Serialized Form (Reporter 0.12.9 API)

Package eu.isas.reporter.calculation.clustering.keys
- Class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey
  
  class PeptideClusterClassKey extends Object implements Serializable
  - Serialized Fields
    
    cTerm
    
    Boolean cTerm
    
    Boolean indicating whether the peptides are C-term.
    
    forbiddenPtms
    
    ArrayList<String> forbiddenPtms
    
    The PTMs not carried by the peptides in this class.
    
    forbiddenPtmsAsSet
    
    HashSet<String> forbiddenPtmsAsSet
    
    The PTMs not carried by the peptides in this class as set.
    
    notModified
    
    boolean notModified
    
    Indicates whether the peptides are not modified.
    
    nTerm
    
    Boolean nTerm
    
    Boolean indicating whether the peptides are N-term.
    
    possiblePtms
    
    ArrayList<String> possiblePtms
    
    The PTMs eventually carried by the peptides in this class.
    
    possiblePtmsAsSet
    
    HashSet<String> possiblePtmsAsSet
    
    The PTMs eventually carried by the peptides in this class as set.
    
    starred
    
    Boolean starred
    
    Indicates whether the peptides must be starred.
- Class eu.isas.reporter.calculation.clustering.keys.ProteinClusterClassKey
  
  class ProteinClusterClassKey extends Object implements Serializable
  - Serialized Fields
    
    starred
    
    Boolean starred
    
    Indicates whether the proteins must be starred.
- Class eu.isas.reporter.calculation.clustering.keys.PsmClusterClassKey
  
  class PsmClusterClassKey extends Object implements Serializable
  - Serialized Fields
    
    file
    
    String file
    
    The name of the spectrum file.
    
    starred
    
    Boolean starred
    
    Indicates whether the PSMs must be starred.

Package eu.isas.reporter.gui

Class eu.isas.reporter.gui.JumpToPanel

class JumpToPanel extends JPanel implements Serializable
- Serialized Fields
  - currentProteinKeys
    
    ArrayList<Long> currentProteinKeys
    
    The current list of protein keys. Can be different from the complete list, e.g., only include validated proteins.
  - currentSelection
    
    HashMap<JumpToPanel.JumpType,Integer> currentSelection
    
    Currently selected item.
  - findJLabel
    
    JLabel findJLabel
  - indexLabel
    
    JLabel indexLabel
  - inputTxt
    
    JTextField inputTxt
  - jumpType
    
    JumpToPanel.JumpType jumpType
    
    The type of data to jump to in that panel.
  - keyPressedCounter
    
    int keyPressedCounter
    
    Counts the number of times the users has pressed a key on the keyboard in the search field.
  - lastInput
    
    HashMap<JumpToPanel.JumpType,String> lastInput
    
    The text to display by default.
  - lastLabel
    
    HashMap<JumpToPanel.JumpType,String> lastLabel
    
    The text to display by default.
  - nextButton
    
    JButton nextButton
  - possibilities
    
    HashMap<JumpToPanel.JumpType,ArrayList<Long>> possibilities
    
    Items matching the criterion for each type.
  - previousButton
    
    JButton previousButton
  - reporterGUI
    
    ReporterGUI reporterGUI
    
    Instance of the main GUI class.
  - types
    
    HashMap<JumpToPanel.JumpType,ArrayList<eu.isas.reporter.gui.JumpToPanel.Type>> types
    
    Type of each possible item.
  - waitingTime
    
    int waitingTime
    
    The time to wait between keys typed before updating the search.
  - welcomeText
    
    HashMap<JumpToPanel.JumpType,String> welcomeText
    
    The text to display by default.

Class eu.isas.reporter.gui.LabellingEfficiencyDialog

class LabellingEfficiencyDialog extends JDialog implements Serializable

Serialized Fields

addDbButton
```
JButton addDbButton
```
addIdFilesButton
```
JButton addIdFilesButton
```
addSpectraFilesJButton
```
JButton addSpectraFilesJButton
```
backgroundPanel
```
JPanel backgroundPanel
```
closeButton
```
JButton closeButton
```
databaseFileLabel
```
JLabel databaseFileLabel
```
efficiencyPanel
```
JPanel efficiencyPanel
```
efficiencyTable
```
JTable efficiencyTable
```
efficiencyTableScrollPane
```
JScrollPane efficiencyTableScrollPane
```
fastaTxt
```
JTextField fastaTxt
```
fileSelectiontPanel
```
JPanel fileSelectiontPanel
```
idFilesLabel
```
JLabel idFilesLabel
```
labellingEfficiency
```
HashMap<String,Double> labellingEfficiency
```
Map of the labeling efficiency: PTM name | efficiency.

lastSelectedFolder

com.compomics.util.io.file.LastSelectedFolder lastSelectedFolder

The last selected folder.

modificationFactory

com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory

The modification factory.

msFileHandler

com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler

The handler for mass spectrometry files.

normalIcon
```
Image normalIcon
```
The normal icon.
parentFrame
```
Frame parentFrame
```
The parent frame.

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

A simple progress dialog.

psdbParent
```
eu.isas.peptideshaker.utils.PsdbParent psdbParent
```
The psdb parent used to manage the data.
sortedModifications
```
ArrayList<String> sortedModifications
```
List of the sorted modifications.
spectrumFiles
```
ArrayList<File> spectrumFiles
```
The spectrum files loaded.
spectrumFilesLabel
```
JLabel spectrumFilesLabel
```
txtIdFileLocation
```
JTextField txtIdFileLocation
```
txtSpectraFileLocation
```
JTextField txtSpectraFileLocation
```
waitingIcon
```
Image waitingIcon
```
The waiting icon.

