEP
double deltaPEP
The difference in identification algorithm level PEP with the next best peptide assumption with sequence difference across all search engines. -
fractionPEP
HashMap<String,Double> fractionPEP
The fraction confidence map. -
fractionScore
HashMap<String,Double> fractionScore
The fraction confidence map. -
hidden
boolean hidden
Boolean indicating whether this is a hidden match. -
intermediateScores
HashMap<Integer,Double> intermediateScores
Map of the intermediate scores. Score index > value -
manualValidation
boolean manualValidation
Boolean indicating whether the validation confidence was manually updated. -
matchValidationLevel
MatchValidationLevel matchValidationLevel
The validation level of a given match. -
precursorIntensityAveragePerFraction
HashMap<String,Double> precursorIntensityAveragePerFraction
The average precursor intensity per fraction. -
precursorIntensityPerFraction
HashMap<String,ArrayList<Double>> precursorIntensityPerFraction
The precursor intensity per fraction. -
precursorIntensitySummedPerFraction
HashMap<String,Double> precursorIntensitySummedPerFraction
The summed precursor intensity per fraction. -
probability
double probability
The probability of the match. -
proteinInferenceGroupClass
int proteinInferenceGroupClass
Protein groups can belong to the following groups according to the static field indexing. -
qcFilters
HashMap<String,Boolean> qcFilters
The results of the validation quality filters. -
score
double score
The score of the match. -
starred
boolean starred
Boolean indicating whether this is a starred match. -
validatedPeptidesPerFraction
HashMap<String,Integer> validatedPeptidesPerFraction
The number of validated peptides per fraction. -
validatedSpectraPerFraction
HashMap<String,Integer> validatedSpectraPerFraction
The number of validated spectra per fraction.
-
-
-
Package com.compomics.util.experiment.identification.protein_inference.fm_index
-
Class com.compomics.util.experiment.identification.protein_inference.fm_index.AccessionMetaData extends Object implements Serializable
- serialVersionUID:
- 8320902054239025L
-
Class com.compomics.util.experiment.identification.protein_inference.fm_index.CacheElement extends ExperimentObject implements Serializable
-
Serialized Fields
-
cachedPrimary
ArrayList<MatrixContent> cachedPrimary
-
massFirst
Double massFirst
-
massSecond
Double massSecond
-
sequence
String sequence
-
-
-
Class com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex extends ExperimentObject implements Serializable
-
Serialized Fields
-
aaMasses
double[] aaMasses
List of all amino acid masses. -
aaMassIndexes
int[] aaMassIndexes
List of all indexes for valid amino acid masses. -
accessionMetaData
HashMap<String,AccessionMetaData> accessionMetaData
The accessions ending positions in the index, important for getSequences function. -
accessions
ArrayList<String[]> accessions
List of all accession IDs in the FASTA file. -
allPermutations
int[][][] allPermutations
All permutations. -
boundaries
ArrayList<int[]> boundaries
Storing the starting positions of the protein sequences. -
BSubstitutions
int[] BSubstitutions
Characters that can be substituted by B. -
cache
HashMap<String,CacheElement>[] cache
List of cached intermediate tag to proteome mapping results. -
decoyAccessions
HashSet<String> decoyAccessions
The decoy accessions contained in this index. -
fmodc
ArrayList<String> fmodc
-
fmodcaa
ArrayList<String>[] fmodcaa
-
fmodcaaMass
ArrayList<Double>[] fmodcaaMass
-
fmodcMass
ArrayList<Double> fmodcMass
-
fmodcp
ArrayList<String> fmodcp
-
fmodcpaa
ArrayList<String>[] fmodcpaa
-
fmodcpaaMass
ArrayList<Double>[] fmodcpaaMass
-
fmodcpMass
ArrayList<Double> fmodcpMass
-
fmodn
ArrayList<String> fmodn
-
fmodnaa
ArrayList<String>[] fmodnaa
-
fmodnaaMass
ArrayList<Double>[] fmodnaaMass
-
fmodnMass
ArrayList<Double> fmodnMass
-
fmodnp
ArrayList<String> fmodnp
-
fmodnpaa
ArrayList<String>[] fmodnpaa
-
fmodnpaaMass
ArrayList<Double>[] fmodnpaaMass
-
fmodnpMass
ArrayList<Double> fmodnpMass
-
hasCTermDirectionModification
boolean hasCTermDirectionModification
-
hasFixedModification_CatTerminus
boolean hasFixedModification_CatTerminus
-
hasFixedModification_NatTerminus
boolean hasFixedModification_NatTerminus
-
hasModificationatTerminus
boolean hasModificationatTerminus
-
hasNTermDirectionModification
boolean hasNTermDirectionModification
-
indexChunkSize
int indexChunkSize
Byte size of index chuck. -
indexParts
int indexParts
Number of chunks of complete index. -
indexStringLengths
ArrayList<Integer> indexStringLengths
Length of the indexed string (all concatenated protein sequences). -
JSubstitutions
int[] JSubstitutions
Characters that can be substituted by J. -
lessTablesPrimary
ArrayList<int[]> lessTablesPrimary
Less table for doing an update step according to the LF step. -
lessTablesReversed
ArrayList<int[]> lessTablesReversed
Less table for doing an update step according to the LF step reversed. -
longestModificationpattern
int longestModificationpattern
Longest modification pattern. -
lookupMasses
long[] lookupMasses
Mass lookup table. -
lookupMultiplier
double lookupMultiplier
Precision for the masses in lookup table. -
massAccuracyType
SearchParameters.MassAccuracyType massAccuracyType
The mass accuracy type. -
massIndexMaps
ArrayList<MassIndexMap> massIndexMaps
Array list for sorted masses to index mappings. -
massTolerance
double massTolerance
Lookup tolerance mass. -
maxNumberDeletions
int maxNumberDeletions
Number of allowed deletion operations. -
maxNumberInsertions
int maxNumberInsertions
Number of allowed insertion operations. -
maxNumberSubstitutions
int maxNumberSubstitutions
Number of allowed substitution operations. -
maxNumberVariants
int maxNumberVariants
Number of allowed variant operations. -
maxPTMsPerPeptide
int maxPTMsPerPeptide
Maximal number of PTMs per peptide. -
maxXPerTag
int maxXPerTag
Maximum supported number of Xs per tag. -
modificationFlags
boolean[] modificationFlags
List of all modification flags -
modificationLabelsToId
HashMap<String,Integer> modificationLabelsToId
Dictionary label to internal id -
modificationPatternNames
HashMap<String,int[]> modificationPatternNames
Mapping dictionary mod name -> (modificationPattern index, relative starting position, pattern length). -
modificationPatterns
ArrayList<Long[]> modificationPatterns
List for patterns of complex modifications. -
modifictationLabels
String[] modifictationLabels
List of all amino acid masses. -
negativeModificationMass
double negativeModificationMass
-
numMasses
int numMasses
List of all indexes for valid amino acid masses. -
occurrenceTablesPrimary
ArrayList<WaveletTree> occurrenceTablesPrimary
Wavelet tree for storing the burrows wheeler transform. -
occurrenceTablesReversed
ArrayList<WaveletTree> occurrenceTablesReversed
Wavelet tree for storing the burrows wheeler transform reversed. -
onlyTrypticPeptides
boolean onlyTrypticPeptides
Flag for only considering tryptic digested peptides. -
sampling
int sampling
Bit shifting for fast multiplying / dividing operations. -
samplingMask
int samplingMask
Mask of fast modulo operations. -
samplingShift
int samplingShift
Every 2^samplingShift suffix array entry will be sampled. -
SNPs
HashMap<String,ArrayList<SNPElement>> SNPs
-
substitutionMatrix
boolean[][] substitutionMatrix
Allowed substitutions. -
suffixArraysPrimary
ArrayList<int[]> suffixArraysPrimary
Sampled suffix array. -
variantBitsPrimary
ArrayList<Rank> variantBitsPrimary
-
variantBitsReversed
ArrayList<Rank> variantBitsReversed
-
variantMatchingType
PeptideVariantsParameters.VariantType variantMatchingType
Either search with one maximal number of variants or use an upper limit for every variant (insertion / deletion / substitution) -
variantsPrimary
ArrayList<HashSet<int[]>[]> variantsPrimary
-
variantsReversed
ArrayList<HashSet<int[]>[]> variantsReversed
-
vmodc
ArrayList<String> vmodc
-
vmodcaa
ArrayList<String>[] vmodcaa
-
vmodcaaMass
ArrayList<Double>[] vmodcaaMass
-
vmodcMass
ArrayList<Double> vmodcMass
-
vmodcp
ArrayList<String> vmodcp
-
vmodcpaa
ArrayList<String>[] vmodcpaa
-
vmodcpaaMass
ArrayList<Double>[] vmodcpaaMass
-
vmodcpMass
ArrayList<Double> vmodcpMass
-
vmodn
ArrayList<String> vmodn
-
vmodnaa
ArrayList<String>[] vmodnaa
-
vmodnaaMass
ArrayList<Double>[] vmodnaaMass
-
vmodnMass
ArrayList<Double> vmodnMass
-
vmodnp
ArrayList<String> vmodnp
-
vmodnpaa
ArrayList<String>[] vmodnpaa
-
vmodnpaaMass
ArrayList<Double>[] vmodnpaaMass
-
vmodnpMass
ArrayList<Double> vmodnpMass
-
withVariableModifications
boolean withVariableModifications
If true, variable modifications are included. -
Xlookup
long[][] Xlookup
Lookup table for up to maxXPerTag Xs per mass tag. -
ZSubstitutions
int[] ZSubstitutions
Characters that can be substituted by Z.
-
-
-
Class com.compomics.util.experiment.identification.protein_inference.fm_index.MassIndexMap extends ExperimentObject implements Serializable
-
Serialized Fields
-
indexes
int[] indexes
-
mass
double mass
-
-
-
Class com.compomics.util.experiment.identification.protein_inference.fm_index.MatrixContent extends ExperimentObject implements Serializable
-
Serialized Fields
-
allVariants
String allVariants
Current storing of all variant operations. -
allXcomponents
ArrayList<int[]> allXcomponents
Information about all component where the Xs belong to. -
allXMassDiffs
HashMap<Integer,Double> allXMassDiffs
The all X mass differences. -
ambiguousChar
int ambiguousChar
If original character was B, J, X, Z. -
character
int character
Character which was chosen. -
left
int left
Left index. -
length
int length
Current peptide sequence length. -
mass
double mass
Current mass. -
modification
ModificationMatch modification
Index to the modifications list. -
modificationPos
int modificationPos
List of all modifications. -
modifications
ArrayList<ModificationMatch> modifications
List of all modifications. -
numPTMs
int numPTMs
The number of PTMs. -
numSpecificVariants
int[] numSpecificVariants
The specific variants. (0) deletion, (1) insertion, (2) substitution. -
numVariants
int numVariants
List of all modifications. -
numX
int numX
Current number of contained X's. -
peptideSequence
String peptideSequence
Current peptide sequence. -
peptideSequenceSearch
String peptideSequenceSearch
Current peptide sequence needed for search. -
previousContent
MatrixContent previousContent
Index of the originating entry of a particular cell with the pattern searching matrix. -
right
int right
Right index. -
tagComponent
int tagComponent
Information about the component where the X belongs to. -
variant
char variant
Type of edit operation, either deletion 'd', substitution 's' or insertion 'i'. -
XMassDiff
double XMassDiff
The X mass difference,
-
-
-
Class com.compomics.util.experiment.identification.protein_inference.fm_index.Rank extends Object implements Serializable
- serialVersionUID:
- 832090205423902L
-
Serialized Fields
-
bitfield
long[] bitfield
The bit field. -
length
int length
The length. -
sums
int[] sums
The sums. -
sumsSecondLevel
byte[] sumsSecondLevel
The sums.
-
-
Class com.compomics.util.experiment.identification.protein_inference.fm_index.SNPElement extends ExperimentObject implements Serializable
-
Serialized Fields
-
position
int position
-
sourceAA
char sourceAA
-
targetAA
char targetAA
-
-
-
Class com.compomics.util.experiment.identification.protein_inference.fm_index.TagElement extends ExperimentObject implements Serializable
-
Class com.compomics.util.experiment.identification.protein_inference.fm_index.WaveletTree extends Object implements Serializable
- serialVersionUID:
- 83209020542390251L
-
Serialized Fields
-
alphabetDirections
long[] alphabetDirections
Stored alphabet in a 128 bitfield. -
continueLeftRangeQuery
boolean continueLeftRangeQuery
Continue range query for left child. -
continueRightRangeQuery
boolean continueRightRangeQuery
Continue range query for right child. -
firstChar
int firstChar
First character in alphabet. -
lastChar
int lastChar
Last character in alphabet. -
leftChild
WaveletTree leftChild
Left child of the wavelet tree. -
leftRightMask
int leftRightMask
Left right mask. -
lenText
int lenText
Text length. -
less
int[] less
The less table. -
rank
Rank rank
Instance of a rank. -
rightChild
WaveletTree rightChild
Right child of the wavelet tree.
-
-
-
Package com.compomics.util.experiment.identification.spectrum_annotation
-
Class com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
automaticAnnotation
boolean automaticAnnotation
Shall automatic annotation be used. -
deNovoCharge
int deNovoCharge
The charge for the fragment ions in the de novo sequencing. -
fragmentIonAccuracy
double fragmentIonAccuracy
Fragment ion accuracy used for peak matching. -
fragmentIonPpm
boolean fragmentIonPpm
Indicates whether the fragment ion accuracy is in ppm. -
intensityLimit
double intensityLimit
The intensity threshold to use. The type of threshold is defined according to the IntensityThreshold enum. -
intensityThresholdType
AnnotationParameters.IntensityThresholdType intensityThresholdType
The type of intensity threshold. -
neutralLossesAuto
boolean neutralLossesAuto
If true neutral losses will be automatically deduced from the spectrum identification assumption. -
neutralLossesList
ArrayList<NeutralLoss> neutralLossesList
List of neutral losses to annotate. -
relatedIons
boolean relatedIons
If true related ions will be annotated by default. -
reporterIons
boolean reporterIons
If true reporter ions will be annotated by default. -
selectedIonsMap
HashMap<Ion.IonType,HashSet<Integer>> selectedIonsMap
The types of ions to annotate. -
showAllPeaks
boolean showAllPeaks
If true, all peaks are shown, false displays the annotated peaks, and the non-annotated in the background. -
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. -
tiesResolution
SpectrumAnnotator.TiesResolution tiesResolution
The method to use for resolution of ties when multiple peaks can be assigned to a fragment. -
yAxisZoomExcludesBackgroundPeaks
boolean yAxisZoomExcludesBackgroundPeaks
If true, the automatic y-axis zoom excludes background peaks. False includes all peaks in the auto zoom.
-
-
-
Class com.compomics.util.experiment.identification.spectrum_annotation.NeutralLossesMap extends ExperimentObject implements Serializable
- serialVersionUID:
- -4690159937753713106L
-
Serialized Fields
-
accountedNeutralLosses
ArrayList<String> accountedNeutralLosses
Cache for the accounted neutral losses. -
forwardBoundaries
HashMap<String,Integer> forwardBoundaries
Map indicating for each neutral loss when they should start being accounted for the forward ions (b ions for instance). -
rewindBoundaries
HashMap<String,Integer> rewindBoundaries
Map indicating for each neutral loss when they should start being accounted for the reverse ions (y ions for instance).
-
-
-
Package com.compomics.util.experiment.identification.spectrum_assumptions
-
Class com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption extends SpectrumIdentificationAssumption implements Serializable
-
Serialized Fields
-
peptide
Peptide peptide
The theoretic peptide.
-
-
-
Class com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption extends SpectrumIdentificationAssumption implements Serializable
-
Serialized Fields
-
tag
Tag tag
List of mass gaps.
-
-
-
-
Package com.compomics.util.experiment.io.biology.protein
-
Class com.compomics.util.experiment.io.biology.protein.FastaParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
decoyFlag
String decoyFlag
The flag for decoy proteins in the accession. -
decoySuffix
boolean decoySuffix
Boolean indicating whether the decoy flag is a suffix or a prefix. -
targetDecoy
boolean targetDecoy
Boolean indicating whether the FASTA file should be processed as target-decoy or only target. -
targetDecoyFileNameTag
String targetDecoyFileNameTag
The tag added after adding decoy sequences to a FASTA file.
-
-
-
Class com.compomics.util.experiment.io.biology.protein.Header extends ExperimentObject implements Serializable
- serialVersionUID:
- 7665784733371863163L
-
Serialized Fields
-
databaseType
ProteinDatabase databaseType
Extracted database name. As there are no standard database names, this is only an internally consistent naming scheme included to be able to later separate the databases. For example when linking to the online version of the database. The links themselves are not included as these might change outside the control of the compomics-utilities library. Note that the type is set to unknown by default, and is set to the correct type during the parsing of the header. -
iAccession
String iAccession
The accession String is the unique identifier for the sequence in the respective database. Note that for NCBI, the accession number also defines a unique moment in time.
Accession String is the second element in the abbreviated header String. -
iAddenda
StringBuffer iAddenda
This StringBuffer holds all the addenda for this header. -
iDescription
String iDescription
The description is a more or less elaborate description of the protein in question.
The description is the third element (and final) in the abbreviated header String. -
iDescriptionProteinName
String iDescriptionProteinName
Protein name, the protein name extracted from the protein description. For example: "GRP78_HUMAN 78 kDa glucose-regulated protein OS=Homo sapiens GN=HSPA5 PE=1 SV=2" returns "GRP78_HUMAN". -
iDescriptionShort
String iDescriptionShort
A short protein description, removing all but the protein description itself. For example: "GRP78_HUMAN 78 kDa glucose-regulated protein OS=Homo sapiens GN=HSPA5 PE=1 SV=2" becomes "78 kDa glucose-regulated protein". -
iEnd
int iEnd
This variable holds a possible end index for the associated sequence. -
iForeignAccession
String iForeignAccession
The foreign accession String is an accession String in another database of significance. Most notably used for SwissProt accessions that are kept in the NCBI database.
The foreign accession String is an addendum to the foreign ID String in the abbreviated header String. -
iForeignDescription
String iForeignDescription
The foreign Description is a description for an entry in another DB. Most notably, the SwissProt short description for an entry that is found within NCBI.
The foreign description is an addendum to the foreign accession String in the abbreviated header String. -
iForeignID
String iForeignID
The foreign ID is the ID of another database this entry is originally from. Most notably used for SwissProt entries in NCBI.
The foreign ID String is an addendum to the accession String in the abbreviated header String. -
iGeneName
String iGeneName
The name of the gene the protein comes from. Note that this is only available for UniProt and NextProt based databases. -
iID
String iID
The ID String corresponds to the String that is present as the first element following the opening '>'. It is most notably 'sw' for SwissProt, and 'gi' for NCBI.
ID is the first element in the abbreviated header String. -
iProteinEvidence
Integer iProteinEvidence
The protein evidence for the protein. Note that this is only available for UniProt-based databases. -
iRawHeader
String iRawHeader
This variable holds the raw complete unformatted header. Only trailing white space is removed. -
iRest
String iRest
This variable holds all unidentified parts for the Header. If the String was not (recognized as) a standard SwissProt or NCBI header, this variable holds the entire header. -
iStart
int iStart
This variable holds a possible start index for the associated sequence. -
iTaxonomy
String iTaxonomy
The name of the taxonomy the protein comes from. Note that this is only available for UniProt-based databases.
-
-
-
Package com.compomics.util.experiment.io.identification
-
Class com.compomics.util.experiment.io.identification.MzIdentMLIdfileSearchParametersConverter extends ExperimentObject implements Serializable
-
Serialized Fields
-
mzIdentMLFile
File mzIdentMLFile
The mzIdentML file. -
parametersReport
String parametersReport
The parameters report. -
searchParameters
SearchParameters searchParameters
The search parameters. -
species
String species
The species. -
waitingHandler
WaitingHandler waitingHandler
The waiting handler.
-
-
-
-
Package com.compomics.util.experiment.io.identification.idfilereaders
-
Class com.compomics.util.experiment.io.identification.idfilereaders.PepNovoIdfileReader extends ExperimentObject implements Serializable
-
Serialized Fields
-
cTermCorrection
double cTermCorrection
The mass to add to the C-terminal gap so that is corresponds to a peptide fragment. -
identificationFile
File identificationFile
The file to parse. -
nTermCorrection
double nTermCorrection
The mass to add to the N-terminal gap so that is corresponds to a peptide fragment.
-
-
-
Class com.compomics.util.experiment.io.identification.idfilereaders.PNovoIdfileReader extends ExperimentObject implements Serializable
-
Serialized Fields
-
identificationFile
File identificationFile
The file to parse.
-
-
-
Class com.compomics.util.experiment.io.identification.idfilereaders.TideIdfileReader extends ExperimentObject implements Serializable
-
Class com.compomics.util.experiment.io.identification.idfilereaders.XTandemIdfileReader extends ExperimentObject implements Serializable
-
Serialized Fields
-
allMatches
HashMap<Integer,SpectrumMatch> allMatches
Map of all matches indexed by X!Tandem spectrum id. -
inputFile
File inputFile
The input file. -
softwareVersion
String softwareVersion
The software version. -
specNumber
int specNumber
The spectrum number. -
spectrumFileName
String spectrumFileName
The PSM filename.
-
-
-
-
Package com.compomics.util.experiment.io.mass_spectrometry.mgf
-
Class com.compomics.util.experiment.io.mass_spectrometry.mgf.MgfIndex extends ExperimentObject implements Serializable
-
Serialized Fields
-
duplicatedSpectrumTitles
HashMap<String,Integer> duplicatedSpectrumTitles
Map of duplicated spectrum titles and how often they are duplicated. -
fileName
String fileName
The name of the indexed file. -
indexMap
HashMap<String,Long> indexMap
The map of all indexes: spectrum title > index in the file. -
lastModified
Long lastModified
The last time the indexed file was modified. -
maxCharge
Integer maxCharge
The maximal charge. -
maxIntensity
Double maxIntensity
The maximal precursor intensity of the file. -
maxMz
Double maxMz
The maximal m/z in all precursors of the file. -
maxPeakCount
Integer maxPeakCount
The maximal peak count. -
maxRT
Double maxRT
The maximum RT found in the spectra. -
minRT
Double minRT
The minimum RT found in the spectra. -
peakPicked
Boolean peakPicked
Indicates if the spectra seem to be peak picked or not. A null value indicated that the check for peak picking was not performed. -
precursorChargesMissing
Boolean precursorChargesMissing
Indicates if there are spectra where the precursor charge is missing. A null value indicated that the check was not performed. -
precursorMzMap
HashMap<Integer,Double> precursorMzMap
Map of the precursor mz values. -
spectrumCount
Integer spectrumCount
Returns the number of spectra in the file as counted by the begin ions tags. Null if not set. -
spectrumNumberIndexMap
HashMap<String,Integer> spectrumNumberIndexMap
A map of all the spectrum titles and which rank they have in the file, i.e., the first spectrum has rank 0, the second rank 1, etc. -
spectrumTitles
ArrayList<String> spectrumTitles
List of spectrum titles.
-
-
-
-
Package com.compomics.util.experiment.mass_spectrometry.spectra
-
Class com.compomics.util.experiment.mass_spectrometry.spectra.Peak extends ExperimentObject implements Serializable
-
Serialized Fields
-
intensity
double intensity
The intensity of the peak. -
mz
double mz
The mass over charge ratio of the peak.
-
-
-
Class com.compomics.util.experiment.mass_spectrometry.spectra.Precursor extends ExperimentObject implements Serializable
-
Serialized Fields
-
intensity
double intensity
The measured intensity of the precursor. -
mz
double mz
The measured m/z of the precursor. -
possibleCharges
int[] possibleCharges
The charge of the precursor. -
rt
double rt
The retention time when the precursor was isolated.
-
-
-
Class com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum extends ExperimentObject implements Serializable
-
Serialized Fields
-
intensity
double[] intensity
The array of the intensities of the peaks. -
mz
double[] mz
The array of the m/z of the peaks. Note: throughout the code, it is assumed that the m/z array is sorted by ascending m/z. Only minimal sanity check is conducted. -
precursor
Precursor precursor
The precursor if any.
-
-
-
-
Package com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui
-
Class com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.gui.ThermoRawFileParserParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
advancedSettingsWarningLabel
JLabel advancedSettingsWarningLabel
-
backgourdPanel
JPanel backgourdPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the editing was canceled. -
installationPanel
JPanel installationPanel
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
outputFormatCmb
JComboBox outputFormatCmb
-
outputPepXmlLabel
JLabel outputPepXmlLabel
-
peakPickingCmb
JComboBox peakPickingCmb
-
peakPickingLabel
JLabel peakPickingLabel
-
-
-
-
Package com.compomics.util.experiment.personalization
-
Class com.compomics.util.experiment.personalization.ExperimentObject extends Object implements Serializable
-
Serialized Fields
-
id
long id
Unique identifier. -
urParams
HashMap<Long,UrParameter> 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
-
controlSamples
ArrayList<String> controlSamples
List of control samples. The index should be the same as for the sample assignment. -
normalizationFactors
NormalizationFactors normalizationFactors
The normalization factors. -
reporterMethod
ReporterMethod reporterMethod
The reporter method. -
sampleAssignement
HashMap<String,String> sampleAssignement
The sample assignment to the various reporter ions indexed by their name. -
sampleIndexes
HashMap<String,Integer> sampleIndexes
The sample index map. The key is the sample reference and the element the index as a zero based integer.
-
-
-
Class com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory extends ExperimentObject implements Serializable
-
Serialized Fields
-
methods
HashMap<String,ReporterMethod> methods
The reporter methods. -
methodsNames
ArrayList<String> methodsNames
The reporter methods names.
-
-
-
-
Package com.compomics.util.experiment.refinement_parameters
-
Class com.compomics.util.experiment.refinement_parameters.PepnovoAssumptionDetails extends ExperimentObject implements Serializable
- serialVersionUID:
- -4163506699889716493L
-
Serialized Fields
-
mH
double mH
The PepNovo M+H. -
rankScore
double rankScore
The PepNovo rank score.
-
-
-
Package com.compomics.util.experiment.units
-
Class com.compomics.util.experiment.units.UnitOfMeasurement extends ExperimentObject implements Serializable
-
Serialized Fields
-
abbreviation
String abbreviation
The abbreviated name of the unit. -
fullName
String fullName
The full name of the unit. -
metricsPrefix
MetricsPrefix metricsPrefix
The metrics prefix.
-
-
-
-
Package com.compomics.util.general
-
Class com.compomics.util.general.BoxedObject extends ExperimentObject implements Serializable
-
Serialized Fields
-
object
K object
The object to box.
