Example 1 with PsmTableModel
use of eu.isas.peptideshaker.gui.tablemodels.PsmTableModel in project peptide-shaker by compomics.
the class OverviewPanel method clearData.
/**
* Clear all the data.
*/
public void clearData() {
displaySpectrum = true;
displayCoverage = true;
displayProteins = true;
displayPeptidesAndPSMs = true;
proteinKeys = new long[0];
peptideKeys = new long[0];
psmKeys = new long[0];
PsmTableModel psmTableModel = (PsmTableModel) psmTable.getModel();
psmTableModel.reset();
PeptideTableModel peptideTableModel = (PeptideTableModel) peptideTable.getModel();
peptideTableModel.reset();
ProteinTableModel proteinTableModel = (ProteinTableModel) proteinTable.getModel();
proteinTableModel.reset();
psmTableModel.fireTableDataChanged();
peptideTableModel.fireTableDataChanged();
proteinTableModel.fireTableDataChanged();
currentProteinSequence = "";
spectrumPanel = null;
sequenceCoverageInnerPanel.removeAll();
sequencePtmsPanel.removeAll();
sequenceVariationsPanel.removeAll();
fragmentIonsJScrollPane.setViewportView(null);
bubbleJPanel.removeAll();
spectrumJPanel.removeAll();
secondarySpectrumPlotsJPanel.removeAll();
((TitledBorder) proteinsLayeredPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Proteins" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
proteinsLayeredPanel.repaint();
((TitledBorder) peptidesPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Peptides" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
peptidesPanel.repaint();
((TitledBorder) psmsPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Peptide Spectrum Matches" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
psmsPanel.repaint();
((TitledBorder) spectrumMainPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
spectrumMainPanel.repaint();
((TitledBorder) sequenceCoverageTitledPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Protein Sequence Coverage" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
sequenceCoverageTitledPanel.repaint();
}
Also used :
PsmTableModel(eu.isas.peptideshaker.gui.tablemodels.PsmTableModel)
ProteinTableModel(eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel)
TitledBorder(javax.swing.border.TitledBorder)
PeptideTableModel(eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel)
Example 2 with PsmTableModel
use of eu.isas.peptideshaker.gui.tablemodels.PsmTableModel in project peptide-shaker by compomics.
the class OverviewPanel method initComponents.
/**
* This method is called from within the constructor to initialize the form.
* WARNING: Do NOT modify this code. The content of this method is always
* regenerated by the Form Editor.
*/
@SuppressWarnings("unchecked")
private // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
void initComponents() {
selectJPopupMenu = new javax.swing.JPopupMenu();
selectAllMenuItem = new javax.swing.JMenuItem();
deselectAllMenuItem = new javax.swing.JMenuItem();
sequenceCoverageJPopupMenu = new javax.swing.JPopupMenu();
coverageShowAllPeptidesJRadioButtonMenuItem = new javax.swing.JRadioButtonMenuItem();
coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem = new javax.swing.JRadioButtonMenuItem();
coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItem = new javax.swing.JRadioButtonMenuItem();
jSeparator1 = new javax.swing.JPopupMenu.Separator();
coverageShowPossiblePeptidesJCheckBoxMenuItem = new javax.swing.JCheckBoxMenuItem();
coveragePeptideTypesButtonGroup = new javax.swing.ButtonGroup();
sequenceCoverageExportPopupMenu = new javax.swing.JPopupMenu();
sequenceCoveragePlotExportMenuItem = new javax.swing.JMenuItem();
sequenceCoverageSequenceExportMenuItem = new javax.swing.JMenuItem();
backgroundLayeredPane = new javax.swing.JLayeredPane();
overviewJPanel = new javax.swing.JPanel();
overviewJSplitPane = new javax.swing.JSplitPane();
proteinsJPanel = new javax.swing.JPanel();
proteinsLayeredPane = new javax.swing.JLayeredPane();
proteinsLayeredPanel = new javax.swing.JPanel();
proteinScrollPane = new javax.swing.JScrollPane();
proteinTable = new JTable() {
protected JTableHeader createDefaultTableHeader() {
return new JTableHeader(columnModel) {
public String getToolTipText(MouseEvent e) {
java.awt.Point p = e.getPoint();
int index = columnModel.getColumnIndexAtX(p.x);
int realIndex = columnModel.getColumn(index).getModelIndex();
String tip = (String) proteinTableToolTips.get(realIndex);
return tip;
}
};
}
};
proteinsHelpJButton = new javax.swing.JButton();
exportProteinsJButton = new javax.swing.JButton();
hideProteinsJButton = new javax.swing.JButton();
contextMenuProteinsBackgroundPanel = new javax.swing.JPanel();
coverageJSplitPane = new javax.swing.JSplitPane();
sequenceCoverageJPanel = new javax.swing.JPanel();
sequenceCoverageLayeredPane = new javax.swing.JLayeredPane();
sequenceCoverageTitledPanel = new javax.swing.JPanel();