Class eu.isas.reporter.gui.MethodSettingsDialog

class MethodSettingsDialog extends JDialog implements Serializable
- Serialized Fields
  - backgroundPanel
    
    JPanel backgroundPanel
  - browseConfigButton
    
    JButton browseConfigButton
  - configFilePanel
    
    JPanel configFilePanel
  - isotopeCorrectionPanel
    
    JPanel isotopeCorrectionPanel
  - methodsFactory
    
    com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory methodsFactory
    
    The compomics reporter methods factory.
  - newDialog
    
    NewDialog newDialog
    
    The parent dialog.
  - okButton
    
    JButton okButton
  - reagentsTable
    
    JTable reagentsTable
  - reagentsTableJScrollPane
    
    JScrollPane reagentsTableJScrollPane
  - saveConfigButton
    
    JButton saveConfigButton
  - txtConfigurationFileLocation
    
    JTextField txtConfigurationFileLocation
  - valuesChanged
    
    boolean valuesChanged
    
    Boolean indicating of the user has made changes to the table.

Class eu.isas.reporter.gui.NewDialog

class NewDialog extends JDialog implements Serializable

Serialized Fields

aboutButton
```
JButton aboutButton
```
addDbButton
```
JButton addDbButton
```
addIdFilesButton
```
JButton addIdFilesButton
```
addSpectraFilesJButton
```
JButton addSpectraFilesJButton
```
advancedSettingsPanel
```
JPanel advancedSettingsPanel
```
backgroundPanel
```
JPanel backgroundPanel
```
cancelled
```
boolean cancelled
```
Boolean indicating whether the user canceled the project creation
controlSamples
```
ArrayList<String> controlSamples
```
List of control samples.
databaseFileLabel
```
JLabel databaseFileLabel
```
DEFAULT_REPORTER_ION_TOLERANCE_ITRAQ
```
double DEFAULT_REPORTER_ION_TOLERANCE_ITRAQ
```
The default reporter ion tolerance for iTRAQ data.
DEFAULT_REPORTER_ION_TOLERANCE_TMT
```
double DEFAULT_REPORTER_ION_TOLERANCE_TMT
```
The default reporter ion tolerance for TMT data.
displayPreferences
```
DisplayPreferences displayPreferences
```
The display preferences for this project.
editProcessingButton
```
JButton editProcessingButton
```
editQuantPrefsButton
```
JButton editQuantPrefsButton
```
fastaFile
```
File fastaFile
```
The FASTA file.
fastaTxt
```
JTextField fastaTxt
```
fileSelectiontPanel
```
JPanel fileSelectiontPanel
```
idFilesLabel
```
JLabel idFilesLabel
```
loadButton
```
JButton loadButton
```
methodSettingsButton
```
JButton methodSettingsButton
```

methodsFactory

com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory methodsFactory

The compomics reporter methods factory.

methodsFile
```
File methodsFile
```
The current methods file.
moveBottomButton
```
JButton moveBottomButton
```
moveDownButton
```
JButton moveDownButton
```
moveTopButton
```
JButton moveTopButton
```
moveUpButton
```
JButton moveUpButton
```

msFileHandler

com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler

The handler for mass spectrometry files.

orderSettingsPanel
```
JPanel orderSettingsPanel
```
processingLbl
```
JLabel processingLbl
```

processingParameters

com.compomics.util.parameters.tools.ProcessingParameters processingParameters

The processing parameters.

processingTxt
```
JTextField processingTxt
```

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

A simple progress dialog.

projectDetails

eu.isas.peptideshaker.preferences.ProjectDetails projectDetails

The project details.

psdbParent
```
eu.isas.peptideshaker.utils.PsdbParent psdbParent
```
The psdb parent used to manage the data.
quantificationPreferencesTxt
```
JTextField quantificationPreferencesTxt
```
quantPreferencesLabel
```
JLabel quantPreferencesLabel
```
reagents
```
ArrayList<String> reagents
```
List of reagents used in this reporter method
reporterGUI
```
ReporterGUI reporterGUI
```
The reporter class.

reporterIonQuantification

com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification

A reporter ion quantification object containing the input from the user.

reporterMethodComboBox
```
JComboBox reporterMethodComboBox
```
reporterMethodLabel
```
JLabel reporterMethodLabel
```
reporterPublicationLabel
```
JLabel reporterPublicationLabel
```
reporterSettings
```
ReporterSettings reporterSettings
```
The reporter settings.
sampleAssignmentJScrollPane
```
JScrollPane sampleAssignmentJScrollPane
```
sampleAssignmentTable
```
JTable sampleAssignmentTable
```
sampleAssignmentTableToolTips
```
ArrayList<String> sampleAssignmentTableToolTips
```
The sample assignment table column header tooltips.
sampleNames
```
HashMap<String,String> sampleNames
```
List of all sample names.
samplePanel
```
JPanel samplePanel
```

selectedMethod

com.compomics.util.experiment.quantification.reporterion.ReporterMethod selectedMethod

The method selected.

spectrumFiles
```
ArrayList<File> spectrumFiles
```
The spectrum files loaded.
spectrumFilesLabel
```
JLabel spectrumFilesLabel
```
txtIdFileLocation
```
JTextField txtIdFileLocation
```
txtSpectraFileLocation
```
JTextField txtSpectraFileLocation
```
welcomeDialog
```
WelcomeDialog welcomeDialog
```

Class eu.isas.reporter.gui.ReagentOrderDialog

class ReagentOrderDialog extends JDialog implements Serializable
- Serialized Fields
  - cancelButton
    
    JButton cancelButton
  - cancelled
    
    boolean cancelled
    
    Boolean indicating whether the user canceled the project creation
  - controlSamples
    
    ArrayList<String> controlSamples
    
    List of control samples.
  - methodsFactory
    
    com.compomics.util.experiment.quantification.reporterion.ReporterMethodFactory methodsFactory
    
    The compomics reporter methods factory.
  - methodsFile
    
    File methodsFile
    
    The current methods file.
  - moveBottomButton
    
    JButton moveBottomButton
  - moveDownButton
    
    JButton moveDownButton
  - moveTopButton
    
    JButton moveTopButton
  - moveUpButton
    
    JButton moveUpButton
  - okButton
    
    JButton okButton
  - orderSettingsPanel
    
    JPanel orderSettingsPanel
  - reagents
    
    ArrayList<String> reagents
    
    List of reagents used in this reporter method.
  - reporterGUI
    
    ReporterGUI reporterGUI
    
    The ReporterGUI parent.
  - reporterIonQuantification
    
    com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification
    
    The reporter ion quantifications.
  - reporterMethodComboBox
    
    JComboBox reporterMethodComboBox
  - reporterMethodLabel
    
    JLabel reporterMethodLabel
  - sampleAssignmentJScrollPane
    
    JScrollPane sampleAssignmentJScrollPane
  - sampleAssignmentTable
    
    JTable sampleAssignmentTable
  - sampleAssignmentTableToolTips
    
    ArrayList<String> sampleAssignmentTableToolTips
    
    The sample assignment table column header tooltips.
  - samplePanel
    
    JPanel samplePanel
  - selectedMethod
    
    com.compomics.util.experiment.quantification.reporterion.ReporterMethod selectedMethod
    
    The method selected.