-
-
-
Class com.compomics.util.general.UnknownElementMassException extends Exception implements Serializable
-
Serialized Fields
-
element
String element
The element symbol that was not recognized. -
logger
org.apache.log4j.Logger logger
-
-
-
-
Package com.compomics.util.general.servlet
-
Class com.compomics.util.general.servlet.MassCalcServlet extends javax.servlet.http.HttpServlet implements Serializable
-
Serialized Fields
-
logger
org.apache.log4j.Logger logger
-
-
-
-
Package com.compomics.util.gui
-
Class com.compomics.util.gui.AaMass extends JDialog implements Serializable
-
Serialized Fields
-
daLbl
JLabel daLbl
-
massLbl
JLabel massLbl
-
massTxt
JTextField massTxt
-
sequenceLbl
JLabel sequenceLbl
-
sequenceTxt
JTextField sequenceTxt
-
-
-
Class com.compomics.util.gui.AminoAcidPatternDialog extends JDialog implements Serializable
-
Serialized Fields
-
addJMenuItem
JMenuItem addJMenuItem
-
backgroundPanel
JPanel backgroundPanel
-
cancel
boolean cancel
A boolean indicating whether the used clicked the cancel button. -
cancelButton
JButton cancelButton
-
deleteSelectedRowJMenuItem
JMenuItem deleteSelectedRowJMenuItem
-
editable
boolean editable
A boolean indicating whether the pattern can be edited. -
exampleLabel
JLabel exampleLabel
-
exampleSequence
String exampleSequence
The example sequence. -
jSeparator3
JSeparator jSeparator3
-
jSeparator4
JSeparator jSeparator4
-
moveDownJMenuItem
JMenuItem moveDownJMenuItem
-
moveUpJMenuItem
JMenuItem moveUpJMenuItem
-
okButton
JButton okButton
-
pattern
AminoAcidPattern pattern
The pattern displayed. -
patternDesignPanel
JPanel patternDesignPanel
-
patternDesignScrollPane
JScrollPane patternDesignScrollPane
-
patternDesignTable
JTable patternDesignTable
-
patternDesignTableToolTips
ArrayList<String> patternDesignTableToolTips
The pattern design table column header tooltips. -
patternTestEditorPane
JEditorPane patternTestEditorPane
-
patternTestJScrollPane
JScrollPane patternTestJScrollPane
-
popupJMenu
JPopupMenu popupJMenu
-
rightClickHelpLabel
JLabel rightClickHelpLabel
-
testPanel
JPanel testPanel
-
-
-
Class com.compomics.util.gui.DummyFrame extends JFrame implements Serializable
-
Class com.compomics.util.gui.ExportFormatSelectionDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
buttonGroup
ButtonGroup buttonGroup
-
canceled
boolean canceled
True if the user canceled the dialog. -
cancelJButton
JButton cancelJButton
-
excelJRadioButton
JRadioButton excelJRadioButton
-
exportJButton
JButton exportJButton
-
formatTypeJPanel
JPanel formatTypeJPanel
-
textJRadioButton
JRadioButton textJRadioButton
-
-
-
Class com.compomics.util.gui.FlamableJFrame extends JFrame implements Serializable
-
Serialized Fields
-
logger
org.apache.log4j.Logger logger
-
-
-
Class com.compomics.util.gui.JExceptionDialog extends JDialog implements Serializable
-
Class com.compomics.util.gui.JFrameForBytes extends JFrame implements Serializable
-
Class com.compomics.util.gui.JLabelAndComponentPanel extends JPanel implements Serializable
-
Serialized Fields
-
logger
org.apache.log4j.Logger logger
-
-
-
Class com.compomics.util.gui.JTableForDB extends AlternateRowColoursJTable implements Serializable
-
Class com.compomics.util.gui.PrivacyParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
confidentialLabel
JLabel confidentialLabel
-
normalIcon
Image normalIcon
The normal dialog icon. -
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
settingsPanel
JPanel settingsPanel
-
updatesCheck
JCheckBox updatesCheck
-
utilitiesUserParameters
UtilitiesUserParameters utilitiesUserParameters
The user preferences.
-
-
-
Class com.compomics.util.gui.SampleSelection extends JDialog implements Serializable
-
Class com.compomics.util.gui.VennDiagramDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
contextMenuPlotBackgroundPanel
JPanel contextMenuPlotBackgroundPanel
-
dataPanel
JPanel dataPanel
-
datasetAColorJPanel
JPanel datasetAColorJPanel
-
datasetAScrollPane
JScrollPane datasetAScrollPane
-
datasetATextArea
JTextArea datasetATextArea
-
datasetATextField
JTextField datasetATextField
-
datasetBColorJPanel
JPanel datasetBColorJPanel
-
datasetBScrollPane
JScrollPane datasetBScrollPane
-
datasetBTextArea
JTextArea datasetBTextArea
-
datasetBTextField
JTextField datasetBTextField
-
datasetCColorJPanel
JPanel datasetCColorJPanel
-
datasetCScrollPane
JScrollPane datasetCScrollPane
-
datasetCTextArea
JTextArea datasetCTextArea
-
datasetCTextField
JTextField datasetCTextField
-
datasetDColorJPanel
JPanel datasetDColorJPanel
-
datasetDScrollPane
JScrollPane datasetDScrollPane
-
datasetDTextArea
JTextArea datasetDTextArea
-
datasetDTextField
JTextField datasetDTextField
-
dialogParent
Frame dialogParent
The dialog parent. -
exportPlotMenuItem
JMenuItem exportPlotMenuItem
-
fontSizeMenu
JMenu fontSizeMenu
-
jSeparator1
JPopupMenu.Separator jSeparator1
-
jSeparator2
JPopupMenu.Separator jSeparator2
-
lastSelectedFolder
LastSelectedFolder lastSelectedFolder
The last selected folder. -
legendCheckBoxMenuItem
JCheckBoxMenuItem legendCheckBoxMenuItem
-
legendFontSizeMenuItem
JMenuItem legendFontSizeMenuItem
-
legendLocationMenuItem
JMenuItem legendLocationMenuItem
-
normalIcon
Image normalIcon
The normal icon for the parent dialog. -
plotHelpJButton
JButton plotHelpJButton
-
plotLayeredPane
JLayeredPane plotLayeredPane
-
plotOptionsJButton
JButton plotOptionsJButton
-
plotPopupMenu
JPopupMenu plotPopupMenu
-
valueFontSizeMenuItem
JMenuItem valueFontSizeMenuItem
-
vennDiagramPanel
VennDiagramPanel vennDiagramPanel
The Venn diagram panel. -
waitingIcon
Image waitingIcon
The icon to use when busy. -
xyPlotPanel
JPanel xyPlotPanel
-
-
-
Class com.compomics.util.gui.VennDiagramLegendLocationDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
datasetALabel
JLabel datasetALabel
-
datasetBLabel
JLabel datasetBLabel
-
datasetCLabel
JLabel datasetCLabel
-
datasetDLabel
JLabel datasetDLabel
-
downDatasetAButton
JButton downDatasetAButton
-
downDatasetBButton
JButton downDatasetBButton
-
downDatasetCButton
JButton downDatasetCButton
-
downDatasetDButton
JButton downDatasetDButton
-
leftDatasetAButton
JButton leftDatasetAButton
-
leftDatasetBButton
JButton leftDatasetBButton
-
leftDatasetCButton
JButton leftDatasetCButton
-
leftDatasetDButton
JButton leftDatasetDButton
-
legendLocationPanel
JPanel legendLocationPanel
-
legendShiftSize
double legendShiftSize
Legend shift size. -
okButton
JButton okButton
-
rightDatasetAButton
JButton rightDatasetAButton
-
rightDatasetBButton
JButton rightDatasetBButton
-
rightDatasetCButton
JButton rightDatasetCButton
-
rightDatasetDButton
JButton rightDatasetDButton
-
shiftSizeLabel
JLabel shiftSizeLabel
-
shiftSizeSpinner
JSpinner shiftSizeSpinner
-
upDatasetAButton
JButton upDatasetAButton
-
upDatasetBButton
JButton upDatasetBButton
-
upDatasetCButton
JButton upDatasetCButton
-
upDatasetDButton
JButton upDatasetDButton
-
vennDiagramDialog
VennDiagramDialog vennDiagramDialog
The VennDiagramDialog parent.
-
-
-
Class com.compomics.util.gui.VennDiagramPanel extends JPanel implements Serializable
-
Serialized Fields
-
chartPanel
org.jfree.chart.ChartPanel chartPanel
The chart panel. -
currentVennDiagramType
VennDiagramPanel.VennDiagramType currentVennDiagramType
The current Venn diagram type. -
datasetAColor
Color datasetAColor
The color for dataset A. -
datasetBColor
Color datasetBColor
The color for dataset B. -
datasetCColor
Color datasetCColor
The color for dataset C. -
datasetDColor
Color datasetDColor
The color for dataset D. -
fontSizeLegend
int fontSizeLegend
The font size to use for the legend. -
fontSizeValues
int fontSizeValues
The font size to use for the values. -
groupNames
HashMap<String,String> groupNames
The current Venn diagram group names. -
legendDatasetAFourWay
no.uib.jsparklines.data.XYDataPoint legendDatasetAFourWay
The legend location of Dataset A in a four-way Venn diagram. -
legendDatasetAThreeWay
no.uib.jsparklines.data.XYDataPoint legendDatasetAThreeWay
The legend location of Dataset A in a one to three way Venn diagram. -
legendDatasetBFourWay
no.uib.jsparklines.data.XYDataPoint legendDatasetBFourWay
The legend location of Dataset B in a four-way Venn diagram. -
legendDatasetBThreeWay
no.uib.jsparklines.data.XYDataPoint legendDatasetBThreeWay
The legend location of Dataset B in a one to three way Venn diagram. -
legendDatasetCFourWay
no.uib.jsparklines.data.XYDataPoint legendDatasetCFourWay
The legend location of Dataset C in a four-way Venn diagram. -
legendDatasetCThreeWay
no.uib.jsparklines.data.XYDataPoint legendDatasetCThreeWay
The legend location of Dataset C in a one to three way Venn diagram. -
legendDatasetDFourWay
no.uib.jsparklines.data.XYDataPoint legendDatasetDFourWay
The legend location of Dataset D in a four-way Venn diagram. -
plotPanel
JPanel plotPanel
-
showLegend
boolean showLegend
If true, the legend is shown. -
tooltipToDatasetMap
HashMap<String,String> tooltipToDatasetMap
Map each dataset tooltip back to the given dataset. -
vennDiagramResults
HashMap<String,ArrayList<String>> vennDiagramResults
The current Venn diagram results/data.
-
-
-
Class com.compomics.util.gui.VisibleTableColumnsDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
deselectAllMenuItem
JMenuItem deselectAllMenuItem
-
okButton
JButton okButton
-
selectAllMenuItem
JMenuItem selectAllMenuItem
-
selectedColumnsTable
JTable selectedColumnsTable
-
selectedValuesTableScrollPane
JScrollPane selectedValuesTableScrollPane
-
selectJPopupMenu
JPopupMenu selectJPopupMenu
-
visibleTableColumnsDialogParent
VisibleTableColumnsDialogParent visibleTableColumnsDialogParent
The VisibleTableColumnsDialogParent.
-
-
-
Class com.compomics.util.gui.XYPlotFiltersDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
filtersScrollPane
JScrollPane filtersScrollPane
-
filtersTable
JTable filtersTable
-
filterTypesLabel
JLabel filterTypesLabel
-
okButton
JButton okButton
-
xyPlottingDialog
XYPlottingDialog xyPlottingDialog
The XYPlottingDialog parent.
-
-
-
Class com.compomics.util.gui.XYPlottingDialog extends JDialog implements Serializable
-
Serialized Fields
-
allTableColumns
ArrayList<TableColumn> allTableColumns
The table columns. -
backgroundPanel
JPanel backgroundPanel
-
binSizeSpinner
JSpinner binSizeSpinner
-
binsLabel
JLabel binsLabel
-
bubbleScalingFactor
double bubbleScalingFactor
The bubble scaling factor in percent. 1.0 means no scaling. -
bubbleSize
double bubbleSize
The bubble size. -
bubbleSizeComboBox
JComboBox bubbleSizeComboBox
-
bubbleSizeLabel
JLabel bubbleSizeLabel
-
cellRenderers
HashMap<Integer,TableCellRenderer> cellRenderers
The cell renderers for the table. -
chartPanel
org.jfree.chart.ChartPanel chartPanel
The chart panel. -
colorGradient
no.uib.jsparklines.renderers.util.GradientColorCoding.ColorGradient colorGradient
The color gradient to use. -
colorLabel
JLabel colorLabel
-
colorsComboBox
JComboBox colorsComboBox
-
colummnNames
Vector<String> colummnNames
The column names. -
contextMenuPlotBackgroundPanel
JPanel contextMenuPlotBackgroundPanel
-
contextMenuSelectedValuesTableBackgroundPanel
JPanel contextMenuSelectedValuesTableBackgroundPanel
-
dataPointToRowNumber
HashMap<String,Integer> dataPointToRowNumber
The data point to model row number map. -
densityPlotRadioButton
JRadioButton densityPlotRadioButton
-
dialogParent
Frame dialogParent
The dialog parent. -
dragButtonGroup
ButtonGroup dragButtonGroup
-
dragEnd
Point dragEnd
The ending location of the mouse dragging. -
dragSettingsPanel
JPanel dragSettingsPanel
-
dragStart
Point dragStart
The starting location of the mouse dragging. -
dragToSelectRadioButton
JRadioButton dragToSelectRadioButton
-
dragToZoomRadioButton
JRadioButton dragToZoomRadioButton
-
editFiltersButton
JButton editFiltersButton
-
exportPlotMenuItem
JMenuItem exportPlotMenuItem
-
exportSelectedValuesMenuItem
JMenuItem exportSelectedValuesMenuItem
-
filterPanel
JPanel filterPanel
-
filters
HashMap<String,String> filters
The data filters. -
hideColumnsMenuItem
JMenuItem hideColumnsMenuItem
-
histogramColor
Color histogramColor
The color used for the bars in the histograms. -
histogramRadioButton
JRadioButton histogramRadioButton
-
isPlotting
boolean isPlotting
If true, the plot is currently being updated. -
lastSelectedFolder
LastSelectedFolder lastSelectedFolder
The last selected folder. -
logAcisPanel
JPanel logAcisPanel
-
maxColumnWidths
HashMap<Integer,Integer> maxColumnWidths
The maximum column widths for the table. -
minColumnWidths
HashMap<Integer,Integer> minColumnWidths
The minimum column widths for the table. -
mouseDragged
boolean mouseDragged
If true, the mouse is currently being dragged. -
normalIcon
Image normalIcon
The normal icon for the parent dialog. -
numberOfBins
int numberOfBins
The number if bins for the histograms. -
plotHelpJButton
JButton plotHelpJButton
-
plotLayeredPane
JLayeredPane plotLayeredPane
-
plotOptionsJButton
JButton plotOptionsJButton
-
plotPanel
JPanel plotPanel
-
plotPopupMenu
JPopupMenu plotPopupMenu
-
plotTypeButtonGroup
ButtonGroup plotTypeButtonGroup
-
plotTypePanel
JPanel plotTypePanel
-
progressDialog
ProgressDialogX progressDialog
The progress dialog. -
regressionLineCheckBoxMenuItem
JCheckBoxMenuItem regressionLineCheckBoxMenuItem
-
rowsAfterDataFiltering
ArrayList<Integer> rowsAfterDataFiltering
The rows remaining after applying the data filters. -
selectedDataPoints
HashMap<Integer,ArrayList<Integer>> selectedDataPoints
The currently selected data points. The keys are the series keys, while the elements are the lists of data indexes. -
selectedModelRows
ArrayList<Integer> selectedModelRows
The index of the selected rows. -
selectedValuesLayeredPane
JLayeredPane selectedValuesLayeredPane
-
selectedValuesPanel
JPanel selectedValuesPanel
-
selectedValuesScrollPane
JScrollPane selectedValuesScrollPane
-
selectedValuesTable
JTable selectedValuesTable
-
selectedValuesTableHelpJButton
JButton selectedValuesTableHelpJButton
-
selectedValuesTableOptionsJButton
JButton selectedValuesTableOptionsJButton
-
selectedValuesTablePopupMenu
JPopupMenu selectedValuesTablePopupMenu
-
selectionActive
boolean selectionActive
If true, selection is currently being performed. -
showRegressionLine
boolean showRegressionLine
If true, the regression line is shown. -
sizeLogCheckBox
JCheckBox sizeLogCheckBox
-
tableModel
TableModel tableModel
The table model. -
tableToolTips
ArrayList<String> tableToolTips
The table column header tool tips. -
useGradientColorCoding
boolean useGradientColorCoding
If true, gradient color coding is used. -
userDefinedBinSize
boolean userDefinedBinSize
If true, the user defined bin size will be used instead of the automatic one. -
visibleColumns
HashMap<Integer,Boolean> visibleColumns
Boolean indicators of which columns to show. -
waitingIcon
Image waitingIcon
The icon to use when busy. -
xAxisComboBox
JComboBox xAxisComboBox
-
xAxisLabel
JLabel xAxisLabel
-
xAxisLogCheckBox
JCheckBox xAxisLogCheckBox
-
xAxisPanel
JPanel xAxisPanel
-
xyPlotPanel
JPanel xyPlotPanel
-
xyPlotRadioButton
JRadioButton xyPlotRadioButton
-
yAxisComboBox
JComboBox yAxisComboBox
-
yAxisLabel
JLabel yAxisLabel
-
yAxisLogCheckBox
JCheckBox yAxisLogCheckBox
-
-
-
-
Package com.compomics.util.gui.atoms
-
Class com.compomics.util.gui.atoms.AtomChainDialog extends JDialog implements Serializable
-
Serialized Fields
-
addOnly
boolean addOnly
If true, then only adding atoms is allowed. -
atomChainAdded
AtomChain atomChainAdded
The added atom chain edited by the user. -
atomChainRemoved
AtomChain atomChainRemoved
The removed atom chain edited by the user. -
atomPanelIndex
int atomPanelIndex
The atom panel index. -
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the input. -
compositionLbl
JLabel compositionLbl
-
compositionPanel
JPanel compositionPanel
-
compositionTxt
JTextField compositionTxt
-
editPanel
JPanel editPanel
-
elementsPanel
JPanel elementsPanel
-
elementsScrollPane
JScrollPane elementsScrollPane
-
helpJButton
JButton helpJButton
-
MassLbl
JLabel MassLbl
-
massTxt
JTextField massTxt
-
okButton
JButton okButton
-
settingUpGUI
boolean settingUpGUI
True if the GUI is currently being set up.
-
-
-
Class com.compomics.util.gui.atoms.AtomPanel extends JPanel implements Serializable
-
Serialized Fields
-
addLabel
JLabel addLabel
-
atomChainDialog
AtomChainDialog atomChainDialog
The parent dialog. -
atomCmb
JComboBox atomCmb
-
isotopeCmb
JComboBox isotopeCmb
-
isotopesMap
HashMap<String,Integer> isotopesMap
Map of the isotopes as displayed: displayed string | isotope number. -
occurenceSpinner
JSpinner occurenceSpinner
-
panelIndex
int panelIndex
The panel index. -
removeLabel
JLabel removeLabel
-
-
-
-
Package com.compomics.util.gui.enzymes
-
Class com.compomics.util.gui.enzymes.EnzymesDialog extends JDialog implements Serializable
-
Serialized Fields
-
addUserEnzyme
JButton addUserEnzyme
-
defaultEnzymesTableToolTips
ArrayList<String> defaultEnzymesTableToolTips
The default enzymes table column header tooltips. -
deleteEnzymeButton
JButton deleteEnzymeButton
-
enzymeFactory
EnzymeFactory enzymeFactory
The enzymes factory. -
enzymesEditorPanel
JPanel enzymesEditorPanel
-
enzymesHelpJButton
JButton enzymesHelpJButton
-
enzymesPanel
JPanel enzymesPanel
-
enzymesScrollPane
JScrollPane enzymesScrollPane
-
enzymesTable
JTable enzymesTable
-
exportEnzymesLabel
JLabel exportEnzymesLabel
-
importEnzymesLabel
JLabel importEnzymesLabel
-
notSelectedRowHtmlTagFontColor
String notSelectedRowHtmlTagFontColor
The color to use for the HTML tags for the rows that are not selected, in HTML color code. -
okButton
JButton okButton
-
resetEnzymesLabel
JLabel resetEnzymesLabel
-
selectedRowHtmlTagFontColor
String selectedRowHtmlTagFontColor
The color to use for the HTML tags for the selected rows, in HTML color code. -
userEnzymesTableToolTips
ArrayList<String> userEnzymesTableToolTips
The user enzymes table column header tooltips.
-
-
-
Class com.compomics.util.gui.enzymes.NewEnzymeDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
butNotAfterLabel
JLabel butNotAfterLabel
-
butNotAfterTxt
JTextField butNotAfterTxt
-
butNotBeforeLabel
JLabel butNotBeforeLabel
-
butNotBeforeTxt
JTextField butNotBeforeTxt
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the dialog was canceled by the user. -
cleavageRulesPanel
JPanel cleavageRulesPanel
-
cleavesAfterLabel
JLabel cleavesAfterLabel
-
cleavesAfterTxt
JTextField cleavesAfterTxt
-
cleavesBeforeLabel
JLabel cleavesBeforeLabel
-
cleavesBeforeTxt
JTextField cleavesBeforeTxt
-
enzymeFactory
EnzymeFactory enzymeFactory
The enzymes factory. -
enzymesDialog
EnzymesDialog enzymesDialog
The parent enzymes dialog. -
helpJButton
JButton helpJButton
-
nameLabel
JLabel nameLabel
-
nameTxt
JTextField nameTxt
-
okButton
JButton okButton
-
psiMsAccessionJTextField
JTextField psiMsAccessionJTextField
-
psiMsAccessionLabel
JLabel psiMsAccessionLabel
-
psiMsLinkLabel
JLabel psiMsLinkLabel
-
psMsMappingPanel
JPanel psMsMappingPanel
-
-
-
-
Package com.compomics.util.gui.error_handlers
-
Class com.compomics.util.gui.error_handlers.BugReport extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
clearJButton
JButton clearJButton
-
exitButton
JButton exitButton
-
gitHubProjectName
String gitHubProjectName
The GitHub name of the tool, e.g., "peptide-shaker". -
googleGroup
String googleGroup
The name of the Google Group. -
googleGroupName
String googleGroupName
The human readable name of the the Google Group. -
infoJEditorPane
JEditorPane infoJEditorPane
-
infoJPanel
JPanel infoJPanel
-
infoJScrollPane
JScrollPane infoJScrollPane
-
lastSelectedFolder
LastSelectedFolder lastSelectedFolder
The folder to open in the file selection dialog. -
logFile
File logFile
The log file to display. -
logJPanel
JPanel logJPanel
-
logJScrollPane
JScrollPane logJScrollPane
-
logTxt
JTextArea logTxt
-
saveJButton
JButton saveJButton
-
toolName
String toolName
The name of the tool to get the bug report for, e.g., "PeptideShaker". -
toolVersion
String toolVersion
The version number of the tool the log files belongs to.
-
-
-
Class com.compomics.util.gui.error_handlers.HelpDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
closeJButton
JButton closeJButton
-
dialogParent
JDialog dialogParent
The parent of the parent is a JDialog. -
frameParent
Frame frameParent
The parent of the parent is a Frame. -
jScrollPane1
JScrollPane jScrollPane1
-
textJEditorPane
JEditorPane textJEditorPane
-
-
-
-
Package com.compomics.util.gui.error_handlers.notification
-
Class com.compomics.util.gui.error_handlers.notification.NotesDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
notesEditorPane
JEditorPane notesEditorPane
-
notesScrollPane
JScrollPane notesScrollPane
-
okButton
JButton okButton
-
-
-
Class com.compomics.util.gui.error_handlers.notification.NotificationDialog extends JDialog implements Serializable
-
Serialized Fields
-
notificationDialogParent
NotificationDialogParent notificationDialogParent
The notification dialog parent. -
notificationLabel
JLabel notificationLabel
-
notificationPanel
JPanel notificationPanel
-
notificationType
String notificationType
The notification type.
-
-
-
-
Package com.compomics.util.gui.export.graphics
-
Class com.compomics.util.gui.export.graphics.ExportGraphicsDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
buttonGroup
ButtonGroup buttonGroup
-
cancelJButton
JButton cancelJButton
-
chartPanel
org.jfree.chart.ChartPanel chartPanel
The chart panel to export. -
exportJButton
JButton exportJButton
-
frame
JFrame frame
The parent frame. -
graphicsPanel
Component graphicsPanel
The panel to export. -
lastSelectedFolder
LastSelectedFolder lastSelectedFolder
The last selected folder. -
normalIcon
Image normalIcon
The normal icon. -
pdfJRadioButton
JRadioButton pdfJRadioButton
-
plottingTypeJPanel
JPanel plottingTypeJPanel
-
pngJRadioButton
JRadioButton pngJRadioButton
-
progressDialog
ProgressDialogX progressDialog
The progress dialog. -
svgJRadioButton
JRadioButton svgJRadioButton
-
tiffJRadioButton
JRadioButton tiffJRadioButton
-
waitingIcon
Image waitingIcon
The waiting icon.
-
-
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Package com.compomics.util.gui.export.report
-
Class com.compomics.util.gui.export.report.ReportEditor extends JDialog implements Serializable
-
Serialized Fields
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advancedFeaturesCheck
JCheckBox advancedFeaturesCheck
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
columnDelimiterLabel
JLabel columnDelimiterLabel
-
commaRadioButton
JRadioButton commaRadioButton
-
decoysCheck
JCheckBox decoysCheck
-
delimiterButtonGroup
ButtonGroup delimiterButtonGroup
-
editable
boolean editable
A boolean indicating whether the report can be edited. -
exportFactory
ExportFactory exportFactory
The export factory. -
featuresList
ArrayList<ExportFeature> featuresList
The list of implemented features for the selected section. -
featuresScrollPane
JScrollPane featuresScrollPane
-
featuresTable
JTable featuresTable
-
headerCheckBox
JCheckBox headerCheckBox
-
lineNumberCheckBox
JCheckBox lineNumberCheckBox
-
mainTitleTxt
JTextField mainTitleTxt
-
maintTitleCheckBox
JCheckBox maintTitleCheckBox
-
matchesLbl
JLabel matchesLbl
-
nameTxt
JTextField nameTxt
-
numberOfSeparationLinesLabel
JLabel numberOfSeparationLinesLabel
-
okButton
JButton okButton
-
oldName
String oldName
The original name of the report. -
reporterSettingsPanel
JPanel reporterSettingsPanel
-
reporterTypePanel
JPanel reporterTypePanel
-
reportTitleLabel
JLabel reportTitleLabel
-
rowDelimiterLabel
JLabel rowDelimiterLabel
-
sectionContentPanel
JPanel sectionContentPanel
-
sectionName
String sectionName
The selected section name. -
sectionsPanel
JPanel sectionsPanel
-
sectionsScrollPane
JScrollPane sectionsScrollPane
-
sectionsTable
JTable sectionsTable
-
sectionTitleCheckBox
JCheckBox sectionTitleCheckBox
-
selection
HashMap<String,ArrayList<ExportFeature>> selection
The original selection. -
semicolonRadioButton
JRadioButton semicolonRadioButton
-
separationLinesSpinner
JSpinner separationLinesSpinner
-
spaceRadioButton
JRadioButton spaceRadioButton
-
structureLabel
JLabel structureLabel
-
subFeaturesCheck
JCheckBox subFeaturesCheck
-
tabRadioButton
JRadioButton tabRadioButton
-
validatedCheck
JCheckBox validatedCheck
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Package com.compomics.util.gui.file_handling
-
Class com.compomics.util.gui.file_handling.FileDisplayDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
canceled
boolean canceled
True if the dialog was canceled by the user. -
files
ArrayList<File> files
The list of files. -
okButton
JButton okButton
-
selectedFilesEditorPane
JEditorPane selectedFilesEditorPane
-
selectedFilesScrollPane
JScrollPane selectedFilesScrollPane
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-
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Class com.compomics.util.gui.file_handling.FileSelectionDialog extends JDialog implements Serializable
-
Serialized Fields
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the dialog. -
fileList
JList fileList
-
fileListScrollPane
JScrollPane fileListScrollPane
-
fileMap
HashMap<String,File> fileMap
A map of the parameter files indexed by their name. -
helpLabel
JLabel helpLabel
-
okButton
JButton okButton
-
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Package com.compomics.util.gui.filtering
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Class com.compomics.util.gui.filtering.FilterDialog extends JDialog implements Serializable
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Serialized Fields
-
addItemMenuItem
JMenuItem addItemMenuItem
-
allModifications
ArrayList<String> allModifications
The modifications that can be used for filtering. -
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the filtering. -
descriptionLbl
JLabel descriptionLbl
-
descriptionScrollPane
JScrollPane descriptionScrollPane
-
descriptionTxt
JTextArea descriptionTxt
-
exceptionsPanel
JPanel exceptionsPanel
-
exceptionsScrollPane
JScrollPane exceptionsScrollPane
-
exceptionsTxt
JTextArea exceptionsTxt
-
filterItemsPanel
JPanel filterItemsPanel
-
filterItemsTable
JTable filterItemsTable
-
filterItemsTableScrollPane
JScrollPane filterItemsTableScrollPane
-
filterPanel
JPanel filterPanel
-
filterSettingsPanel
JPanel filterSettingsPanel
-
filterSplitPane
JSplitPane filterSplitPane
-
helpLbl
JLabel helpLbl
-
itemPopupMenu
JPopupMenu itemPopupMenu
-
itemsNames
ArrayList<String> itemsNames
The names of the items to display. -
manualSelectionSplitPane
JSplitPane manualSelectionSplitPane
-
manualValidationPanel
JPanel manualValidationPanel
-
manualValidationScrollPane
JScrollPane manualValidationScrollPane
-
manualValidationTxt
JTextArea manualValidationTxt
-
matchFilter
MatchFilter matchFilter
The original filter. -
nameLbl
JLabel nameLbl
-
nameTxt
JTextField nameTxt
-
okButton
JButton okButton
-
propertiesPanel
JPanel propertiesPanel
-
removeItemMenuItem
JMenuItem removeItemMenuItem
-
-
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Class com.compomics.util.gui.filtering.FilterParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
peptideHideFilters
HashMap<String,PeptideFilter> peptideHideFilters
The peptide hide filters. -
peptideStarFilters
HashMap<String,PeptideFilter> peptideStarFilters
The peptide star filters. -
proteinHideFilters
HashMap<String,ProteinFilter> proteinHideFilters
The protein hide filters. -
proteinStarFilters
HashMap<String,ProteinFilter> proteinStarFilters
The protein star filters. -
psmHideFilters
HashMap<String,PsmFilter> psmHideFilters
The psm hide filters. -
psmStarFilters
HashMap<String,PsmFilter> psmStarFilters
The psm star filters.