sequencePtmsPanel = new javax.swing.JPanel();
sequenceCoverageInnerPanel = new javax.swing.JPanel();
sequenceVariationsPanel = new javax.swing.JPanel();
sequenceCoveragetHelpJButton = new javax.swing.JButton();
exportSequenceCoverageContextJButton = new javax.swing.JButton();
hideCoverageJButton = new javax.swing.JButton();
sequenceCoverageOptionsJButton = new javax.swing.JButton();
contextMenuSequenceCoverageBackgroundPanel = new javax.swing.JPanel();
peptidesPsmSpectrumFragmentIonsJSplitPane = new javax.swing.JSplitPane();
peptidesPsmJSplitPane = new javax.swing.JSplitPane();
peptidesJPanel = new javax.swing.JPanel();
peptidesLayeredPane = new javax.swing.JLayeredPane();
peptidesPanel = new javax.swing.JPanel();
peptideScrollPane = new javax.swing.JScrollPane();
peptideTable = new JTable() {
protected JTableHeader createDefaultTableHeader() {
return new JTableHeader(columnModel) {
public String getToolTipText(MouseEvent e) {
java.awt.Point p = e.getPoint();
int index = columnModel.getColumnIndexAtX(p.x);
int realIndex = columnModel.getColumn(index).getModelIndex();
String tip = (String) peptideTableToolTips.get(realIndex);
return tip;
}
};
}
};
peptidesHelpJButton = new javax.swing.JButton();
exportPeptidesJButton = new javax.swing.JButton();
hidePeptideAndPsmsJButton = new javax.swing.JButton();
contextMenuPeptidesBackgroundPanel = new javax.swing.JPanel();
psmJPanel = new javax.swing.JPanel();
psmsLayeredPane = new javax.swing.JLayeredPane();
psmsPanel = new javax.swing.JPanel();
spectraScrollPane = new javax.swing.JScrollPane();
psmTable = new JTable() {
protected JTableHeader createDefaultTableHeader() {
return new JTableHeader(columnModel) {
public String getToolTipText(MouseEvent e) {
java.awt.Point p = e.getPoint();
int index = columnModel.getColumnIndexAtX(p.x);
int realIndex = columnModel.getColumn(index).getModelIndex();
String tip = (String) psmTableToolTips.get(realIndex);
return tip;
}
};
}
};
psmsHelpJButton = new javax.swing.JButton();
exportPsmsJButton = new javax.swing.JButton();
hidePeptideAndPsmsJButton2 = new javax.swing.JButton();
contextMenuPsmsBackgroundPanel = new javax.swing.JPanel();
spectrumMainJPanel = new javax.swing.JPanel();
spectrumLayeredPane = new javax.swing.JLayeredPane();
spectrumMainPanel = new javax.swing.JPanel();
slidersSplitPane = new javax.swing.JSplitPane();
spectrumJTabbedPane = new javax.swing.JTabbedPane();
fragmentIonJPanel = new javax.swing.JPanel();
fragmentIonsJScrollPane = new javax.swing.JScrollPane();
ionTableJToolBar = new javax.swing.JToolBar();
ionTableAnnotationMenuPanel = new javax.swing.JPanel();
bubblePlotTabJPanel = new javax.swing.JPanel();
bubbleJPanel = new javax.swing.JPanel();
bubblePlotJToolBar = new javax.swing.JToolBar();
bubbleAnnotationMenuPanel = new javax.swing.JPanel();
spectrumContainerJPanel = new javax.swing.JPanel();
spectrumJToolBar = new javax.swing.JToolBar();
spectrumAnnotationMenuPanel = new javax.swing.JPanel();
spectrumSplitPane = new javax.swing.JSplitPane();
secondarySpectrumPlotsJPanel = new javax.swing.JPanel();
spectrumOuterJPanel = new javax.swing.JPanel();
spectrumPaddingPanel = new javax.swing.JPanel();
spectrumJPanel = new javax.swing.JPanel();
slidersPanel = new javax.swing.JPanel();
accuracySlider = new javax.swing.JSlider();
intensitySlider = new javax.swing.JSlider();
spectrumHelpJButton = new javax.swing.JButton();
exportSpectrumJButton = new javax.swing.JButton();
hideSpectrumPanelJButton = new javax.swing.JButton();
maximizeSpectrumPanelJButton = new javax.swing.JButton();
contextMenuSpectrumBackgroundPanel = new javax.swing.JPanel();
toolBar = new javax.swing.JToolBar();
showProteinsBeforeSeparator = new javax.swing.JPopupMenu.Separator();
showProteinsJButton = new javax.swing.JButton();
showProteinsAfterSeparator = new javax.swing.JPopupMenu.Separator();
showPeptidesAndPsmsJButton = new javax.swing.JButton();
showPeptidesAfterSeparator = new javax.swing.JPopupMenu.Separator();
showSpectrumJButton = new javax.swing.JButton();
showSpectrumAfterSeparator = new javax.swing.JPopupMenu.Separator();
showCoverageJButton = new javax.swing.JButton();
showCoverageAfterSeparator = new javax.swing.JPopupMenu.Separator();
selectAllMenuItem.setText("Select All");
selectAllMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
selectAllMenuItemActionPerformed(evt);
}
});
selectJPopupMenu.add(selectAllMenuItem);
deselectAllMenuItem.setText("Deselect All");
deselectAllMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
deselectAllMenuItemActionPerformed(evt);
}
});
selectJPopupMenu.add(deselectAllMenuItem);
coveragePeptideTypesButtonGroup.add(coverageShowAllPeptidesJRadioButtonMenuItem);
coverageShowAllPeptidesJRadioButtonMenuItem.setSelected(true);
coverageShowAllPeptidesJRadioButtonMenuItem.setText("All Peptides");
coverageShowAllPeptidesJRadioButtonMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
coverageShowAllPeptidesJRadioButtonMenuItemActionPerformed(evt);
}
});
sequenceCoverageJPopupMenu.add(coverageShowAllPeptidesJRadioButtonMenuItem);
coveragePeptideTypesButtonGroup.add(coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem);
coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem.setText("Enzymatic Peptides");
coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItemActionPerformed(evt);
}
});
sequenceCoverageJPopupMenu.add(coverageShowEnzymaticPeptidesOnlyJRadioButtonMenuItem);
coveragePeptideTypesButtonGroup.add(coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItem);
coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItem.setText("Non Enzymatic Peptides");
coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItemActionPerformed(evt);
}
});
sequenceCoverageJPopupMenu.add(coverageShowTruncatedPeptidesOnlyJRadioButtonMenuItem);
sequenceCoverageJPopupMenu.add(jSeparator1);
coverageShowPossiblePeptidesJCheckBoxMenuItem.setSelected(true);
coverageShowPossiblePeptidesJCheckBoxMenuItem.setText("Possible Coverage");
coverageShowPossiblePeptidesJCheckBoxMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
coverageShowPossiblePeptidesJCheckBoxMenuItemActionPerformed(evt);
}
});
sequenceCoverageJPopupMenu.add(coverageShowPossiblePeptidesJCheckBoxMenuItem);
sequenceCoveragePlotExportMenuItem.setText("Sequence Coverage Plot");
sequenceCoveragePlotExportMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
sequenceCoveragePlotExportMenuItemActionPerformed(evt);
}
});
sequenceCoverageExportPopupMenu.add(sequenceCoveragePlotExportMenuItem);
sequenceCoverageSequenceExportMenuItem.setText("Protein Sequence");
sequenceCoverageSequenceExportMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
sequenceCoverageSequenceExportMenuItemActionPerformed(evt);
}
});
sequenceCoverageExportPopupMenu.add(sequenceCoverageSequenceExportMenuItem);
setOpaque(false);
addComponentListener(new java.awt.event.ComponentAdapter() {
public void componentResized(java.awt.event.ComponentEvent evt) {
formComponentResized(evt);
}
});
overviewJPanel.setBackground(new java.awt.Color(255, 255, 255));
overviewJPanel.setOpaque(false);
overviewJPanel.setPreferredSize(new java.awt.Dimension(900, 800));
overviewJSplitPane.setBorder(null);
overviewJSplitPane.setDividerLocation(300);
overviewJSplitPane.setDividerSize(0);
overviewJSplitPane.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
overviewJSplitPane.setResizeWeight(0.5);
proteinsJPanel.setOpaque(false);
// NOI18N
proteinsLayeredPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Proteins", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("sansserif", 1, 14)));
proteinsLayeredPanel.setOpaque(false);
proteinTable.setModel(new ProteinTableModel());
proteinTable.setGridColor(new java.awt.Color(204, 204, 204));
proteinTable.setOpaque(false);
proteinTable.setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
proteinTable.addMouseMotionListener(new java.awt.event.MouseMotionAdapter() {
public void mouseMoved(java.awt.event.MouseEvent evt) {
proteinTableMouseMoved(evt);
}
});
proteinTable.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
proteinTableMouseClicked(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
proteinTableMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
proteinTableMouseReleased(evt);
}
});
proteinTable.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
proteinTableKeyReleased(evt);
}
});
proteinScrollPane.setViewportView(proteinTable);
proteinTable.getAccessibleContext().setAccessibleName("ProteinTable");
javax.swing.GroupLayout proteinsLayeredPanelLayout = new javax.swing.GroupLayout(proteinsLayeredPanel);
proteinsLayeredPanel.setLayout(proteinsLayeredPanelLayout);
proteinsLayeredPanelLayout.setHorizontalGroup(proteinsLayeredPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 938, Short.MAX_VALUE).addGroup(proteinsLayeredPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(proteinsLayeredPanelLayout.createSequentialGroup().addContainerGap().addComponent(proteinScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 918, Short.MAX_VALUE).addContainerGap())));
proteinsLayeredPanelLayout.setVerticalGroup(proteinsLayeredPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 255, Short.MAX_VALUE).addGroup(proteinsLayeredPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(proteinsLayeredPanelLayout.createSequentialGroup().addContainerGap().addComponent(proteinScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 243, Short.MAX_VALUE).addContainerGap())));
proteinsLayeredPane.add(proteinsLayeredPanel);
proteinsLayeredPanel.setBounds(0, 0, 950, 300);
// NOI18N
proteinsHelpJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help_no_frame_grey.png")));
proteinsHelpJButton.setToolTipText("Help");