Class eu.isas.reporter.gui.ReporterGUI

class ReporterGUI extends JFrame implements Serializable

Serialized Fields

aboutMenuItem
```
JMenuItem aboutMenuItem
```
backgroundPanel
```
JPanel backgroundPanel
```
categoriesMenuItem
```
JMenuItem categoriesMenuItem
```
clusterBuilder
```
ClusterBuilder clusterBuilder
```
The cluster builder.
displayFeaturesGenerator
```
eu.isas.peptideshaker.utils.DisplayFeaturesGenerator displayFeaturesGenerator
```
The display features generator provides display features for the identified matches.
displayPreferences
```
DisplayPreferences displayPreferences
```
The display preferences.

exceptionHandler

com.compomics.util.exceptions.ExceptionHandler exceptionHandler

The exception handler.

exitMenuItem
```
JMenuItem exitMenuItem
```
exportFollowUpJMenuItem
```
JMenuItem exportFollowUpJMenuItem
```
exportMenu
```
JMenu exportMenu
```

exportQuantificationFeaturesMenuItem

JMenuItem exportQuantificationFeaturesMenuItem

fileMenu
```
JMenu fileMenu
```
helpMenu
```
JMenu helpMenu
```
helpMenuItem
```
JMenuItem helpMenuItem
```
identificationFeaturesGenerator
```
com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator
```
The identification features generator provides identification related metrics on the identified matches.
javaOptionsMenuItem
```
JMenuItem javaOptionsMenuItem
```
jSeparator1
```
JPopupMenu.Separator jSeparator1
```
jSeparator16
```
JPopupMenu.Separator jSeparator16
```
jSeparator17
```
JPopupMenu.Separator jSeparator17
```
jSeparator2
```
JPopupMenu.Separator jSeparator2
```
jSeparator3
```
JPopupMenu.Separator jSeparator3
```
jSeparator4
```
JPopupMenu.Separator jSeparator4
```
jumpToPanel
```
JumpToPanel jumpToPanel
```
The Jump To panel.

kMeansClutering

com.compomics.util.math.clustering.KMeansClustering kMeansClutering

The k-means clustering results.

lastSelectedFolder
```
com.compomics.util.io.file.LastSelectedFolder lastSelectedFolder
```
The last folder opened by the user. Defaults to user.home.
logReportMenu
```
JMenuItem logReportMenu
```
menuBar
```
JMenuBar menuBar
```
newMenuItem
```
JMenuItem newMenuItem
```
openMenuItem
```
JMenuItem openMenuItem
```
overviewJPanel
```
JPanel overviewJPanel
```
overviewPanel
```
OverviewPanel overviewPanel
```
the overview panel
privacyMenuItem
```
JMenuItem privacyMenuItem
```

processingParameters

com.compomics.util.parameters.tools.ProcessingParameters processingParameters

The processing parameters.

processingSettingsMenuItem
```
JMenuItem processingSettingsMenuItem
```

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

A simple progress dialog.

projectSaved
```
boolean projectSaved
```
Boolean indicating whether the project has been saved.
psdbParent
```
eu.isas.peptideshaker.utils.PsdbParent psdbParent
```
The psdb parent used to manage the data.
quantificationFeaturesGenerator
```
QuantificationFeaturesGenerator quantificationFeaturesGenerator
```
The quantification features generator provides quantification features on the identified matches.
quantificationOptionsMenu
```
JMenu quantificationOptionsMenu
```
reagentOrderMenuItem
```
JMenuItem reagentOrderMenuItem
```

reporterIonQuantification

com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification

The reporter ion quantification containing the quantification parameters.

reporterSettings
```
ReporterSettings reporterSettings
```
The reporter settings
saveAsMenuItem
```
JMenuItem saveAsMenuItem
```
saveMenuItem
```
JMenuItem saveMenuItem
```
scoreAndConfidenceDecimalFormat
```
DecimalFormat scoreAndConfidenceDecimalFormat
```
The decimal format use for the score and confidence columns.
selectedPeptides
```
ArrayList<Long> selectedPeptides
```
List of the currently selected peptides.
selectedProteins
```
ArrayList<Long> selectedProteins
```
List of the currently selected proteins.
selectedPsms
```
ArrayList<Long> selectedPsms
```
List of the currently selected PSMs.
tabPanel
```
JTabbedPane tabPanel
```

utilitiesUserParameters

com.compomics.util.parameters.UtilitiesUserParameters utilitiesUserParameters

The utilities user preferences.

Class eu.isas.reporter.gui.WelcomeDialog

class WelcomeDialog extends JDialog implements Serializable

Serialized Fields

aboutMenuItem
```
JMenuItem aboutMenuItem
```
backgroundPanel
```
JPanel backgroundPanel
```
bugReportMenuItem
```
JMenuItem bugReportMenuItem
```
compomicsButton
```
JButton compomicsButton
```
gettingStartedJButton1
```
JButton gettingStartedJButton1
```
gettingStartedMenuItem
```
JMenuItem gettingStartedMenuItem
```
helpMenu
```
JMenu helpMenu
```
isasButton
```
JButton isasButton
```
javaSettingsMenuItem
```
JMenuItem javaSettingsMenuItem
```
jSeparator1
```
JSeparator jSeparator1
```
jSeparator2
```
JPopupMenu.Separator jSeparator2
```
lowMemoryWarningLabel
```
JLabel lowMemoryWarningLabel
```
newJButton
```
JButton newJButton
```
openExampleDatasetJButton
```
JButton openExampleDatasetJButton
```
openJButton
```
JButton openJButton
```
pathSettingsMenu
```
JMenuItem pathSettingsMenu
```
probeButton
```
JButton probeButton
```

progressDialog

com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog

The progress dialog.