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Package com.compomics.util.gui.genes
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Class com.compomics.util.gui.genes.GeneDetailsDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
chromosomeLabel
JLabel chromosomeLabel
-
chromosomeNameTxt
JTextField chromosomeNameTxt
-
detailsPanel
JPanel detailsPanel
-
ensemlbIdLabel
JLabel ensemlbIdLabel
-
geneIdTxt
JTextField geneIdTxt
-
geneMaps
GeneMaps geneMaps
The gene maps. -
geneNameLabel
JLabel geneNameLabel
-
geneNameTxt
JTextField geneNameTxt
-
goAnnotationLabel
JLabel goAnnotationLabel
-
goTable
JTable goTable
-
goTableScrollPane
JScrollPane goTableScrollPane
-
goTermDescriptions
ArrayList<String> goTermDescriptions
The GO term descriptions attached to this protein match. -
notSelectedRowHtmlTagFontColor
String notSelectedRowHtmlTagFontColor
The color to use for the HTML tags for the rows that are not selected, in HTML color code. -
okButton
JButton okButton
-
proteinAccessionColumn
ArrayList<String> proteinAccessionColumn
The protein accession column in the table. Only used if more than one accession. -
proteinAccessions
String[] proteinAccessions
The protein accessions of this match. -
proteinDetailsProvider
ProteinDetailsProvider proteinDetailsProvider
The protein details provider. -
selectedRowHtmlTagFontColor
String selectedRowHtmlTagFontColor
The color to use for the HTML tags for the selected rows, in HTML color code.
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-
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Class com.compomics.util.gui.genes.SpeciesDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
Deprecated. -
cancelButton
JButton cancelButton
Deprecated. -
canceled
boolean canceled
Deprecated.Boolean indicating whether the user canceled the editing. -
chickenLabel
JLabel chickenLabel
Deprecated. -
comma1Label
JLabel comma1Label
Deprecated. -
comma2Label
JLabel comma2Label
Deprecated. -
comma3Label
JLabel comma3Label
Deprecated. -
comma4Label
JLabel comma4Label
Deprecated. -
dialogParent
JDialog dialogParent
Deprecated.The dialog parent, if any. -
ensemblCategoryJComboBox
JComboBox ensemblCategoryJComboBox
Deprecated. -
ensemblVersionLabel
JLabel ensemblVersionLabel
Deprecated. -
geneFactory
ProteinGeneDetailsProvider geneFactory
Deprecated.The gene factory. -
humanLabel
JLabel humanLabel
Deprecated. -
mouseLabel
JLabel mouseLabel
Deprecated. -
normalImage
Image normalImage
Deprecated.The icon to display when processing is finished. -
okButton
JButton okButton
Deprecated. -
parentFrame
Frame parentFrame
Deprecated.The frame parent, if any. -
popularSpeciesLabel
JLabel popularSpeciesLabel
Deprecated. -
progressDialog
ProgressDialogX progressDialog
Deprecated.The progress dialog. -
ratLabel
JLabel ratLabel
Deprecated. -
selectedSpeciesList
ArrayList<String> selectedSpeciesList
Deprecated.The selected species. -
speciesFactory
SpeciesFactory speciesFactory
Deprecated.The species factory -
speciesJComboBox
JComboBox speciesJComboBox
Deprecated. -
speciesPanel
JPanel speciesPanel
Deprecated. -
speciesToTaxonMap
HashMap<String,Integer> speciesToTaxonMap
Deprecated.A species name to taxon map. -
unknownSpeciesLabel
JLabel unknownSpeciesLabel
Deprecated. -
updateMappingsButton
JButton updateMappingsButton
Deprecated. -
waitingImage
Image waitingImage
Deprecated.The icon to display when waiting. -
zebrafishLabel
JLabel zebrafishLabel
Deprecated.
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Package com.compomics.util.gui.isotopic_calculator
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Class com.compomics.util.gui.isotopic_calculator.IsotopeDistributionGui extends JFrame implements Serializable
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Serialized Fields
-
calculateButton
JButton calculateButton
-
headerTable
JPanel headerTable
-
iCharge
double iCharge
The charge -
iElements
HashMap<String,MolecularFormula> iElements
HashMap with the molecular formula for all the aminoacids -
iSequence
AASequenceImpl iSequence
The amino acid sequence -
jpanContent
JPanel jpanContent
-
lblComp
JLabel lblComp
-
lblMass
JLabel lblMass
-
lblPeptide
JLabel lblPeptide
-
logger
org.apache.log4j.Logger logger
-
spectrumPanel
JPanel spectrumPanel
-
spinCharge
JSpinner spinCharge
-
table1
AlternateRowColoursJTable table1
-
txtSequence
JTextArea txtSequence
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-
-
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Package com.compomics.util.gui.modification
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Class com.compomics.util.gui.modification.ModificationDialog extends JDialog implements Serializable
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Serialized Fields
-
addNeutralLoss
JButton addNeutralLoss
-
addReporterIon
JButton addReporterIon
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atomChainAdded
AtomChain atomChainAdded
The atom chain added by the modification. -
atomChainRemoved
AtomChain atomChainRemoved
The atom chain removed by the modification. -
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the edition has been canceled by the user. -
categoryCmb
JComboBox categoryCmb
-
categoryLabel
JLabel categoryLabel
-
compositionLabel
JLabel compositionLabel
-
compositionTxt
JTextField compositionTxt
-
currentPtm
Modification currentPtm
The edited Modification. -
cvTermSplitPane
JSplitPane cvTermSplitPane
-
editable
boolean editable
Boolean indicating whether the user can edit the Modification or not. -
helpJButton
JButton helpJButton
-
massLabel
JLabel massLabel
-
massTxt
JTextField massTxt
-
modificationFactory
ModificationFactory modificationFactory
The post translational modifications factory. -
nameLabel
JLabel nameLabel
-
nameShortLabel
JLabel nameShortLabel
-
nameShortTxt
JTextField nameShortTxt
-
nameTxt
JTextField nameTxt
-
neutralLosses
ArrayList<NeutralLoss> neutralLosses
The neutral losses. -
neutralLossesAndReportIonsTabbedPane
JTabbedPane neutralLossesAndReportIonsTabbedPane
-
neutralLossesJScrollPane
JScrollPane neutralLossesJScrollPane
-
neutralLossesPanel
JPanel neutralLossesPanel
-
neutralLossesTable
JTable neutralLossesTable
-
neutralLossesTableToolTips
ArrayList<String> neutralLossesTableToolTips
The neutral losses table column header tooltips. -
okButton
JButton okButton
-
pattern
AminoAcidPattern pattern
The amino acid pattern of the modification -
patternLabel
JLabel patternLabel
-
patternTxt
JTextField patternTxt
-
propertiesPanel
JPanel propertiesPanel
-
psiModAccessionJTextField
JTextField psiModAccessionJTextField
-
psiModAccessionLabel
JLabel psiModAccessionLabel
-
psiModLabel
JLabel psiModLabel
-
psiModLinkLabel
JLabel psiModLinkLabel
-
psiModNameJTextField
JTextField psiModNameJTextField
-
psiModNameLabel
JLabel psiModNameLabel
-
psiModPanel
JPanel psiModPanel
-
removeNeutralLoss
JButton removeNeutralLoss
-
removerReporterIon
JButton removerReporterIon
-
reporterIons
ArrayList<ReporterIon> reporterIons
The reporter ions. -
reporterIonsAndNeutralLossesPanel
JPanel reporterIonsAndNeutralLossesPanel
-
reporterIonsJScrollPane
JScrollPane reporterIonsJScrollPane
-
reporterIonsPanel
JPanel reporterIonsPanel
-
reporterIonsTable
JTable reporterIonsTable
-
reporterIonTableToolTips
ArrayList<String> reporterIonTableToolTips
The reporter ion table column header tooltips. -
typeCmb
JComboBox typeCmb
-
typeLabel
JLabel typeLabel
-
unimodAccessionJTextField
JTextField unimodAccessionJTextField
-
unimodAccessionLabel
JLabel unimodAccessionLabel
-
unimodLabel
JLabel unimodLabel
-
unimodLinkLabel
JLabel unimodLinkLabel
-
unimodMappingPanel
JPanel unimodMappingPanel
-
unimodNameJTextField
JTextField unimodNameJTextField
-
unimodNameLabel
JLabel unimodNameLabel
-
unimodPanel
JPanel unimodPanel
-
-
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Class com.compomics.util.gui.modification.ModificationsDialog extends JDialog implements Serializable
-
Serialized Fields
-
addUserModification
JButton addUserModification
-
defaultModificationsTable
JTable defaultModificationsTable
-
defaultModsPanel
JPanel defaultModsPanel
-
defaultModsPopupMenu
JPopupMenu defaultModsPopupMenu
-
defaultModsScrollPane
JScrollPane defaultModsScrollPane
-
defaultModsTableToolTips
ArrayList<String> defaultModsTableToolTips
The default mods table column header tooltips. -
deleteUserModification
JButton deleteUserModification
-
editUserModification
JButton editUserModification
-
editUserPtmJMenuItem
JMenuItem editUserPtmJMenuItem
-
exportDefaultModsLabel
JLabel exportDefaultModsLabel
-
exportUserModsLabel
JLabel exportUserModsLabel
-
findJLabel
JLabel findJLabel
-
modificationFactory
ModificationFactory modificationFactory
The post translational modifications factory. -
modificationsEditorPanel
JPanel modificationsEditorPanel
-
modificationsHelpJButton
JButton modificationsHelpJButton
-
modificationsSplitPane
JSplitPane modificationsSplitPane
-
notSelectedRowHtmlTagFontColor
String notSelectedRowHtmlTagFontColor
The color to use for the HTML tags for the rows that are not selected, in HTML color code. -
okButton
JButton okButton
-
searchCurrentSelection
int searchCurrentSelection
The search current selection. -
searchIndexLabel
JLabel searchIndexLabel
-
searchInputTxt
JTextField searchInputTxt
-
searchNextButton
JButton searchNextButton
-
searchPossibilities
ArrayList<Integer> searchPossibilities
The lines of the Modifications concerned by the search. -
searchPreviousButton
JButton searchPreviousButton
-
searchWelcomeText
String searchWelcomeText
The search text to display by default. -
selectedRowHtmlTagFontColor
String selectedRowHtmlTagFontColor
The color to use for the HTML tags for the selected rows, in HTML color code. -
sparklineColor
Color sparklineColor
The color used for the sparkline bar chart plots. -
userModificationsTable
JTable userModificationsTable
-
userModsPanel
JPanel userModsPanel
-
userModsPopupMenu
JPopupMenu userModsPopupMenu
-
userModsScrollPane
JScrollPane userModsScrollPane
-
userModsTableToolTips
ArrayList<String> userModsTableToolTips
The user mods table column header tooltips. -
viewDefaultModsJMenuItem
JMenuItem viewDefaultModsJMenuItem
-
-
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Class com.compomics.util.gui.modification.ModificationTable extends JTable implements Serializable
-
Serialized Fields
-
annotationParameters
AnnotationParameters annotationParameters
The annotation parameters. -
areaChart
boolean areaChart
If true, area charts are used, false results in bar charts. -
identification
Identification identification
The identification object. -
maxAreaChartValue
double maxAreaChartValue
The max value for the area charts. -
modification
Modification modification
The PTM to analyze. -
modificationParameters
ModificationParameters modificationParameters
The modification parameters. -
modificationSequenceMatchingParameters
SequenceMatchingParameters modificationSequenceMatchingParameters
The modification sequence matching parameters. -
modificationSites
ArrayList<Integer> modificationSites
A list of the modification site indexes. -
nModifications
int nModifications
Number of PTMs. -
peptideMatch
PeptideMatch peptideMatch
The peptide match. -
sequenceProvider
SequenceProvider sequenceProvider
The protein sequence provider. -
spectrumProvider
SpectrumProvider spectrumProvider
The spectrum provider. -
tooltips
ArrayList<String> tooltips
The table tooltips.
-
-
-
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Package com.compomics.util.gui.parameters
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Class com.compomics.util.gui.parameters.SparklineColorsDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
doubtfulColorLabel
JLabel doubtfulColorLabel
-
doubtfulColorPanel
JPanel doubtfulColorPanel
-
falsePositiveColorLabel
JLabel falsePositiveColorLabel
-
falsePositiveColorPanel
JPanel falsePositiveColorPanel
-
mirroredPeakColorLabel3
JLabel mirroredPeakColorLabel3
-
mirroredPeakColorPanel2
JPanel mirroredPeakColorPanel2
-
notFoundColorLabel
JLabel notFoundColorLabel
-
notFoundColorPanel
JPanel notFoundColorPanel
-
notValidatedColorLabel
JLabel notValidatedColorLabel
-
notValidatedColorPanel
JPanel notValidatedColorPanel
-
okButton
JButton okButton
-
possibleColorLabel
JLabel possibleColorLabel
-
possibleColorPanel
JPanel possibleColorPanel
-
sparklineColorsPanel
JPanel sparklineColorsPanel
-
utilitiesUserParameters
UtilitiesUserParameters utilitiesUserParameters
The utilities user parameters object. -
validatedColorLabel
JLabel validatedColorLabel
-
validatedColorPanel
JPanel validatedColorPanel
-
-
-
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Package com.compomics.util.gui.parameters.identification
-
Class com.compomics.util.gui.parameters.identification.IdentificationParametersEditionDialog extends JDialog implements Serializable
-
Serialized Fields
-
advancedSettingsLabel
JLabel advancedSettingsLabel
-
annotationSettings
AnnotationParameters annotationSettings
The peak annotation settings. -
attributesPanel
JPanel attributesPanel
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
databaseProcessingButton
JButton databaseProcessingButton
-
editable
boolean editable
Boolean indicating whether the parameters can be edited. -
exportLabel
JLabel exportLabel
-
fastaPreferences
FastaParameters fastaPreferences
The FASTA processing preferences. -
fractionsButton
JButton fractionsButton
-
fractionSettings
FractionParameters fractionSettings
The fraction settings. -
geneMappingButton
JButton geneMappingButton
-
genePreferences
GeneParameters genePreferences
The gene preferences. -
identificationParametersFactory
IdentificationParametersFactory identificationParametersFactory
The identification parameters factory. -
idValidationPreferences
IdMatchValidationParameters idValidationPreferences
The identification validation preferences. -
importLabel
JLabel importLabel
-
lastSelectedFolder
LastSelectedFolder lastSelectedFolder
The last selected folder -
matchesFiltersButton
JButton matchesFiltersButton
-
nameLabel
JLabel nameLabel
-
nameTxt
JTextField nameTxt
-
normalIcon
Image normalIcon
The normal icon. -
parentFrame
Frame parentFrame
The parent frame. -
peptideAssumptionFilter
PeptideAssumptionFilter peptideAssumptionFilter
The PSM filter. -
peptideVariantsButton
JButton peptideVariantsButton
-
peptideVariantsPreferences
PeptideVariantsParameters peptideVariantsPreferences
The peptide variants preferences. -
proteinInferenceButton
JButton proteinInferenceButton
-
proteinInferencePreferences
ProteinInferenceParameters proteinInferencePreferences
The protein inference preferences. -
psmScoringButton
JButton psmScoringButton
-
psmScoringPreferences
PsmScoringParameters psmScoringPreferences
The PSM scores to use. -
ptmLocalizationButton
JButton ptmLocalizationButton
-
ptmScoringPreferences
ModificationLocalizationParameters ptmScoringPreferences
The PTM localization scoring preferences. -
qualityControlButton
JButton qualityControlButton
-
saveButton
JButton saveButton
-
scrollPane
JScrollPane scrollPane
-
searchParameters
SearchParameters searchParameters
The parameters used for the spectrum matching. -
sequenceMatchingButton
JButton sequenceMatchingButton
-
sequenceMatchingPreferences
SequenceMatchingParameters sequenceMatchingPreferences
The peptide to protein matching preferences. -
settingsOuterPanel
JPanel settingsOuterPanel
-
settingsPanel
JPanel settingsPanel
-
showAdvancedSettings
boolean showAdvancedSettings
If yes, the advanced settings are shown. -
spectrumAnnotationButton
JButton spectrumAnnotationButton
-
spectrumMatchingButton
JButton spectrumMatchingButton
-
validationButton
JButton validationButton
-
waitingIcon
Image waitingIcon
The waiting icon.
-
-
-
Class com.compomics.util.gui.parameters.identification.IdentificationParametersNameDialog extends JDialog implements Serializable
-
Serialized Fields
-
attributesPanel
JPanel attributesPanel
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
decriptionLbl
JLabel decriptionLbl
-
descriptionTxt
JTextArea descriptionTxt
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
jScrollPane1
JScrollPane jScrollPane1
-
nameLbl
JLabel nameLbl
-
nameTxt
JTextField nameTxt
-
okButton
JButton okButton
-
originalDescription
String originalDescription
The original description. -
parentFrame
Frame parentFrame
The parent frame.
-
-
-
Class com.compomics.util.gui.parameters.identification.IdentificationParametersOverviewDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
helpLbl
JLabel helpLbl
-
identificationParametersFactory
IdentificationParametersFactory identificationParametersFactory
The identification parameters factory. -
okButton
JButton okButton
-
parametersPopupMenu
JPopupMenu parametersPopupMenu
-
removeMenuItem
JMenuItem removeMenuItem
-
settingsTable
JTable settingsTable
-
settingsTableScrollPane
JScrollPane settingsTableScrollPane
-
tablePanel
JPanel tablePanel
-
-
-
-
Package com.compomics.util.gui.parameters.identification.advanced
-
Class com.compomics.util.gui.parameters.identification.advanced.AnnotationParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
aBox
JCheckBox aBox
-
accuracySpinner
JSpinner accuracySpinner
-
annotationLevelLabel
JLabel annotationLevelLabel
-
annotationLevelPercentLabel
JLabel annotationLevelPercentLabel
-
annotationPreferencesHelpJButton
JButton annotationPreferencesHelpJButton
-
backgroundPanel
JPanel backgroundPanel
-
bBox
JCheckBox bBox
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
cBox
JCheckBox cBox
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
fragmentIonAccuracyLabel
JLabel fragmentIonAccuracyLabel
-
fragmentIonAccuracyTypeLabel
JLabel fragmentIonAccuracyTypeLabel
-
highResolutionBox
JCheckBox highResolutionBox
-
immoniumBox
JCheckBox immoniumBox
-
intensitySpinner
JSpinner intensitySpinner
-
intensityThresholdCmb
JComboBox intensityThresholdCmb
-
ionsPanel
JPanel ionsPanel
-
maxFragmentIonAccuracy
double maxFragmentIonAccuracy
The fragment ion accuracy used for the search. -
neutralLossesMap
HashMap<String,Boolean> neutralLossesMap
Map of the neutral losses selection. -
neutralLossesTable
JTable neutralLossesTable
-
neutralLossPanel
JPanel neutralLossPanel
-
neutralLossScrollPane
JScrollPane neutralLossScrollPane
-
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
peakMatchingPanel
JPanel peakMatchingPanel
-
precursorBox
JCheckBox precursorBox
-
relatedBox
JCheckBox relatedBox
-
reporterBox
JCheckBox reporterBox
-
reporterIons
ArrayList<Integer> reporterIons
List of possible reporter ions. -
xBox
JCheckBox xBox
-
yBox
JCheckBox yBox
-
zBox
JCheckBox zBox
-
-
-
Class com.compomics.util.gui.parameters.identification.advanced.BackgroundSpeciesDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
True of the dialog was canceled by the user. -
fastaSummary
FastaSummary fastaSummary
The search parameters. -
genePreferences
GeneParameters genePreferences
The gene preferences. -
helpJButton
JButton helpJButton
-
mappingPanel
JPanel mappingPanel
-
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
speciesCmb
JComboBox speciesCmb
-
speciesFactory
SpeciesFactory speciesFactory
The species factory. -
speciesLabel
JLabel speciesLabel
-
speciesMap
HashMap<String,Integer> speciesMap
A map from the species names used in the drop down menu to the taxon.
-
-
-
Class com.compomics.util.gui.parameters.identification.advanced.FractionParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgrounPanel
JPanel backgrounPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
fractionsPanel
JPanel fractionsPanel
-
helpJButton
JButton helpJButton
-
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
proteinMwLabel
JLabel proteinMwLabel
-
proteinMwSpinner
JSpinner proteinMwSpinner
-
-
-
Class com.compomics.util.gui.parameters.identification.advanced.GeneParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
autoUpdateCmb
JComboBox autoUpdateCmb
-
autoUpdateLabel
JLabel autoUpdateLabel
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
True of the dialog was canceled by the user. -
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
genePreferences
GeneParameters genePreferences
The gene preferences. -
helpJButton
JButton helpJButton
-
mappingPanel
JPanel mappingPanel
-
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
useMappingCmb
JComboBox useMappingCmb
-
useMappingLabel
JLabel useMappingLabel
-
-
-
Class com.compomics.util.gui.parameters.identification.advanced.MatchesImportParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
filterPanel
JPanel filterPanel
-
helpJButton
JButton helpJButton
-
isotopesLbl
JLabel isotopesLbl
-
isotopesRangeLabel
JLabel isotopesRangeLabel
-
maxIsotopesTxt
JTextField maxIsotopesTxt
-
maxMissedCleavagesTxt
JTextField maxMissedCleavagesTxt
-
minIsotopesTxt
JTextField minIsotopesTxt
-
minMissedCleavagesTxt
JTextField minMissedCleavagesTxt
-
missedCleavagesLabel
JLabel missedCleavagesLabel
-
missedCleavagesRangeLabel
JLabel missedCleavagesRangeLabel
-
nAAmaxTxt
JTextField nAAmaxTxt
-
nAAminTxt
JTextField nAAminTxt
-
okButton
JButton okButton
-
peptideLengthLabel
JLabel peptideLengthLabel
-
peptideLengthRangeLabel
JLabel peptideLengthRangeLabel
-
precDevTxt
JTextField precDevTxt
-
precursorAccuracyLabel
JLabel precursorAccuracyLabel
-
ptmsCheck
JCheckBox ptmsCheck
-
unitCmb
JComboBox unitCmb
-
-
-
Class com.compomics.util.gui.parameters.identification.advanced.ModificationLocalizationParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
alignOnConfidentCmb
JComboBox alignOnConfidentCmb
-
alignOnConfidentLbl
JLabel alignOnConfidentLbl
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
helpJButton
JButton helpJButton
-
jSeparator1
JSeparator jSeparator1
-
neutralLossesCmb
JComboBox neutralLossesCmb
-
neutralLossesLabel
JLabel neutralLossesLabel
-
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
ptmScoringPanel
JPanel ptmScoringPanel
-
scoreCmb
JComboBox scoreCmb
-
scoreTypeLabel
JLabel scoreTypeLabel
-
siteAlignmentPanel
JPanel siteAlignmentPanel
-
thresholdLabel
JLabel thresholdLabel
-
thresholdTxt
JTextField thresholdTxt
-
-
-
Class com.compomics.util.gui.parameters.identification.advanced.PeptideVariantsParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
aaSubstitutionsTableJPanel
JPanel aaSubstitutionsTableJPanel
-
backgrounPanel
JPanel backgrounPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
deletionsLbl
JLabel deletionsLbl
-
deletionsLbl1
JLabel deletionsLbl1
-
deletionsLbl2
JLabel deletionsLbl2
-
deletionsLbl3
JLabel deletionsLbl3
-
deletionsSpinner
JSpinner deletionsSpinner
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
helpJButton
JButton helpJButton
-
insertionsSpinner
JSpinner insertionsSpinner
-
maxVariantsJPanel
JPanel maxVariantsJPanel
-
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
specificVariantsComboBox
JComboBox specificVariantsComboBox
-
specificVariantsLbl
JLabel specificVariantsLbl
-
subsitutionsSpinner
JSpinner subsitutionsSpinner
-
substitutionMatrixComboBox
JComboBox substitutionMatrixComboBox
-
substitutionMatrixTable
JTable substitutionMatrixTable
-
substitutionMatrixTableJScrollPane
JScrollPane substitutionMatrixTableJScrollPane
-
swapSpinner
JSpinner swapSpinner
-
totalVariantsLbl
JLabel totalVariantsLbl
-
totalVariantsSpinner
JSpinner totalVariantsSpinner
-
-
-
Class com.compomics.util.gui.parameters.identification.advanced.ProteinInferenceParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
confidenceLbl
JLabel confidenceLbl
-
confidenceTxt
JTextField confidenceTxt
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
helpJButton
JButton helpJButton
-
modificationsLbl
JLabel modificationsLbl
-
modificatoinsCmb
JComboBox modificatoinsCmb
-
normalIcon
Image normalIcon
The normal dialog icon. -
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
proteinGroupPanel
JPanel proteinGroupPanel
-
simplifyConfidenceCmb
JComboBox simplifyConfidenceCmb
-
simplifyConfidenceLbl
JLabel simplifyConfidenceLbl
-
simplifyConfidenceLbl1
JLabel simplifyConfidenceLbl1
-
simplifyEnzymaticityCmb
JComboBox simplifyEnzymaticityCmb
-
simplifyEnzymaticityLbl
JLabel simplifyEnzymaticityLbl
-
simplifyEvidenceCmb
JComboBox simplifyEvidenceCmb
-
simplifyEvidenceLbl
JLabel simplifyEvidenceLbl
-
simplifyGroupsCmb
JComboBox simplifyGroupsCmb
-
simplifyGroupsLbl
JLabel simplifyGroupsLbl
-
simplifyVariantsCmb
JComboBox simplifyVariantsCmb
-
simplifyVariantsLbl
JLabel simplifyVariantsLbl
-
waitingIcon
Image waitingIcon
The waiting dialog icon.