proteinsHelpJButton.setBorder(null);
proteinsHelpJButton.setBorderPainted(false);
proteinsHelpJButton.setContentAreaFilled(false);
// NOI18N
proteinsHelpJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help_no_frame.png")));
proteinsHelpJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
proteinsHelpJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
proteinsHelpJButtonMouseExited(evt);
}
});
proteinsHelpJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
proteinsHelpJButtonActionPerformed(evt);
}
});
proteinsLayeredPane.setLayer(proteinsHelpJButton, javax.swing.JLayeredPane.POPUP_LAYER);
proteinsLayeredPane.add(proteinsHelpJButton);
proteinsHelpJButton.setBounds(930, 0, 10, 19);
// NOI18N
exportProteinsJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame_grey.png")));
exportProteinsJButton.setToolTipText("Copy to File");
exportProteinsJButton.setBorder(null);
exportProteinsJButton.setBorderPainted(false);
exportProteinsJButton.setContentAreaFilled(false);
// NOI18N
exportProteinsJButton.setDisabledIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame_grey.png")));
exportProteinsJButton.setEnabled(false);
// NOI18N
exportProteinsJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame.png")));
exportProteinsJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
exportProteinsJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
exportProteinsJButtonMouseExited(evt);
}
});
exportProteinsJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
exportProteinsJButtonActionPerformed(evt);
}
});
proteinsLayeredPane.setLayer(exportProteinsJButton, javax.swing.JLayeredPane.POPUP_LAYER);
proteinsLayeredPane.add(exportProteinsJButton);
exportProteinsJButton.setBounds(920, 0, 10, 19);
// NOI18N
hideProteinsJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/hide_grey.png")));
hideProteinsJButton.setToolTipText("Hide Proteins (Shift+Ctrl+P)");
hideProteinsJButton.setBorder(null);
hideProteinsJButton.setBorderPainted(false);
hideProteinsJButton.setContentAreaFilled(false);
// NOI18N
hideProteinsJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/hide.png")));
hideProteinsJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
hideProteinsJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
hideProteinsJButtonMouseExited(evt);
}
});
hideProteinsJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
hideProteinsJButtonActionPerformed(evt);
}
});
proteinsLayeredPane.setLayer(hideProteinsJButton, javax.swing.JLayeredPane.POPUP_LAYER);
proteinsLayeredPane.add(hideProteinsJButton);
hideProteinsJButton.setBounds(910, 0, 10, 19);
contextMenuProteinsBackgroundPanel.setOpaque(false);
javax.swing.GroupLayout contextMenuProteinsBackgroundPanelLayout = new javax.swing.GroupLayout(contextMenuProteinsBackgroundPanel);
contextMenuProteinsBackgroundPanel.setLayout(contextMenuProteinsBackgroundPanelLayout);
contextMenuProteinsBackgroundPanelLayout.setHorizontalGroup(contextMenuProteinsBackgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 40, Short.MAX_VALUE));
contextMenuProteinsBackgroundPanelLayout.setVerticalGroup(contextMenuProteinsBackgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 19, Short.MAX_VALUE));
proteinsLayeredPane.setLayer(contextMenuProteinsBackgroundPanel, javax.swing.JLayeredPane.POPUP_LAYER);
proteinsLayeredPane.add(contextMenuProteinsBackgroundPanel);
contextMenuProteinsBackgroundPanel.setBounds(910, 0, 40, 19);
javax.swing.GroupLayout proteinsJPanelLayout = new javax.swing.GroupLayout(proteinsJPanel);
proteinsJPanel.setLayout(proteinsJPanelLayout);
proteinsJPanelLayout.setHorizontalGroup(proteinsJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(proteinsLayeredPane, javax.swing.GroupLayout.DEFAULT_SIZE, 960, Short.MAX_VALUE));
proteinsJPanelLayout.setVerticalGroup(proteinsJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(proteinsLayeredPane, javax.swing.GroupLayout.DEFAULT_SIZE, 300, Short.MAX_VALUE));
overviewJSplitPane.setTopComponent(proteinsJPanel);
coverageJSplitPane.setBorder(null);
coverageJSplitPane.setDividerLocation(350);
coverageJSplitPane.setDividerSize(0);
coverageJSplitPane.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
coverageJSplitPane.setResizeWeight(1.0);
sequenceCoverageJPanel.setOpaque(false);
sequenceCoverageTitledPanel.setBackground(new java.awt.Color(255, 255, 255));
// NOI18N
sequenceCoverageTitledPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Protein Sequence Coverage", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("sansserif", 1, 14)));
sequenceCoverageTitledPanel.setOpaque(false);
sequencePtmsPanel.setBackground(new java.awt.Color(255, 255, 255));
sequencePtmsPanel.setOpaque(false);
sequencePtmsPanel.setLayout(new javax.swing.BoxLayout(sequencePtmsPanel, javax.swing.BoxLayout.LINE_AXIS));
sequenceCoverageInnerPanel.setOpaque(false);