quantifyJButton
```
JButton quantifyJButton
```
recentProjectsLabel
```
JLabel recentProjectsLabel
```
reporterGUI
```
ReporterGUI reporterGUI
```
The Reporter parent frame.
reshakeJButton
```
JButton reshakeJButton
```
searchJButton
```
JButton searchJButton
```
settingsLabel
```
JLabel settingsLabel
```
settingsMenu
```
JMenu settingsMenu
```
settingsPopupMenu
```
JPopupMenu settingsPopupMenu
```

Package eu.isas.reporter.gui.export
- Class eu.isas.reporter.gui.export.ReportDialog
  
  class ReportDialog extends JDialog implements Serializable
  - Serialized Fields
    
    addReportLabel
    
    JLabel addReportLabel
    
    addReportMenuItem
    
    JMenuItem addReportMenuItem
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    customReportsPanel
    
    JPanel customReportsPanel
    
    editReportMenuItem
    
    JMenuItem editReportMenuItem
    
    exitButton
    
    JButton exitButton
    
    exportFactory
    
    ReporterExportFactory exportFactory
    
    The export factory.
    
    exportReportButton
    
    JButton exportReportButton
    
    exportSchemesNames
    
    ArrayList<String> exportSchemesNames
    
    List of the available export schemes.
    
    helpLabel
    
    JLabel helpLabel
    
    removeReportMenuItem
    
    JMenuItem removeReportMenuItem
    
    reportDocumentationMenuItem
    
    JMenuItem reportDocumentationMenuItem
    
    reportDocumentationPopupMenu
    
    JPopupMenu reportDocumentationPopupMenu
    
    reporterGUI
    
    ReporterGUI reporterGUI
    
    The main GUI instance.
    
    reportPopUpMenuSeparator
    
    JPopupMenu.Separator reportPopUpMenuSeparator
    
    reportsTable
    
    JTable reportsTable
    
    reportsTableScrollPane
    
    JScrollPane reportsTableScrollPane
Package eu.isas.reporter.gui.resultpanels
- Class eu.isas.reporter.gui.resultpanels.OverviewPanel
  
  class OverviewPanel extends JPanel implements Serializable
  - Serialized Fields
    
    allChartPanels
    
    ArrayList<org.jfree.chart.ChartPanel> allChartPanels
    
    List with all the chart panels.
    
    allOrderedProteinKeys
    
    long[] allOrderedProteinKeys
    
    The complete list of ordered protein keys.
    
    backgroundLayeredPane
    
    JLayeredPane backgroundLayeredPane
    
    chartMaximized
    
    boolean chartMaximized
    
    True of a single chart is maximized.
    
    clusterPopupMenu
    
    JPopupMenu clusterPopupMenu
    
    contextMenuProteinsBackgroundPanel
    
    JPanel contextMenuProteinsBackgroundPanel
    
    contextMenuRatioPlotBackgroundPanel
    
    JPanel contextMenuRatioPlotBackgroundPanel
    
    exportProteinsJButton
    
    JButton exportProteinsJButton
    
    exportRatioPlotContextJButton
    
    JButton exportRatioPlotContextJButton
    
    geneMaps
    
    com.compomics.util.experiment.biology.genes.GeneMaps geneMaps
    
    The gene maps.
    
    identification
    
    com.compomics.util.experiment.identification.Identification identification
    
    Utilities Identification containing the identification objects.
    
    identificationFeaturesGenerator
    
    com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator
    
    PeptideShaker identification features generator.
    
    lineChartChartPanel
    
    org.jfree.chart.ChartPanel lineChartChartPanel
    
    The current line chart chart panel.
    
    matchesJTabbedPane
    
    JTabbedPane matchesJTabbedPane
    
    maximizeChartJButton
    
    JButton maximizeChartJButton
    
    maximizeIconChartPanel
    
    org.jfree.chart.ChartPanel maximizeIconChartPanel
    
    The current chart panel where the maximize icon is showing.
    
    maxLegendSize
    
    int maxLegendSize
    
    The maximum number of elements in a legend.
    
    notSelectedProteinProfileColor
    
    Color notSelectedProteinProfileColor
    
    The color used for the not selected protein profiles.
    
    numberOfClustersMenuItem
    
    JMenuItem numberOfClustersMenuItem
    
    overviewJPanel
    
    JPanel overviewJPanel
    
    overviewJSplitPane
    
    JSplitPane overviewJSplitPane
    
    peptideKeys
    
    long[] peptideKeys
    
    A list of peptides in the peptide table.
    
    peptideScrollPane
    
    JScrollPane peptideScrollPane
    
    peptideTable
    
    JTable peptideTable
    
    plotPanel
    
    JPanel plotPanel
    
    progressDialog
    
    com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog
    
    A simple progress dialog.
    
    proteinKeys
    
    long[] proteinKeys
    
    A list of proteins in the protein table.
    
    proteinPeptidePsmLayeredPanel
    
    JPanel proteinPeptidePsmLayeredPanel
    
    proteinScrollPane
    
    JScrollPane proteinScrollPane
    
    proteinsHelpJButton
    
    JButton proteinsHelpJButton
    
    proteinsJPanel
    
    JPanel proteinsJPanel
    
    proteinsLayeredPane
    
    JLayeredPane proteinsLayeredPane
    
    proteinTable
    
    JTable proteinTable
    
    proteinTableToolTips
    
    ArrayList<String> proteinTableToolTips
    
    The protein table column header tooltips.
    
    psmKeys
    
    long[] psmKeys
    
    A list of PSMs in the PSM table.
    