-
-
-
Class com.compomics.util.gui.parameters.identification.advanced.PsmScoringParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
addJMenuItem
JMenuItem addJMenuItem
-
advocateNames
ArrayList<String> advocateNames
List of the advocates in the table. -
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
defaultScores
HashSet<Integer> defaultScores
The scores to use by default. -
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
helpJButton
JButton helpJButton
-
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
psmScoresJScrollPane
JScrollPane psmScoresJScrollPane
-
psmScoresJTable
JTable psmScoresJTable
-
psmScoresPopupMenu
JPopupMenu psmScoresPopupMenu
-
psmScoresTableToolTips
ArrayList<String> psmScoresTableToolTips
The table column header tooltips. -
removeJMenuItem
JMenuItem removeJMenuItem
-
scoresNames
ArrayList<String> scoresNames
List of the scores in the table. -
scoresSelectionJPanel
JPanel scoresSelectionJPanel
-
spectrumMatchingScores
HashMap<Integer,HashSet<Integer>> spectrumMatchingScores
The scores used to score the spectrum matches for every advocate in a map: advocate index > list of score indexes.
-
-
-
Class com.compomics.util.gui.parameters.identification.advanced.SequenceMatchingParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
annotationPreferencesHelpJButton
JButton annotationPreferencesHelpJButton
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
matchingCmb
JComboBox matchingCmb
-
matchingMethodLbl
JLabel matchingMethodLbl
-
maxPtmsPerTagLbl
JLabel maxPtmsPerTagLbl
-
maxPtmsPerTagTextField
JTextField maxPtmsPerTagTextField
-
minAaScoreLbl
JLabel minAaScoreLbl
-
minAaScoreSpinner
JSpinner minAaScoreSpinner
-
minTagLengthLbl
JLabel minTagLengthLbl
-
minTagLengthTextField
JTextField minTagLengthTextField
-
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
sequenceMatchingPanel
JPanel sequenceMatchingPanel
-
tagMatchingCmb
JComboBox tagMatchingCmb
-
tagMatchingLbl
JLabel tagMatchingLbl
-
xLbl
JLabel xLbl
-
xSpinner
JSpinner xSpinner
-
-
-
Class com.compomics.util.gui.parameters.identification.advanced.ValidationParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
helpJButton
JButton helpJButton
-
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
peptideFdrLabel
JLabel peptideFdrLabel
-
peptideFdrTxt
JTextField peptideFdrTxt
-
processingParamsPanel
JPanel processingParamsPanel
-
proteinFdrLabel
JLabel proteinFdrLabel
-
proteinFdrTxt
JTextField proteinFdrTxt
-
psmFdrLabel
JLabel psmFdrLabel
-
psmFdrTxt
JTextField psmFdrTxt
-
-
-
Class com.compomics.util.gui.parameters.identification.advanced.ValidationQCParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
addPeptideFilterMenuItem
JMenuItem addPeptideFilterMenuItem
-
addProteinFilterMenuItem
JMenuItem addProteinFilterMenuItem
-
addPsmFilterMenuItem
JMenuItem addPsmFilterMenuItem
-
allModifications
ArrayList<String> allModifications
The modifications that can be used for filtering. -
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the dialog was canceled. -
confidenceCheck
JCheckBox confidenceCheck
-
dbCheck
JCheckBox dbCheck
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
editPeptideFilterMenuItem
JMenuItem editPeptideFilterMenuItem
-
editProteinFilterMenuItem
JMenuItem editProteinFilterMenuItem
-
editPsmFilterMenuItem
JMenuItem editPsmFilterMenuItem
-
generalSettingsPanel
JPanel generalSettingsPanel
-
helpJButton
JButton helpJButton
-
helpLbl
JLabel helpLbl
-
markDoubtfulLabel
JLabel markDoubtfulLabel
-
nTargetCheck
JCheckBox nTargetCheck
-
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
peptideFilters
ArrayList<Filter> peptideFilters
List of the peptide quality filters. -
peptideFiltersPanel
JPanel peptideFiltersPanel
-
peptidePopupMenu
JPopupMenu peptidePopupMenu
-
peptideScrollPane
JScrollPane peptideScrollPane
-
peptideTable
JTable peptideTable
-
proteinFilters
ArrayList<Filter> proteinFilters
List of the protein quality filters. -
proteinFiltersPanel
JPanel proteinFiltersPanel
-
proteinPopupMenu
JPopupMenu proteinPopupMenu
-
proteinScrollPane
JScrollPane proteinScrollPane
-
proteinTable
JTable proteinTable
-
psmFilters
ArrayList<Filter> psmFilters
List of the PSM quality filters. -
psmFiltersPanel
JPanel psmFiltersPanel
-
psmPopupMenu
JPopupMenu psmPopupMenu
-
psmScrollPane
JScrollPane psmScrollPane
-
psmTable
JTable psmTable
-
removePeptideFilterMenuItem
JMenuItem removePeptideFilterMenuItem
-
removeProteinFilterMenuItem
JMenuItem removeProteinFilterMenuItem
-
removePsmFilterMenuItem
JMenuItem removePsmFilterMenuItem
-
userInput
boolean userInput
Boolean indicating whether the settings have been changed. -
validationQCPreferencesDialogPanel
JPanel validationQCPreferencesDialogPanel
-
-
-
-
Package com.compomics.util.gui.parameters.identification.algorithm
-
Class com.compomics.util.gui.parameters.identification.algorithm.AndromedaParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
advancedSettingsWarningLabel
JLabel advancedSettingsWarningLabel
-
ammoniaLossCmb
JComboBox ammoniaLossCmb
-
ammoniaLossLabel
JLabel ammoniaLossLabel
-
backgroundPanel
JPanel backgroundPanel
-
cancelled
boolean cancelled
Boolean indicating whether the used canceled the editing. -
closeButton
JButton closeButton
-
decoyModeCmb
JComboBox decoyModeCmb
-
decoyModeLabel
JLabel decoyModeLabel
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
empiricalCorrectionCombo
JComboBox empiricalCorrectionCombo
-
empiricalCorrectionLabel
JLabel empiricalCorrectionLabel
-
equalILCombo
JComboBox equalILCombo
-
equalILLabel
JLabel equalILLabel
-
fragmentAllCmb
JComboBox fragmentAllCmb
-
fragmentAllLabel
JLabel fragmentAllLabel
-
fragMethodCmb
JComboBox fragMethodCmb
-
fragMethodLabel
JLabel fragMethodLabel
-
higherChargeCombo
JComboBox higherChargeCombo
-
higherChargeLabel
JLabel higherChargeLabel
-
maxCombinationsLabel
JLabel maxCombinationsLabel
-
maxCombinationsTxt
JTextField maxCombinationsTxt
-
maxPepLengthNoEnzymeTxt
JTextField maxPepLengthNoEnzymeTxt
-
maxPeptideMassLabel
JLabel maxPeptideMassLabel
-
maxPeptideMassTxt
JTextField maxPeptideMassTxt
-
maxPtmsLabel
JLabel maxPtmsLabel
-
maxPtmsTxt
JTextField maxPtmsTxt
-
minPepLengthNoEnzymeTxt
JTextField minPepLengthNoEnzymeTxt
-
neutralLossesCmb
JComboBox neutralLossesCmb
-
neutralLossesLabel
JLabel neutralLossesLabel
-
numberMatchesLabel
JLabel numberMatchesLabel
-
numberMatchesTxt
JTextField numberMatchesTxt
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
peptideLengthNoEnzymeDividerLabel
JLabel peptideLengthNoEnzymeDividerLabel
-
peptideLengthNoEnzymeLabel
JLabel peptideLengthNoEnzymeLabel
-
settingsInnerPanel
JPanel settingsInnerPanel
-
settingsPanel
JPanel settingsPanel
-
settingsScrollPane
JScrollPane settingsScrollPane
-
topPeaksLabel
JLabel topPeaksLabel
-
topPeaksTxt
JTextField topPeaksTxt
-
topPeaksWindowLabel
JLabel topPeaksWindowLabel
-
topPeaksWindowTxt
JTextField topPeaksWindowTxt
-
waterLossCombo
JComboBox waterLossCombo
-
waterLossLabel
JLabel waterLossLabel
-
-
-
Class com.compomics.util.gui.parameters.identification.algorithm.CometParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
advancedSettingsWarningLabel
JLabel advancedSettingsWarningLabel
-
backgroundPanel
JPanel backgroundPanel
-
batchSizeLabel
JLabel batchSizeLabel
-
batchSizeTxt
JTextField batchSizeTxt
-
cancelled
boolean cancelled
Boolean indicating whether the used canceled the editing. -
clearMzRangeDividerLabel
JLabel clearMzRangeDividerLabel
-
clearMzRangeLabel
JLabel clearMzRangeLabel
-
clearMzRangeLowerTxt
JTextField clearMzRangeLowerTxt
-
clearMzRangeUpperTxt
JTextField clearMzRangeUpperTxt
-
closeButton
JButton closeButton
-
correlationScoreTypeCmb
JComboBox correlationScoreTypeCmb
-
correlationScoreTypeLabel
JLabel correlationScoreTypeLabel
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
enzymeTypeCmb
JComboBox enzymeTypeCmb
-
enzymeTypeLabel
JLabel enzymeTypeLabel
-
fragmentBinOffsetLabel
JLabel fragmentBinOffsetLabel
-
fragmentBinOffsetTxt
JTextField fragmentBinOffsetTxt
-
fragmentIonsPanel
JPanel fragmentIonsPanel
-
isotopeCorrectionCmb
JComboBox isotopeCorrectionCmb
-
isotopeCorrectionLabel
JLabel isotopeCorrectionLabel
-
maxFragmentChargeLabel
JLabel maxFragmentChargeLabel
-
maxFragmentChargeTxt
JTextField maxFragmentChargeTxt
-
maxPepLengthTxt
JTextField maxPepLengthTxt
-
maxPrecursorMassTxt
JTextField maxPrecursorMassTxt
-
maxPtmsLabel
JLabel maxPtmsLabel
-
maxPtmsTxt
JTextField maxPtmsTxt
-
minPeakIntensityLbl
JLabel minPeakIntensityLbl
-
minPeakIntensityTxt
JTextField minPeakIntensityTxt
-
minPeaksLbl
JLabel minPeaksLbl
-
minPeaksTxt
JTextField minPeaksTxt
-
minPepLengthTxt
JTextField minPepLengthTxt
-
minPrecursorMassTxt
JTextField minPrecursorMassTxt
-
numberMatchesLabel
JLabel numberMatchesLabel
-
numberMatchesTxt
JTextField numberMatchesTxt
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
outputFormatCmb
JComboBox outputFormatCmb
-
outputPanel
JPanel outputPanel
-
outputPepXmlLabel
JLabel outputPepXmlLabel
-
peptideLengthDividerLabel
JLabel peptideLengthDividerLabel
-
peptideLengthLabel
JLabel peptideLengthLabel
-
precursorMassDividerLabel
JLabel precursorMassDividerLabel
-
precursorMassLabel
JLabel precursorMassLabel
-
printExpecScoreLabel
JLabel printExpecScoreLabel
-
printExpectScoreCmb
JComboBox printExpectScoreCmb
-
removeMethionineCmb
JComboBox removeMethionineCmb
-
removeMethionineLabel
JLabel removeMethionineLabel
-
removePrecursorPeakCombo
JComboBox removePrecursorPeakCombo
-
removePrecursorPeakLabel
JLabel removePrecursorPeakLabel
-
removePrecursorPeakToleranceLbl
JLabel removePrecursorPeakToleranceLbl
-
removePrecursorPeakToleranceTxt
JTextField removePrecursorPeakToleranceTxt
-
requireVariablePtmCmb
JComboBox requireVariablePtmCmb
-
requireVariablePtmLabel
JLabel requireVariablePtmLabel
-
searchSettingsPanel
JPanel searchSettingsPanel
-
spectrumProcessingPanel
JPanel spectrumProcessingPanel
-
tabbedPane
JTabbedPane tabbedPane
-
-
-
Class com.compomics.util.gui.parameters.identification.algorithm.DirecTagParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
adjustPrecursorMassCmb
JComboBox adjustPrecursorMassCmb
-
adjustPrecursorMassLabel
JLabel adjustPrecursorMassLabel
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
True if the dialog was canceled by the user. -
complementScoreWeightLabel
JLabel complementScoreWeightLabel
-
complementScoreWeightTextField
JTextField complementScoreWeightTextField
-
complementToleranceLabel
JLabel complementToleranceLabel
-
complementToleranceTextField
JTextField complementToleranceTextField
-
deisotopingModeLabel
JLabel deisotopingModeLabel
-
deisptopingModeTextField
JTextField deisptopingModeTextField
-
directTagPanel
JPanel directTagPanel
-
duplicateSpectraLabel
JLabel duplicateSpectraLabel
-
duplicateSpectraPerChargeCmb
JComboBox duplicateSpectraPerChargeCmb
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
intensityScoreWeightLabel
JLabel intensityScoreWeightLabel
-
intensityScoreWeightTextField
JTextField intensityScoreWeightTextField
-
isotopeToleranceLabel
JLabel isotopeToleranceLabel
-
isotopeToleranceTextField
JTextField isotopeToleranceTextField
-
maxPeakCountLabel
JLabel maxPeakCountLabel
-
maxPeakCountTextField
JTextField maxPeakCountTextField
-
maxPrecursorAdjustmentLabel
JLabel maxPrecursorAdjustmentLabel
-
maxPrecursorAdjustmentTextField
JTextField maxPrecursorAdjustmentTextField
-
maxTagCountLabel
JLabel maxTagCountLabel
-
maxTagCountSpinner
JSpinner maxTagCountSpinner
-
minPrecursorAdjustmentLabel
JLabel minPrecursorAdjustmentLabel
-
minPrecursorAdjustmentTextField
JTextField minPrecursorAdjustmentTextField
-
mzFidelityScoreWeightLabel
JLabel mzFidelityScoreWeightLabel
-
mzFidelityScoreWeightTextField
JTextField mzFidelityScoreWeightTextField
-
numberOfChargeStatesLabel
JLabel numberOfChargeStatesLabel
-
numberOfChargeStatesTextField
JTextField numberOfChargeStatesTextField
-
numberOfIntensityClassesLabel
JLabel numberOfIntensityClassesLabel
-
numberOfIntensityClassesTextField
JTextField numberOfIntensityClassesTextField
-
numVariableModsLabel
JLabel numVariableModsLabel
-
numVariableModsTextField
JTextField numVariableModsTextField
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
outputSuffixLabel
JLabel outputSuffixLabel
-
outputSuffixTextField
JTextField outputSuffixTextField
-
precursorAdjustmentStepLabel
JLabel precursorAdjustmentStepLabel
-
precursorAdjustmentStepTextField
JTextField precursorAdjustmentStepTextField
-
tagLengthLabel
JLabel tagLengthLabel
-
tagLengthTextField
JTextField tagLengthTextField
-
ticCutoffLabel
JLabel ticCutoffLabel
-
ticCutoffTextField
JTextField ticCutoffTextField
-
useSpectrumChargeStateCmb
JComboBox useSpectrumChargeStateCmb
-
useSpectrumChargeStateLabel
JLabel useSpectrumChargeStateLabel
-
-
-
Class com.compomics.util.gui.parameters.identification.algorithm.MetaMorpheusParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
advancedSettingsWarningLabel
JLabel advancedSettingsWarningLabel
-
backgroundPanel
JPanel backgroundPanel
-
cancelled
boolean cancelled
Boolean indicating whether the used canceled the editing. -
closeButton
JButton closeButton
-
deconvIntRatioLbl
JLabel deconvIntRatioLbl
-
deconvIntRatioTxt
JTextField deconvIntRatioTxt
-
deconvMassToleranceLbl
JLabel deconvMassToleranceLbl
-
deconvMassToleranceTxt
JTextField deconvMassToleranceTxt
-
deconvMassToleranceTypeCmb
JComboBox deconvMassToleranceTypeCmb
-
deconvMassToleranceTypeLbl
JLabel deconvMassToleranceTypeLbl
-
decoyTypeCmb
JComboBox decoyTypeCmb
-
decoyTypeLbl
JLabel decoyTypeLbl
-
deisotopingPanel
JPanel deisotopingPanel
-
dissociationTypeCombo
JComboBox dissociationTypeCombo
-
dissociationTypeLbl
JLabel dissociationTypeLbl
-
doPrecDeconvCmb
JComboBox doPrecDeconvCmb
-
doPrecDeconvLbl
JLabel doPrecDeconvLbl
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
excludeOneHitWondersCmb
JComboBox excludeOneHitWondersCmb
-
excludeOneHitWondersLbl
JLabel excludeOneHitWondersLbl
-
fragmentationTerminusCmb
JComboBox fragmentationTerminusCmb
-
fragmentationTerminusLbl
JLabel fragmentationTerminusLbl
-
gptmPanel
JPanel gptmPanel
-
gPtmScrollPane
JScrollPane gPtmScrollPane
-
gPtmTable
JTable gPtmTable
-
inSilicoDigestionPanel
JPanel inSilicoDigestionPanel
-
intitiatorMethBehaviorCombo
JComboBox intitiatorMethBehaviorCombo
-
intitiatorMethBehaviorLabel
JLabel intitiatorMethBehaviorLabel
-
jSeparator1
JSeparator jSeparator1
-
massDiffAcceptorTypeCmb
JComboBox massDiffAcceptorTypeCmb
-
massDiffAcceptorTypeLbl
JLabel massDiffAcceptorTypeLbl
-
maxFragmentSizeLbl
JLabel maxFragmentSizeLbl
-
maxFragmentSizeTxt
JTextField maxFragmentSizeTxt
-
maxHetroVariantsLbl
JLabel maxHetroVariantsLbl
-
maxHetroVariantsTxt
JTextField maxHetroVariantsTxt
-
maxModIsoformsLbl
JLabel maxModIsoformsLbl
-
maxModIsoformsTxt
JTextField maxModIsoformsTxt
-
maxNumModPeptideLbl
JLabel maxNumModPeptideLbl
-
maxNumModPeptideTxt
JTextField maxNumModPeptideTxt
-
maxPepLengthTxt
JTextField maxPepLengthTxt
-
minAllowedIntensityRatioToBasePeakLbl
JLabel minAllowedIntensityRatioToBasePeakLbl
-
minAllowedIntensityRatioToBasePeakTxt
JTextField minAllowedIntensityRatioToBasePeakTxt
-
minPepLengthTxt
JTextField minPepLengthTxt
-
minVariantDepthLabel
JLabel minVariantDepthLabel
-
minVariantDepthTxt
JTextField minVariantDepthTxt
-
modifiedPeptidesAreDifferentCmb
JComboBox modifiedPeptidesAreDifferentCmb
-
modifiedPeptidesAreDifferentLbl
JLabel modifiedPeptidesAreDifferentLbl
-
normalizePeaksAcrossAllWindowsCmb
JComboBox normalizePeaksAcrossAllWindowsCmb
-
normalizePeaksAcrossAllWindowsLbl
JLabel normalizePeaksAcrossAllWindowsLbl
-
numberOfPartitionsLbl
JLabel numberOfPartitionsLbl
-
numberOfPartitionsTxt
JTextField numberOfPartitionsTxt
-
numberOfWindowsLbl
JLabel numberOfWindowsLbl
-
numberOfWindowsTxt
JTextField numberOfWindowsTxt
-
numPeaksPerWindowLbl
JLabel numPeaksPerWindowLbl
-
numPeaksPerWindowTxt
JTextField numPeaksPerWindowTxt
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
outputPanel
JPanel outputPanel
-
peakTrimmingPanel
JPanel peakTrimmingPanel
-
peptideLengthDividerLabel
JLabel peptideLengthDividerLabel
-
peptideLengthJLabel
JLabel peptideLengthJLabel
-
proteinGroupingPanel
JPanel proteinGroupingPanel
-
runGptmLbl
JLabel runGptmLbl
-
runGtpmCmb
JComboBox runGtpmCmb
-
scoreCutoffLabel
JLabel scoreCutoffLabel
-
scoreCutoffTxt
JTextField scoreCutoffTxt
-
searchPanel
JPanel searchPanel
-
searchTargetComboBox
JComboBox searchTargetComboBox
-
searchTargetLabel
JLabel searchTargetLabel
-
searchTypeCombo
JComboBox searchTypeCombo
-
searchTypeLabel
JLabel searchTypeLabel
-
tabbedPane
JTabbedPane tabbedPane
-
trimMs1Cmb
JComboBox trimMs1Cmb
-
trimMs1Lbl
JLabel trimMs1Lbl
-
trimMsMsCmb
JComboBox trimMsMsCmb
-
trimMsMsLbl
JLabel trimMsMsLbl
-
useDeltaScoreCmb
JComboBox useDeltaScoreCmb
-
useDeltaScoreLbl
JLabel useDeltaScoreLbl
-
useProvidedPrecCmb
JComboBox useProvidedPrecCmb
-
useProvidedPrecLabel
JLabel useProvidedPrecLabel
-
windowWidthThompsonLbl
JLabel windowWidthThompsonLbl
-
windowWidthThompsonTxt
JTextField windowWidthThompsonTxt
-
writeMzidCmb
JComboBox writeMzidCmb
-
writeMzidLbl
JLabel writeMzidLbl
-
writePepXmlCmb
JComboBox writePepXmlCmb
-
writePepXmlLbl
JLabel writePepXmlLbl
-
-
-
Class com.compomics.util.gui.parameters.identification.algorithm.MsAmandaParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
advancedSearchSettingsPanel
JPanel advancedSearchSettingsPanel
-
advancedSettingsWarningLabel
JLabel advancedSettingsWarningLabel
-
backgroundPanel
JPanel backgroundPanel
-
cancelled
boolean cancelled
Boolean indicating whether the used canceled the editing. -
closeButton
JButton closeButton
-
decoyDatabaseCmb
JComboBox decoyDatabaseCmb
-
decoyDatabaseLabel
JLabel decoyDatabaseLabel
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
instrumentCmb
JComboBox instrumentCmb
-
instrumentLabel
JLabel instrumentLabel
-
maxModPerPeptideCmb
JComboBox maxModPerPeptideCmb
-
maxModPerPeptideLabel
JLabel maxModPerPeptideLabel
-
maxNeutralLossesPerPeptideCmb
JComboBox maxNeutralLossesPerPeptideCmb
-
maxNeutralLossesPerPeptideLabel
JLabel maxNeutralLossesPerPeptideLabel
-
maxPeptideLengthTxt
JTextField maxPeptideLengthTxt
-
maxPotentialModSitePerPeptideCmb
JComboBox maxPotentialModSitePerPeptideCmb
-
maxPotentialModSitePerPeptideLabel
JLabel maxPotentialModSitePerPeptideLabel
-
maxProteinsLoadedLabel
JLabel maxProteinsLoadedLabel
-
maxProteinsLoadedTxt
JTextField maxProteinsLoadedTxt
-
maxPtmNeutalLossesPerPeptideCmb
JComboBox maxPtmNeutalLossesPerPeptideCmb
-
maxPtmNeutalLossesPerPeptideLabel
JLabel maxPtmNeutalLossesPerPeptideLabel
-
maxRankLabel
JLabel maxRankLabel
-
maxRankTxt
JTextField maxRankTxt
-
maxSpectraLoadedLabel
JLabel maxSpectraLoadedLabel
-
maxSpectraLoadedTxt
JTextField maxSpectraLoadedTxt
-
maxVariableModPerPeptideCmb
JComboBox maxVariableModPerPeptideCmb
-
maxVariableModPerPeptideLabel
JLabel maxVariableModPerPeptideLabel
-
minPeptideLengthTxt
JTextField minPeptideLengthTxt
-
monoIsotopicCmb
JComboBox monoIsotopicCmb
-
monoIsotopicLabel
JLabel monoIsotopicLabel
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
outputFormatCmb
JComboBox outputFormatCmb
-
outputFormatLabel
JLabel outputFormatLabel
-
peptideLengthDividerLabel
JLabel peptideLengthDividerLabel
-
peptideLengthLabel
JLabel peptideLengthLabel
-
performDeisotopingCmb
JComboBox performDeisotopingCmb
-
performDeisotopingLabel
JLabel performDeisotopingLabel
-
rankTargetAndDecoySeparatelyCmb
JComboBox rankTargetAndDecoySeparatelyCmb
-
rankTargetAndDecoySeparatelyLabel
JLabel rankTargetAndDecoySeparatelyLabel
-
-
-
Class com.compomics.util.gui.parameters.identification.algorithm.MsgfParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
additionalOutputCmb
JComboBox additionalOutputCmb
-
additionalOutputLabel
JLabel additionalOutputLabel
-
advancedSearchSettingsPanel
JPanel advancedSearchSettingsPanel
-
advancedSettingsWarningLabel
JLabel advancedSettingsWarningLabel
-
backgroundPanel
JPanel backgroundPanel
-
cancelled
boolean cancelled
Boolean indicating whether the used canceled the editing. -
closeButton
JButton closeButton
-
decoyDatabaseCmb
JComboBox decoyDatabaseCmb
-
decoyDatabaseLabel
JLabel decoyDatabaseLabel
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
fragmentationMethodCmb
JComboBox fragmentationMethodCmb
-
fragmentationMethodLabel
JLabel fragmentationMethodLabel
-
instrumentCmb
JComboBox instrumentCmb
-
instrumentLabel
JLabel instrumentLabel
-
maxPepLengthTxt
JTextField maxPepLengthTxt
-
maxPtmsLabel
JLabel maxPtmsLabel
-
maxPtmsTxt
JTextField maxPtmsTxt
-
minPepLengthTxt
JTextField minPepLengthTxt
-
numberMatchesLabel
JLabel numberMatchesLabel
-
numberMatchesTxt
JTextField numberMatchesTxt
-
numberOfTasksLabel
JLabel numberOfTasksLabel
-
numberOfTasksTxt
JTextField numberOfTasksTxt
-
numberTerminiLabel
JLabel numberTerminiLabel
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
peptideLengthDividerLabel
JLabel peptideLengthDividerLabel
-
peptideLengthLabel
JLabel peptideLengthLabel
-
protocolCmb
JComboBox protocolCmb
-
protocolLabel
JLabel protocolLabel
-
terminiCmb
JComboBox terminiCmb
-
-
-
Class com.compomics.util.gui.parameters.identification.algorithm.MyriMatchParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
advancedSearchSettingsPanel
JPanel advancedSearchSettingsPanel
-
advancedSettingsPanel
JPanel advancedSettingsPanel
-
advancedSettingsWarningLabel
JLabel advancedSettingsWarningLabel
-
backgroundPanel
JPanel backgroundPanel
-
cancelled
boolean cancelled
Boolean indicating whether the used canceled the editing. -
classSizeMultiplierLabel
JLabel classSizeMultiplierLabel
-
classSizeMultiplierTxt
JTextField classSizeMultiplierTxt
-
closeButton
JButton closeButton
-
computeXCorrCmb
JComboBox computeXCorrCmb
-
computeXCorrlLabel
JLabel computeXCorrlLabel
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
fragmentationMethodCmb
JComboBox fragmentationMethodCmb
-
fragmentationMethodLabel
JLabel fragmentationMethodLabel
-
maxPeakCountLabel
JLabel maxPeakCountLabel
-
maxPeakCountTxt
JTextField maxPeakCountTxt
-
maxPepLengthTxt
JTextField maxPepLengthTxt
-
maxPrecursorMassTxt
JTextField maxPrecursorMassTxt
-
maxPtmsLabel
JLabel maxPtmsLabel
-
maxPtmsTxt
JTextField maxPtmsTxt
-
minPepLengthTxt
JTextField minPepLengthTxt
-
minPrecursorMassTxt
JTextField minPrecursorMassTxt
-
numbBatchesLabel
JLabel numbBatchesLabel
-
numbBatchesTxt
JTextField numbBatchesTxt
-
numberMatchesLabel
JLabel numberMatchesLabel
-
