Package eu.isas.peptideshaker.gui

Class PeptideShakerGUI

java.lang.Object
java.awt.Component
java.awt.Container
java.awt.Window
java.awt.Frame
javax.swing.JFrame
eu.isas.peptideshaker.gui.PeptideShakerGUI
All Implemented Interfaces:
com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent, com.compomics.util.gui.error_handlers.notification.NotificationDialogParent, ClipboardOwner, ImageObserver, MenuContainer, Serializable, Accessible, RootPaneContainer, WindowConstants
public class PeptideShakerGUI extends JFrame implements ClipboardOwner, com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent, com.compomics.util.gui.error_handlers.notification.NotificationDialogParent
The main PeptideShaker frame.
Author:
Harald Barsnes, Marc Vaudel
See Also:

  • Field Details

    • OVER_VIEW_TAB_INDEX

      public static final int OVER_VIEW_TAB_INDEX
      The Overview tab index.
      See Also:

    • SPECTRUM_ID_TAB_INDEX

      public static final int SPECTRUM_ID_TAB_INDEX
      The SpectrumID tab index.
      See Also:

    • PROTEIN_FRACTIONS_TAB_INDEX

      public static final int PROTEIN_FRACTIONS_TAB_INDEX
      The Protein Fractions tab index.
      See Also:

    • MODIFICATIONS_TAB_INDEX

      public static final int MODIFICATIONS_TAB_INDEX
      The Modifications tab index.
      See Also:

    • STRUCTURES_TAB_INDEX

      public static final int STRUCTURES_TAB_INDEX
      The Structures tab index.
      See Also:

    • ANNOTATION_TAB_INDEX

      public static final int ANNOTATION_TAB_INDEX
      The Annotation tab index.
      See Also:

    • GO_ANALYSIS_TAB_INDEX

      public static final int GO_ANALYSIS_TAB_INDEX
      The GO Analysis tab index.
      See Also:

    • VALIDATION_TAB_INDEX

      public static final int VALIDATION_TAB_INDEX
      The Validation tab index.
      See Also:

    • QC_PLOTS_TAB_INDEX

      public static final int QC_PLOTS_TAB_INDEX
      The QC Plots tab index.
      See Also:

    • TITLED_BORDER_HORIZONTAL_PADDING

      public static String TITLED_BORDER_HORIZONTAL_PADDING
      The horizontal padding used before and after the text in the titled borders. (Needed to make it look as good in Java 7 as it did in Java 6...)

    • TITLED_BORDER_HORIZONTAL_PADDING_HTML

      public static String TITLED_BORDER_HORIZONTAL_PADDING_HTML
      The horizontal padding used before and after the text in the titled borders. (Needed to make it look as good in Java 7 as it did in Java 6...)

    • DARK_THEME_BACKGROUND_COLOR

      public static final Color DARK_THEME_BACKGROUND_COLOR
      The dark theme background color.

  • Constructor Details

    • PeptideShakerGUI

      public PeptideShakerGUI()
      Creates a new PeptideShaker frame.

    • PeptideShakerGUI

      public PeptideShakerGUI(File psdbFile, String zipURL, String zipUrlDownloadFolder, String pxAccession, boolean pxAccessionPrivate, boolean showWelcomeDialog)
      Creates a new PeptideShaker frame.
      Parameters:
      psdbFile - the psdb file to load
      zipURL - the URL to a zipped psdb file to download and load, can be null
      zipUrlDownloadFolder - the folder to download the URL to, can be null
      pxAccession - a PX accession to open in the PRIDE Reshake, can be null
      pxAccessionPrivate - if true, the PX accession is private
      showWelcomeDialog - boolean indicating if the Welcome Dialog is to be shown

  • Method Details

    • main

      public static void main(String[] args)
      The main method used to start PeptideShaker.
      Parameters:
      args - the arguments

    • loadUserParameters

      public void loadUserParameters()
      Loads the user parameters.

    • setProject

      public void setProject(com.compomics.util.experiment.ProjectParameters projectParameters)
      Sets the project.
      Parameters:
      projectParameters - the experiment

    • updateFrameTitle

      public void updateFrameTitle()
      Add the experiment title to the frame title.

    • resetFrameTitle

      public void resetFrameTitle()
      Reset the frame title.

