Serialized Form

  • Package eu.isas.searchgui.gui

    • Class eu.isas.searchgui.gui.AdvancedParametersDialog

      class AdvancedParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • advancedParamatersPanel
          JPanel advancedParamatersPanel
        • checkMgfFileSizeComboBox
          JComboBox checkMgfFileSizeComboBox
        • checkMgfFileSizeLabel
          JLabel checkMgfFileSizeLabel
        • checkSpectrumChargesComboBox
          JComboBox checkSpectrumChargesComboBox
        • checkSpectrumChargesLabel
          JLabel checkSpectrumChargesLabel
        • closeButton
          JButton closeButton
        • duplicateTitlesComboBox
          JComboBox duplicateTitlesComboBox
        • duplicateTitlesLabel
          JLabel duplicateTitlesLabel
        • groupResultFilesCmb
          JComboBox groupResultFilesCmb
        • groupResultFilesTxt
          JLabel groupResultFilesTxt
        • highSpectrumChargeRangeTxt
          JTextField highSpectrumChargeRangeTxt
        • identificationParametersPanel
          JPanel identificationParametersPanel
        • includeDataCmb
          JComboBox includeDataCmb
        • includeDataTxt
          JLabel includeDataTxt
        • includeDateCmb
          JComboBox includeDateCmb
        • includeDateLbl
          JLabel includeDateLbl
        • lowSpectrumChargeRangeTxt
          JTextField lowSpectrumChargeRangeTxt
        • maxMgfFileSizeLabel
          JLabel maxMgfFileSizeLabel
        • maxSpectraPerFileLabel
          JLabel maxSpectraPerFileLabel
        • mgfMaxSizeTxt
          JTextField mgfMaxSizeTxt
        • mgfReducedSizeTxt
          JTextField mgfReducedSizeTxt
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • outputPanel
          JPanel outputPanel
        • peakPickingComboBox
          JComboBox peakPickingComboBox
        • peakPickingLabel
          JLabel peakPickingLabel
        • refMassLbl
          JLabel refMassLbl
        • refMassTxt
          JTextField refMassTxt
        • renameCmb
          JComboBox renameCmb
        • renameXTandemFileLabel
          JLabel renameXTandemFileLabel
        • spectrumChargeRangeDelimiterLabel
          JLabel spectrumChargeRangeDelimiterLabel
        • spectrumChargeRangeLabel
          JLabel spectrumChargeRangeLabel
        • spectrumProcessingPanel
          JPanel spectrumProcessingPanel
        • zipIdFilesCmb
          JComboBox zipIdFilesCmb
        • zipIdFilesLabel
          JLabel zipIdFilesLabel

    • Class eu.isas.searchgui.gui.AlignedListCellRenderer

      class 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 eu.isas.searchgui.gui.PeptideShakerParametersDialog

      class PeptideShakerParametersDialog extends JDialog implements Serializable

      • Serialized Fields

        • advancedPanel
          JPanel advancedPanel
        • backgroundPanel
          JPanel backgroundPanel
        • browseMascotFilesButton
          JButton browseMascotFilesButton
        • cancelButton
          JButton cancelButton
        • canceled
          boolean canceled
          Boolean indicating whether the user canceled the action.
        • clearMascotFilesButton
          JButton clearMascotFilesButton
        • editOutputButton
          JButton editOutputButton
        • editPeptideShakerLocationButton
          JButton editPeptideShakerLocationButton
        • editProjectSettingsButton
          JButton editProjectSettingsButton
        • fileNamePanel
          JPanel fileNamePanel
        • lowMemoryWarningLabel
          JLabel lowMemoryWarningLabel
        • mascotDatFiles
          ArrayList<File> mascotDatFiles
          The list of Mascot dat files.
        • mascotFilesLabel
          JLabel mascotFilesLabel
        • mascotFilesTextField
          JTextField mascotFilesTextField
        • okButton
          JButton okButton
        • openDialogHelpJButton
          JButton openDialogHelpJButton
        • outputFileLabel
          JLabel outputFileLabel
        • outputFileTextField
          JTextField outputFileTextField
        • peptideShakerInstallationJTextField
          JTextField peptideShakerInstallationJTextField
        • peptideShakerInstallationPanel
          JPanel peptideShakerInstallationPanel
        • peptideShakerLocationLabel
          JLabel peptideShakerLocationLabel
        • progressDialog
          com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog
          The progress dialog.
        • projectDetailsPanel
          JPanel projectDetailsPanel
        • projectNameIdTxt
          JTextField projectNameIdTxt
        • projectReferenceLabel
          JLabel projectReferenceLabel
        • projectSettingsLbl
          JLabel projectSettingsLbl
        • projectSettingsTxt
          JTextField projectSettingsTxt
        • searchGUI
          SearchGUI searchGUI
          The SearchGUI parent.