sequenceCoverageInnerPanel.setLayout(new javax.swing.BoxLayout(sequenceCoverageInnerPanel, javax.swing.BoxLayout.LINE_AXIS));
sequenceVariationsPanel.setBackground(new java.awt.Color(255, 255, 255));
sequenceVariationsPanel.setOpaque(false);
sequenceVariationsPanel.setLayout(new javax.swing.BoxLayout(sequenceVariationsPanel, javax.swing.BoxLayout.LINE_AXIS));
javax.swing.GroupLayout sequenceCoverageTitledPanelLayout = new javax.swing.GroupLayout(sequenceCoverageTitledPanel);
sequenceCoverageTitledPanel.setLayout(sequenceCoverageTitledPanelLayout);
sequenceCoverageTitledPanelLayout.setHorizontalGroup(sequenceCoverageTitledPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(sequenceCoverageTitledPanelLayout.createSequentialGroup().addContainerGap().addGroup(sequenceCoverageTitledPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(sequenceVariationsPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE).addComponent(sequenceCoverageInnerPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE).addComponent(sequencePtmsPanel, javax.swing.GroupLayout.DEFAULT_SIZE, 918, Short.MAX_VALUE)).addContainerGap()));
sequenceCoverageTitledPanelLayout.setVerticalGroup(sequenceCoverageTitledPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(sequenceCoverageTitledPanelLayout.createSequentialGroup().addGap(0, 0, 0).addComponent(sequencePtmsPanel, javax.swing.GroupLayout.PREFERRED_SIZE, 7, javax.swing.GroupLayout.PREFERRED_SIZE).addGap(2, 2, 2).addComponent(sequenceCoverageInnerPanel, javax.swing.GroupLayout.DEFAULT_SIZE, 167, Short.MAX_VALUE).addGap(2, 2, 2).addComponent(sequenceVariationsPanel, javax.swing.GroupLayout.PREFERRED_SIZE, 7, javax.swing.GroupLayout.PREFERRED_SIZE).addGap(0, 0, 0)));
sequenceCoverageLayeredPane.add(sequenceCoverageTitledPanel);
sequenceCoverageTitledPanel.setBounds(0, 0, 950, 230);
// NOI18N
sequenceCoveragetHelpJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help_no_frame_grey.png")));
sequenceCoveragetHelpJButton.setToolTipText("Help");
sequenceCoveragetHelpJButton.setBorder(null);
sequenceCoveragetHelpJButton.setBorderPainted(false);
sequenceCoveragetHelpJButton.setContentAreaFilled(false);
// NOI18N
sequenceCoveragetHelpJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help_no_frame.png")));
sequenceCoveragetHelpJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
sequenceCoveragetHelpJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
sequenceCoveragetHelpJButtonMouseExited(evt);
}
});
sequenceCoveragetHelpJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
sequenceCoveragetHelpJButtonActionPerformed(evt);
}
});
sequenceCoverageLayeredPane.setLayer(sequenceCoveragetHelpJButton, javax.swing.JLayeredPane.POPUP_LAYER);
sequenceCoverageLayeredPane.add(sequenceCoveragetHelpJButton);
sequenceCoveragetHelpJButton.setBounds(930, 0, 10, 19);
// NOI18N
exportSequenceCoverageContextJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame_grey.png")));
exportSequenceCoverageContextJButton.setToolTipText("Export");
exportSequenceCoverageContextJButton.setBorder(null);
exportSequenceCoverageContextJButton.setBorderPainted(false);
exportSequenceCoverageContextJButton.setContentAreaFilled(false);
// NOI18N
exportSequenceCoverageContextJButton.setDisabledIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame_grey.png")));
exportSequenceCoverageContextJButton.setEnabled(false);
// NOI18N
exportSequenceCoverageContextJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame.png")));
exportSequenceCoverageContextJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
exportSequenceCoverageContextJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
exportSequenceCoverageContextJButtonMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
exportSequenceCoverageContextJButtonMouseReleased(evt);
}
});
sequenceCoverageLayeredPane.setLayer(exportSequenceCoverageContextJButton, javax.swing.JLayeredPane.POPUP_LAYER);
sequenceCoverageLayeredPane.add(exportSequenceCoverageContextJButton);
exportSequenceCoverageContextJButton.setBounds(920, 0, 10, 19);
// NOI18N
hideCoverageJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/hide_grey.png")));
hideCoverageJButton.setToolTipText("Hide Coverage (Shift+Ctrl+E)");
hideCoverageJButton.setBorder(null);
hideCoverageJButton.setBorderPainted(false);
hideCoverageJButton.setContentAreaFilled(false);
// NOI18N
hideCoverageJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/hide.png")));
hideCoverageJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
hideCoverageJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
hideCoverageJButtonMouseExited(evt);
}
});
hideCoverageJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
hideCoverageJButtonActionPerformed(evt);
}
});
sequenceCoverageLayeredPane.setLayer(hideCoverageJButton, javax.swing.JLayeredPane.POPUP_LAYER);