    • getLastSelectedFolder

      public com.compomics.util.io.file.LastSelectedFolder getLastSelectedFolder()
      Returns the last selected folder.
      Returns:
      the last selected folder

    • setLastSelectedFolder

      public void setLastSelectedFolder(com.compomics.util.io.file.LastSelectedFolder lastSelectedFolder)
      Set the last selected folder.
      Parameters:
      lastSelectedFolder - the folder to set

    • editPathSettings

      public void editPathSettings(WelcomeDialog welcomeDialog)
      Opens a dialog allowing the setting of paths.
      Parameters:
      welcomeDialog - reference to the Welcome dialog, can be null

    • initiateDisplay

      public void initiateDisplay()
      Initiate the display by displaying the data in the currently selected tab. Was previously a part of the displayResults methods, but had to be split into a separate method due to threading issues.

    • displayResults

      public void displayResults()
      This method will display results in all panels.

    • disableSpectrumDisplay

      public void disableSpectrumDisplay()
      Method called to disable the spectrum display.

    • setUpLogFile

      public void setUpLogFile(boolean redirectOutputStream)
      Set up the log file. Redirects the error and output streams to the log file.
      Parameters:
      redirectOutputStream - if true, redirects the output stream

    • getUserParameters

      public UserParameters getUserParameters()
      Returns the user parameters.
      Returns:
      the user parameters

    • getUtilitiesUserParameters

      public com.compomics.util.parameters.UtilitiesUserParameters getUtilitiesUserParameters()
      Specified by:
      getUtilitiesUserParameters in interface com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent

    • setUtilitiesUserParameters

      public void setUtilitiesUserParameters(com.compomics.util.parameters.UtilitiesUserParameters utilitiesUserParameters)
      Set the utilities user parameters.
      Parameters:
      utilitiesUserParameters - the utilities user parameters

    • setDefaultParameters

      public void setDefaultParameters()
      Set the default parameters.

    • updateAnnotationMenu

      public void updateAnnotationMenu()
      Updates the ions used for fragment annotation.

    • updateSpectrumAnnotations

      public void updateSpectrumAnnotations()
      Updates the annotations in the selected tab.

    • updateModificationColorCoding

      public void updateModificationColorCoding()
      Update the modification color coding in all tabs.

    • getProjectParameters

      public com.compomics.util.experiment.ProjectParameters getProjectParameters()
      Returns the project parameters.
      Returns:
      the project parameters

    • getIdentification

      public com.compomics.util.experiment.identification.Identification getIdentification()
      Returns the identification displayed.
      Returns:
      the identification displayed

    • getSequenceProvider

      public com.compomics.util.experiment.io.biology.protein.SequenceProvider getSequenceProvider()
      Returns the sequence provider.
      Returns:
      the sequence provider

    • getSpectrumProvider

      public com.compomics.util.experiment.mass_spectrometry.SpectrumProvider getSpectrumProvider()
      Returns the spectrum provider.
      Returns:
      the spectrum provider

    • setSequenceProvider

      public void setSequenceProvider(com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider)
      Sets the sequence provider.
      Parameters:
      sequenceProvider - the sequence provider

    • getProteinDetailsProvider

      public com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider getProteinDetailsProvider()
      Returns the protein details provider.
      Returns:
      the protein details provider

    • setProteinDetailsProvider

      public void setProteinDetailsProvider(com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider)
      Sets the protein details provider.
      Parameters:
      proteinDetailsProvider - the protein details provider

    • setMsFileHandler

      public void setMsFileHandler(com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler)
      Sets the mass spectrometry file handler.
      Parameters:
      msFileHandler - The mass spectrometry file handler.