    • Class eu.isas.searchgui.gui.SearchGUI

      class SearchGUI extends JFrame implements Serializable

      • Serialized Fields

        • aboutButton
          JButton aboutButton
        • aboutMenuItem
          JMenuItem aboutMenuItem
        • addSettingsButton
          JButton addSettingsButton
        • addSpectraButton
          JButton addSpectraButton
        • advancedSettingsMenuItem
          JMenuItem advancedSettingsMenuItem
        • andromedaButton
          JButton andromedaButton
        • andromedaLinkLabel
          JLabel andromedaLinkLabel
        • andromedaSettingsButton
          JButton andromedaSettingsButton
        • andromedaSupportButton
          JButton andromedaSupportButton
        • clearSpectraButton
          JButton clearSpectraButton
        • cometButton
          JButton cometButton
        • cometLinkLabel
          JLabel cometLinkLabel
        • cometSettingsButton
          JButton cometSettingsButton
        • cometSupportButton
          JButton cometSupportButton
        • configFolder
          File configFolder
          The config folder.
        • databaseFileTxt
          JTextField databaseFileTxt
        • databaseSettingsLbl
          JLabel databaseSettingsLbl
        • direcTagButton
          JButton direcTagButton
        • direcTagLinkLabel
          JLabel direcTagLinkLabel
        • direcTagSettingsButton
          JButton direcTagSettingsButton
        • direcTagSupportButton
          JButton direcTagSupportButton
        • editDatabaseDetailsButton
          JButton editDatabaseDetailsButton
        • editEnzymesEditMenuItem
          JMenuItem editEnzymesEditMenuItem
        • editIdSettingsFilesMenuItem
          JMenuItem editIdSettingsFilesMenuItem
        • editMenu
          JMenu editMenu
        • editModificationsEditMenuItem
          JMenuItem editModificationsEditMenuItem
        • editModificationsMenuItem
          JMenuItem editModificationsMenuItem
        • editReporterSettingsLabel
          JLabel editReporterSettingsLabel
        • editResultFolderButton
          JButton editResultFolderButton
        • editSearchEngineLocationsMenuItem
          JMenuItem editSearchEngineLocationsMenuItem
        • editSettingsButton
          JButton editSettingsButton
        • enableAndromedaJCheckBox
          JCheckBox enableAndromedaJCheckBox
        • enableCometJCheckBox
          JCheckBox enableCometJCheckBox
        • enableDirecTagJCheckBox
          JCheckBox enableDirecTagJCheckBox
        • enableMetaMorpheusJCheckBox
          JCheckBox enableMetaMorpheusJCheckBox
        • enableMsAmandaJCheckBox
          JCheckBox enableMsAmandaJCheckBox
        • enableMsgfJCheckBox
          JCheckBox enableMsgfJCheckBox
        • enableMyriMatchJCheckBox
          JCheckBox enableMyriMatchJCheckBox
        • enableNovorJCheckBox
          JCheckBox enableNovorJCheckBox
        • enableOmssaJCheckBox
          JCheckBox enableOmssaJCheckBox
        • enableSageJCheckBox
          JCheckBox enableSageJCheckBox
        • enableTideJCheckBox
          JCheckBox enableTideJCheckBox
        • enableXTandemJCheckBox
          JCheckBox enableXTandemJCheckBox
        • enzymeFactory
          com.compomics.util.experiment.biology.enzymes.EnzymeFactory enzymeFactory
          The enzyme factory.
        • exceptionHandler
          com.compomics.util.exceptions.exception_handlers.FrameExceptionHandler exceptionHandler
          Handler for exceptions.
        • exitMenuItem
          JMenuItem exitMenuItem
        • fastaFile
          File fastaFile
          The FASTA file.
        • fileMenu
          JMenu fileMenu
        • helpMenu
          JMenu helpMenu
        • helpMenuItem
          JMenuItem helpMenuItem
        • identificationParameters
          com.compomics.util.parameters.identification.IdentificationParameters identificationParameters
          The search parameters.