numberMatchesTxt
JTextField numberMatchesTxt
-
numberTerminiLabel
JLabel numberTerminiLabel
-
numIntensityClassesLabel
JLabel numIntensityClassesLabel
-
numIntensityClassesTxt
JTextField numIntensityClassesTxt
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
outputFormatCmb
JComboBox outputFormatCmb
-
outputFormatLabel
JLabel outputFormatLabel
-
peptideLengthDividerLabel
JLabel peptideLengthDividerLabel
-
peptideLengthLabel
JLabel peptideLengthLabel
-
precursorMassDividerLabel
JLabel precursorMassDividerLabel
-
precursorMassLabel
JLabel precursorMassLabel
-
scrollPane
JScrollPane scrollPane
-
terminiCmb
JComboBox terminiCmb
-
ticCutoffPercentageLabel
JLabel ticCutoffPercentageLabel
-
ticCutoffPercentageTxt
JTextField ticCutoffPercentageTxt
-
useSmartPlusThreeModelCmb
JComboBox useSmartPlusThreeModelCmb
-
useSmartPlusThreeModelLabel
JLabel useSmartPlusThreeModelLabel
-
-
-
Class com.compomics.util.gui.parameters.identification.algorithm.NovorParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
True if the dialog was canceled by the user. -
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
fragmentationMethodCmb
JComboBox fragmentationMethodCmb
-
fragmentationMethodLabel
JLabel fragmentationMethodLabel
-
massAnalyzerCmb
JComboBox massAnalyzerCmb
-
massAnalyzerLabel
JLabel massAnalyzerLabel
-
novorPanel
JPanel novorPanel
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
-
-
Class com.compomics.util.gui.parameters.identification.algorithm.OmssaParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
advancedSearchSettingsPanel
JPanel advancedSearchSettingsPanel
-
advancedSettingsWarningLabel
JLabel advancedSettingsWarningLabel
-
backgroundPanel
JPanel backgroundPanel
-
cancelled
boolean cancelled
Boolean indicating whether the used canceled the editing. -
chargeEstimationCombo
JComboBox chargeEstimationCombo
-
chargeReductionLabel
JLabel chargeReductionLabel
-
cleaveNterminalMethionineCmb
JComboBox cleaveNterminalMethionineCmb
-
cleaveNterminalMethionineLbl
JLabel cleaveNterminalMethionineLbl
-
closeButton
JButton closeButton
-
consecutiveIonProbabilityLbl
JLabel consecutiveIonProbabilityLbl
-
consecutiveIonProbabilityTxt
JTextField consecutiveIonProbabilityTxt
-
correlationCorrectionScoreCmb
JComboBox correlationCorrectionScoreCmb
-
correlationCorrectionScoreLbl
JLabel correlationCorrectionScoreLbl
-
cTermIonsCmb
JComboBox cTermIonsCmb
-
cTermIonsLbl
JLabel cTermIonsLbl
-
databaseProcessingPanel
JPanel databaseProcessingPanel
-
doublyChargedNPeaksLbl
JLabel doublyChargedNPeaksLbl
-
doublyChargedNpeaksTxt
JTextField doublyChargedNpeaksTxt
-
doublyChargedWindowWidthLbl
JLabel doublyChargedWindowWidthLbl
-
doublyChargedWindowWidthTxt
JTextField doublyChargedWindowWidthTxt
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
eliminatePrecursorCombo
JComboBox eliminatePrecursorCombo
-
eValueLbl
JLabel eValueLbl
-
forwardIonsFirstCmb
JComboBox forwardIonsFirstCmb
-
forwardIonsFirstLbl
JLabel forwardIonsFirstLbl
-
fractionChargeLbl
JLabel fractionChargeLbl
-
fractionChargeTxt
JTextField fractionChargeTxt
-
highIntensityLbl
JLabel highIntensityLbl
-
highIntensityTxt
JTextField highIntensityTxt
-
hitListLbl
JLabel hitListLbl
-
hitlistTxt
JTextField hitlistTxt
-
intensityIncrementLbl
JLabel intensityIncrementLbl
-
intensityIncrementTxt
JTextField intensityIncrementTxt
-
iterativeReplaceEvalueLbl
JLabel iterativeReplaceEvalueLbl
-
iterativeReplaceEvalueTxt
JTextField iterativeReplaceEvalueTxt
-
iterativeSearchSettingsPanel
JPanel iterativeSearchSettingsPanel
-
iterativeSequenceEvalueLbl
JLabel iterativeSequenceEvalueLbl
-
iterativeSequenceEvalueTxt
JTextField iterativeSequenceEvalueTxt
-
iterativeSpectraEvalueLbl
JLabel iterativeSpectraEvalueLbl
-
iterativeSpectraEvalueTxt
JTextField iterativeSpectraEvalueTxt
-
jSeparator1
JSeparator jSeparator1
-
lowIntensityLbl
JLabel lowIntensityLbl
-
lowIntensityTxt
JTextField lowIntensityTxt
-
maxEvalueTxt
JTextField maxEvalueTxt
-
maxFragmentChargeLbl
JLabel maxFragmentChargeLbl
-
maxFragmentChargeTxt
JTextField maxFragmentChargeTxt
-
maxFragmentsPerSeriesLbl
JLabel maxFragmentsPerSeriesLbl
-
maxFragmentsPerSeriesTxt
JTextField maxFragmentsPerSeriesTxt
-
maxLaddersLbl
JLabel maxLaddersLbl
-
maxLaddersTxt
JTextField maxLaddersTxt
-
maxPepLengthTxt
JTextField maxPepLengthTxt
-
minAnnotatedMostIntensePeaksLbl
JLabel minAnnotatedMostIntensePeaksLbl
-
minAnnotatedMostIntensePeaksTxt
JTextField minAnnotatedMostIntensePeaksTxt
-
minAnnotatedPeaksLbl
JLabel minAnnotatedPeaksLbl
-
minAnnotatedPeaksTxt
JTextField minAnnotatedPeaksTxt
-
minPepLengthTxt
JTextField minPepLengthTxt
-
minPrecChargeMultipleChargedFragmentsTxt
JTextField minPrecChargeMultipleChargedFragmentsTxt
-
minPrecPerSpectrumLbl
JLabel minPrecPerSpectrumLbl
-
minPrecPerSpectrumTxt
JTextField minPrecPerSpectrumTxt
-
minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel
JLabel minPrecursorChargeConsideredMultiplyChargedFragmentsJLabel
-
neutronLbl
JLabel neutronLbl
-
neutronTxt
JTextField neutronTxt
-
nHitsPerSpectrumPerChargeLbl
JLabel nHitsPerSpectrumPerChargeLbl
-
nHitsPerSpectrumPerChargeTxt
JTextField nHitsPerSpectrumPerChargeTxt
-
nPeaksLbl
JLabel nPeaksLbl
-
nPeaksTxt
JTextField nPeaksTxt
-
okButton
JButton okButton
-
omssaOutputFormatComboBox
JComboBox omssaOutputFormatComboBox
-
omssaOutputFormatLabel
JLabel omssaOutputFormatLabel
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
outputParametersPanel
JPanel outputParametersPanel
-
peptideLengthDividerLabel1
JLabel peptideLengthDividerLabel1
-
peptideLengthJLabel
JLabel peptideLengthJLabel
-
plusOneChargeAutomaticLbl
JLabel plusOneChargeAutomaticLbl
-
plusOneChargeCmb
JComboBox plusOneChargeCmb
-
precursorChargeEstimationLabel
JLabel precursorChargeEstimationLabel
-
precursorMassScalingLabel
JLabel precursorMassScalingLabel
-
precursorScalingCombo
JComboBox precursorScalingCombo
-
searchPositiveIonsCmb
JComboBox searchPositiveIonsCmb
-
searchPositiveIonsLbl
JLabel searchPositiveIonsLbl
-
searchSettingsPanel
JPanel searchSettingsPanel
-
searchSettingsScrollPane
JScrollPane searchSettingsScrollPane
-
semiEnzymaticParametersPanel
JPanel semiEnzymaticParametersPanel
-
sequenceMappingCmb
JComboBox sequenceMappingCmb
-
sequenceMappingLbl
JLabel sequenceMappingLbl
-
singlyChargedNPeaksLbl
JLabel singlyChargedNPeaksLbl
-
singlyChargedNpeaksTxt
JTextField singlyChargedNpeaksTxt
-
singlyChargedWindowWidthLbl
JLabel singlyChargedWindowWidthLbl
-
singlyChargedWindowWidthTxt
JTextField singlyChargedWindowWidthTxt
-
spectrumProcessingPanel
JPanel spectrumProcessingPanel
-
tabbedPane
JTabbedPane tabbedPane
-
-
-
Class com.compomics.util.gui.parameters.identification.algorithm.PepNovoParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
True if the dialog was canceled by the user. -
correctPrecursorMassCmb
JComboBox correctPrecursorMassCmb
-
correctPrecursorMassLabel
JLabel correctPrecursorMassLabel
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
estimateChargeCmb
JComboBox estimateChargeCmb
-
estimateChargeLabel
JLabel estimateChargeLabel
-
hitListLengthLabel
JLabel hitListLengthLabel
-
hitListLengthSpinner
JSpinner hitListLengthSpinner
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
pepNovoPanel
JPanel pepNovoPanel
-
-
-
Class com.compomics.util.gui.parameters.identification.algorithm.PNovoParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
activationTypeCmb
JComboBox activationTypeCmb
-
activationTypeLabel
JLabel activationTypeLabel
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
True if the dialog was canceled by the user. -
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
maxPrecursorMassLabel
JLabel maxPrecursorMassLabel
-
maxPrecursorMassTextField
JTextField maxPrecursorMassTextField
-
minPrecursorMassLabel
JLabel minPrecursorMassLabel
-
minPrecursorMassTextField
JTextField minPrecursorMassTextField
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
pNovoPanel
JPanel pNovoPanel
-
-
-
Class com.compomics.util.gui.parameters.identification.algorithm.TideParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
advancedSettingsWarningLabel
JLabel advancedSettingsWarningLabel
-
backgroundPanel
JPanel backgroundPanel
-
cancelled
boolean cancelled
Boolean indicating whether the used canceled the editing. -
chargesCombo
JComboBox chargesCombo
-
chargesLabel
JLabel chargesLabel
-
closeButton
JButton closeButton
-
decoyFormatCombo
JComboBox decoyFormatCombo
-
decoyformatLabel
JLabel decoyformatLabel
-
decoySeedLabel
JLabel decoySeedLabel
-
decoySeedTxt
JTextField decoySeedTxt
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
enzymeTypeCmb
JComboBox enzymeTypeCmb
-
enzymeTypeLabel
JLabel enzymeTypeLabel
-
exactPvalueCombo
JComboBox exactPvalueCombo
-
exactPvalueLabel
JLabel exactPvalueLabel
-
indexPanel
JPanel indexPanel
-
keepTerminalAaCombo
JComboBox keepTerminalAaCombo
-
keepTerminalAaLabel
JLabel keepTerminalAaLabel
-
maxPepLengthTxt
JTextField maxPepLengthTxt
-
maxPrecursorMassTxt
JTextField maxPrecursorMassTxt
-
maxPtmsLabel
JLabel maxPtmsLabel
-
maxPtmsTxt
JTextField maxPtmsTxt
-
maxSpectrumMzTxt
JTextField maxSpectrumMzTxt
-
maxVariablePtmsPerTypeLabel
JLabel maxVariablePtmsPerTypeLabel
-
maxVariablePtmsPerTypeTxt
JTextField maxVariablePtmsPerTypeTxt
-
minPeaksLbl
JLabel minPeaksLbl
-
minPeaksTxt
JTextField minPeaksTxt
-
minPepLengthTxt
JTextField minPepLengthTxt
-
minPrecursorMassTxt
JTextField minPrecursorMassTxt
-
minSpectrumMzTxt
JTextField minSpectrumMzTxt
-
monoPrecursorCmb
JComboBox monoPrecursorCmb
-
monoPrecursorLabel
JLabel monoPrecursorLabel
-
mzBinOffsetLabel
JLabel mzBinOffsetLabel
-
mzBinOffsetTxt
JTextField mzBinOffsetTxt
-
mzBinWidthLabel
JLabel mzBinWidthLabel
-
mzBinWidthTxt
JTextField mzBinWidthTxt
-
numberMatchesLabel
JLabel numberMatchesLabel
-
numberMatchesTxt
JTextField numberMatchesTxt
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
outputFormatCombo
JComboBox outputFormatCombo
-
outputFormatLabel
JLabel outputFormatLabel
-
peptideLengthDividerLabel
JLabel peptideLengthDividerLabel
-
peptideLengthLabel
JLabel peptideLengthLabel
-
peptideListCmb
JComboBox peptideListCmb
-
peptideListLabel
JLabel peptideListLabel
-
precursorMassDividerLabel
JLabel precursorMassDividerLabel
-
precursorMassLabel
JLabel precursorMassLabel
-
removeMethionineCmb
JComboBox removeMethionineCmb
-
removeMethionineLabel
JLabel removeMethionineLabel
-
removePrecursorPeakCombo
JComboBox removePrecursorPeakCombo
-
removePrecursorPeakLabel
JLabel removePrecursorPeakLabel
-
removePrecursorPeakToleranceLbl
JLabel removePrecursorPeakToleranceLbl
-
removePrecursorPeakToleranceTxt
JTextField removePrecursorPeakToleranceTxt
-
removeTempFoldersCmb
JComboBox removeTempFoldersCmb
-
removeTempFoldersLabel
JLabel removeTempFoldersLabel
-
searchPanel
JPanel searchPanel
-
spectrumMzDividerLabel
JLabel spectrumMzDividerLabel
-
spectrumMzLabel
JLabel spectrumMzLabel
-
spScoreCombo
JComboBox spScoreCombo
-
spScoreLabel
JLabel spScoreLabel
-
tabbedPane
JTabbedPane tabbedPane
-
useFlankingCmb
JComboBox useFlankingCmb
-
useFlankingLabel
JLabel useFlankingLabel
-
useNeutralLossCmb
JComboBox useNeutralLossCmb
-
useNeutralLossLabel
JLabel useNeutralLossLabel
-
-
-
Class com.compomics.util.gui.parameters.identification.algorithm.XTandemParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
advancedSearchSettingsPanel
JPanel advancedSearchSettingsPanel
-
advancedSettingsWarningLabel
JLabel advancedSettingsWarningLabel
-
backgroundPanel
JPanel backgroundPanel
-
cancelled
boolean cancelled
Boolean indicating whether the used canceled the editing. -
closeButton
JButton closeButton
-
dynamicRangeLbl
JLabel dynamicRangeLbl
-
dynamicRangeTxt
JTextField dynamicRangeTxt
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
eValueLbl
JLabel eValueLbl
-
eValueTxt
JTextField eValueTxt
-
fragmentIonMassAccuracyInDa
double fragmentIonMassAccuracyInDa
The fragment ion mass accuracy. -
jSeparator1
JSeparator jSeparator1
-
maxEValueRefineTxt
JTextField maxEValueRefineTxt
-
maxEValueRefinmentLbl
JLabel maxEValueRefinmentLbl
-
minFragmentMzTxt
JTextField minFragmentMzTxt
-
minFragMzLbl
JLabel minFragMzLbl
-
minPeaksLbl
JLabel minPeaksLbl
-
minPeaksTxt
JTextField minPeaksTxt
-
minPrecMassLbl
JLabel minPrecMassLbl
-
minPrecMassTxt
JTextField minPrecMassTxt
-
modificationComplexityLbl
JLabel modificationComplexityLbl
-
modificationComplexityTxt
JTextField modificationComplexityTxt
-
modificationFactory
ModificationFactory modificationFactory
The post translational modifications factory. -
modificationProfile
ModificationParameters modificationProfile
The modification profile used for the search. -
modificationsJScrollPane
JScrollPane modificationsJScrollPane
-
modificationsTable
JTable modificationsTable
-
modificationTableToolTips
ArrayList<String> modificationTableToolTips
The modification table column header tooltips. -
modProfileChanged
boolean modProfileChanged
Boolean indicating whether the modification profile has been changed. Note that it only checks if the user has made changed to the selection, not if the end result is different or not. -
noiseSuppressionCmb
JComboBox noiseSuppressionCmb
-
noiseSuppressionLabel
JLabel noiseSuppressionLabel
-
nPeaksLbl
JLabel nPeaksLbl
-
nPeaksTxt
JTextField nPeaksTxt
-
okButton
JButton okButton
-
openDialogHelpJButton
JButton openDialogHelpJButton
-
openModificationSettingsJButton
JButton openModificationSettingsJButton
-
outputHistogramsCmb
JComboBox outputHistogramsCmb
-
outputHistogramsLabel
JLabel outputHistogramsLabel
-
outputProteinsCmb
JComboBox outputProteinsCmb
-
outputProteinsLabel
JLabel outputProteinsLabel
-
outputResultsCmb
JComboBox outputResultsCmb
-
outputResultsLabel
JLabel outputResultsLabel
-
outputSequencesCmb
JComboBox outputSequencesCmb
-
outputSequencesLabel
JLabel outputSequencesLabel
-
outputSettingsPanel
JPanel outputSettingsPanel
-
outputSpectraCmb
JComboBox outputSpectraCmb
-
outputSpectraLabel
JLabel outputSpectraLabel
-
parentMonoisotopicMassIsotopeErrorCmb
JComboBox parentMonoisotopicMassIsotopeErrorCmb
-
parentMonoisotopicMassIsotopeErrorLabel
JLabel parentMonoisotopicMassIsotopeErrorLabel
-
pointMutationLabel
JLabel pointMutationLabel
-
pointMutationsCmb
JComboBox pointMutationsCmb
-
potentialModificationsCmb
JComboBox potentialModificationsCmb
-
quickAcetylCmb
JComboBox quickAcetylCmb
-
quickAcetylLabel
JLabel quickAcetylLabel
-
quickPyroCmb
JComboBox quickPyroCmb
-
quickPyroLabel
JLabel quickPyroLabel
-
refinementCmb
JComboBox refinementCmb
-
refinementLabel
JLabel refinementLabel
-
refinementModificationsJPanel
JPanel refinementModificationsJPanel
-
refinementModificationsLabel
JLabel refinementModificationsLabel
-
refinementSettingsPanel
JPanel refinementSettingsPanel
-
semiEnzymaticCmb
JComboBox semiEnzymaticCmb
-
semiEnzymaticLabel
JLabel semiEnzymaticLabel
-
skylinePathValueLbl
JLabel skylinePathValueLbl
-
skylineTxt
JTextField skylineTxt
-
snapsCmb
JComboBox snapsCmb
-
snapsLabel
JLabel snapsLabel
-
spectrumImportSettingsPanel
JPanel spectrumImportSettingsPanel
-
spectrumSynthesisCmb
JComboBox spectrumSynthesisCmb
-
spectrumSynthesisLabel
JLabel spectrumSynthesisLabel
-
stpBiasCmb
JComboBox stpBiasCmb
-
stpBiasLabel
JLabel stpBiasLabel
-
tabbedPane
JTabbedPane tabbedPane
-
unanticipatedCleavageCmb
JComboBox unanticipatedCleavageCmb
-
unanticipatedCleavageLabel
JLabel unanticipatedCleavageLabel
-
usePotentialModsLabel
JLabel usePotentialModsLabel
-
-
-
-
Package com.compomics.util.gui.parameters.identification.pride
-
Class com.compomics.util.gui.parameters.identification.pride.EnzymeParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
enzymeFactory
EnzymeFactory enzymeFactory
The enzyme factory. -
enzymeLabel
JLabel enzymeLabel
-
enzymesCmb
JComboBox enzymesCmb
-
mappingPanel
JPanel mappingPanel
-
okButton
JButton okButton
-
prideEnzymeNameLabel
JLabel prideEnzymeNameLabel
-
prideEnzymeNameTextField
JTextField prideEnzymeNameTextField
-
selectionCanceled
boolean selectionCanceled
True of the enzyme selection was canceled by the user.
-
-
-
-
Package com.compomics.util.gui.parameters.identification.search
-
Class com.compomics.util.gui.parameters.identification.search.SearchParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
addFixedModification
JButton addFixedModification
-
addVariableModification
JButton addVariableModification
-
availableModsPanel
JPanel availableModsPanel
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the cancel button was pressed. -
currentPtmSearchString
String currentPtmSearchString
The current Modification search string. -
digestionCmb
JComboBox digestionCmb
-
digestionLabel
JLabel digestionLabel
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
enzymeFactory
EnzymeFactory enzymeFactory
The enzyme factory. -
enzymeLabel
JLabel enzymeLabel
-
enzymesCmb
JComboBox enzymesCmb
-
fixedModificationsLabel
JLabel fixedModificationsLabel
-
fixedModsJScrollPane
JScrollPane fixedModsJScrollPane
-
fixedModsPanel
JPanel fixedModsPanel
-
fixedModsTable
JTable fixedModsTable
-
forwardIons
String[] forwardIons
Convenience array for forward ion type selection. -
fragmentIon1Cmb
JComboBox fragmentIon1Cmb
-
fragmentIon2Cmb
JComboBox fragmentIon2Cmb
-
fragmentIonAccuracyTxt
JTextField fragmentIonAccuracyTxt
-
fragmentIonLbl
JLabel fragmentIonLbl
-
fragmentIonType1Lbl
JLabel fragmentIonType1Lbl
-
fragmentIonUnit
JComboBox fragmentIonUnit
-
isotopeMaxTxt
JTextField isotopeMaxTxt
-
isotopeMinTxt
JTextField isotopeMinTxt
-
isotopeRangeLabel
JLabel isotopeRangeLabel
-
isotopesLbl
JLabel isotopesLbl
-
keyPressedCounter
int keyPressedCounter
Counts the number of times the users has pressed a key on the keyboard in the search field. -
lastSelectedFolder
LastSelectedFolder lastSelectedFolder
The last selected folder to use. -
maxMissedCleavagesLabel
JLabel maxMissedCleavagesLabel
-
maxMissedCleavagesTxt
JTextField maxMissedCleavagesTxt
-
maxPrecursorChargeTxt
JTextField maxPrecursorChargeTxt
-
minPrecursorChargeTxt
JTextField minPrecursorChargeTxt
-
modificationFactory
ModificationFactory modificationFactory
The post translational modifications factory. -
modificationsJScrollPane
JScrollPane modificationsJScrollPane
-
modificationsLayeredPane
JLayeredPane modificationsLayeredPane
-
modificationsListCombo
JComboBox modificationsListCombo
-
modificationsPanel
JPanel modificationsPanel
-
modificationsTable
JTable modificationsTable
-
modificationTableToolTips
ArrayList<String> modificationTableToolTips
The modification table column header tooltips. -
modificationTypesSplitPane
JSplitPane modificationTypesSplitPane
-
normalIcon
Image normalIcon
The normal dialog icon. -
okButton
JButton okButton
-
openDialogHelpJButton1
JButton openDialogHelpJButton1
-
openModificationSettingsJButton
JButton openModificationSettingsJButton
-
parentFrame
Frame parentFrame
The dialog parent frame. -
precursorChargeLbl
JLabel precursorChargeLbl
-
precursorChargeRangeLabel
JLabel precursorChargeRangeLabel
-
precursorIonAccuracyTxt
JTextField precursorIonAccuracyTxt
-
precursorIonLbl
JLabel precursorIonLbl
-
precursorIonUnit
JComboBox precursorIonUnit
-
proteaseAndFragmentationPanel
JPanel proteaseAndFragmentationPanel
-
refMass
Double refMass
Reference mass for the conversion of the fragment ion tolerance from ppm to Dalton. -
removeFixedModification
JButton removeFixedModification
-
removeVariableModification
JButton removeVariableModification
-
rewindIons
String[] rewindIons
Convenience array for rewind ion type selection. -
searchParameters
SearchParameters searchParameters
-
specificityComboBox
JComboBox specificityComboBox
-
specificityLabel
JLabel specificityLabel
-
utilitiesUserParameters
UtilitiesUserParameters utilitiesUserParameters
The utilities user parameters. -
variableModificationsLabel
JLabel variableModificationsLabel
-
variableModsJScrollPane
JScrollPane variableModsJScrollPane
-
variableModsPanel
JPanel variableModsPanel
-
variableModsTable
JTable variableModsTable
-
waitingIcon
Image waitingIcon
The waiting dialog icon. -
waitingTime
int waitingTime
The time to wait between keys typed before updating the search.
-
-
-
Class com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog extends JDialog implements Serializable
-
Serialized Fields
-
accessionsSample
ArrayList<String> accessionsSample
Accessions of the sampled proteins. -
accessionsSpinner
JSpinner accessionsSpinner
-
backgroundPanel
JPanel backgroundPanel
-
browseButton
JButton browseButton
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the database selection was canceled by the user. -
databaseHelpSettingsJLabel
JLabel databaseHelpSettingsJLabel
-
databaseInformationPanel
JPanel databaseInformationPanel
-
dbEditable
boolean dbEditable
Boolean indicating whether the database can be changed. -
dbNameTxt
JTextField dbNameTxt
-
decoyButton
JButton decoyButton
-
editFastaParametersJLabel
JLabel editFastaParametersJLabel
-
fastaParameters
FastaParameters fastaParameters
The parameters used to parse the FASTA file. -
fastaSummary
FastaSummary fastaSummary
Summary information on the FASTA file content. -
fileLabel
JLabel fileLabel
-
fileTxt
JTextField fileTxt
-
headersSample
HashMap<String,Header> headersSample
Sample of protein headers from the database. -
lastModifiedLabel
JLabel lastModifiedLabel
-
lastModifiedTxt
JTextField lastModifiedTxt
-
lastSelectedFolder
LastSelectedFolder lastSelectedFolder
The last selected folder. -
nameLabel
JLabel nameLabel
-
normalImange
Image normalImange
The normal icon. -
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
previewPanel
JPanel previewPanel
-
proteinIterator
FastaIterator proteinIterator
A protein iterator to fill the sample. -
proteinLabel
JLabel proteinLabel
-
proteinsSample
HashMap<String,Protein> proteinsSample
Sample of proteins from the database. -
proteinTxt
JTextArea proteinTxt
-
proteinYxtScrollPane
JScrollPane proteinYxtScrollPane
-
selectedFastaFile
String selectedFastaFile
The selected FASTA file. -
sizeLabel
JLabel sizeLabel
-
sizeTxt
JTextField sizeTxt
-
speciesJTextField
JTextField speciesJTextField
-
speciesLabel
JLabel speciesLabel
-
targetDecoyTxt
JLabel targetDecoyTxt
-
typeJTextField
JTextField typeJTextField
-
typeLabel
JLabel typeLabel
-
utilitiesUserParameters
UtilitiesUserParameters utilitiesUserParameters
The utilities user parameters. -
versionLabel
JLabel versionLabel
-
versionTxt
JTextField versionTxt
-
waitingImage
Image waitingImage
The icon to display when waiting.