    • setIdentification

      public void setIdentification(com.compomics.util.experiment.identification.Identification identification)
      Sets the identification.
      Parameters:
      identification - the identification

    • getFilterParameters

      public com.compomics.util.gui.filtering.FilterParameters getFilterParameters()
      Return the filter parameters to use.
      Returns:
      the filter parameters to use

    • getDisplayParameters

      public DisplayParameters getDisplayParameters()
      Return the display parameters to use.
      Returns:
      the display parameters to use

    • setFilterParameters

      public void setFilterParameters(com.compomics.util.gui.filtering.FilterParameters filterParameters)
      Sets the filter parameters to use.
      Parameters:
      filterParameters - the filter parameters to use

    • setDisplayParameters

      public void setDisplayParameters(DisplayParameters displayParameters)
      Sets the display parameters to use.
      Parameters:
      displayParameters - the display parameters to use

    • getSpectrumCountingParameters

      public com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters getSpectrumCountingParameters()
      Returns the spectrum counting parameters.
      Returns:
      the spectrum counting parameters

    • setSpectrumCountingParameters

      public void setSpectrumCountingParameters(com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters)
      Sets new spectrum counting parameters.
      Parameters:
      spectrumCountingParameters - new spectrum counting parameters

    • getIdentificationParameters

      public com.compomics.util.parameters.identification.IdentificationParameters getIdentificationParameters()
      Returns the identification parameters.
      Returns:
      the identification parameters

    • setIdentificationParameters

      public void setIdentificationParameters(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters)
      Sets the identification parameters.
      Parameters:
      identificationParameters - the identification parameters

    • getProcessingParameters

      public com.compomics.util.parameters.tools.ProcessingParameters getProcessingParameters()
      Returns the initial processing preferences.
      Returns:
      the initial processing preferences

    • setProcessingParameters

      public void setProcessingParameters(com.compomics.util.parameters.tools.ProcessingParameters processingParameters)
      Sets the initial processing preferences.
      Parameters:
      processingParameters - the initial processing preferences

    • resetModificationFactory

      public void resetModificationFactory()
      Resets the modification factory.

    • getSparklineColor

      public Color getSparklineColor()
      Get the sparklines color.
      Returns:
      the sparklineColor

    • setSparklineColor

      public void setSparklineColor(Color sparklineColor)
      Set the sparklines color.
      Parameters:
      sparklineColor - the sparklineColor to set

    • getSparklineColorNonValidated

      public Color getSparklineColorNonValidated()
      Get the non-validated sparklines color.
      Returns:
      the non-validated sparklineColor

    • setSparklineColorNonValidated

      public void setSparklineColorNonValidated(Color sparklineColorNonValidated)
      Set the non-validated sparklines color.
      Parameters:
      sparklineColorNonValidated - the non-validated sparklineColor to set

    • getSparklineColorNotFound

      public Color getSparklineColorNotFound()
      Get the not found sparklines color.
      Returns:
      the not found sparklineColor

    • getSparklineColorPossible

      public Color getSparklineColorPossible()
      Get the possible sparklines color.
      Returns:
      the possible sparklineColor

    • setSparklineColorPossible

      public void setSparklineColorPossible(Color sparklineColorPossible)
      Set the possible sparklines color.
      Parameters:
      sparklineColorPossible - the possible sparklineColor to set

    • getBubbleScale

      public double getBubbleScale()
      Returns the bubble plot scale value.
      Returns:
      the bubble plot scale value

    • setSelectedItems

      public void setSelectedItems(long proteinKey, long peptideKey, String spectrumFile, String spectrumTitle)
      Sets the keys of the selected protein, peptide and PSM.
      Parameters:
      proteinKey - the key of the selected protein
      peptideKey - the key of the selected peptide
      spectrumFile - the file of the selected spectrum
      spectrumTitle - the title of the selected spectrum

    • updateSelectionInCurrentTab

      public void updateSelectionInCurrentTab()
      Updates the selected items in the currently opened tab.

    • resetSelectedItems

      public void resetSelectedItems()
      Resets the items selection.

    • setSelectedItems

      public void setSelectedItems()
      Sets the selected item based on the selected tab.

    • getSelectedProteinKey

      public long getSelectedProteinKey()
      Returns the key of the selected protein.
      Returns:
      the key of the selected protein

    • getSelectedPeptideKey

      public long getSelectedPeptideKey()
      Returns the key of the selected peptide.
      Returns:
      the key of the selected peptide

    • getSelectedSpectrumFile

      public String getSelectedSpectrumFile()
      Returns the currently selected spectrum file.
      Returns:
      the file of the selected spectrum

    • getSelectedSpectrumTitle

      public String getSelectedSpectrumTitle()
      Returns the currently selected spectrum title.
      Returns:
      the title of the selected spectrum

    • clearData

      public void clearData(boolean clearDatabaseFolder, boolean updateGuiComponents)
      Clear the data from the previous experiment.
      Parameters:
      clearDatabaseFolder - decides if the database folder is to be cleared or not
      updateGuiComponents - true if the GUI components are to be updated

    • clearParameters

      public void clearParameters()
      Clears the project parameters.