        • identificationParametersFactory
          com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory identificationParametersFactory
          The identification parameters factory.
        • identificationParametersFile
          File identificationParametersFile
          The identification settings file.
        • inputFilesPanel
          JPanel inputFilesPanel
        • javaSettingsJMenuItem
          JMenuItem javaSettingsJMenuItem
        • jMenuItem1
          JMenuItem jMenuItem1
        • jSeparator1
          JPopupMenu.Separator jSeparator1
        • jSeparator16
          JPopupMenu.Separator jSeparator16
        • jSeparator17
          JPopupMenu.Separator jSeparator17
        • jSeparator2
          JPopupMenu.Separator jSeparator2
        • 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
        • metaMorpheusButton
          JButton metaMorpheusButton
        • metaMorpheusLinkLabel
          JLabel metaMorpheusLinkLabel
        • metaMorpheusSettingsButton
          JButton metaMorpheusSettingsButton
        • metaMorpheusSupportButton
          JButton metaMorpheusSupportButton
        • modificationFactory
          com.compomics.util.experiment.biology.modifications.ModificationFactory modificationFactory
          The modifications factory.
        • modificationOptionsPopupMenu
          JPopupMenu modificationOptionsPopupMenu
        • msAmandaButton
          JButton msAmandaButton
        • msAmandaLinkLabel
          JLabel msAmandaLinkLabel
        • msAmandaSettingsButton
          JButton msAmandaSettingsButton
        • msAmandaSupportButton
          JButton msAmandaSupportButton
        • msconvertButton
          JButton msconvertButton
        • msconvertCheckBox
          JCheckBox msconvertCheckBox
        • msconvertLabel
          JLabel msconvertLabel
        • msConvertParameters
          com.compomics.util.experiment.mass_spectrometry.proteowizard.MsConvertParameters msConvertParameters
          The msconvert parameters.
        • msconvertSettingsButton
          JButton msconvertSettingsButton
        • msconvertSupportButton
          JButton msconvertSupportButton
        • msFileHandler
          com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler
          The ms file handler.
        • msgfButton
          JButton msgfButton
        • msgfLinkLabel
          JLabel msgfLinkLabel
        • msgfSettingsButton
          JButton msgfSettingsButton
        • msgfSupportButton
          JButton msgfSupportButton
        • myriMatchButton
          JButton myriMatchButton
        • myriMatchLinkLabel
          JLabel myriMatchLinkLabel
        • myriMatchSettingsButton
          JButton myriMatchSettingsButton
        • myrimatchSupportButton
          JButton myrimatchSupportButton
        • nonThermoRawFilesSelected
          boolean nonThermoRawFilesSelected
          Boolean indicating whether non-Thermo raw files are selected.
        • novorButton
          JButton novorButton
        • novorLinkLabel
          JLabel novorLinkLabel
        • novorSettingsButton
          JButton novorSettingsButton
        • novorSupportButton
          JButton novorSupportButton
        • omssaButton
          JButton omssaButton
        • omssaLinkLabel
          JLabel omssaLinkLabel
        • omssaSettingsButton
          JButton omssaSettingsButton
        • omssaSupportButton
          JButton omssaSupportButton
        • outputFolder
          File outputFolder
          The output folder.
        • outputFolderTxt
          JTextField outputFolderTxt
        • peptideShakerButton
          JButton peptideShakerButton
        • peptideShakerCheckBox
          JCheckBox peptideShakerCheckBox
        • peptideShakerLabel
          JLabel peptideShakerLabel
        • peptideShakerSettingsButton
          JButton peptideShakerSettingsButton
        • peptideShakerSupportButton