-
-
-
-
Package com.compomics.util.gui.parameters.proteowizard
-
Class com.compomics.util.gui.parameters.proteowizard.MsConvertParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
addFilterMenu
JMenu addFilterMenu
-
backgourdPanel
JPanel backgourdPanel
-
browseButton
JButton browseButton
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the editing was canceled. -
filterHelpLabel
JLabel filterHelpLabel
-
filterIndexes
ArrayList<Integer> filterIndexes
List of the indexes of the filters to use. -
filters
HashMap<Integer,String> filters
Map of the filters to use. -
filtersLbl
JLabel filtersLbl
-
filtersPopupMenu
JPopupMenu filtersPopupMenu
-
filtersTable
JTable filtersTable
-
filtersTableScrollPane
JScrollPane filtersTableScrollPane
-
folderHelpLabel
JLabel folderHelpLabel
-
installationJTextField
JTextField installationJTextField
-
installationPanel
JPanel installationPanel
-
lastSelectedFolder
String lastSelectedFolder
The selected folder. -
msconvertParameters
JPanel msconvertParameters
-
okButton
JButton okButton
-
outputFormatCmb
JComboBox outputFormatCmb
-
outputFormatLbl
JLabel outputFormatLbl
-
removeFilterMenuItem
JMenuItem removeFilterMenuItem
-
utilitiesUserParameters
UtilitiesUserParameters utilitiesUserParameters
The utilities preferences.
-
-
-
-
Package com.compomics.util.gui.parameters.tools
-
Class com.compomics.util.gui.parameters.tools.ProcessingParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
editable
boolean editable
Boolean indicating whether the processing and identification parameters should be edited upon clicking on OK. -
nThreadsSpinner
JSpinner nThreadsSpinner
-
okButton
JButton okButton
-
performanceLbl
JLabel performanceLbl
-
performancePanel
JPanel performancePanel
-
processingTypeCmb
JComboBox processingTypeCmb
-
processingTypeLbl
JLabel processingTypeLbl
-
processingTypePanel
JPanel processingTypePanel
-
-
-
-
Package com.compomics.util.gui.protein
-
Class com.compomics.util.gui.protein.FastaParametersDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the user canceled the editing. -
decoyFlagTxt
JTextField decoyFlagTxt
-
decoySuffixLabel
JLabel decoySuffixLabel
-
decoyTagLabel
JLabel decoyTagLabel
-
decoyTypeComboBox
JComboBox<String> decoyTypeComboBox
-
decoyTypeLabel
JLabel decoyTypeLabel
-
editable
boolean editable
Boolean indicating whether the settings can be edited by the user. -
fastaSuffixTxt
JTextField fastaSuffixTxt
-
fileProcessingPanel
JPanel fileProcessingPanel
-
helpJButton
JButton helpJButton
-
okButton
JButton okButton
-
parentFrame
Frame parentFrame
The parent frame. -
targetDecoyComboBox
JComboBox<String> targetDecoyComboBox
-
targetDecoyLabel
JLabel targetDecoyLabel
-
-
-
Class com.compomics.util.gui.protein.SequenceModificationPanel extends JPanel implements Serializable
-
Serialized Fields
-
fragmentIonRectangles
HashMap<String,Rectangle> fragmentIonRectangles
A map of the rectangles used to draw each profile peak. This map is later used for the tooltip for each peak. -
iBarWidth
int iBarWidth
The width of the bars. -
iBaseFont
Font iBaseFont
The font to use. -
iHorizontalSpace
int iHorizontalSpace
The horizontal space. -
iMaxBarHeight
double iMaxBarHeight
The maximum bar height. -
iSequenceComponents
String[] iSequenceComponents
Elementary data for composing the Panel. -
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 -
iXStart
int iXStart
The x-axis start position. -
iYStart
int iYStart
The y-axis start position. -
profiles
ArrayList<ModificationProfile> profiles
The list of modification profiles. -
score1Name
String score1Name
The name of the score above of the sequence. -
score2Name
String score2Name
The name of the score under of the sequence.
-
-
-
-
Package com.compomics.util.gui.renderers
-
Class com.compomics.util.gui.renderers.AlignedListCellRenderer extends DefaultListCellRenderer implements Serializable
-
Serialized Fields
-
align
int align
One of the following constants defined in SwingConstants: LEFT, CENTER (the default for image-only labels), RIGHT, LEADING (the default for text-only labels) or TRAILING.
-
-
-
Class com.compomics.util.gui.renderers.ByteArrayRenderer extends DefaultTableCellRenderer implements Serializable
-
Serialized Fields
-
iData
byte[] iData
This byte[] is the actual data cached by the renderer. -
logger
org.apache.log4j.Logger logger
-
-
-
Class com.compomics.util.gui.renderers.GraphicsPanelTableCellRenderer extends JLabel implements Serializable
-
Serialized Fields
-
delegate
TableCellRenderer delegate
A reference to a standard table cell renderer. -
maxXAxisValue
double maxXAxisValue
The maxium x-axis value. -
minXAxisValue
double minXAxisValue
The minimum x-axis value.
-
-
-
Class com.compomics.util.gui.renderers.TimestampRenderer extends DefaultTableCellRenderer implements Serializable
-
Serialized Fields
-
logger
org.apache.log4j.Logger logger
-
-
-
Class com.compomics.util.gui.renderers.ToolTipComboBoxRenderer extends BasicComboBoxRenderer implements Serializable
-
Serialized Fields
-
align
int align
The horizontal alignment of the text. -
backgroundColor
Color backgroundColor
The background color for the list. Defaults to white if not set. -
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. -
tooltips
Vector tooltips
The tooltips for each element in the list.
-
-
-
-
Package com.compomics.util.gui.spectrum
-
Class com.compomics.util.gui.spectrum.ChromatogramPanel extends GraphicsPanel implements Serializable
-
Class com.compomics.util.gui.spectrum.FragmentIonTable extends JTable implements Serializable
-
Serialized Fields
-
allAnnotations
ArrayList<IonMatch[]> allAnnotations
The spectrum annotations map. -
allSpectra
ArrayList<Spectrum> allSpectra
The list of spectra. Needed for intensity normalization. -
currentFragmentIonTypes
HashSet<Integer> currentFragmentIonTypes
The list of currently selected fragment ion types. -
currentPeptide
Peptide currentPeptide
The current peptide. -
modificationParameters
ModificationParameters modificationParameters
The modification parameters. -
modificationSequenceMatchingParameters
SequenceMatchingParameters modificationSequenceMatchingParameters
The modification sequence matching parameters. -
neutralLosses
NeutralLossesMap neutralLosses
The list of the currently selected neutral loss types. -
peptideSequence
String peptideSequence
The current peptide sequence. -
sequenceProvider
SequenceProvider sequenceProvider
The protein sequence provider. -
singleCharge
boolean singleCharge
If true, singly charge ions are included in the table. -
tooltips
ArrayList<String> tooltips
The table tooltips. -
twoCharges
boolean twoCharges
If true, doubly charged ions are included in the table.
-
-
-
Class com.compomics.util.gui.spectrum.GraphicsPanel extends JPanel implements Serializable
-
Serialized Fields
-
alphaLevel
float alphaLevel
The opacity of the spectra. 0 means completely see-through, 1 means opaque. -
ANNOTATED_STATUS
int ANNOTATED_STATUS
This status indicates that annotation (if present) will be displayed, while limiting the user to zooming in/out. -
annotateHighestPeak
boolean annotateHighestPeak
If more than one peak is within the accuracy range of an annotation setting this to true will always select the most intense of possible peaks. Setting this variable to false will instead select the most accurate peak. -
backgroundPeakWidth
float backgroundPeakWidth
The width used for the background peaks. -
currentGraphicsPanelType
GraphicsPanel.GraphicsPanelType currentGraphicsPanelType
Sets the current GraphicsPanel type, default to centroid spectrum. -
currentPadding
int currentPadding
The current padding (distance between the axes and the border of the panel). -
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. -
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. -
iAnnotations
Vector iAnnotations
The Vector that holds a set of Annotation instances. -
iAnnotationsMirroredSpectra
Vector iAnnotationsMirroredSpectra
The Vector that holds a set of Annotation instances for the mirrored spectra. -
iAnnotationYAxisThreshold
double iAnnotationYAxisThreshold
The percent non-inclusive, minimal y-axis value (compared to the highest point in the spectrum) a point should have before being eligible for annotation. Default is '0.0'. -
iAreaUnderCurveColor
ArrayList<Color> iAreaUnderCurveColor
Colors in which the chromatogram polyline is rendered. Indexed by dataset. -
iAreaUnderCurveColorMirroredSpectra
ArrayList<Color> iAreaUnderCurveColorMirroredSpectra
Colors in which the chromatogram polyline is rendered for the mirrored spectra. Indexed by dataset. -
iClicked
boolean iClicked
Boolean that indicates whether a point has been marked by clicking. -
iClickedDataSetIndex
int iClickedDataSetIndex
Int that indicates which dataset contains the clicked point. -
iClickedDataSetIndexMirrored
int iClickedDataSetIndexMirrored
Int that indicates which dataset contains the clicked point in the mirrored spectra. -
iClickedIndex
int iClickedIndex
Int that indicates which point was clicked. -
iClickedIndexMirrored
int iClickedIndexMirrored
Int that indicates which point was clicked in the mirrored spectra. -
iClickedList
Vector iClickedList
The Vector that holds all points clicked up to now. -
iClickedListDatasetIndices
Vector iClickedListDatasetIndices
The Vector that holds the dataset indices of all points clicked up to now. -
iClickedListDatasetIndicesMirrored
Vector iClickedListDatasetIndicesMirrored
The Vector that holds the dataset indices of all points clicked up to now in the mirrored spectra. -
iClickedListMirrored
Vector iClickedListMirrored
The Vector that holds all points clicked up to now in the mirrored spectra. -
iClickedMirrored
boolean iClickedMirrored
Boolean that indicates whether a point has been marked by clicking in the mirrored spectra. -
iCurrentDrawStyle
GraphicsPanel.DrawingStyle iCurrentDrawStyle
This variable holds the current drawing style. -
iDataPointAndLineColor
ArrayList<Color> iDataPointAndLineColor
Colors in which the data points and peaks are rendered. Indexed by dataset. -
iDataPointAndLineColorMirroredSpectra
ArrayList<Color> iDataPointAndLineColorMirroredSpectra
Colors in which the data points and peaks are rendered for the mirrored spectra. Indexed by dataset. -
iDotRadius
int iDotRadius
This variable holds the dot radius; only used when drawing style is DOTS style. -
iDragged
boolean iDragged
This boolean is set to 'true' when dragging is performed. -
iDragXLoc
int iDragXLoc
The current dragging location. -
iEndXLoc
int iEndXLoc
When the mouse is dragged, this represents the X-coordinate of the ending location. -
iFilename
String iFilename
The spectrum or chromatogram filename. -
iFilenameColor
Color iFilenameColor
This is the color the filename should be presented in. -
iFilenameMirrorredSpectrum
String iFilenameMirrorredSpectrum
The spectrum or chromatogram filename for the mirrored spectrum or chromatogram. -
iHighLight
boolean iHighLight
Boolean that will be 'true' when a point needs highlighting. -
iHighLightDatasetIndex
int iHighLightDatasetIndex
Index of the dataset containing the point that needs to be highlighted. -
iHighLightDatasetIndexMirrored
int iHighLightDatasetIndexMirrored
Index of the dataset containing the point that needs to be highlighted in the mirrored spectra. -
iHighLightIndex
int iHighLightIndex
Index of the point that needs to be highlighted. -
iHighLightIndexMirrored
int iHighLightIndexMirrored
Index of the point that needs to be highlighted in the mirrored spectra. -
iHighLightMirrored
boolean iHighLightMirrored
Boolean that will be 'true' when a point needs highlighting in the mirrored spectra. -
iMinDrag
int iMinDrag
Minimal dragging distance in pixels. -
iMSLevel
int iMSLevel
The ms level of the current spectrum. O is assumed to mean no ms level given. -
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.) -
iPointDetectionTolerance
int iPointDetectionTolerance
The deviation (both left and right) allowed for point highlighting detection. -
iPointSize
Integer iPointSize
Size for the point on a polygon. -
iPrecursorCharge
String iPrecursorCharge
This String holds the charge for the precursor. -
iPrecursorChargeMirorredSpectrum
String iPrecursorChargeMirorredSpectrum
This String holds the charge for the precursor for the mirrored spectrum. -
iPrecursorMZ
double iPrecursorMZ
This variable holds the precursor M/Z. -
iPrecursorMZMirroredSpectrum
double iPrecursorMZMirroredSpectrum
This variable holds the precursor M/Z for the mirrored spectrum. -
iSpecPanelListeners
ArrayList iSpecPanelListeners
The list of SpectrumPanelListeners. -
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. -
iStoredSequence
Vector iStoredSequence
The Vector that holds a set of stored points from a previously established list. -
iStoredSequenceDatasetIndices
Vector iStoredSequenceDatasetIndices
The Vector that holds the dataset indices of stored points from a previously established list. -
iStoredSequenceDatasetIndicesMirrored
Vector iStoredSequenceDatasetIndicesMirrored
The Vector that holds the dataset indices of stored points from a previously established list in the mirrored spectra. -
iStoredSequenceMirrored
Vector iStoredSequenceMirrored
The Vector that holds a set of stored points from a previously established list in the mirrored spectra. -
iTopPadding
int iTopPadding
Effective distance from the panel top border to 5 pixels above the top of the highest point (or y-tick mark). -
iXAxisData
ArrayList<double[]> 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. -
iXAxisDataInPixels
ArrayList<int[]> 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). -
iXAxisDataInPixelsMirroredSpectrum
ArrayList<int[]> 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). -
iXAxisDataMirroredSpectrum
ArrayList<double[]> 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. -
iXAxisLabel
String iXAxisLabel
The label (and unit between brackets, if available) for the x-axis. Defaults to "m/z". -
iXAxisMax
double iXAxisMax
The maximum x-axis value to display. -
iXAxisMin
double iXAxisMin
The minimum x-axis value to display. -
iXAxisStartAtZero
boolean iXAxisStartAtZero
This boolean is set to 'true' if the x-axis should start at zero. -
iXPadding
int iXPadding
Effective distance from the x-axis to the panel border. -
iXScaleUnit
double iXScaleUnit
Scale unit for the X axis. -
iXUnit
int iXUnit
Graphical unit for the X axis. -
iYAxisData
ArrayList<double[]> 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. -
iYAxisDataInPixels
ArrayList<int[]> 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). -
iYAxisDataInPixelsMirroredSpectrum
ArrayList<int[]> 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). -
iYAxisDataMirroredSpectrum
ArrayList<double[]> 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. -
iYAxisLabel
String iYAxisLabel
The label (and unit between brackets, if available) for the y-axis. Defaults to "Int". -
iYAxisMax
double iYAxisMax
The maximum y-axis value to display. -
iYAxisMin
double iYAxisMin
The minimum y-axis value to display. -
iYScaleUnit
double iYScaleUnit
Scale unit for the Y axis. -
iYUnit
int iYUnit
Graphical unit for the Y axis. -
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. -
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. -
padding
int padding
The padding (distance between the axes and the border of the panel). -
peakWaterMarkColor
Color peakWaterMarkColor
The color to use for the non-annotated peaks when only the annotated peaks are to be shown. -
peakWidth
float peakWidth
The width used for the annotated peaks. -
referenceAreasXAxis
HashMap<String,ReferenceArea> referenceAreasXAxis
A hashmap of the current x-axis reference areas. Key is the name of the reference area. -
referenceAreasYAxis
HashMap<String,ReferenceArea> referenceAreasYAxis
A hashmap of the current y-axis reference areas. Key is the name of the reference area. -
scientificPattern
String scientificPattern
The number format pattern for scientific annotation. -
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. -
showAllPeaks
boolean showAllPeaks
If false, only the annotated peaks will be shown. Note that this setting is ignored in profile mode! -
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. -
subscriptAnnotationNumbers
boolean subscriptAnnotationNumbers
If true, all numbers in peak annotations are subscripted. -
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. -
xAxisZoomRangeLowerValue
double xAxisZoomRangeLowerValue
The lower range for the current zoom range. -
xAxisZoomRangeUpperValue
double xAxisZoomRangeUpperValue
The upper range for the current zoom range. -
xTagCount
int xTagCount
The number of X-axis tags. -
yAxisZoomExcludesBackgroundPeaks
boolean yAxisZoomExcludesBackgroundPeaks
If true, the automatic y-axis zoom excludes the background peaks. False includes all peaks in the zoom. -
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. -
yTagCount
int yTagCount
The number of Y-axis tags.
-
-
-
Class com.compomics.util.gui.spectrum.IntensityHistogram extends JPanel implements Serializable
-
Serialized Fields
-
chartPanel
org.jfree.chart.ChartPanel chartPanel
The chart panel for external access.
-
-
-
Class com.compomics.util.gui.spectrum.IonLabelColorTableModel extends DefaultTableModel implements Serializable
-
Class com.compomics.util.gui.spectrum.IsotopicDistributionPanel extends GraphicsPanel implements Serializable
-
Serialized Fields
-
aSpectrumPeakColor
Color aSpectrumPeakColor
The color used for the peaks. Default to red. -
aSpectrumProfileModeLineColor
Color aSpectrumProfileModeLineColor
The color used for the area under the curve. Defaults to pink. -
iElements
HashMap<String,MolecularFormula> iElements
HashMap with the molecular formula for all the amino acids. -
logger
org.apache.log4j.Logger logger
-
peptideCharges
ArrayList<Integer> peptideCharges
The charges of the peptides. Indexed by dataset. -
peptideSequences
ArrayList<AASequenceImpl> peptideSequences
The peptide sequences to display the isotopic distribution for.
-
-
-
Class com.compomics.util.gui.spectrum.MassErrorBubblePlot extends JPanel implements Serializable
-
Serialized Fields
-
chartPanel
org.jfree.chart.ChartPanel chartPanel
The chart panel. -
currentlyUsedIonMatches
IonMatch[] currentlyUsedIonMatches
The array of currently used ions. -
dataSeriesfragmentIonColors
ArrayList<Color> dataSeriesfragmentIonColors
The data series fragment ion colors. -
useRelativeError
boolean useRelativeError
If true the relative error (ppm) is used instead of the absolute error (Da).
-
-
-
Class com.compomics.util.gui.spectrum.MassErrorPlot extends JPanel implements Serializable
-
Serialized Fields
-
annotations
IonMatch[] annotations
The complete list of possible spectrum annotations. -
chartPanel
org.jfree.chart.ChartPanel chartPanel
The chart panel.
-
-
-
Class com.compomics.util.gui.spectrum.SequenceFragmentationPanel extends JPanel implements Serializable
-
Serialized Fields
-
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. -
fontColor
Color fontColor
Color for the peptide sequence. -
forwardColor
Color forwardColor
Color for the forward ion -
forwardIon
int forwardIon
the forward ion type (for instance B ion) as indexed by the PeptideFragmentIon static fields -
iBarWidth
int iBarWidth
The width of the bars. -
iHighlightModifications
boolean iHighlightModifications
If true the modification are highlighted with a background color. -
iHorizontalSpace
int iHorizontalSpace
The horizontal space. -
iIonMatches
IonMatch[] iIonMatches
The array of fragment ion matches. -
iMaxBarHeight
double iMaxBarHeight
The maximum bar height. -
iPeptideSequenceFont
Font iPeptideSequenceFont
The font to use for the peptide sequence.. -
iSequenceComponents
String[] iSequenceComponents
Elementary data for composing the Panel. -
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 -
iXStart
int iXStart
The x-axis start position. -
modificationProfile
ModificationParameters modificationProfile
The modification profile. -
rewindColor
Color rewindColor
Color for the rewind ion -
rewindIon
int rewindIon
the rewind ion type (for instance B ion) as indexed by the PeptideFragmentIon static fields -
tooltipRectangles
HashMap<String,Rectangle> tooltipRectangles
A map of the rectangles that have tooltips, i.e., the fragment ion peaks and the PTM highlighting. -
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.
-
-
-
Class com.compomics.util.gui.spectrum.SpectrumPanel extends GraphicsPanel implements Serializable
-
-
Package com.compomics.util.gui.tablemodels
-
Class com.compomics.util.gui.tablemodels.SelfUpdatingTableModel extends DefaultTableModel implements Serializable
-
Serialized Fields
-
isScrolling
boolean isScrolling
When true this indicates that the user is currently scrolling in the table and that the table should not update. -
lastColumnSorted
int lastColumnSorted
Indicates which column was last changed. -
lastLoadingRunnable
com.compomics.util.gui.tablemodels.SelfUpdatingTableModel.LoadingRunnable lastLoadingRunnable
The last loading runnable. -
loadingPool
ExecutorService loadingPool
Executor for the loading threads. -
progressDialog
ProgressDialogX progressDialog
A progress dialog. -
rowEndLoading
int rowEndLoading
The view end index of the rows being loaded. -
rowStartLoading
int rowStartLoading
The view start index of the rows being loaded. -
selfUpdating
boolean selfUpdating
If false, the table will not update automatically. -
sortAscending
boolean sortAscending
If true the current sorting is ascending. -
unsorted
boolean unsorted
If true the table has not yet been sorted. -
updateMutex
Semaphore updateMutex
Mutex for the table update. -
updatingPool
ExecutorService updatingPool
Executor for the updating threads. -
viewIndexes
ArrayList<Integer> viewIndexes
List of view indexes.
-
-
-
-
Package com.compomics.util.gui.utils
-
Class com.compomics.util.gui.utils.ConnectionDialog extends JDialog implements Serializable
-
Serialized Fields
-
btnCancel
JButton btnCancel
-
btnOK
JButton btnOK
-
cmbConfigurations
JComboBox cmbConfigurations
-
iConnections
ArrayList 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. -
iLastInitiatedConfiguration
String iLastInitiatedConfiguration
-
iPropsFile
String iPropsFile
-
iTarget
Connectable iTarget
-
logger
org.apache.log4j.Logger logger
-
txtDriver
JTextField txtDriver
-
txtPassword
JPasswordField txtPassword
-
txtUrl
JTextField txtUrl
-
txtUser
JTextField txtUser
-
-
-
Class com.compomics.util.gui.utils.DateChooser extends JDialog implements Serializable
-
-
Package com.compomics.util.gui.utils.user_choice
-
Class com.compomics.util.gui.utils.user_choice.ListChooser extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
cancelButton
JButton cancelButton
-
canceled
boolean canceled
Boolean indicating whether the selection has been cancelled. -
items
ArrayList<String> items
The list of items the user will choose from. -
itemsLabel
JLabel itemsLabel
-
itemsPanel
JPanel itemsPanel
-
itemsTable
JTable itemsTable
-
itemsTableScrollPane
JScrollPane itemsTableScrollPane
-
okButton
JButton okButton
-
tableToolTips
ArrayList<String> tableToolTips
Table column header tooltips.
-
-
-
-
Package com.compomics.util.gui.utils.user_choice.list_choosers
-
Class com.compomics.util.gui.utils.user_choice.list_choosers.ModificationChooser extends ListChooser implements Serializable
-
Serialized Fields
-
modificationsFactory
ModificationFactory modificationsFactory
The modifications factory. -
modificationsList
ArrayList<String> modificationsList
List of modifications to display.
-
-
-
Class com.compomics.util.gui.utils.user_choice.list_choosers.StringListChooser extends ListChooser implements Serializable
-
-
Package com.compomics.util.gui.variants.aa_substitutions
-
Class com.compomics.util.gui.variants.aa_substitutions.AaSubstitutionMatrixTableModel extends DefaultTableModel implements Serializable
-
Serialized Fields
-
aaSubstitutionMatrix
AaSubstitutionMatrix aaSubstitutionMatrix
The substitution matrix to display. -
aminoAcids
char[] aminoAcids
The possible amino acids represented by their single character code. -
editable
boolean editable
Boolean indicating whether the table can be edited.
-
-
-
-
Package com.compomics.util.gui.waiting.waitinghandlers
-
Class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialog extends JDialog implements Serializable
-
Serialized Fields
-
iProgress
JProgressBar iProgress
-
logger
org.apache.log4j.Logger logger
-
-
-
Class com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX extends JDialog implements Serializable
-
Serialized Fields
-
canceled
boolean canceled
Boolean indicating whether the process has been canceled. -
displayProgress
boolean displayProgress
Set if the waiting handler is to show the progress for the current process or not. Useful when running subprocesses that one wants to be able to cancel but do not want to show the progress for. -
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. -
finished
boolean finished
Boolean indicating whether the process has been completed. -
mutex
SimpleSemaphore mutex
Mutex to synchronize multiple threads. -
normalIcon
Image normalIcon
The dialog/frame icon to use when done. -
progressBar
JProgressBar progressBar
-
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. -
waitingActionListener
WaitingActionListener waitingActionListener
The waiting action listener. -
waitingHandlerParentDialog
JDialog waitingHandlerParentDialog
The waitingHandlerParent dialog. -
waitingHandlerParentFrame
Frame waitingHandlerParentFrame
The waitingHandlerParent frame. -
waitingIcon
Image waitingIcon
The dialog/frame icon to use when waiting.
-
-
-
Class com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog extends JDialog implements Serializable
-
Serialized Fields
-
backgroundPanel
JPanel backgroundPanel
-
closeDialogWhenImportCompletesCheckBox
JCheckBox closeDialogWhenImportCompletesCheckBox
-
closeJButton
JButton closeJButton
-
currentTipIndex
int currentTipIndex
The current tip index. -
dialog
JDialog dialog
Needed for the shaking feature. -
displayProgress
boolean displayProgress
Set if the waiting handler is to show the progress for the current process or not. Useful when running subprocesses that one wants to be able to cancel but do not want to show the progress for. -
lastSelectedFolder
String lastSelectedFolder
The last selected folder -
layeredPane
JLayeredPane layeredPane
-
lineBreak
String lineBreak
The line break type. -
naturalLocation
Point naturalLocation
Used in the shaking feature. -
nextJButton
JButton nextJButton
-
normalIcon
Image normalIcon
The dialog/frame icon to use when done. -
okButton
JButton okButton
-
primaryMutex
SimpleSemaphore primaryMutex
Mutex to synchronize multiple threads on the primary error bar. -
processName
String processName
The name of the process we are waiting for, e.g., 'Import Data' or 'Search'. -
processProgressPanel
JPanel processProgressPanel
-
progressBar
JProgressBar progressBar
-
reportScrollPane
JScrollPane reportScrollPane
-
reportTextArea
JTextArea reportTextArea
-
runCanceled
boolean runCanceled
Boolean indicating whether the process is canceled. -
runFinished
boolean runFinished
Boolean indicating whether the process is finished. -
saveReportLabel
JLabel saveReportLabel
-
secondaryJProgressBar
JProgressBar secondaryJProgressBar
-
secondaryMutex
SimpleSemaphore secondaryMutex
Mutex to synchronize multiple threads on the secondary error bar. -
secondaryProgressBarSplitPane
JSplitPane secondaryProgressBarSplitPane
-
shakeTimer
Timer shakeTimer
Timer for the shaking feature. -
shakeWhenFinished
boolean shakeWhenFinished
If true, the dialog will shake when completed. Mainly a PeptideShaker feature. -
showTipOfTheDayCheckBox
JCheckBox showTipOfTheDayCheckBox
-
tempJProgressBar
JProgressBar tempJProgressBar
-
textMutex
SimpleSemaphore textMutex
Mutex to synchronize multiple threads writing text. -
tipOfTheDayEditorPane
JEditorPane tipOfTheDayEditorPane
-
tipOfTheDayJPanel
JPanel tipOfTheDayJPanel
-
tipOfTheDayLayeredPane
JLayeredPane tipOfTheDayLayeredPane
-
tipOfTheDayScrollPane
JScrollPane tipOfTheDayScrollPane
-
tips
ArrayList<String> tips
An array list of the tip of the day. -
toolName
String toolName
The name of the tool using the waiting dialog. Used for the report. -
toolVersion
String toolVersion
The version number of the tool using the waiting dialog. Used for the report. -
waitingActionListener
WaitingActionListener waitingActionListener
The waiting action listener. -
waitingHandlerParent
Frame waitingHandlerParent
The waitingHandlerParent. -
waitingIcon
Image waitingIcon
The dialog/frame icon to use when waiting.