    • getOverviewPanel

      public OverviewPanel getOverviewPanel()
      Returns the OverviewPanel.
      Returns:
      the OverviewPanel

    • getProteinFractionsPanel

      public ProteinFractionsPanel getProteinFractionsPanel()
      Returns the fractions panel.
      Returns:
      the fractions panel

    • getValidationPanel

      public ValidationPanel getValidationPanel()
      Returns the validation panel.
      Returns:
      the validation panel

    • getModificationsPanel

      public ModificationsPanel getModificationsPanel()
      Returns the modification panel.
      Returns:
      the modification panel

    • getProteinStructurePanel

      public ProteinStructurePanel getProteinStructurePanel()
      Returns the ProteinStructurePanel.
      Returns:
      the ProteinStructurePanel

    • getSpectrumIdentificationPanel

      public SpectrumIdentificationPanel getSpectrumIdentificationPanel()
      Returns the SpectrumIdentificationPanel.
      Returns:
      the SpectrumIdentificationPanel

    • getGOPanel

      public GOEAPanel getGOPanel()
      Returns the GO Panel.
      Returns:
      the GO Panel

    • getPreferredColumnWidth

      public int getPreferredColumnWidth(JTable table, int colIndex, int margin)
      Gets the preferred width of the column specified by colIndex. The column will be just wide enough to show the column head and the widest cell in the column. Margin pixels are added to the left and right (resulting in an additional width of 2*margin pixels.
      Note that this method iterates all rows in the table to get the perfect width of the column!
      Parameters:
      table - the table
      colIndex - the colum index
      margin - the margin to add
      Returns:
      the preferred width of the column

    • enableSpectrumExport

      public void enableSpectrumExport(boolean enable)
      Enable or disable the spectrum export in the overview panel.
      Parameters:
      enable - if true the spectrum export in the overview panel will be enabled

    • updateMainMatch

      public void updateMainMatch(String mainMatch, int proteinInferenceType)
      Update the protein match in the different tabs.
      Parameters:
      mainMatch - the protein match to use
      proteinInferenceType - the protein inference group type

    • setDataSaved

      public void setDataSaved(boolean dataSaved)
      Set whether the current data has been saved to a psdb file or not.
      Parameters:
      dataSaved - whether the current data has been saved to a psdb file or not

    • getSelectedTab

      public int getSelectedTab()
      Returns the selected tab as indexed by the static fields.
      Returns:
      the selected tab as indexed by the static fields

    • getDisplayedProteins

      public long[] getDisplayedProteins()
      Returns a list of keys of the currently displayed proteins.
      Returns:
      a list of keys of the currently displayed proteins

    • getDisplayedPeptides

      public long[] getDisplayedPeptides()
      Returns a list of keys of the currently displayed peptides.
      Returns:
      a list of keys of the currently displayed peptides

    • getDisplayedSpectrumMatches

      public long[] getDisplayedSpectrumMatches()
      Returns a list of keys of the currently displayed spectrum matches.
      Returns:
      a list of keys of the currently displayed spectrum matches

    • getDisplayedAssumptions

      public long[] getDisplayedAssumptions()
      Returns a list of keys of the currently displayed assumptions.
      Returns:
      a list of keys of the currently displayed assumptions

    • openProteinLinks

      public void openProteinLinks(String links)
      Opens one or more protein links in the default web browser.
      Parameters:
      links - the links to open

    • getScoreAndConfidenceDecimalFormat

      public DecimalFormat getScoreAndConfidenceDecimalFormat()
      Returns the decimal format used for the score and confidence columns.
      Returns:
      the decimal format used for the score and confidence columns

    • catchException

      public void catchException(Exception e)
      Method called whenever an exception is caught.
      Parameters:
      e - the exception caught

    • getExceptionHandler

      public com.compomics.util.exceptions.exception_handlers.FrameExceptionHandler getExceptionHandler()
      Returns the exception handler.
      Returns:
      the exception handler

    • close

      public void close()
      Closes the frame by first checking if the project ought to be saved.