          JButton peptideShakerSupportButton
        • postProcessingPanel
          JPanel postProcessingPanel
        • preProcessingPanel
          JPanel preProcessingPanel
        • privacyMenuItem
          JMenuItem privacyMenuItem
        • processingMenuItem
          JMenuItem processingMenuItem
        • processingParameters
          com.compomics.util.parameters.tools.ProcessingParameters processingParameters
          The processing preferences.
        • rawFiles
          ArrayList<File> rawFiles
          The raw files.
        • reporterButton
          JButton reporterButton
        • reporterCheckBox
          JCheckBox reporterCheckBox
        • reporterLabel
          JLabel reporterLabel
        • reporterPostProcessPanel
          JPanel reporterPostProcessPanel
        • resourceSettingsMenuItem
          JMenuItem resourceSettingsMenuItem
        • resultFolderLbl
          JLabel resultFolderLbl
        • sageButton
          JButton sageButton
        • sageLinkLabel
          JLabel sageLinkLabel
        • sageSettingsButton
          JButton sageSettingsButton
        • sageSupportButton
          JButton sageSupportButton
        • searchButton
          JButton searchButton
        • searchEnginesLocationPanel
          JPanel searchEnginesLocationPanel
        • searchEnginesPanel
          JPanel searchEnginesPanel
        • searchEnginesScrollPane
          JScrollPane searchEnginesScrollPane
        • searchGUIPublicationLabel
          JLabel searchGUIPublicationLabel
        • searchHandler
          SearchHandler searchHandler
          The SearchCLI instance.
        • searchSettingsLbl
          JLabel searchSettingsLbl
        • settingsComboBox
          JComboBox settingsComboBox
        • settingsTabDisplayed
          boolean settingsTabDisplayed
          A boolean indicating if the user has visited the Parameters tab. If the user does not visit the settings tab before starting the search a warning is displayed.s
        • spectrumFiles
          ArrayList<File> spectrumFiles
          The spectrum files.
        • spectrumFilesLabel
          JLabel spectrumFilesLabel
        • spectrumFilesTxt
          JTextField spectrumFilesTxt
        • taskEditorPanel
          JPanel taskEditorPanel
        • thermoRawFileParserButton
          JButton thermoRawFileParserButton
        • thermoRawFileParserCheckBox
          JCheckBox thermoRawFileParserCheckBox
        • thermoRawFileParserLabel
          JLabel thermoRawFileParserLabel
        • thermoRawFileParserParameters
          com.compomics.util.experiment.mass_spectrometry.thermo_raw_file_parser.ThermoRawFileParserParameters thermoRawFileParserParameters
          The ThermoRawFileParser parameters.
        • thermoRawFileParserSettingsButton
          JButton thermoRawFileParserSettingsButton
        • thermoRawFileParserSupportButton
          JButton thermoRawFileParserSupportButton
        • tideButton
          JButton tideButton
        • tideLinkLabel
          JLabel tideLinkLabel
        • tideSettingsButton
          JButton tideSettingsButton
        • tideSupportButton
          JButton tideSupportButton
        • utilitiesUserParameters
          com.compomics.util.parameters.UtilitiesUserParameters utilitiesUserParameters
          The utilities user parameters.
        • validSpectrumTitles
          boolean validSpectrumTitles
          If true, then one of the currently processed spectra has duplicate titles.
        • waitingDialog
          com.compomics.util.gui.waiting.waitinghandlers.WaitingDialog waitingDialog
          The dialog displayed during the search.
        • xtandemButton
          JButton xtandemButton
        • xtandemLinkLabel
          JLabel xtandemLinkLabel
        • xtandemSettingsButton
          JButton xtandemSettingsButton
        • xtandemSupportButton
          JButton xtandemSupportButton