    psmScrollPane
    
    JScrollPane psmScrollPane
    
    psmTable
    
    JTable psmTable
    
    ratioPlotHelpJButton
    
    JButton ratioPlotHelpJButton
    
    ratioPlotOptionsJButton
    
    JButton ratioPlotOptionsJButton
    
    ratioPlotsJPanel
    
    JPanel ratioPlotsJPanel
    
    ratioPlotsMainLayeredPane
    
    JLayeredPane ratioPlotsMainLayeredPane
    
    ratioPlotsTitledPanel
    
    JPanel ratioPlotsTitledPanel
    
    reporterGUI
    
    ReporterGUI reporterGUI
    
    The main GUI class.
    
    selectedChartPanel
    
    org.jfree.chart.ChartPanel selectedChartPanel
    
    The currently selected chart panel.
Package eu.isas.reporter.gui.settings
- Class eu.isas.reporter.gui.settings.ReporterSettingsDialog
  
  class ReporterSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    cancelButton
    
    JButton cancelButton
    
    canceled
    
    boolean canceled
    
    Boolean indicating whether the editing of the settings has been canceled.
    
    editable
    
    boolean editable
    
    Boolean indicating whether the user can edit the settings.
    
    modificationParameters
    
    com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters
    
    The modification parameters of the search.
    
    normalizationButton
    
    JButton normalizationButton
    
    normalizationSettings
    
    NormalizationSettings normalizationSettings
    
    The normalization settings.
    
    okButton
    
    JButton okButton
    
    ratioEstimationButton
    
    JButton ratioEstimationButton
    
    ratioEstimationSettings
    
    RatioEstimationSettings ratioEstimationSettings
    
    The ratio estimation settings
    
    reporterIonSelectionButton
    
    JButton reporterIonSelectionButton
    
    reporterIonSelectionSettings
    
    ReporterIonSelectionSettings reporterIonSelectionSettings
    
    The settings for the selection of the reporter ions in spectra
    
    reporterMethod
    
    com.compomics.util.experiment.quantification.reporterion.ReporterMethod reporterMethod
    
    The reporter method used.
    
    settingsPanel
    
    JPanel settingsPanel
Package eu.isas.reporter.gui.settings.display
- Class eu.isas.reporter.gui.settings.display.ClusteringSettingsDialog
  
  class ClusteringSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    cancelButton
    
    JButton cancelButton
    
    canceled
    
    boolean canceled
    
    Boolean indicating whether the editing of the settings has been canceled.
    
    classesColors
    
    HashMap<String,Color> classesColors
    
    The classes color coding.
    
    editable
    
    boolean editable
    
    Boolean indicating whether the settings can be edited.
    
    okButton
    
    JButton okButton
    
    peptideClasses
    
    ArrayList<String> peptideClasses
    
    The available peptide classes.
    
    peptideClassesMap
    
    HashMap<String,PeptideClusterClassKey> peptideClassesMap
    
    The peptide classes map.
    
    peptideClassesScrollPane
    
    JScrollPane peptideClassesScrollPane
    
    peptideClassesTable
    
    JTable peptideClassesTable
    
    peptidesClassesLbl
    
    JLabel peptidesClassesLbl
    
    proteinClasses
    
    ArrayList<String> proteinClasses
    
    The available protein classes.
    
    proteinClassesMap
    
    HashMap<String,ProteinClusterClassKey> proteinClassesMap
    
    The protein classes map.
    
    proteinClassesScrollPane
    
    JScrollPane proteinClassesScrollPane
    
    proteinClassesTable
    
    JTable proteinClassesTable
    
    proteinsClassesLbl
    
    JLabel proteinsClassesLbl
    
    psmClasses
    
    ArrayList<String> psmClasses
    
    The available PSM classes.
    
    psmClassesMap
    
    HashMap<String,PsmClusterClassKey> psmClassesMap
    
    The PSM classes map.
    
    psmClassesScrollPane
    
    JScrollPane psmClassesScrollPane
    
    psmClassesTable
    
    JTable psmClassesTable
    
    psmsClassesLbl
    
    JLabel psmsClassesLbl
    
    selectedPeptideClasses
    
    ArrayList<String> selectedPeptideClasses
    
    The selected peptide classes.
    
    selectedProteinClasses
    
    ArrayList<String> selectedProteinClasses
    
    The selected protein classes.
    
    selectedPsmClasses
    
    ArrayList<String> selectedPsmClasses
    
    The selected PSM classes.
    
    selectionPanel
    
    JPanel selectionPanel
Package eu.isas.reporter.gui.settings.quantification
- Class eu.isas.reporter.gui.settings.quantification.NormalizationSettingsDialog
  
  class NormalizationSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    cancelButton
    
    JButton cancelButton
    
    canceled
    
    boolean canceled
    
    Boolean indicating whether the editing of the settings has been canceled.
    
    contaminantsBrowseButton
    
    JButton contaminantsBrowseButton
    
    contaminantsClearButton
    
    JButton contaminantsClearButton
    
    contaminantsFile
    
    File contaminantsFile
    
    FASTA file containing the contaminant proteins.
    
    contaminantsTxt
    
    JTextField contaminantsTxt
    
    jLabel1
    
    JLabel jLabel1
    
    jLabel2
    
    JLabel jLabel2
    
    matchesNormalizationPanel
    
    JPanel matchesNormalizationPanel
    
    okButton
    
    JButton okButton
    
    peptideNormalizationCmb
    
    JComboBox peptideNormalizationCmb
    
    peptideNormalizationLbl
    
    JLabel peptideNormalizationLbl
    
    peptideNormalizationType
    
    NormalizationType peptideNormalizationType
    
    The selected peptide normalization type.
    
    proteinNormalizationCmb
    
    JComboBox proteinNormalizationCmb
    
    proteinNormalizationLbl
    
    JLabel proteinNormalizationLbl
    
    proteinNormalizationType
    
    NormalizationType proteinNormalizationType
    
    The selected protein normalization type.
    
    psmNormalizationCmb
    
    JComboBox psmNormalizationCmb
    
    psmNormalizationLbl
    
    JLabel psmNormalizationLbl
    
    psmNormalizationType
    
    NormalizationType psmNormalizationType
    
    The selected PSM normalization type.
    
    specialProteinsPanel
    
    JPanel specialProteinsPanel
    
    stableProteinsBrowseButton
    
    JButton stableProteinsBrowseButton
    
    stableProteinsClearButton
    
    JButton stableProteinsClearButton
    
    stableProteinsFile
    
    File stableProteinsFile
    
    FASTA file containing the stable proteins.
    