sequenceCoverageLayeredPane.add(hideCoverageJButton);
hideCoverageJButton.setBounds(910, 0, 10, 19);
// NOI18N
sequenceCoverageOptionsJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/contextual_menu_gray.png")));
sequenceCoverageOptionsJButton.setToolTipText("Coverage Options");
sequenceCoverageOptionsJButton.setBorder(null);
sequenceCoverageOptionsJButton.setBorderPainted(false);
sequenceCoverageOptionsJButton.setContentAreaFilled(false);
// NOI18N
sequenceCoverageOptionsJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/contextual_menu_black.png")));
sequenceCoverageOptionsJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseReleased(java.awt.event.MouseEvent evt) {
sequenceCoverageOptionsJButtonMouseReleased(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
sequenceCoverageOptionsJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
sequenceCoverageOptionsJButtonMouseExited(evt);
}
});
sequenceCoverageLayeredPane.setLayer(sequenceCoverageOptionsJButton, javax.swing.JLayeredPane.POPUP_LAYER);
sequenceCoverageLayeredPane.add(sequenceCoverageOptionsJButton);
sequenceCoverageOptionsJButton.setBounds(895, 5, 10, 19);
contextMenuSequenceCoverageBackgroundPanel.setOpaque(false);
javax.swing.GroupLayout contextMenuSequenceCoverageBackgroundPanelLayout = new javax.swing.GroupLayout(contextMenuSequenceCoverageBackgroundPanel);
contextMenuSequenceCoverageBackgroundPanel.setLayout(contextMenuSequenceCoverageBackgroundPanelLayout);
contextMenuSequenceCoverageBackgroundPanelLayout.setHorizontalGroup(contextMenuSequenceCoverageBackgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 50, Short.MAX_VALUE));
contextMenuSequenceCoverageBackgroundPanelLayout.setVerticalGroup(contextMenuSequenceCoverageBackgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 19, Short.MAX_VALUE));
sequenceCoverageLayeredPane.setLayer(contextMenuSequenceCoverageBackgroundPanel, javax.swing.JLayeredPane.POPUP_LAYER);
sequenceCoverageLayeredPane.add(contextMenuSequenceCoverageBackgroundPanel);
contextMenuSequenceCoverageBackgroundPanel.setBounds(890, 0, 50, 19);
javax.swing.GroupLayout sequenceCoverageJPanelLayout = new javax.swing.GroupLayout(sequenceCoverageJPanel);
sequenceCoverageJPanel.setLayout(sequenceCoverageJPanelLayout);
sequenceCoverageJPanelLayout.setHorizontalGroup(sequenceCoverageJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(sequenceCoverageLayeredPane, javax.swing.GroupLayout.DEFAULT_SIZE, 960, Short.MAX_VALUE));
sequenceCoverageJPanelLayout.setVerticalGroup(sequenceCoverageJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(sequenceCoverageLayeredPane, javax.swing.GroupLayout.DEFAULT_SIZE, 48, Short.MAX_VALUE));
coverageJSplitPane.setRightComponent(sequenceCoverageJPanel);
peptidesPsmSpectrumFragmentIonsJSplitPane.setBorder(null);
peptidesPsmSpectrumFragmentIonsJSplitPane.setDividerLocation(450);
peptidesPsmSpectrumFragmentIonsJSplitPane.setDividerSize(0);
peptidesPsmSpectrumFragmentIonsJSplitPane.setResizeWeight(0.5);
peptidesPsmJSplitPane.setBorder(null);
peptidesPsmJSplitPane.setDividerLocation(175);
peptidesPsmJSplitPane.setDividerSize(0);
peptidesPsmJSplitPane.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
peptidesPsmJSplitPane.setResizeWeight(0.5);
peptidesJPanel.setOpaque(false);
// NOI18N
peptidesPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Peptides", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("sansserif", 1, 14)));
peptidesPanel.setOpaque(false);
peptideTable.setModel(new PeptideTableModel());
peptideTable.setSelectionMode(javax.swing.ListSelectionModel.SINGLE_SELECTION);
peptideTable.addMouseMotionListener(new java.awt.event.MouseMotionAdapter() {
public void mouseMoved(java.awt.event.MouseEvent evt) {
peptideTableMouseMoved(evt);
}
});
peptideTable.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
peptideTableMouseClicked(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
peptideTableMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
peptideTableMouseReleased(evt);
}
});
peptideTable.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
peptideTableKeyReleased(evt);
}
});
peptideScrollPane.setViewportView(peptideTable);
javax.swing.GroupLayout peptidesPanelLayout = new javax.swing.GroupLayout(peptidesPanel);
peptidesPanel.setLayout(peptidesPanelLayout);
peptidesPanelLayout.setHorizontalGroup(peptidesPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 438, Short.MAX_VALUE).addGroup(peptidesPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(peptidesPanelLayout.createSequentialGroup().addContainerGap().addComponent(peptideScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 418, Short.MAX_VALUE).addContainerGap())));