-
-
-
-
Package com.compomics.util.io.export
-
Class com.compomics.util.io.export.ExportScheme extends ExperimentObject implements Serializable
- serialVersionUID:
- -4712918049667194600L
-
Serialized Fields
-
editable
boolean editable
A boolean indicating whether the scheme can be modified. -
exportFeaturesMap
HashMap<String,ArrayList<ExportFeature>> exportFeaturesMap
Map of the features to export indexed by feature type. -
header
boolean header
Boolean indicating whether column headers shall be included. -
includeDecoy
Boolean includeDecoy
Indicates whether decoy matches should be included. -
includeSectionTitles
boolean includeSectionTitles
Indicates whether the title of every section shall be included. -
indexes
boolean indexes
Boolean indicating whether the line shall be indexed. -
mainTitle
String mainTitle
The title of the report. -
name
String name
The name of the scheme. -
sectionList
ArrayList<String> sectionList
Ordered list of the features in that scheme. -
separationLines
int separationLines
indicates how many lines shall be used to separate sections. -
separator
String separator
The separator used to separate columns. -
validatedOnly
Boolean validatedOnly
Indicates whether only validated matches should be included.
-
-
-
Package com.compomics.util.io.file
-
Class com.compomics.util.io.file.LastSelectedFolder extends ExperimentObject implements Serializable
- serialVersionUID:
- 7612497861284156966L
-
-
Package com.compomics.util.io.ftp
-
Class com.compomics.util.io.ftp.FtpConnectionException extends FtpProtocolException implements Serializable
-
Serialized Fields
-
logger
org.apache.log4j.Logger logger
-
-
-
Class com.compomics.util.io.ftp.FtpLoginException extends FtpProtocolException implements Serializable
-
Serialized Fields
-
logger
org.apache.log4j.Logger logger
-
-
-
Class com.compomics.util.io.ftp.FtpProtocolException extends IOException implements Serializable
-
Serialized Fields
-
logger
org.apache.log4j.Logger logger
-
-
-
-
Package com.compomics.util.io.json
-
Class com.compomics.util.io.json.JsonMarshaller extends ExperimentObject implements Serializable
-
Serialized Fields
-
builder
com.google.gson.GsonBuilder builder
GsonBuilder that can be used to append interfaces so the parser knows how to handle them. -
gson
com.google.gson.Gson gson
GSON parser instance to convert JSON to Java objects and back.
-
-
-
-
Package com.compomics.util.io.json.marshallers
-
Class com.compomics.util.io.json.marshallers.IdentificationParametersMarshaller extends JsonMarshaller implements Serializable
-
Class com.compomics.util.io.json.marshallers.PrideMarshaller extends JsonMarshaller implements Serializable
-
Class com.compomics.util.io.json.marshallers.PTMFactoryMarshaller extends JsonMarshaller implements Serializable
-
-
Package com.compomics.util.math.statistics.distributions
-
Class com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution extends ExperimentObject implements Serializable
- serialVersionUID:
- -5258258835569357886L
-
Serialized Fields
-
distributionDown
NormalDistribution distributionDown
Distribution equivalent to the left of the distribution. -
distributionUp
NormalDistribution distributionUp
Distribution equivalent to the right of the distribution. -
mean
double mean
The mean. -
stdDown
double stdDown
The standard deviation on the left of the distribution. -
stdUp
double stdUp
The standard deviation on the right of the distribution.
-
-
Class com.compomics.util.math.statistics.distributions.NormalDistribution extends ExperimentObject implements Serializable
-
Serialized Fields
-
mean
double mean
The mean of the distribution. -
normalDistributionImpl
org.apache.commons.math.distribution.NormalDistributionImpl normalDistributionImpl
The apache normal distribution implementation. -
std
double std
The standard deviation of the distribution.
-
-
-
-
Package com.compomics.util.parameters
-
Class com.compomics.util.parameters.UtilitiesUserParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- -4343570286224891504L
-
Serialized Fields
-
autoUpdate
boolean autoUpdate
Indicates whether the tool should check for updates. -
checkDuplicateTitles
boolean checkDuplicateTitles
If true, the selected spectra will be checked for duplicate spectrum titles. -
checkMgfSize
boolean checkMgfSize
If true, the mgf files will be checked for size. -
checkPeakPicking
boolean checkPeakPicking
If true, the selected spectra will be checked for peak picking. -
checkSpectrumCharges
boolean checkSpectrumCharges
If true, the spectra will be checked for missing charges. -
dbFolder
String dbFolder
The user last used database folder. -
deNovoGuiPath
String deNovoGuiPath
The path to the DeNovoGUI installation (if any). Set to null if no path is provided. -
displayedTips
ArrayList<String> displayedTips
The list of already displayed tips. -
gzip
boolean gzip
Boolean indicating whether the output files should be gzipped. -
includeDateInOutputName
boolean includeDateInOutputName
Indicates whether the date should be included in the output. -
javaHome
String javaHome
The Java Home, for example, C:\Program Files\Java\jdk1.8.0_25\bin. Null if not set. Note that this setting will be ignored of a JavaHome.txt file is found. -
lastSelectedFolder
LastSelectedFolder lastSelectedFolder
The last selected folder. -
localPrideFolder
String localPrideFolder
The local PRIDE projects folder. -
maxSpectrumChargeRange
int maxSpectrumChargeRange
The minimum charge added when the charge is missing for a given spectrum. -
memoryParameter
int memoryParameter
The memory to use. -
mgfMaxSize
double mgfMaxSize
If an mgf file exceeds this limit, the user will be asked for a split. -
mgfNSpectra
int mgfNSpectra
Number of spectra allowed in the split file. -
minSpectrumChargeRange
int minSpectrumChargeRange
The maximum charge added when the charge is missing for a given spectrum. -
outputData
boolean outputData
Indicates whether data files (mgf and FASTA) should be copied in the output. -
outputFolder
String outputFolder
The user last used output folder. -
outputOption
OutputParameters outputOption
The way output files should be exported. -
peptideSelected
Color peptideSelected
The color of the selected peptide. -
peptideShakerPath
String peptideShakerPath
The path to the PeptideShaker installation (if any). Set to null if no path is provided. -
proteoWizardPath
String proteoWizardPath
The path to the ProteoWizard installation (if any). Set to null if no path is provided. -
readTweets
ArrayList<String> readTweets
The list of already read tweets. -
refMass
double refMass
Reference mass for the conversion of the fragment ion tolerance from ppm to Dalton. -
relimsPath
String relimsPath
The path to the Relims installation (if any). Set to null if no path is provided. -
renameXTandemFile
boolean renameXTandemFile
If true the X! Tandem file will be renamed. -
reporterPath
String reporterPath
The path to the Reporter installation (if any). Set to null if no path is provided. -
searchGuiPath
String searchGuiPath
The path to the SearchGUI installation (if any). Makes it possible to start SearchGUI directly from PeptideShaker. Set to null if no path is provided. -
sortPsmsOnRt
boolean sortPsmsOnRt
If true, the PSMs are sorted on retention time, false sorts on PSM score. -
sparklineColorDoubtful
Color sparklineColorDoubtful
The color used for the doubtful matches in sparkline bar chart plots. -
sparklineColorFalsePositive
Color sparklineColorFalsePositive
The color used for the false positive in sparkline bar chart plots. -
sparklineColorNonValidated
Color sparklineColorNonValidated
The color used for the non-validated sparkline bar chart plots. -
sparklineColorNotFound
Color sparklineColorNotFound
The color used for the not found sparkline bar chart plots. -
sparklineColorPossible
Color sparklineColorPossible
The color used for the possible values sparkline bar chart plots. -
sparklineColorValidated
Color sparklineColorValidated
The color used for the sparkline bar chart plots. -
spectrumAnnotatedMirroredPeakColor
Color spectrumAnnotatedMirroredPeakColor
The color to use for the annotated mirrored peaks. -
spectrumAnnotatedPeakColor
Color spectrumAnnotatedPeakColor
The color to use for the annotated peaks. -
spectrumAnnotatedPeakWidth
float spectrumAnnotatedPeakWidth
The width to use for the annotated peaks. -
spectrumBackgroundPeakColor
Color spectrumBackgroundPeakColor
The color to use for the background peaks. -
spectrumBackgroundPeakWidth
float spectrumBackgroundPeakWidth
The width to use for the background peaks. -
spectrumFolder
String spectrumFolder
The user last used spectrum folder.
-
-
-
Package com.compomics.util.parameters.identification
-
Class com.compomics.util.parameters.identification.IdentificationParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
annotationParameters
AnnotationParameters annotationParameters
The peak annotation parameters. -
defaultDescription
boolean defaultDescription
Indicates whether the description is automatically generated. -
description
String description
The description of the parameters. -
fastaParameters
FastaParameters fastaParameters
The FASTA processing parameters. -
fractionParameters
FractionParameters fractionParameters
The fraction settings. -
geneParameters
GeneParameters geneParameters
The gene parameters. -
idValidationParameters
IdMatchValidationParameters idValidationParameters
The identification validation parameters. -
marshallableParameterType
String marshallableParameterType
Name of the type of marshalled parameter. -
modificationLocalizationParameters
ModificationLocalizationParameters modificationLocalizationParameters
The modification localization parameters. -
name
String name
The name of the parameters. -
peptideAssumptionFilter
PeptideAssumptionFilter peptideAssumptionFilter
The PSM filter. -
peptideVariantsParameters
PeptideVariantsParameters peptideVariantsParameters
The peptide variants parameters. -
proteinInferenceParameters
ProteinInferenceParameters proteinInferenceParameters
The protein inference parameters. -
psmScoringParameters
PsmScoringParameters psmScoringParameters
The PSM scores to use. -
searchParameters
SearchParameters searchParameters
The parameters used for the spectrum matching. -
sequenceMatchingParameters
SequenceMatchingParameters sequenceMatchingParameters
The peptide to protein matching parameters. -
version
String version
Version number.
-
-
-
-
Package com.compomics.util.parameters.identification.advanced
-
Class com.compomics.util.parameters.identification.advanced.FractionParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
fractionMolecularWeightRanges
HashMap<String,no.uib.jsparklines.data.XYDataPoint> fractionMolecularWeightRanges
The list of fraction molecular weights. The key is the fraction name. -
proteinConfidenceMwPlots
Double proteinConfidenceMwPlots
The minimum confidence required for a protein to be included in the calculation of the average molecular weight plot in the Fractions tab of PeptideShaker.
-
-
-
Class com.compomics.util.parameters.identification.advanced.GeneParameters extends ExperimentObject implements Serializable
-
Class com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
defaultPeptideFDR
double defaultPeptideFDR
The default peptide FDR. -
defaultProteinFDR
double defaultProteinFDR
The default protein FDR. -
defaultPsmFDR
double defaultPsmFDR
The default PSM FDR. -
validationQCPreferences
ValidationQcParameters validationQCPreferences
The validation quality control preferences.
-
-
-
Class com.compomics.util.parameters.identification.advanced.ModificationLocalizationParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
alignNonConfidentModifications
boolean alignNonConfidentModifications
Boolean indicating whether the non confidently localized modification should be aligned on the confident sites. -
dScoreThreshold
double dScoreThreshold
The D-score threshold. -
probabilisticScoreCalculation
boolean probabilisticScoreCalculation
Boolean indicating whether a probabilistic score is to be calculated. -
probabilisticScoreNeutralLosses
boolean probabilisticScoreNeutralLosses
Boolean indicating whether neutral losses shall be accounted for in the calculation of the probabilistic score. -
probabilisticScoreThreshold
double probabilisticScoreThreshold
The probabilistic score threshold. -
selectedProbabilisticScore
ModificationLocalizationScore selectedProbabilisticScore
The probabilistic score selected. -
sequenceMatchingParameters
SequenceMatchingParameters sequenceMatchingParameters
The preferences to use when matching modifications to amino acid sequences.
-
-
-
Class com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
aaSubstitutionMatrix
AaSubstitutionMatrix aaSubstitutionMatrix
The amino acid substitution matrix selected. -
fixedVariants
HashMap<String,ArrayList<SNPElement>> fixedVariants
SNP positions for fixed variants -
nAaDeletions
int nAaDeletions
The number of amino acid deletions allowed. -
nAaInsertions
int nAaInsertions
The number of amino acid insertions allowed. -
nAaSubstitutions
int nAaSubstitutions
The number of amino acid substitutions allowed. -
nAaSwap
int nAaSwap
The number of amino acid swap allowed. -
nVariants
int nVariants
Total number of variants allowed per peptide. -
variantType
PeptideVariantsParameters.VariantType variantType
Boolean indicating whether specific variant counts should be used.
-
-
-
Class com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
confidenceThreshold
double confidenceThreshold
Confidence below which a peptide is considered absent. -
modificationRefinement
boolean modificationRefinement
Refine based on terminal and pattern modifications. -
simplifyGroupsConfidence
boolean simplifyGroupsConfidence
Simplify groups based on peptide confidenc level. -
simplifyGroupsEnzymaticity
boolean simplifyGroupsEnzymaticity
Simplify groups based on enzymaticity. -
simplifyGroupsEvidence
boolean simplifyGroupsEvidence
Simplify groups based on UniProt evidence level. -
simplifyGroupsVariants
boolean simplifyGroupsVariants
Simplify groups based on variant matching. -
simplifyProteinGroups
boolean simplifyProteinGroups
Simplify protein groups.
-
-
-
Class com.compomics.util.parameters.identification.advanced.PsmScoringParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
defaultScores
HashSet<Integer> defaultScores
The scores to use by default. -
minDecoysInBin
int minDecoysInBin
The minimal number of decoys to include in a bin to set the bin size of the score histogram. -
spectrumMatchingScores
HashMap<Integer,HashSet<Integer>> spectrumMatchingScores
The scores used to score the spectrum matches for every advocate in a map: advocate index > list of score indexes.
-
-
-
Class com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
enzymaticTagsOnly
Boolean enzymaticTagsOnly
Boolean deciding whether tags should only be mapped to enzymatic peptides. -
limitX
double limitX
Limit the share of X's a match can contain, range [0.0-1.0]. -
maxPtmsPerTagPeptide
int maxPtmsPerTagPeptide
The maximum number of PTMs per peptide when mapping tags. -
minAminoAcidScore
Integer minAminoAcidScore
The minimum amino acid score [0-100]. Used when converting Novor peptides into tags. -
minTagLength
Integer minTagLength
The minimum tag length. Used when converting Novor peptides into tags. -
sequenceMatchingType
SequenceMatchingParameters.MatchingType sequenceMatchingType
The amino acid matching type.
-
-
-
Class com.compomics.util.parameters.identification.advanced.ValidationQcParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
confidenceMargin
Double confidenceMargin
The margin in number of resolution over the confidence threshold. -
dbSize
boolean dbSize
Indicates whether the database size should be checked. -
firstDecoy
boolean firstDecoy
Indicates whether the number of hits before the first decoy should be checked. -
peptideFilters
ArrayList<Filter> peptideFilters
List of QC filters for peptides. -
proteinFilters
ArrayList<Filter> proteinFilters
List of QC filters for proteins. -
psmFilters
ArrayList<Filter> psmFilters
List of QC filters for PSMs.
-
-
-
-
Package com.compomics.util.parameters.identification.search
-
Class com.compomics.util.parameters.identification.search.DigestionParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
cleavageParameter
DigestionParameters.CleavageParameter cleavageParameter
Boolean indicating whether the sample was not digested. -
enzymes
ArrayList<Enzyme> enzymes
List of enzyme used. -
nMissedCleavages
HashMap<String,Integer> nMissedCleavages
Number of allowed missed cleavages. -
specificity
HashMap<String,DigestionParameters.Specificity> specificity
The specificity of the enzyme.
-
-
-
Class com.compomics.util.parameters.identification.search.ModificationParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- 342611308111304721L
-
Serialized Fields
-
backUp
HashMap<String,Modification> backUp
Back-up mapping of the modifications for portability. -
colors
HashMap<String,Integer> colors
Mapping of the expected modification names to the color used. -
fixedModifications
ArrayList<String> fixedModifications
List of the expected fixed modifications. -
refinementFixedModifications
ArrayList<String> refinementFixedModifications
List of variable modifications searched during the second pass search. -
refinementVariableModifications
ArrayList<String> refinementVariableModifications
List of variable modifications searched during the second pass search. -
variableModifications
ArrayList<String> variableModifications
List of the expected variable modifications.
-
-
Class com.compomics.util.parameters.identification.search.SearchParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
algorithmParameters
HashMap<Integer,IdentificationAlgorithmParameter> algorithmParameters
The algorithm specific parameters. -
digestionParameters
DigestionParameters digestionParameters
The digestion preferences. -
flanking
boolean flanking
Report the flanking amino acids of a mapped peptide. -
forwardIons
ArrayList<Integer> forwardIons
The forward ions to consider (a, b or c). -
fragmentAccuracyType
SearchParameters.MassAccuracyType fragmentAccuracyType
The fragment accuracy type. Default is Da. -
fragmentIonMZTolerance
double fragmentIonMZTolerance
The MS2 ion tolerance. -
marshallableParameterType
String marshallableParameterType
Name of the type of marshalled parameter. -
maxChargeSearched
int maxChargeSearched
The minimal charge searched (in absolute value). -
maxIsotopicCorrection
int maxIsotopicCorrection
The maximal isotope correction. -
minChargeSearched
int minChargeSearched
The minimal charge searched (in absolute value). -
minIsotopicCorrection
int minIsotopicCorrection
The minimal isotope correction. -
modificationParameters
ModificationParameters modificationParameters
The expected modifications. Modified peptides will be grouped and displayed according to this classification. -
precursorAccuracyType
SearchParameters.MassAccuracyType precursorAccuracyType
The precursor accuracy type. Default is ppm. -
precursorTolerance
double precursorTolerance
The precursor mass tolerance. -
refMass
double refMass
Reference mass for the conversion of the fragment ion tolerance from ppm to Dalton. -
rewindIons
ArrayList<Integer> rewindIons
The rewind ions to consider (x, y or z). -
version
String version
Version number.
-
-
-
-
Package com.compomics.util.parameters.identification.tool_specific
-
Class com.compomics.util.parameters.identification.tool_specific.AndromedaParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- 9056661756332085205L
-
Serialized Fields
-
decoyMode
AndromedaParameters.AndromedaDecoyMode decoyMode
The decoy mode. -
dependentLosses
Boolean dependentLosses
Boolean indicating whether neutral losses should be sequence dependent. -
empiricalCorrection
Boolean empiricalCorrection
Boolean indicating whether the empirical correction should be used. -
equalIL
Boolean equalIL
Boolean indicating whether I and L should be considered indistinguishable. -
fragmentAll
Boolean fragmentAll
Boolean indicating whether the fragment all option should be used. -
fragmentationMethod
FragmentationMethod fragmentationMethod
The fragmentation method used. -
higherCharge
Boolean higherCharge
Boolean indicating whether the higher charge option should be used. -
includeAmmonia
Boolean includeAmmonia
Boolean indicating whether ammonia losses should be accounted for. -
includeWater
Boolean includeWater
Boolean indicating whether water losses should be accounted for. -
maxCombinations
Integer maxCombinations
The maximum number of combinations. -
maxNumberOfModifications
Integer maxNumberOfModifications
The maximal number of modifications. -
maxPeptideLengthNoEnzyme
Integer maxPeptideLengthNoEnzyme
The maximal peptide length when no enzyme is used. -
maxPeptideMass
Double maxPeptideMass
The maximal peptide mass. -
minPeptideLengthNoEnzyme
Integer minPeptideLengthNoEnzyme
The minimal peptide length when no enzyme is used. -
numberOfCandidates
Integer numberOfCandidates
The number of candidates to report. -
ptmIndexes
HashMap<Integer,String> ptmIndexes
Map of the Andromeda indexes used for user modifications in this search. -
topPeaks
Integer topPeaks
The top peaks number. -
topPeaksWindow
Integer topPeaksWindow
The top peaks window size.
-
-
Class com.compomics.util.parameters.identification.tool_specific.CometParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- -2996752557726296967L
-
Serialized Fields
-
batchSize
Integer batchSize
When this parameter is set to a non-zero value, say 5000, this causes Comet to load and search about 5000 spectra at a time, looping through sets of 5000 spectra until all data have been analyzed. Set this parameter to 0 to load and search all spectra at once. -
enzymeType
Integer enzymeType
The enzyme type: 1 for a semi-enzyme search, 2 for a full-enzyme search, 8 for a semi-enzyme search, unspecific cleavage on peptide's C-terminus and 9 for a semi-enzyme search, unspecific cleavage on peptide's N-terminus. -
fragmentBinOffset
Double fragmentBinOffset
The fragment bin offset. -
isotopeCorrection
Integer isotopeCorrection
Isotope correction setting. 0: analyzes no isotope offsets, just the given precursor mass, 1: searches 0, +1 isotope offsets, 2: searches 0, +1, +2 isotope offsets, 3: searches 0, +1, +2, +3 isotope offsets, 4: searches -8, -4, 0, +4, +8 isotope offsets (for +4/+8 stable isotope labeling). -
lowerClearMzRange
Double lowerClearMzRange
Defines the lower m/z value to clear out in each MS/MS spectra. -
maxFragmentCharge
Integer maxFragmentCharge
The maximum fragment charge. -
maxPeptideLength
Integer maxPeptideLength
The maximal peptide length. Maximum length for Comet is 63. -
maxPrecursorMass
Double maxPrecursorMass
The maximum precursor mass. -
maxVariableMods
Integer maxVariableMods
The maximum number of variable modifications per peptide. -
minPeakIntensity
Double minPeakIntensity
The minimum peak intensity. -
minPeaks
Integer minPeaks
The minimum allowed number of peaks in a spectrum. -
minPeptideLength
Integer minPeptideLength
The minimum peptide length. -
minPrecursorMass
Double minPrecursorMass
The minimum precursor mass. -
numberOfSpectrumMatches
Integer numberOfSpectrumMatches
The maximum number of spectrum matches. -
printExpectScore
Boolean printExpectScore
A boolean flag this determines whether or not the expectation score (E-value) is reported in .out and SQT formats. Note that the E-value is always reported in pepXML output. This parameter is only relevant for results reported in .out and SQT formats. -
removeMethionine
Boolean removeMethionine
This parameter controls whether Comet will automatically remove the N-terminal methionine from a sequence entry. -
removePrecursor
Integer removePrecursor
Remove precursor peak. An input value of 0 will not perform any precursor removal. An input value of 1 will remove all peaks around the precursor m/z. An input value of 2 will remove all charge reduced precursor peaks as expected to be present for ETD/ECD spectra. An input value of 3 will remove the HPO3 (-80) and H3PO4 (-98) precursor phosphate neutral loss peaks. -
removePrecursorTolerance
Double removePrecursorTolerance
This parameter specifies the mass tolerance (in Da) around each precursor m/z that would be removed when the remove_precursor_peak option is invoked. -
requireVariableMods
Boolean requireVariableMods
Controls whether the peptides must contain at least one variable modification i.e. force all reported peptides to have a variable modification. -
selectedOutputFormat
CometParameters.CometOutputFormat selectedOutputFormat
The selected output format. -
theoreticalFragmentIonsSumOnly
Boolean theoreticalFragmentIonsSumOnly
The correlation score type. This parameter specifies how theoretical fragment ion peaks are represented. -
upperClearMzRange
Double upperClearMzRange
Defines the upper m/z value to clear out in each MS/MS spectra. -
useSparseMatrix
Boolean useSparseMatrix
Deprecated.from Comet release 2015.02 all searches use this internal data representation by defaultControls whether or not internal sparse matrix data representation is used.
-
-
Class com.compomics.util.parameters.identification.tool_specific.DirecTagParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- -3107089648450731330L
-
Serialized Fields
-
adjustPrecursorMass
boolean adjustPrecursorMass
If true, the preprocessing step will correct the precursor mass by adjusting it through a specified range in steps of a specified length, finally choosing the optimal adjustment. The optimal adjustment is the one that maximizes the sum of products of all complementary peaks in the spectrum. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
complementMzTolerance
double complementMzTolerance
When adjusting the precursor mass, this parameter controls how much tolerance there is on each side of the calculated m/z when looking for a peaks complement. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
complementScoreWeight
double complementScoreWeight
This parameter controls how complement scores are combined to form a total score. Peaks that match to complementary ions within the spectrum are more trustworthy than other peaks. DirecTag assesses the number and concordance of complementary ions for each tag. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
deisotopingMode
int deisotopingMode
Deisotoping a spectrum (consolidating isotopic peak intensities into the monoisotopic peaks intensity) during preprocessing will significantly improve precursor adjustment, and it may be desirable to keep the deisotoped spectrum around for candidate scoring as well. Set to 0, no deisotoping will be used. Set to 1, deisotoping will be used for precursor adjustment only. Set to 2, deisotoping will be used for both precursor adjustment and for candidate scoring. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
duplicateSpectra
boolean duplicateSpectra
If DirecTag determines a spectrum to be multiply charged and this parameter is true, the spectrum will be copied and treated as if it was all possible charge states from +2 to +<NumChargeStates>. If this parameter is false, the spectrum will simply be treated as a +2. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
intensityScoreWeight
double intensityScoreWeight
This parameter controls how intensity scores are combined to form a total score. DirecTag scores tags on the basis of their peak intensities. Tags that contain intense peaks are more likely to be correct than those that contain average peaks. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
isotopeMzTolerance
double isotopeMzTolerance
When deisotoping a spectrum, an isotopic peak is one that is the mass of a neutron higher than another peak, tolerating variation based on the value of this parameter. Deisotoping actually traverses the spectrum at multiple charge states, starting from the highest (NumChargeStates) and ending at the lowest. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
maxDynamicMods
int maxDynamicMods
This parameter sets the maximum number of modified residues that may be in any candidate sequence. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
maxPeakCount
int maxPeakCount
Another way of increasing the effectiveness of the MVH scoring algorithm when used for tagging is to set an upper bound on the number of peaks in a spectrum before generating tags. This step tends to get rid of most noise peaks and makes tagging much more feasible because so many fewer false positives are generated. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
maxPrecursorAdjustment
double maxPrecursorAdjustment
When adjusting the precursor mass, this parameter sets the upper mass limit of adjustment allowable from the original precursor mass, measured in Daltons. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
maxTagCount
int maxTagCount
This parameter sets the maximum number of sequence tags to report for each spectrum. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
minPrecursorAdjustment
double minPrecursorAdjustment
When adjusting the precursor mass, this parameter sets the lower mass limit of adjustment allowable from the original precursor mass, measured in Daltons. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
mzFidelityScoreWeight
double mzFidelityScoreWeight
This parameter controls how mzFidelity scores are combined to form a total score. m/z fidelity for a tag can be characterized through SSE. DirecTag evaluates the consistency of fragment ion m/z values for each tag. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
numChargeStates
int numChargeStates
Controls the number of charge states that DirecTag will handle during all stages of the program. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
numIntensityClasses
int numIntensityClasses
Before scoring any candidates, experimental spectra have their peaks stratified into the number of intensity classes specified by this parameter. Spectra that are very dense in peaks will likely benefit from more intensity classes in order to best take advantage of the variation in peak intensities. Spectra that are very sparse will not see much benefit from using many intensity classes. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
outputSuffix
String outputSuffix
The output of a DirecTag job will be a TAGS file for each input file. The string specified by this parameter will be appended to each TAGS0.5 filename. It is useful for differentiating jobs within a single directory. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
precursorAdjustmentStep
double precursorAdjustmentStep
When adjusting the precursor mass, this parameter sets the size of the steps between adjustments, measured in Daltons. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
tagLength
int tagLength
A sequence tag is generated from the gaps between a number of peaks equal to this parameter plus one. Longer tag lengths are more specific, but harder to find because many consecutive ion fragments are rare. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
ticCutoffPercentage
double ticCutoffPercentage
In order to maximize the effectiveness of the MVH scoring algorithm, an important step in preprocessing the experimental spectra is filtering out noise peaks. Noise peaks are filtered out by sorting the original peaks in descending order of intensity, and then picking peaks from that list until the cumulative ion current of the picked peaks divided by the total ion current (TIC) is greater than or equal to this parameter. Lower percentages mean that less of the spectra total intensity will be allowed to pass through preprocessing. See the section on Advanced Usage for tips on how to use this parameter optimally. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
useChargeStateFromMS
boolean useChargeStateFromMS
If true, DirecTag will use the charge state from the input data if it is available. If false, or if charge state is not available from a particular spectrum, DirecTag will use its internal algorithm to determine charge state. (http://fenchurch.mc.vanderbilt.edu/bumbershoot/directag) -
variableModifications
ArrayList<String> variableModifications
The variable modifications in the order used.