    stableProteinsTxt
    
    JTextField stableProteinsTxt
- Class eu.isas.reporter.gui.settings.quantification.RatioEstimationSettingsDialog
  
  class RatioEstimationSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    
    addModifications
    
    JButton addModifications
    
    allPTMs
    
    JList allPTMs
    
    allPtmsScrollPane
    
    JScrollPane allPtmsScrollPane
    
    availablePtmsLabel
    
    JLabel availablePtmsLabel
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    cancelButton
    
    JButton cancelButton
    
    canceled
    
    boolean canceled
    
    Boolean indicating whether the editing of the settings has been canceled.
    
    excludeMiscleavedCmb
    
    JComboBox excludeMiscleavedCmb
    
    excludeMissingIntensitiesCmb
    
    JComboBox excludeMissingIntensitiesCmb
    
    excludePeptidesLabel
    
    JLabel excludePeptidesLabel
    
    excludeSharedCmb
    
    JComboBox excludeSharedCmb
    
    helpLabel
    
    JLabel helpLabel
    
    helpLinkLabel
    
    JLabel helpLinkLabel
    
    idSelectionPanel
    
    JPanel idSelectionPanel
    
    jLabel1
    
    JLabel jLabel1
    
    jLabel2
    
    JLabel jLabel2
    
    jLabel3
    
    JLabel jLabel3
    
    modificationParameters
    
    com.compomics.util.parameters.identification.search.ModificationParameters modificationParameters
    
    The modification profile of the search.
    
    okButton
    
    JButton okButton
    
    peptidesLabel
    
    JLabel peptidesLabel
    
    peptideValidationCmb
    
    JComboBox peptideValidationCmb
    
    proteinGroupJPanel
    
    JPanel proteinGroupJPanel
    
    proteinsLabel
    
    JLabel proteinsLabel
    
    proteinValidationCmb
    
    JComboBox proteinValidationCmb
    
    psmsLabel
    
    JLabel psmsLabel
    
    psmValidationCmb
    
    JComboBox psmValidationCmb
    
    ratioEstimationsPanel
    
    JPanel ratioEstimationsPanel
    
    removeModification
    
    JButton removeModification
    
    resolutionLabel
    
    JLabel resolutionLabel
    
    resolutionTxt
    
    JTextField resolutionTxt
    
    selectedPTMs
    
    JList selectedPTMs
    
    selectedPtmsScrollPane
    
    JScrollPane selectedPtmsScrollPane
    
    uniquePeptidesLbl
    
    JLabel uniquePeptidesLbl
    
    uniquePeptidesSpinner
    
    JSpinner uniquePeptidesSpinner
    
    widthTxt
    
    JTextField widthTxt
    
    windowWidthLabel
    
    JLabel windowWidthLabel
- Class eu.isas.reporter.gui.settings.quantification.ReporterIonSelectionSettingsDialog
  
  class ReporterIonSelectionSettingsDialog extends JDialog implements Serializable
  - Serialized Fields
    
    backgroundPanel
    
    JPanel backgroundPanel
    
    cancelButton
    
    JButton cancelButton
    
    canceled
    
    boolean canceled
    
    Boolean indicating whether the editing of the settings has been canceled.
    
    ionSelectionComboBox
    
    JComboBox ionSelectionComboBox
    
    ionSelectionLabel
    
    JLabel ionSelectionLabel
    
    ionToleranceTxt
    
    JTextField ionToleranceTxt
    
    ms2SpectrumReportersOption
    
    JRadioButton ms2SpectrumReportersOption
    
    ms3SpectrumReportersOption
    
    JRadioButton ms3SpectrumReportersOption
    
    mzToleranceLabel
    
    JLabel mzToleranceLabel
    
    mzTolTxt
    
    JTextField mzTolTxt
    
    okButton
    
    JButton okButton
    
    ppmCmb
    
    JComboBox ppmCmb
    
    precursorMatchingReportersOption
    
    JRadioButton precursorMatchingReportersOption
    
    reporterIonMzToleranceLabel
    
    JLabel reporterIonMzToleranceLabel
    
    reporterLocationButtonGroup
    
    ButtonGroup reporterLocationButtonGroup
    
    reporterLocationPanel
    
    JPanel reporterLocationPanel
    
    reporterMethod
    
    com.compomics.util.experiment.quantification.reporterion.ReporterMethod reporterMethod
    
    The reporter method used.
    
    rtToleranceLabel
    
    JLabel rtToleranceLabel
    
    rtTolTxt
    
    JTextField rtTolTxt
    
    spectrumAnalysisPanel
    
    JPanel spectrumAnalysisPanel
Package eu.isas.reporter.gui.tablemodels
- Class eu.isas.reporter.gui.tablemodels.PeptideTableModel
  
  class PeptideTableModel extends com.compomics.util.gui.tablemodels.SelfUpdatingTableModel implements Serializable
  - Serialized Fields
    
    batchSize
    
    int batchSize
    
    The batch size.
    
    displayFeaturesGenerator
    
    eu.isas.peptideshaker.utils.DisplayFeaturesGenerator displayFeaturesGenerator
    
    The display features generator.
    
    displayPreferences
    
    DisplayPreferences displayPreferences
    
    The display preferences.
    
    exceptionHandler
    
    com.compomics.util.exceptions.ExceptionHandler exceptionHandler
    
    The exception handler catches exceptions.
    
    identification
    
    com.compomics.util.experiment.identification.Identification identification
    
    The identification.
    
    identificationFeaturesGenerator
    
    com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator
    
    The identification features generator.
    
    identificationParameters
    
    com.compomics.util.parameters.identification.IdentificationParameters identificationParameters
    
    The identification parameters.
    
    peptideKeys
    
    long[] peptideKeys
    
    A list of ordered peptide keys.
    
    proteinAccession
    
    String proteinAccession
    
    The main accession of the protein match to which the list of peptides is attached.
    
    quantificationFeaturesGenerator
    
    QuantificationFeaturesGenerator quantificationFeaturesGenerator
    
    The quantification feature generator.
    
