Package eu.isas.peptideshaker.gui.tabpanels

Class ModificationsPanel

java.lang.Object
java.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
eu.isas.peptideshaker.gui.tabpanels.ModificationsPanel
All Implemented Interfaces:
ImageObserver, MenuContainer, Serializable, Accessible
public class ModificationsPanel extends JPanel
The Modifications tab.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Field Details

    • NO_MODIFICATION

      public static final String NO_MODIFICATION
      The modification name for no modification.
      See Also:

  • Constructor Details

    • ModificationsPanel

      public ModificationsPanel(PeptideShakerGUI peptideShakerGUI)
      Creates a new Modifications tab.
      Parameters:
      peptideShakerGUI - the PeptideShaker parent frame

  • Method Details

    • getDisplayedProteinMatches

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

    • getDisplayedPeptides

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

    • getDisplayedSpectrumMatches

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

    • showSparkLines

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

    • getSelectedModification

      public String getSelectedModification()
      Returns the selected modification name.
      Returns:
      the selected modification name

    • displayResults

      public void displayResults()
      Displays the results.

    • updateSelection

      public void updateSelection()
      Tries to find the last selected peptide.

    • updatePeptideTable

      public void updatePeptideTable(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog)
      Updates the peptide table.
      Parameters:
      progressDialog - the progress dialog

    • updateRelatedPeptidesTable

      public void updateRelatedPeptidesTable(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog)
      Updates the related peptides table.
      Parameters:
      progressDialog - a progress dialog

    • updateGraphics

      public void updateGraphics(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog)
      Updates the graphics components.
      Parameters:
      progressDialog - the progress dialog

    • updateSpectrum

      public void updateSpectrum(long spectrumMatchKey, Long secondSpectrumMatchKey)
      Update the spectra according to the currently selected PSM.
      Parameters:
      spectrumMatchKey - the main spectrum match key
      secondSpectrumMatchKey - the secondary spectrum key

    • getSelectedPsmsKeys

      public long[] getSelectedPsmsKeys()
      Returns the keys of the selected PSMs.
      Returns:
      the keys of the selected PSMs

    • 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

    • showSpectrumAnnotationMenu

      public void showSpectrumAnnotationMenu()
      Makes sure that the annotation menu bar is visible.

    • 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 modification color coding.

    • updateModificationProfiles

      public void updateModificationProfiles(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX progressDialog)
      Redraws the modification profiles. For example if the modification colors are updated.
      Parameters:
      progressDialog - the progress dialog

    • updateSeparators

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

    • newItemSelection

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