    • restart

      public void restart()
      Closes and restarts PeptideShaker. Does not work inside the IDE of course.
      Specified by:
      restart in interface com.compomics.software.dialogs.JavaHomeOrMemoryDialogParent

    • updateAnnotationMenus

      public void updateAnnotationMenus(com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters specificAnnotationParameters, int precursorCharge, HashSet<String> modNames)
      Update the annotation menu bar with the current annotation preferences.
      Parameters:
      specificAnnotationParameters - the specific annotation parameters
      precursorCharge - the precursor charges
      modNames - the names of the modifications

    • getSpecificAnnotationParameters

      public com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters getSpecificAnnotationParameters(String spectrumFile, String spectrumTitle, com.compomics.util.experiment.identification.SpectrumIdentificationAssumption spectrumIdentificationAssumption)
      Returns the specific annotation parameters corresponding to the given spectrum, hit, and the menu selections.
      Parameters:
      spectrumFile - The file name of the spectrum.
      spectrumTitle - The title of the spectrum.
      spectrumIdentificationAssumption - The spectrum annotation preferences.
      Returns:
      the specific annotation parameters corresponding to the given spectrum, hit, and the menu selection

    • getAnnotationMenuBar

      public JMenuBar getAnnotationMenuBar()
      Returns the annotation menu bar.
      Returns:
      the annotation menu bar

    • updateAnnotationMenuBarVisableOptions

      public void updateAnnotationMenuBarVisableOptions(boolean showSpectrumOptions, boolean showBubblePlotOptions, boolean showIonTableOptions, boolean showPtmPlotOptions, boolean showSingleSpectrumExportOptions)
      Updates the visible menu items on the settings menu of the annotation menu bar.
      Parameters:
      showSpectrumOptions - if true, the spectrum options are shown
      showBubblePlotOptions - if true, the bubble plot options are shown
      showIonTableOptions - if true, the ion table options are shown
      showPtmPlotOptions - if true, the PTM plot option is shown
      showSingleSpectrumExportOptions - if true, the single spectrum export options are shown

    • updateRecentProjectsList

      public void updateRecentProjectsList()
      Add the list of recently used files to the file menu.

    • loadRecentProjectsList

      public void loadRecentProjectsList(JPopupMenu menu, WelcomeDialog welcomeDialog)
      Add the list of recently used files to the file menu.
      Parameters:
      menu - the menu to add the recent files list to
      welcomeDialog - the welcome dialog reference

    • getProjectDetails

      public ProjectDetails getProjectDetails()
      Returns the project details.
      Returns:
      the project details

    • setProjectDetails

      public void setProjectDetails(ProjectDetails projectDetails)
      Sets the project details.
      Parameters:
      projectDetails - the project details

    • importPeptideShakerZipFromURL

      public void importPeptideShakerZipFromURL(String zipURL, String destinationFolder)
      Imports a PeptideShaker zip file from a URL.
      Parameters:
      zipURL - the PeptideShaker zip file to import
      destinationFolder - the folder to download and unzip the project in

    • importPeptideShakerZipFile

      public void importPeptideShakerZipFile(File zipFile)
      Imports information from a PeptideShaker zip file.
      Parameters:
      zipFile - the PeptideShaker zip file to import

    • importPeptideShakerFile

      public void importPeptideShakerFile(File psFile, boolean importFromZip)
      Imports information from a PeptideShaker file.
      Parameters:
      psFile - The PeptideShaker file to import.
      importFromZip - flag that determines if psdb was imported from a zip file

    • lostOwnership

      public void lostOwnership(Clipboard clipboard, Transferable contents)
      Specified by:
      lostOwnership in interface ClipboardOwner

    • exportSelectedSpectraAsMgf

      public void exportSelectedSpectraAsMgf() throws IOException
      Export the current spectrum as an mgf.
      Throws:
      IOException - Exception thrown whenever an error occurred while writing the mgf file

    • exportAnnotatedSpectrum

      public void exportAnnotatedSpectrum() throws IOException
      Export the current spectrum annotation.
      Throws:
      IOException - exception thrown whenever an error occurred while reading or writing a file

    • exportSpectrumAsFigure

      public void exportSpectrumAsFigure()
      Export the current spectrum as a figure.