    reporterIonQuantification
    
    com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification
    
    The reporter ion quantification.
    
    sampleIndexes
    
    ArrayList<String> sampleIndexes
    
    The sample indexes.
    
    showScores
    
    boolean showScores
    
    Indicates whether the scores should be displayed instead of the confidence
    
    spectrumProvider
    
    com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider
    
    The spectrum provider.
- Class eu.isas.reporter.gui.tablemodels.ProteinTableModel
  
  class ProteinTableModel extends com.compomics.util.gui.tablemodels.SelfUpdatingTableModel implements Serializable
  - Serialized Fields
    
    batchSize
    
    int batchSize
    
    The batch size.
    
    displayFeaturesGenerator
    
    eu.isas.peptideshaker.utils.DisplayFeaturesGenerator displayFeaturesGenerator
    
    The display features generator provides display features.
    
    displayPreferences
    
    DisplayPreferences displayPreferences
    
    The display preferences.
    
    exceptionHandler
    
    com.compomics.util.exceptions.ExceptionHandler exceptionHandler
    
    The exception handler catches exceptions.
    
    geneMaps
    
    com.compomics.util.experiment.biology.genes.GeneMaps geneMaps
    
    The gene maps.
    
    identification
    
    com.compomics.util.experiment.identification.Identification identification
    
    The identification of this project.
    
    identificationFeaturesGenerator
    
    com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator
    
    The identification features generator provides identification information on the matches.
    
    proteinDetailsProvider
    
    com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider
    
    The protein details provider.
    
    proteinKeys
    
    long[] proteinKeys
    
    The list of the keys of the protein matches being displayed.
    
    quantificationFeaturesGenerator
    
    QuantificationFeaturesGenerator quantificationFeaturesGenerator
    
    The quantification feature generator.
    
    reporterIonQuantification
    
    com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification
    
    The reporter ion quantification.
    
    sampleIndexes
    
    ArrayList<String> sampleIndexes
    
    The sample indexes.
    
    sequenceProvider
    
    com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider
    
    The protein sequences provider.
    
    showScores
    
    boolean showScores
    
    If true the scores will be shown.
    
    spectrumProvider
    
    com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider
    
    The spectrum provider.
- Class eu.isas.reporter.gui.tablemodels.PsmTableModel
  
  class PsmTableModel extends com.compomics.util.gui.tablemodels.SelfUpdatingTableModel implements Serializable
  - Serialized Fields
    
    batchSize
    
    int batchSize
    
    The batch size.
    
    displayFeaturesGenerator
    
    eu.isas.peptideshaker.utils.DisplayFeaturesGenerator displayFeaturesGenerator
    
    The display features generator.
    
    displayPreferences
    
    DisplayPreferences displayPreferences
    
    The display preferences.
    
    exceptionHandler
    
    com.compomics.util.exceptions.ExceptionHandler exceptionHandler
    
    The exception handler catches exceptions.
    
    identification
    
    com.compomics.util.experiment.identification.Identification identification
    
    The identification of this project.
    
    identificationParameters
    
    com.compomics.util.parameters.identification.IdentificationParameters identificationParameters
    
    The identification parameters.
    
    inputMap
    
    eu.isas.peptideshaker.scoring.maps.InputMap inputMap
    
    The ID input map.
    
    psmKeys
    
    long[] psmKeys
    
    A list of ordered PSM keys.
    
    quantificationFeaturesGenerator
    
    QuantificationFeaturesGenerator quantificationFeaturesGenerator
    
    The quantification feature generator.
    
    reporterIonQuantification
    
    com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification
    
    The reporter ion quantification.
    
    sampleIndexes
    
    ArrayList<String> sampleIndexes
    
    The sample indexes.
    
    showScores
    
    boolean showScores
    
    Indicates whether the scores should be displayed instead of the confidence
    
    spectrumProvider
    
    com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider
    
    The spectrum provider.
Package eu.isas.reporter.preferences
- Class eu.isas.reporter.preferences.DisplayPreferences
  
  class DisplayPreferences extends Object implements Serializable
  - Serialized Fields
    
    clusteringSettings
    
    ClusteringSettings clusteringSettings
    
    The clustering settings.
    
    proteinRatioType
    
    int proteinRatioType
    
    The type of ratio to display.
    
    reagents
    
    ArrayList<String> reagents
    
    The list of the reagents on the user defined order. Null if not set.
- Class eu.isas.reporter.preferences.ProjectDetails
  
  class ProjectDetails extends Object implements Serializable
Package eu.isas.reporter.settings
- Class eu.isas.reporter.settings.ClusteringSettings
  
  class ClusteringSettings extends Object implements Serializable
  - Serialized Fields
    
    classesColors
    
    HashMap<String,Color> classesColors
    
    The classes color coding in a map where the key is the toString() representation of the key.
    
    kMeansClusteringSettings
    
    com.compomics.util.math.clustering.settings.KMeansClusteringSettings kMeansClusteringSettings
    
    The k-means clustering settings.
    
    possiblePeptideClassesKeys
    
    HashMap<String,PeptideClusterClassKey> possiblePeptideClassesKeys
    
    Map of the classes keys indexed by name.
    
    possiblePeptideClassesNames
    
    ArrayList<String> possiblePeptideClassesNames
    
    The possible peptide classes.
    
    possibleProteinClassesKeys
    
    HashMap<String,ProteinClusterClassKey> possibleProteinClassesKeys
    
    Map of the classes keys indexed by name.
    
    possibleProteinClassesNames
    
    ArrayList<String> possibleProteinClassesNames
    
    The possible protein classes.
    
    possiblePsmClassesKeys
    
    HashMap<String,PsmClusterClassKey> possiblePsmClassesKeys
    
    Map of the classes keys indexed by name.
    
    possiblePsmClassesNames
    
    ArrayList<String> possiblePsmClassesNames
    
    The possible PSM classes.
    
    selectedPeptideClasses
    
    ArrayList<String> selectedPeptideClasses
    
    The selected peptide classes.
    
    selectedProteinClasses
    
    ArrayList<String> selectedProteinClasses
    
    The selected protein classes.
    