    • Class eu.isas.searchgui.gui.SoftwareLocationDialog

      class SoftwareLocationDialog extends JDialog implements Serializable

      • Serialized Fields

        • andromedaBrowse
          JButton andromedaBrowse
        • andromedaLocationLabel
          JLabel andromedaLocationLabel
        • andromedaLocationTxt
          JTextField andromedaLocationTxt
        • andromedaValid
          boolean andromedaValid
          True if the Andromeda installation is valid.
        • backgroundPanel
          JPanel backgroundPanel
        • cancelButton
          JButton cancelButton
        • cometBrowse
          JButton cometBrowse
        • cometLocationLabel
          JLabel cometLocationLabel
        • cometLocationTxt
          JTextField cometLocationTxt
        • cometValid
          boolean cometValid
          True if the Comet installation is valid.
        • direcTagBrowse
          JButton direcTagBrowse
        • direcTagLocationLabel
          JLabel direcTagLocationLabel
        • direcTagLocationTxt
          JTextField direcTagLocationTxt
        • direcTagValid
          boolean direcTagValid
          True if the DirecTag installation is valid.
        • enableAndromedaCombo
          JComboBox enableAndromedaCombo
        • enableCometCombo
          JComboBox enableCometCombo
        • enableDirecTagCombo
          JComboBox enableDirecTagCombo
        • enableMetaMorpheusCombo
          JComboBox enableMetaMorpheusCombo
        • enableMsAmandaCombo
          JComboBox enableMsAmandaCombo
        • enableMsgfCombo
          JComboBox enableMsgfCombo
        • enableMyriMatchCombo
          JComboBox enableMyriMatchCombo
        • enableNovorCombo
          JComboBox enableNovorCombo
        • enableOmssaCombo
          JComboBox enableOmssaCombo
        • enableSageCombo
          JComboBox enableSageCombo
        • enableTideCombo
          JComboBox enableTideCombo
        • enableXTandemCombo
          JComboBox enableXTandemCombo
        • guiLoaded
          boolean guiLoaded
          True when the GUI has loaded.
        • makeblastdbBrowse
          JButton makeblastdbBrowse
        • makeblastdbLocationLabel
          JLabel makeblastdbLocationLabel
        • makeblastdbLocationTxt
          JTextField makeblastdbLocationTxt
        • metaMorpheusBrowse
          JButton metaMorpheusBrowse
        • metaMorpheusLocationLabel
          JLabel metaMorpheusLocationLabel
        • metaMorpheusLocationTxt
          JTextField metaMorpheusLocationTxt
        • metaMorpheusValid
          boolean metaMorpheusValid
          True if the MetaMorpheus installation is valid.
        • msAmandaBrowse
          JButton msAmandaBrowse
        • msAmandaLocationLabel
          JLabel msAmandaLocationLabel
        • msAmandaLocationTxt
          JTextField msAmandaLocationTxt
        • msAmandaValid
          boolean msAmandaValid
          True if the MS Amanda installation is valid.
        • msgfBrowse
          JButton msgfBrowse
        • msgfLocationLabel
          JLabel msgfLocationLabel
        • msgfLocationTxt
          JTextField msgfLocationTxt
        • msgfValid
          boolean msgfValid
          True if the MS-GF+ installation is valid.
        • myriMatchBrowse
          JButton myriMatchBrowse
        • myriMatchLocationLabel
          JLabel myriMatchLocationLabel
        • myriMatchLocationTxt
          JTextField myriMatchLocationTxt
        • myriMatchValid
          boolean myriMatchValid
          True if the MyriMatch installation is valid.
        • novorBrowse
          JButton novorBrowse
        • novorLocationLabel
          JLabel novorLocationLabel
        • novorLocationTxt
          JTextField novorLocationTxt
        • novorValid
          boolean novorValid
          True if the Novor installation is valid.
        • okButton
          JButton okButton
        • omssaBrowse
          JButton omssaBrowse
        • omssaLocationLabel
          JLabel omssaLocationLabel
        • omssaLocationTxt
          JTextField omssaLocationTxt
        • omssaValid
          boolean omssaValid
          True if the OMSSA installation is valid.
        • sageBrowse
          JButton sageBrowse
        • sageLocationLabel
          JLabel sageLocationLabel
        • sageLocationTxt
          JTextField sageLocationTxt
        • sageValid
          boolean sageValid
          True if the Sage installation is valid.
        • searchEnginesLocationPanel
          JPanel searchEnginesLocationPanel
        • searchGUIMainFrame
          SearchGUI searchGUIMainFrame
          The SearchGUI main frame.
        • tandemValid
          boolean tandemValid
          True if the X!Tandem installation is valid.
        • tideBrowse
          JButton tideBrowse
        • tideLocationLabel
          JLabel tideLocationLabel
        • tideLocationTxt
          JTextField tideLocationTxt
        • tideValid
          boolean tideValid
          True if the Tide installation is valid.
        • xTandemBrowse
          JButton xTandemBrowse
        • xTandemLocationLabel
          JLabel xTandemLocationLabel
        • xTandemLocationTxt
          JTextField xTandemLocationTxt