-
-
Class com.compomics.util.parameters.identification.tool_specific.MetaMorpheusParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
deconvolutionIntensityRatio
Double deconvolutionIntensityRatio
Deconvolution intensity ratio. -
deconvolutionMassTolerance
Double deconvolutionMassTolerance
Deconvolution mass tolerance. -
deconvolutionMassToleranceType
MetaMorpheusParameters.MetaMorpheusToleranceType deconvolutionMassToleranceType
Deconvolution mass tolerance type: PPM or Absolute. -
decoyType
MetaMorpheusParameters.MetaMorpheusDecoyType decoyType
Decoy type: None, Reverse or Slide. -
dissociationType
MetaMorpheusParameters.MetaMorpheusDissociationType dissociationType
Dissociation type. -
doPrecursorDeconvolution
Boolean doPrecursorDeconvolution
Do precursor deconvolution. -
fragmentationTerminus
MetaMorpheusParameters.MetaMorpheusFragmentationTerminusType fragmentationTerminus
Fragmentation terminus type. -
gPtmCategories
ArrayList<ModificationCategory> gPtmCategories
The modification categories to include in the G-PTM search. -
initiatorMethionineBehavior
MetaMorpheusParameters.MetaMorpheusInitiatorMethionineBehaviorType initiatorMethionineBehavior
Initiator methionine behavior. -
massDiffAcceptorType
MetaMorpheusParameters.MetaMorpheusMassDiffAcceptorType massDiffAcceptorType
Mass difference acceptor type. -
maxFragmentSize
Double maxFragmentSize
Max fragment size. -
maxHeterozygousVariants
Integer maxHeterozygousVariants
Max heterozygous variants. -
maxModificationIsoforms
Integer maxModificationIsoforms
Max modification isoforms. -
maxModsForPeptide
Integer maxModsForPeptide
Maximum number of modifications per peptide. -
maxPeptideLength
Integer maxPeptideLength
Maximum peptide length. -
minAllowedIntensityRatioToBasePeak
Double minAllowedIntensityRatioToBasePeak
Minimum allowed intensity ratio to base peak. -
minPeptideLength
Integer minPeptideLength
Minimum peptide length. -
minVariantDepth
Integer minVariantDepth
Min variant depth. -
modPeptidesAreDifferent
Boolean modPeptidesAreDifferent
Modified peptides are different. -
noOneHitWonders
Boolean noOneHitWonders
No one hit wonders. -
normalizePeaksAcrossAllWindows
Boolean normalizePeaksAcrossAllWindows
Normalize peaks across all windows. -
numberOfPeaksToKeepPerWindow
Integer numberOfPeaksToKeepPerWindow
Number of peaks to keep per window. -
numberOfWindows
Integer numberOfWindows
Number of windows. -
runGptm
boolean runGptm
If true, the G-PTM search is performed. -
scoreCutoff
Double scoreCutoff
Score cut-off. -
searchTarget
Boolean searchTarget
Search target. -
searchType
MetaMorpheusParameters.MetaMorpheusSearchType searchType
Search type. -
totalPartitions
Integer totalPartitions
Number of partitions when doing a modern or non-specific search. -
trimMs1Peaks
Boolean trimMs1Peaks
Trim Ms1 peaks. -
trimMsMsPeaks
Boolean trimMsMsPeaks
Trim MsMs peaks. -
useDeltaScore
boolean useDeltaScore
Use delta score. -
useProvidedPrecursorInfo
Boolean useProvidedPrecursorInfo
Use provided precursor info. -
windowWidthThomson
Double windowWidthThomson
Window width in Thomson. -
writeMzId
Boolean writeMzId
Write mzId output. -
writePepXml
Boolean writePepXml
Write pepXml output.
-
-
-
Class com.compomics.util.parameters.identification.tool_specific.MsAmandaParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- -8458620189315975268L
-
Serialized Fields
-
generateDecoy
boolean generateDecoy
Defines whether a decoy database shall be created and searched against. Decoy FASTS files are generated by reverting protein sequences, accessions are marked with the prefix “REV_”. -
instrumentID
String instrumentID
The MS Amanda instrument ID. -
lowMemoryMode
Boolean lowMemoryMode
Deprecated.since MS Amanda 2.0Defines whether the low memory mode is used. -
maxLoadedProteins
Integer maxLoadedProteins
Maximum number of proteins loaded into memory (1000-500000). -
maxLoadedSpectra
Integer maxLoadedSpectra
Maximum number of spectra loaded into memory (1000-500000). -
maxModifications
Integer maxModifications
Maximum number of occurrences of a specific modification on a peptide (0-10). -
maxModificationSites
Integer maxModificationSites
Maximum number of potential modification sites per modification per peptide (0-20). -
maxNeutralLosses
Integer maxNeutralLosses
Maximum number of water and ammonia losses per peptide (0-5). -
maxNeutralLossesPerModification
Integer maxNeutralLossesPerModification
Maximum number identical modification specific losses per peptide (0-5). -
maxPeptideLength
Integer maxPeptideLength
Maximum peptide length. -
maxRank
Integer maxRank
The maximum rank [1-999]. -
maxVariableModifications
Integer maxVariableModifications
Maximum number of variable modifications per peptide (0-10). -
minPeptideLength
Integer minPeptideLength
Minimum peptide length. -
monoisotopic
boolean monoisotopic
Defines whether monoisotopic mass values shall be used (in contrast to average mass values). -
outputFormat
String outputFormat
The output format: csv or mzIdentML. -
performDeisotoping
Boolean performDeisotoping
Defines whether deisotoping is to be performed. -
reportBothBestHitsForTD
Boolean reportBothBestHitsForTD
False = combine ranks for target and decoy, true = own rankings for target and decoy.
-
-
Class com.compomics.util.parameters.identification.tool_specific.MsgfParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- -2656523093031942973L
-
Serialized Fields
-
additionalOutput
boolean additionalOutput
Output additional features. -
fragmentationType
int fragmentationType
The MS-GF+ fragmentation type ID: 0: As written in the spectrum or CID if no info, 1: CID, 2: ETD, 3: HCD, 4: UVPD. -
instrumentID
int instrumentID
The MS-GF+ instrument ID: 0: Low-res LCQ/LTQ (Default), 1: Orbitrap/FTICR, 2: TOF, 3: Q-Exactive. -
maxPeptideLength
Integer maxPeptideLength
The maximal peptide length. -
minPeptideLength
Integer minPeptideLength
The minimum peptide length. -
numberOfModificationsPerPeptide
Integer numberOfModificationsPerPeptide
The maximum number of modifications per peptide. -
numberOfSpectrumMarches
Integer numberOfSpectrumMarches
The maximum number of spectrum matches. -
numberOfTasks
Integer numberOfTasks
The number of tasks. Null if not set, meaning that it will be internally calculated based on the inputs. More tasks than threads will reduce the memory requirements of the search, but will be slower (how much depends on the inputs). If the spectrum file is particularly large, a larger number of tasks will decrease the possibility of out of memory errors. If the FASTA file being searched is larger than 10MB, more tasks will cause a noticeably longer search time. -
numberTolerableTermini
Integer numberTolerableTermini
The number of tolerable termini. E.g. For trypsin, 0: non-tryptic, 1: semi-tryptic, 2: fully-tryptic peptides only. -
protocol
int protocol
The MS-GF+ protocol ID: 0: Automatic, 1: Phosphorylation, 2: iTRAQ, 3: iTRAQPhospho, 4: TMT, 5: Standard. -
searchDecoyDatabase
boolean searchDecoyDatabase
Indicates whether MS-GF+ is to create and search a decoy database or not.
-
-
Class com.compomics.util.parameters.identification.tool_specific.MyriMatchParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- 8755937399680481097L
-
Serialized Fields
-
classSizeMultiplier
Integer classSizeMultiplier
The multiplier controlling the size of each intensity class relative to the class above it. -
computeXCorr
Boolean computeXCorr
If true, a Sequest-like cross correlation (xcorr) score will be calculated for the top ranking hits in each spectrum’s result set. -
fragmentationRule
String fragmentationRule
The fragmentation rules. CID (b, y), ETD (c, z*) or manual (user-defined (a comma-separated list of [abcxyz] or z* (z+1), e.g. manual:b,y,z) -
lowerIsotopeCorrection
Integer lowerIsotopeCorrection
Deprecated.now general search settingThe lower isotope correction range. -
maxDynamicMods
Integer maxDynamicMods
The maximum number of variable modifications. -
maxPeakCount
Integer maxPeakCount
The max number of peaks to use. -
maxPeptideLength
Integer maxPeptideLength
The maximal peptide length. -
maxPrecursorMass
Double maxPrecursorMass
The maximum precursor mass considered. -
minPeptideLength
Integer minPeptideLength
The minimum peptide length. -
minPrecursorMass
Double minPrecursorMass
The minimum precursor mass considered. -
minTerminiCleavages
Integer minTerminiCleavages
By default, when generating peptides from the protein database, a peptide must start and end at a valid cleavage site. Setting this parameter to 0 or 1 will reduce that requirement, so that neither terminus or only one terminus of the peptide must match one of the cleavage rules specified in the CleavageRules parameter. This parameter is useful to turn a tryptic digest into a semi-tryptic digest. -
numberOfBatches
Integer numberOfBatches
The number of batches per node to strive for when using the MPI-based parallelization features. -
numberOfSpectrumMatches
Integer numberOfSpectrumMatches
The maximum number of spectrum matches. -
numIntensityClasses
Integer numIntensityClasses
The number of intensity classes. -
outputFormat
String outputFormat
The output format. -
ticCutoffPercentage
Double ticCutoffPercentage
The TicCutoffPercentage. -
upperIsotopeCorrection
Integer upperIsotopeCorrection
Deprecated.now general search settingThe upper isotope correction range. -
useSmartPlusThreeModel
Boolean useSmartPlusThreeModel
If true, the UseSmartPlusThreeModel is used.
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Class com.compomics.util.parameters.identification.tool_specific.NovorParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- -1685402448885208852L
-
Class com.compomics.util.parameters.identification.tool_specific.OmssaParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- -6704164074092668637L
-
Serialized Fields
-
cleaveNtermMethionine
boolean cleaveNtermMethionine
Cleave the N-term methionines. -
consecutiveIonProbability
double consecutiveIonProbability
Probability of consecutive ions. -
determineChargePlusOneAlgorithmically
boolean determineChargePlusOneAlgorithmically
Determine charge plus one algorithmically. -
doubleChargeWindow
int doubleChargeWindow
Window width for doubly charged fragments. -
estimateCharge
boolean estimateCharge
Indicates whether the precursor charge estimation option. -
fractionOfPeaksForChargeEstimation
double fractionOfPeaksForChargeEstimation
Fraction of peaks below the precursor to estimate charge >1. -
highIntensityCutOff
double highIntensityCutOff
High intensity cut-off as percentage of the most intense peak. -
hitListLength
int hitListLength
The maximal hit list length. -
intensityCutOffIncrement
double intensityCutOffIncrement
Intensity cut-off increment. -
iterativeReplaceEvalue
double iterativeReplaceEvalue
E-value threshold to replace a hit in the iterative search (0 means replace if better). -
iterativeSequenceEvalue
double iterativeSequenceEvalue
E-value threshold to include a sequence in the iterative search (0 means all). -
iterativeSpectrumEvalue
double iterativeSpectrumEvalue
E-value threshold to include a spectrum in the iterative search (0 means all). -
lowIntensityCutOff
double lowIntensityCutOff
Low intensity cut-off as percentage of the most intense peak. -
maxEValue
double maxEValue
Maximal e-value cut-off. -
maxFragmentCharge
int maxFragmentCharge
Maximum fragment charge. -
maxFragmentPerSeries
int maxFragmentPerSeries
Maximal number of fragment per series. -
maxHitsPerSpectrumPerCharge
int maxHitsPerSpectrumPerCharge
Maximum number of hits searched per spectrum and per charge. -
maxMzLadders
int maxMzLadders
Maximum length of m/z ladders. -
maxPeptideLength
int maxPeptideLength
The maximal peptide length (for semi and non tryptic searches). -
memoryMappedSequenceLibraries
boolean memoryMappedSequenceLibraries
Map sequence in libraries in memory -
minAnnotatedPeaks
int minAnnotatedPeaks
Minimal number of annotated peaks required per spectrum. -
minimalChargeForMultipleChargedFragments
int minimalChargeForMultipleChargedFragments
The minimal charge to be considered for multiple fragment charges. -
minPeaks
int minPeaks
Minimal number of peaks per spectrum. -
minPeptideLength
int minPeptideLength
The minimum peptide length (for semi and non tryptic searches). -
minPrecPerSpectrum
int minPrecPerSpectrum
Minimal precursor per spectrum. -
nAnnotatedMostIntensePeaks
int nAnnotatedMostIntensePeaks
Number of annotated most intense peaks required per spectrum. -
neutronThreshold
double neutronThreshold
Mass after which a the exact mass of a neutron should be considered. -
noProlineRuleSeries
ArrayList<Integer> noProlineRuleSeries
ID numbers of ion series to apply no product ions at proline rule at. NOTE: not implemented for now. -
nPeaksIndoubleChargeWindow
int nPeaksIndoubleChargeWindow
Number of peaks allowed in a doubly charged window. -
nPeaksInSingleChargeWindow
int nPeaksInSingleChargeWindow
Number of peaks allowed in a singly charged window. -
ptmIndexes
HashMap<Integer,String> ptmIndexes
Map of the OMSSA indexes used for user modifications in this search. -
removePrecursor
boolean removePrecursor
Indicates whether the precursor removal option is used. -
scalePrecursor
boolean scalePrecursor
Indicates whether the precursor scaling option is used. -
searchForwardFragmentFirst
boolean searchForwardFragmentFirst
Search forward ions (b1) first. -
searchPositiveIons
boolean searchPositiveIons
Search positive ions (if false, negative ions). -
searchRewindFragments
boolean searchRewindFragments
Search c-terminal ions. -
selectedOutput
String selectedOutput
The selected output type (see omssaOutputTypes). -
singleChargeWindow
int singleChargeWindow
Window width for singly charged fragments. -
useCorrelationCorrectionScore
boolean useCorrelationCorrectionScore
Use correlation correction score.
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Class com.compomics.util.parameters.identification.tool_specific.PepnovoParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- -8056507693211793829L
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Serialized Fields
-
correctPrecursorMass
Boolean correctPrecursorMass
Indicates whether the precursor mass shall be corrected. -
discardLowQualitySpectra
Boolean discardLowQualitySpectra
Indicates whether the low quality spectra shall be discarded. -
estimateCharge
Boolean estimateCharge
Indicates whether the precursor charge estimation option. -
fragmentationModel
String fragmentationModel
PepNovo fragmentation model. -
generateQuery
Boolean generateQuery
Indicates whether a blast query shall be generated. -
hitListLength
Integer hitListLength
The maximal hit list length for PepNovo+. Max is 20. -
pepNovoPtmMap
Map<String,String> pepNovoPtmMap
A map from the PepNovo PTM symbols to the utilities PTM names.
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Class com.compomics.util.parameters.identification.tool_specific.PNovoParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- 7525455518683797145L
-
Serialized Fields
-
acticationType
String acticationType
The activation type (HCD, CID or ETD). -
lowerPrecursorMass
int lowerPrecursorMass
The minimum precursor mass. -
numberOfPeptides
int numberOfPeptides
The number of peptides reported. -
pNovoPtmMap
HashMap<Character,String> pNovoPtmMap
A map from the pNovo PTM character to the utilities PTM names. pNovo PTM character > utilities PTM name. -
pNovoResidueMap
HashMap<Character,Character> pNovoResidueMap
A map from the pNovo character to the original amino acids residue. pNovo PTM character > original amino acids residue. -
upperPrecursorMass
int upperPrecursorMass
The maximum precursor mass.
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Class com.compomics.util.parameters.identification.tool_specific.TideParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- 1049197890002802776L
-
Serialized Fields
-
clipNtermMethionine
Boolean clipNtermMethionine
If true, starting methionine peptides will be included both with and without the starting M. -
computeExactPValues
Boolean computeExactPValues
If true, the exact p-values will be computed. -
computeSpScore
Boolean computeSpScore
If true, the SP score will be computed. -
concatenateTargetDecoy
Boolean concatenateTargetDecoy
If true, target and decoy search results are reported in a single file named "tide-search.txt," and only the top-scoring N matches (as specified via --top-match) are reported for each spectrum, irrespective of whether the matches involve target or decoy peptides. -
decoyFormat
String decoyFormat
The decoy format. -
decoySeed
Integer decoySeed
The seed of the random number generator with the given unsigned integer when generating the decoy decoys. When given the string "time," the seed is set with the system time. -
digestionType
String digestionType
The enzyme digestion type: full-digest or partial-digest. -
fastIndexFolderName
String fastIndexFolderName
The name of the FASTA index folder. -
keepTerminalAminoAcids
String keepTerminalAminoAcids
Keep terminal amino acids when creating decoys. -
maxPeptideLength
Integer maxPeptideLength
The maximal peptide length. -
maxPrecursorMass
Double maxPrecursorMass
The maximum precursor mass considered. -
maxSpectrumMz
Double maxSpectrumMz
The maximum spectrum m/z to search for. Null if no maximum. -
maxVariableModificationsPerPeptide
Integer maxVariableModificationsPerPeptide
The maximum number of variable modifications allowed on a single peptide. The default is no limit (set to null). -
maxVariableModificationsPerTypePerPeptide
Integer maxVariableModificationsPerTypePerPeptide
The maximum number of variable modifications of each type allowed on a single peptide. -
minPeptideLength
Integer minPeptideLength
The minimum peptide length. -
minPrecursorMass
Double minPrecursorMass
The minimum precursor mass considered. -
minSpectrumMz
Double minSpectrumMz
The minimum spectrum m/z to search for. -
minSpectrumPeaks
Integer minSpectrumPeaks
The minimum number of peaks in a spectrum for it to be searched. -
monoisotopicPrecursor
Boolean monoisotopicPrecursor
If true, a monoisotopic precursor mass is used, false uses average. -
mzBinOffset
Double mzBinOffset
In the discretization of the m/z axes of the observed and theoretical spectra, this parameter specifies the location of the left edge of the first bin, relative to mass = 0 (i.e., mz-bin-offset = 0.xx means the left edge of the first bin will be located at +0.xx Da). The parameter must lie in the range 0 ≤ mz-bin-offset ≤ 1. -
mzBinWidth
Double mzBinWidth
Before calculation of the XCorr score, the m/z axes of the observed and theoretical spectra are discretized. This parameter specifies the size of each bin. The exact formula is floor((x/mz-bin-width) + 1.0 - mz-bin-offset), where x is the observed m/z value. For low resolution ion trap ms/ms data 1.0005079 and for high resolution ms/ms 0.02 is recommended. -
mzidOutput
Boolean mzidOutput
If true, mzid output is generated. -
numberOfSpectrumMatches
Integer numberOfSpectrumMatches
The maximum number of spectrum matches per peptide. -
outputFolderName
String outputFolderName
The name of the output folder (relative to the Tide working folder). -
pepXmlOutput
Boolean pepXmlOutput
If true, pepxml output is generated. -
pinOutput
Boolean pinOutput
If true, Percolator input file is generated. -
printPeptides
Boolean printPeptides
If true, a list of all the peptides will be printed to the output folder. -
printProgressIndicatorSize
Integer printProgressIndicatorSize
Show search progress by printing every n spectra searched. Set to 0 to show no search progress. -
removePrecursor
Boolean removePrecursor
If true, the precursor peak will be removed. The range removed is specified by -
removePrecursorTolerance
Double removePrecursorTolerance
The tolerance in (Th) used when removing the precursor using removePrecursor. -
removeTempFolders
Boolean removeTempFolders
If true, the tide output and index folders are removed when the search has completed. -
spectrumCharges
String spectrumCharges
The spectrum charges to search for: 1,2,3 or all. With 'all' every spectrum will be searched and spectra with multiple charge states will be searched once at each charge state. With 1, 2, or 3 only spectra with that charge will be searched. -
sqtOutput
Boolean sqtOutput
If true, SQT output is generated. -
storeSpectraFileName
String storeSpectraFileName
Specify the name of the file where the binarized fragmentation spectra will be stored. Subsequent runs of crux tide-search will execute more quickly if provided with the spectra in binary format. The filename is specified relative to the current working directory, not the Crux output directory (as specified by --output-dir). -
textOutput
Boolean textOutput
If true, tab delimited text file output is generated. -
useFlankingPeaks
Boolean useFlankingPeaks
If true, the search includes flanking peaks around singly charged b and y theoretical ions. Each flanking peak occurs in the adjacent m/z bin and has half the intensity of the primary peak. -
useNeutralLossPeaks
Boolean useNeutralLossPeaks
Controls whether neutral loss ions are considered in the search. Two types of neutral losses are included and are applied only to singly charged b- and y-ions: loss of ammonia (NH3, 17.0086343 Da) and H2O (18.0091422). Each neutral loss peak has intensity 1/5 of the primary peak. -
verbosity
Integer verbosity
The verbosity of the progress output: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info.
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Class com.compomics.util.parameters.identification.tool_specific.XtandemParameters extends ExperimentObject implements Serializable
- serialVersionUID:
- -5898951075262732261L
-
Serialized Fields
-
dynamicRange
double dynamicRange
The dynamic range for spectrum filtering. When the highest peak is given the dynamic range value peaks smaller than one are ignored. e.g. for 100 peaks with an intensity <1% of the highest peak are ignored. -
maxEValue
double maxEValue
Maximal e-value cut-off. -
maximumExpectationValueRefinement
double maximumExpectationValueRefinement
The maximum expectation value for a hit to be considered during the refinement process. -
minFragmentMz
double minFragmentMz
The minimum fragment mass. -
minPeaksPerSpectrum
int minPeaksPerSpectrum
The minimum number of peaks per spectrum. -
minPrecursorMass
double minPrecursorMass
The minimum precursor mass. -
nPeaks
int nPeaks
The number of most intense peaks to consider. -
outputHistograms
boolean outputHistograms
If true histograms will be exported to the result file. -
outputProteins
boolean outputProteins
If true protein details will be exported to the to the result file. -
outputResults
String outputResults
The output results filter: all, valid or stochastic. -
outputSequences
boolean outputSequences
If true protein sequences will be added to the protein details to the result file. -
outputSpectra
boolean outputSpectra
If true spectra will be exported to the result file. -
parentMonoisotopicMassIsotopeError
boolean parentMonoisotopicMassIsotopeError
Sets whether the parent ion mass tolerance is expanded by opening up multiple tolerance windows centered on the first and second 13C isotope peaks for a peptide. -
potentialModificationsForFullRefinment
boolean potentialModificationsForFullRefinment
Sets the modifications to be used during the refinement process. -
proteinPtmComplexity
double proteinPtmComplexity
The value of the command "protein, ptm complexity" (C, a floating point number 0.0–12.0) sets the maximum number of variable modification alternatives that will be tested for a particular peptide. The number of alternatives is 2.0C. If this number is not specified, the default value C = 6.0 will be used. -
proteinQuickAcetyl
boolean proteinQuickAcetyl
Indicates whether the protein quick acetylation option should be triggered. -
quickPyrolidone
boolean quickPyrolidone
Indicates whether the quick pyrolidone option should be triggered. -
refine
boolean refine
Triggers the refinement process. -
refinePointMutations
boolean refinePointMutations
Sets whether point mutations should be search for during the refinement process. -
refineSemi
boolean refineSemi
Sets whether semi enzymatic peptides should be search for during the refinement process. -
refineSnaps
boolean refineSnaps
Indicates whether snAPs should be used during the refinement process. -
refineSpectrumSynthesis
boolean refineSpectrumSynthesis
Sets whether the spectrum synthesis option should be used during the refinement process. -
refineUnanticipatedCleavages
boolean refineUnanticipatedCleavages
Sets whether unexpected cleavages should be search for during the refinement process. -
skylinePath
String skylinePath
The skyline path. -
stpBias
boolean stpBias
Indicates whether the phospho stp bias option should be triggered. -
useNoiseSuppression
boolean useNoiseSuppression
Triggers the noise suppression function. Note: ignored in X!Tandem VENGEANCE (2015.12.15) and newer.
-
-
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Package com.compomics.util.parameters.quantification.spectrum_counting
-
Class com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters extends ExperimentObject implements Serializable
-
Serialized Fields
-
matchValidationLevel
Integer matchValidationLevel
The minimal match validation level to consider as indexed in the MatchValidationLevel enum. -
normalize
Boolean normalize
Indicates whether the spectrum counting index should be normalized. -
referenceMass
Double referenceMass
The reference total mass to use for normalization in μg. -
selectedMethod
SpectrumCountingMethod selectedMethod
The currently selected spectrum counting method. -
unit
UnitOfMeasurement unit
The unit to use for normalization.
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-
-
-
Package com.compomics.util.pride
-
Class com.compomics.util.pride.CvTerm extends ExperimentObject implements Serializable
-
Class com.compomics.util.pride.PtmToPrideMap extends ExperimentObject implements Serializable
- serialVersionUID:
- 2436108005958307507L
-
-
Package com.compomics.util.pride.prideobjects
-
Class com.compomics.util.pride.prideobjects.Contact extends ExperimentObject implements Serializable
- serialVersionUID:
- -9182316910747747823L
-
Class com.compomics.util.pride.prideobjects.ContactGroup extends ExperimentObject implements Serializable
-
Class com.compomics.util.pride.prideobjects.Instrument extends ExperimentObject implements Serializable
-
Class com.compomics.util.pride.prideobjects.Protocol extends ExperimentObject implements Serializable
-
Class com.compomics.util.pride.prideobjects.Reference extends ExperimentObject implements Serializable
- serialVersionUID:
- -5449836209751629549L
-
Class com.compomics.util.pride.prideobjects.ReferenceGroup extends ExperimentObject implements Serializable
-
Class com.compomics.util.pride.prideobjects.Sample extends ExperimentObject implements Serializable
-
-
Package com.compomics.util.sun
-
Class com.compomics.util.sun.TableMap extends AbstractTableModel implements Serializable
-
Serialized Fields
-
logger
org.apache.log4j.Logger logger
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model
TableModel model
-
-
-
Class com.compomics.util.sun.TableSorter extends TableMap implements Serializable
-
Serialized Fields
-
ascending
boolean ascending
-
compares
int compares
-
indexes
int[] indexes
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listMouseListener
MouseAdapter listMouseListener
-
logger
org.apache.log4j.Logger logger
-
sortingColumns
Vector sortingColumns
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-
-