    selectedPsmClasses
    
    ArrayList<String> selectedPsmClasses
    
    The selected PSM classes.
- Class eu.isas.reporter.settings.NormalizationSettings
  
  class NormalizationSettings extends Object implements Serializable
  - Serialized Fields
    
    contaminantsFastaFile
    
    File contaminantsFastaFile
    
    FASTA file containing the contaminants.
    
    peptideNormalization
    
    NormalizationType peptideNormalization
    
    The normalization to conduct at the peptide level.
    
    proteinNormalization
    
    NormalizationType proteinNormalization
    
    The normalization to conduct at the protein level.
    
    psmNormalization
    
    NormalizationType psmNormalization
    
    The normalization to conduct at the PSM level.
    
    stableProteinsFastaFile
    
    File stableProteinsFastaFile
    
    FASTA file containing the proteins to consider stable.
- Class eu.isas.reporter.settings.RatioEstimationSettings
  
  class RatioEstimationSettings extends Object implements Serializable
  - Serialized Fields
    
    excludingPTM
    
    HashSet<String> excludingPTM
    
    List of PTMs to exclude. Peptides presenting these PTMs will not be accounted for during quantification.
    
    ignoreMissedCleavages
    
    boolean ignoreMissedCleavages
    
    Boolean indicating whether peptides presenting missed cleavages should be ignored.
    
    ignoreNullIntensities
    
    boolean ignoreNullIntensities
    
    Boolean indicating whether spectra presenting null intensities should be ignored.
    
    minUnique
    
    int minUnique
    
    Minimum number of unique peptides, ignored if negative.
    
    peptideValidation
    
    com.compomics.util.experiment.identification.validation.MatchValidationLevel peptideValidation
    
    The validation threshold to use for peptide quantification.
    
    percentile
    
    double percentile
    
    Percentage of ratios to consider for the likelihood estimator window setting.
    
    proteinValidation
    
    com.compomics.util.experiment.identification.validation.MatchValidationLevel proteinValidation
    
    The validation threshold to use for protein quantification.
    
    psmValidation
    
    com.compomics.util.experiment.identification.validation.MatchValidationLevel psmValidation
    
    The validation threshold to use for PSM quantification.
    
    ratioResolution
    
    double ratioResolution
    
    Ratio resolution.
- Class eu.isas.reporter.settings.ReporterIonSelectionSettings
  
  class ReporterIonSelectionSettings extends Object implements Serializable
  - Serialized Fields
    
    mostAccurate
    
    boolean mostAccurate
    
    Boolean indicating whether the most accurate ion should be selected.
    
    precursorMzPpm
    
    boolean precursorMzPpm
    
    Indicates if the precursor mz tolerance in ppm.
    
    precursorMzTolerance
    
    double precursorMzTolerance
    
    Precursor mz tolerance used to link quantification to identifications in case these are not recorded on the same spectra. (identification files import only)
    
    precursorRTTolerance
    
    double precursorRTTolerance
    
    Precursor RT tolerance used to link quantification to identifications in case these are not recorded on the same spectra. (identification files import only)
    
    reporterIonsLocation
    
    ReporterIonsLocationType reporterIonsLocation
    
    The location of the reporter ions.
    
    reporterIonsMzTolerance
    
    double reporterIonsMzTolerance
- Class eu.isas.reporter.settings.ReporterPreferences
  
  class ReporterPreferences extends Object implements Serializable
  - Serialized Fields
    
    defaultSettings
    
    ReporterSettings defaultSettings
    
    The default reporter settings.
- Class eu.isas.reporter.settings.ReporterSettings
  
  class ReporterSettings extends Object implements Serializable
  - Serialized Fields
    
    annotationParameters
    
    com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters annotationParameters
    
    The annotation parameters.
    
    normalizationSettings
    
    NormalizationSettings normalizationSettings
    
    The normalization settings.
    
    projectDetails
    
    ProjectDetails projectDetails
    
    The project details.
    
    ratioEstimationSettings
    
    RatioEstimationSettings ratioEstimationSettings
    
    The ratio estimation settings.
    
    reporterIonSelectionSettings
    
    ReporterIonSelectionSettings reporterIonSelectionSettings
    
    The settings for the selection of the reporter ions in spectra.

Serialized Form

Package eu.isas.reporter.calculation.clustering.keys

Class eu.isas.reporter.calculation.clustering.keys.PeptideClusterClassKey

Serialized Fields

cTerm

forbiddenPtms

forbiddenPtmsAsSet

notModified

nTerm

possiblePtms

possiblePtmsAsSet

starred

Class eu.isas.reporter.calculation.clustering.keys.ProteinClusterClassKey

Serialized Fields

starred

Class eu.isas.reporter.calculation.clustering.keys.PsmClusterClassKey

Serialized Fields

file

starred

Package eu.isas.reporter.gui

Class eu.isas.reporter.gui.JumpToPanel

Serialized Fields

currentProteinKeys

currentSelection

findJLabel

indexLabel

inputTxt

jumpType

keyPressedCounter

lastInput

lastLabel

nextButton

possibilities

previousButton

reporterGUI

types

waitingTime

welcomeText

Class eu.isas.reporter.gui.LabellingEfficiencyDialog

Serialized Fields

addDbButton

addIdFilesButton

addSpectraFilesJButton

backgroundPanel

closeButton

databaseFileLabel

efficiencyPanel

efficiencyTable

efficiencyTableScrollPane

fastaTxt

fileSelectiontPanel

idFilesLabel

labellingEfficiency

lastSelectedFolder

modificationFactory

msFileHandler

normalIcon

parentFrame

progressDialog

psdbParent

sortedModifications

spectrumFiles

spectrumFilesLabel

txtIdFileLocation

txtSpectraFileLocation

waitingIcon

Class eu.isas.reporter.gui.MethodSettingsDialog

Serialized Fields

backgroundPanel

browseConfigButton

configFilePanel

isotopeCorrectionPanel

methodsFactory

newDialog

okButton

reagentsTable

reagentsTableJScrollPane

saveConfigButton

txtConfigurationFileLocation

valuesChanged