Package eu.isas.peptideshaker.gui.tabpanels

Class OverviewPanel

java.lang.Object
java.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
eu.isas.peptideshaker.gui.tabpanels.OverviewPanel
All Implemented Interfaces:
ProteinSequencePanelParent, ImageObserver, MenuContainer, Serializable, Accessible
public class OverviewPanel extends JPanel implements ProteinSequencePanelParent
The overview panel displaying the proteins, the peptides and the spectra.
Author:
Harald Barsnes, Marc Vaudel
See Also:

  • Constructor Details

    • OverviewPanel

      public OverviewPanel(PeptideShakerGUI parent)
      Creates a new OverviewPanel.
      Parameters:
      parent - the PeptideShaker parent frame.

  • Method Details

    • updateProteinPanelTitle

      public void updateProteinPanelTitle()
      Updates the protein panel title with the number of validated/confident proteins.

    • updatePeptidePanelTitle

      public void updatePeptidePanelTitle()
      Updates the peptide panel title with the number of validated/confident proteins.

    • updatePsmPanelTitle

      public void updatePsmPanelTitle()
      Updates the PSM panel title with the number of validated/confident

    • showSparkLines

      public void showSparkLines(boolean showSparkLines)
      Displays or hide sparklines in the tables.
      Parameters:
      showSparkLines - boolean indicating whether sparklines shall be displayed or hidden

    • getDisplayedProteins

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

    • getDisplayedPeptides

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

    • getDisplayedSpectrumMatches

      public long[] getDisplayedSpectrumMatches()
      Returns a list of keys of the displayed PSMs
      Returns:
      a list of keys of the displayed PSMs

    • updateSeparators

      public void updateSeparators()
      Method called whenever the component is resized to maintain the look of the GUI.

    • setDisplayOptions

      public void setDisplayOptions(boolean displayProteins, boolean displayPeptidesAndPSMs, boolean displayCoverage, boolean displaySpectrum)
      Sets the whether the protein coverage and the spectrum shall be displayed.
      Parameters:
      displayProteins - boolean indicating whether the proteins shall be displayed
      displayPeptidesAndPSMs - boolean indicating whether the peptides and PSMs shall be displayed
      displayCoverage - boolean indicating whether the protein coverage shall be displayed
      displaySpectrum - boolean indicating whether the spectrum shall be displayed

    • updateBubblePlot

      public void updateBubblePlot()
      Updated the bubble plot with the current PSMs.

    • updateSpectrum

      public void updateSpectrum()
      Updates the spectrum annotation. Used when the user updates the annotation accuracy.

    • displayResults

      public void displayResults()
      Displays the results in the tables.

    • updateProteinTable

      public void updateProteinTable()
      Updates the results in the protein table and reselect the desired protein.

    • getProteinTable

      public JTable getProteinTable()
      Returns the protein table.
      Returns:
      the protein table

    • getSelectedPsmKeys

      public long[] getSelectedPsmKeys()
      Returns the keys of the selected spectra in the PSM table.
      Returns:
      the keys of the selected spectra in the PSM table

    • getSelectedSpectrumTitles

      public TreeMap<String,TreeSet<String>> getSelectedSpectrumTitles()
      Returns the titles of the selected spectra in the PSM table in a map by file name.
      Returns:
      The titles of the selected spectra in the PSM table in a map by file name.

    • getSelectedIdentificationAssumptions

      public HashMap<Long,ArrayList<com.compomics.util.experiment.identification.SpectrumIdentificationAssumption>> getSelectedIdentificationAssumptions()
      Returns a map of the selected spectrum identification assumptions as a map: spectrum key | assumption
      Returns:
      an ArrayList of the keys of the selected spectra in the PSM table

    • getSpectrum

      public Component getSpectrum()
      Returns the spectrum panel.
      Returns:
      the spectrum panel, or null if the spectrum tab is not enabled

    • getSpectrumAndPlots

      public Component getSpectrumAndPlots()
      Returns the extended spectrum panel.
      Returns:
      the extended spectrum panel, or null if the spectrum tab is not enabled

    • getSequenceFragmentationPlot

      public Component getSequenceFragmentationPlot()
      Returns the sequence fragmentation plot panel.
      Returns:
      the sequence fragmentation plot panel, or null if the spectrum tab is not enabled

    • getIntensityHistogramPlot

      public com.compomics.util.gui.spectrum.IntensityHistogram getIntensityHistogramPlot()
      Returns the intensity histogram plot panel.
      Returns:
      the intensity histogram plot panel, or null if the spectrum tab is not enabled

    • getMassErrorPlot

      public com.compomics.util.gui.spectrum.MassErrorPlot getMassErrorPlot()
      Returns the mass error plot panel.
      Returns:
      the mass error plot panel, or null if the spectrum tab is not enabled or the the mass error plot is not showing

    • getBubblePlot

      public Component getBubblePlot()
      Returns the bubble plot.
      Returns:
      the bubble plot

    • isSpectrumEnabled

      public boolean isSpectrumEnabled()
      Returns true of the spectrum tab is enabled.
      Returns:
      true of the spectrum tab is enabled

    • showSeparators

      public void showSeparators(boolean showSeparators)
      Enable or disable the separators.
      Parameters:
      showSeparators - if true the separators are enabled

    • updateScores

      public void updateScores()
      Hides or displays the score columns in the protein and peptide tables.

    • enableDarkTheme

      public void enableDarkTheme(boolean darkTheme)
      Enable or disable the dark theme.
      Parameters:
      darkTheme - enable or disable the dark theme

    • getSelectedSpectrumTabIndex

      public int getSelectedSpectrumTabIndex()
      Returns the current selected tab in the spectrum and fragment ions tabbed pane.
      Returns:
      the current selected tab in the spectrum and fragment ions tabbed pane

    • showSpectrumAnnotationMenu

      public void showSpectrumAnnotationMenu()
      Makes sure that the annotation menu bar is shown in the currently visible spectrum and fragment ions tabbed pane.

    • setIntensitySliderValue

      public void setIntensitySliderValue(int value)
      Set the intensity slider value.
      Parameters:
      value - the intensity slider value

    • setAccuracySliderValue

      public void setAccuracySliderValue(int value)
      Set the accuracy slider value.
      Parameters:
      value - the accuracy slider value

    • updateModificationColors

      public void updateModificationColors()
      Update the PTM color coding.

    • updatePsmOrder

      public void updatePsmOrder()
      Update the PSM order in the PSM table.

    • updatePeptideProteinInference

      public void updatePeptideProteinInference(int proteinInferenceType)
      Update the protein inference type for the currently selected peptide.
      Parameters:
      proteinInferenceType - the protein inference type

    • updateSelection

      public void updateSelection(boolean scrollToVisible)
      Update the selected protein and peptide.
      Parameters:
      scrollToVisible - if true the table also scrolls to make the selected row visible

    • newItemSelection

      public void newItemSelection()
      Provides to the PeptideShakerGUI instance the currently selected protein, peptide and PSM.

    • clearData

      public void clearData()
      Clear all the data.

    • annotationClicked

      public void annotationClicked(ArrayList<ResidueAnnotation> allAnnotation, org.jfree.chart.ChartMouseEvent cme)
      Specified by:
      annotationClicked in interface ProteinSequencePanelParent

    • updateSurroundingAminoAcids

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

    • selfUpdating

      public void selfUpdating(boolean selfUpdating)
      Deactivates the self updating tables.
      Parameters:
      selfUpdating - boolean indicating whether the tables should update their content