peptidesPanelLayout.setVerticalGroup(peptidesPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 125, Short.MAX_VALUE).addGroup(peptidesPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(peptidesPanelLayout.createSequentialGroup().addContainerGap().addComponent(peptideScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 113, Short.MAX_VALUE).addContainerGap())));
peptidesLayeredPane.add(peptidesPanel);
peptidesPanel.setBounds(0, 0, 450, 170);
// NOI18N
peptidesHelpJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help_no_frame_grey.png")));
peptidesHelpJButton.setToolTipText("Help");
peptidesHelpJButton.setBorder(null);
peptidesHelpJButton.setBorderPainted(false);
peptidesHelpJButton.setContentAreaFilled(false);
// NOI18N
peptidesHelpJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help_no_frame.png")));
peptidesHelpJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
peptidesHelpJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
peptidesHelpJButtonMouseExited(evt);
}
});
peptidesHelpJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
peptidesHelpJButtonActionPerformed(evt);
}
});
peptidesLayeredPane.setLayer(peptidesHelpJButton, javax.swing.JLayeredPane.POPUP_LAYER);
peptidesLayeredPane.add(peptidesHelpJButton);
peptidesHelpJButton.setBounds(430, 0, 10, 19);
// NOI18N
exportPeptidesJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame_grey.png")));
exportPeptidesJButton.setToolTipText("Copy to File");
exportPeptidesJButton.setBorder(null);
exportPeptidesJButton.setBorderPainted(false);
exportPeptidesJButton.setContentAreaFilled(false);
// NOI18N
exportPeptidesJButton.setDisabledIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame_grey.png")));
exportPeptidesJButton.setEnabled(false);
// NOI18N
exportPeptidesJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame.png")));
exportPeptidesJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
exportPeptidesJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
exportPeptidesJButtonMouseExited(evt);
}
});
exportPeptidesJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
exportPeptidesJButtonActionPerformed(evt);
}
});
peptidesLayeredPane.setLayer(exportPeptidesJButton, javax.swing.JLayeredPane.POPUP_LAYER);
peptidesLayeredPane.add(exportPeptidesJButton);
exportPeptidesJButton.setBounds(420, 0, 10, 19);
// NOI18N
hidePeptideAndPsmsJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/hide_grey.png")));
hidePeptideAndPsmsJButton.setToolTipText("Hide Peptides & PSMs (Shift+Ctrl+E)");
hidePeptideAndPsmsJButton.setBorder(null);
hidePeptideAndPsmsJButton.setBorderPainted(false);
hidePeptideAndPsmsJButton.setContentAreaFilled(false);
// NOI18N
hidePeptideAndPsmsJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/hide.png")));
hidePeptideAndPsmsJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
hidePeptideAndPsmsJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
hidePeptideAndPsmsJButtonMouseExited(evt);
}
});
hidePeptideAndPsmsJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
hidePeptideAndPsmsJButtonActionPerformed(evt);
}
});
peptidesLayeredPane.setLayer(hidePeptideAndPsmsJButton, javax.swing.JLayeredPane.POPUP_LAYER);
peptidesLayeredPane.add(hidePeptideAndPsmsJButton);
hidePeptideAndPsmsJButton.setBounds(410, 0, 10, 19);
contextMenuPeptidesBackgroundPanel.setOpaque(false);
javax.swing.GroupLayout contextMenuPeptidesBackgroundPanelLayout = new javax.swing.GroupLayout(contextMenuPeptidesBackgroundPanel);
contextMenuPeptidesBackgroundPanel.setLayout(contextMenuPeptidesBackgroundPanelLayout);
contextMenuPeptidesBackgroundPanelLayout.setHorizontalGroup(contextMenuPeptidesBackgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 40, Short.MAX_VALUE));
contextMenuPeptidesBackgroundPanelLayout.setVerticalGroup(contextMenuPeptidesBackgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 19, Short.MAX_VALUE));
peptidesLayeredPane.setLayer(contextMenuPeptidesBackgroundPanel, javax.swing.JLayeredPane.POPUP_LAYER);
peptidesLayeredPane.add(contextMenuPeptidesBackgroundPanel);
contextMenuPeptidesBackgroundPanel.setBounds(400, 0, 40, 19);
javax.swing.GroupLayout peptidesJPanelLayout = new javax.swing.GroupLayout(peptidesJPanel);
peptidesJPanel.setLayout(peptidesJPanelLayout);
peptidesJPanelLayout.setHorizontalGroup(peptidesJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(peptidesLayeredPane, javax.swing.GroupLayout.DEFAULT_SIZE, 450, Short.MAX_VALUE));
peptidesJPanelLayout.setVerticalGroup(peptidesJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(peptidesLayeredPane, javax.swing.GroupLayout.DEFAULT_SIZE, 175, Short.MAX_VALUE));
peptidesPsmJSplitPane.setTopComponent(peptidesJPanel);
psmJPanel.setOpaque(false);
// NOI18N
psmsPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Peptide Spectrum Matches", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("sansserif", 1, 14)));
psmsPanel.setOpaque(false);
psmTable.setModel(new PsmTableModel());
psmTable.addMouseMotionListener(new java.awt.event.MouseMotionAdapter() {