    • exportSequenceFragmentationAsFigure

      public void exportSequenceFragmentationAsFigure()
      Export the current sequence fragmentation as a figure.

    • exportIntensityHistogramAsFigure

      public void exportIntensityHistogramAsFigure()
      Export the current intensity histogram as a figure.

    • exportMassErrorPlotAsFigure

      public void exportMassErrorPlotAsFigure()
      Export the current mass error plot as a figure.

    • exportBubblePlotAsFigure

      public void exportBubblePlotAsFigure()
      Export the current bubble plot as a figure.

    • setDisplayOptions

      public void setDisplayOptions(boolean displayProteins, boolean displayPeptidesAndPsms, boolean displayCoverage, boolean displaySpectrum)
      Update the display options for the overview tab.
      Parameters:
      displayProteins - if the proteins panel is to be displayed
      displayPeptidesAndPsms - if the peptides and PSMs panel is to be displayed
      displayCoverage - if the protein coverage panel is to be displayed
      displaySpectrum - if the spectrum panel is to be displayed

    • getCurrentMassDeltas

      public HashMap<Double,String> getCurrentMassDeltas()
      Get the current delta masses for use when annotating the spectra.
      Returns:
      the current delta masses

    • saveProject

      public void saveProject(boolean aCloseWhenDone, boolean aExportToZipWhenDone)
      Saves the modifications made to the project.
      Parameters:
      aCloseWhenDone - if true, PeptideShaker closes after saving
      aExportToZipWhenDone - if true, the project is also saved as a zip file

    • setUpdated

      public void setUpdated(int tabIndex, boolean updated)
      Sets that the tab was updated.
      Parameters:
      tabIndex - integer indicating which tab (according to the static indexing) was updated.
      updated - boolean indicating whether the tab is updated or not

    • updateTabbedPanes

      public void updateTabbedPanes()
      Update the tabbed panes.

    • getStarHider

      public StarHider getStarHider()
      Returns the object responsible for starring/hiding matches.
      Returns:
      the object responsible for starring/hiding matches

    • getIdentificationFeaturesGenerator

      public com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator getIdentificationFeaturesGenerator()
      Returns the identification features generator.
      Returns:
      the identification features generator

    • resetIdentificationFeaturesGenerator

      public void resetIdentificationFeaturesGenerator()
      Resets the feature generator.

    • setIdentificationFeaturesGenerator

      public void setIdentificationFeaturesGenerator(com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator identificationFeaturesGenerator)
      Sets the feature generator.
      Parameters:
      identificationFeaturesGenerator - the identification features generator

    • resetDisplayFeaturesGenerator

      public void resetDisplayFeaturesGenerator()
      Resets the display features generator.

    • getDisplayFeaturesGenerator

      public DisplayFeaturesGenerator getDisplayFeaturesGenerator()
      Returns the display features generator.
      Returns:
      the display features generator

    • getMetrics

      public com.compomics.util.experiment.identification.peptide_shaker.Metrics getMetrics()
      Returns the metrics saved while loading the files.
      Returns:
      the metrics saved while loading the files

    • setMetrics

      public void setMetrics(com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics)
      Sets the metrics saved while loading the files.
      Parameters:
      metrics - the metrics saved while loading the files

    • getProjectType

      public com.compomics.util.parameters.peptide_shaker.ProjectType getProjectType()
      Returns the project type.
      Returns:
      the project type

    • setProjectType

      public void setProjectType(com.compomics.util.parameters.peptide_shaker.ProjectType projectType)
      Sets the project type.
      Parameters:
      projectType - the project type

    • getGeneMaps

      public com.compomics.util.experiment.biology.genes.GeneMaps getGeneMaps()
      Returns the gene maps.
      Returns:
      the gene maps

    • setGeneMaps

      public void setGeneMaps(com.compomics.util.experiment.biology.genes.GeneMaps geneMaps)
      Sets the gene maps.
      Parameters:
      geneMaps - the gene maps

    • spectrumFileSelectionChanged

      public void spectrumFileSelectionChanged(String spectrumFile)
      Sets the new spectrum file selected.
      Parameters:
      spectrumFile - the name of the new spectrum file

    • saveProjectAs

      public void saveProjectAs(boolean closeWhenDone, boolean aExportToZipWhenDone)
      Save the project to a new location.
      Parameters:
      closeWhenDone - if true, PeptideShaker closes when done saving
      aExportToZipWhenDone - if true, the project is also saved as a zip file

    • getUserSelectedFile

      public File getUserSelectedFile(String aSuggestedFileName, String aFileEnding, String aFileFormatDescription, String aDialogTitle, boolean openDialog)
      Returns the file selected by the user, or null if no file was selected.
      Parameters:
      aSuggestedFileName - the suggested file name, can be null
      aFileEnding - the file type, e.g., .txt
      aFileFormatDescription - the file format description, e.g., (Mascot Generic Format) *.mgf
      aDialogTitle - the title for the dialog
      openDialog - if true an open dialog is shown, false results in a save dialog
      Returns:
      the file selected by the user, or null if no file or folder was selected

    • jumpToTab

      public void jumpToTab(int tabIndex)
      Jumps to the desired tab
      Parameters:
      tabIndex - index of the tab as indexed by the static fields

    • showSparklines

      public boolean showSparklines()
      Returns true if the sparklines are to be shown.
      Returns:
      true if the sparklines are to be show

    • updateSurroundingAminoAcids

      public void updateSurroundingAminoAcids()
      Update the number of surrounding amino acids displayed.

    • checkNewsFeed

      public void checkNewsFeed()
      Displays a news feed at the bottom of the GUI.

    • openExampleFile

      public void openExampleFile()
      Open the PeptideShaker example dataset.

    • updateFilterSettingsField

      public void updateFilterSettingsField(String text)
      Update the filter settings field. (Interface method: not implemented in this class as it is not needed.)
      Parameters:
      text - the text to set

    • exportProjectAsZip

      public void exportProjectAsZip()
      Export the project as a zip file.

    • getNormalIcon

      public Image getNormalIcon()
      Returns the normal icon.
      Returns:
      the normal icon

    • getWaitingIcon

      public Image getWaitingIcon()
      Returns the waiting icon.
      Returns:
      the waiting icon

    • getDefaultPsmSelection

      public long getDefaultPsmSelection(long peptideKey)
      Returns the default PSM, i.e., the "best" PSM for the given peptide.
      Parameters:
      peptideKey - the peptide to get the PSM for
      Returns:
      the key of the default PSM

    • getDefaultPeptideSelection

      public long getDefaultPeptideSelection(long proteinKey)
      Returns the default peptide, i.e., the "best" peptide for the given protein.
      Parameters:
      proteinKey - the protein to get the peptide for
      Returns:
      the key of the default peptide

    • clearGeneMappings

      public void clearGeneMappings()
      Clear the gene mappings.

    • notificationClicked

      public void notificationClicked(String notificationType)
      Specified by:
      notificationClicked in interface com.compomics.util.gui.error_handlers.notification.NotificationDialogParent

    • addNote

      public void addNote(String note)
      Add a note to the current list of notes.
      Parameters:
      note - the note to add, can contain HTML formatting, but not the HTML start and end tags

    • setCurentNotes

      public void setCurentNotes(ArrayList<String> currentNotes)
      Set the list of current notes.
      Parameters:
      currentNotes - the notes to set

    • updateNotesNotificationCounter

      public void updateNotesNotificationCounter()
      Update the notification counter for the notes.

    • showNotesNotification

      public void showNotesNotification()
      Show a note notification pop up.

    • addTip

      public void addTip(String tip)
      Add a tip to the current list of tips.
      Parameters:
      tip - the tip to add, can contain HTML formatting, but not the HTML start and end tags

    • setCurentTips

      public void setCurentTips(ArrayList<String> currentTips)
      Set the list of current tips.
      Parameters:
      currentTips - the tips to set

    • updateTipsNotificationCounter

      public void updateTipsNotificationCounter()
      Update the notification counter for the tips.

    • showTipsNotification

      public void showTipsNotification()
      Show a tip notification pop up.

    • getExtendedProjectReport

      public String getExtendedProjectReport()
      Returns an extended HTML project report.
      Returns:
      an extended HTML project report

    • checkForNewVersion

      public boolean checkForNewVersion()
      Check for new version.
      Returns:
      true if a new version is to be downloaded