public void mouseMoved(java.awt.event.MouseEvent evt) {
psmTableMouseMoved(evt);
}
});
psmTable.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
psmTableMouseClicked(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
psmTableMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
psmTableMouseReleased(evt);
}
});
psmTable.addKeyListener(new java.awt.event.KeyAdapter() {
public void keyReleased(java.awt.event.KeyEvent evt) {
psmTableKeyReleased(evt);
}
});
spectraScrollPane.setViewportView(psmTable);
javax.swing.GroupLayout psmsPanelLayout = new javax.swing.GroupLayout(psmsPanel);
psmsPanel.setLayout(psmsPanelLayout);
psmsPanelLayout.setHorizontalGroup(psmsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 438, Short.MAX_VALUE).addGroup(psmsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(psmsPanelLayout.createSequentialGroup().addContainerGap().addComponent(spectraScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 418, Short.MAX_VALUE).addContainerGap())));
psmsPanelLayout.setVerticalGroup(psmsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 125, Short.MAX_VALUE).addGroup(psmsPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(psmsPanelLayout.createSequentialGroup().addContainerGap().addComponent(spectraScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 113, Short.MAX_VALUE).addContainerGap())));
psmsLayeredPane.add(psmsPanel);
psmsPanel.setBounds(0, 0, 450, 170);
// NOI18N
psmsHelpJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help_no_frame_grey.png")));
psmsHelpJButton.setToolTipText("Help");
psmsHelpJButton.setBorder(null);
psmsHelpJButton.setBorderPainted(false);
psmsHelpJButton.setContentAreaFilled(false);
// NOI18N
psmsHelpJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help_no_frame.png")));
psmsHelpJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
psmsHelpJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
psmsHelpJButtonMouseExited(evt);
}
});
psmsHelpJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
psmsHelpJButtonActionPerformed(evt);
}
});
psmsLayeredPane.setLayer(psmsHelpJButton, javax.swing.JLayeredPane.POPUP_LAYER);
psmsLayeredPane.add(psmsHelpJButton);
psmsHelpJButton.setBounds(430, 0, 10, 19);
// NOI18N
exportPsmsJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame_grey.png")));
exportPsmsJButton.setToolTipText("Copy to File");
exportPsmsJButton.setBorder(null);
exportPsmsJButton.setBorderPainted(false);
exportPsmsJButton.setContentAreaFilled(false);
// NOI18N
exportPsmsJButton.setDisabledIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame_grey.png")));
exportPsmsJButton.setEnabled(false);
// NOI18N
exportPsmsJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame.png")));
exportPsmsJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
exportPsmsJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
exportPsmsJButtonMouseExited(evt);
}
});
exportPsmsJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
exportPsmsJButtonActionPerformed(evt);
}
});
psmsLayeredPane.setLayer(exportPsmsJButton, javax.swing.JLayeredPane.POPUP_LAYER);
psmsLayeredPane.add(exportPsmsJButton);
exportPsmsJButton.setBounds(420, 0, 10, 19);
// NOI18N
hidePeptideAndPsmsJButton2.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/hide_grey.png")));
hidePeptideAndPsmsJButton2.setToolTipText("Hide Peptides & PSMs (Shift+Ctrl+E)");
hidePeptideAndPsmsJButton2.setBorder(null);
hidePeptideAndPsmsJButton2.setBorderPainted(false);
hidePeptideAndPsmsJButton2.setContentAreaFilled(false);
// NOI18N
hidePeptideAndPsmsJButton2.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/hide.png")));
hidePeptideAndPsmsJButton2.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
hidePeptideAndPsmsJButton2MouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
hidePeptideAndPsmsJButton2MouseExited(evt);
}
});
hidePeptideAndPsmsJButton2.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
hidePeptideAndPsmsJButton2ActionPerformed(evt);
}
});
psmsLayeredPane.setLayer(hidePeptideAndPsmsJButton2, javax.swing.JLayeredPane.POPUP_LAYER);
psmsLayeredPane.add(hidePeptideAndPsmsJButton2);
hidePeptideAndPsmsJButton2.setBounds(410, 0, 10, 19);
contextMenuPsmsBackgroundPanel.setOpaque(false);
javax.swing.GroupLayout contextMenuPsmsBackgroundPanelLayout = new javax.swing.GroupLayout(contextMenuPsmsBackgroundPanel);
contextMenuPsmsBackgroundPanel.setLayout(contextMenuPsmsBackgroundPanelLayout);
contextMenuPsmsBackgroundPanelLayout.setHorizontalGroup(contextMenuPsmsBackgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 40, Short.MAX_VALUE));
contextMenuPsmsBackgroundPanelLayout.setVerticalGroup(contextMenuPsmsBackgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 19, Short.MAX_VALUE));
psmsLayeredPane.setLayer(contextMenuPsmsBackgroundPanel, javax.swing.JLayeredPane.POPUP_LAYER);
psmsLayeredPane.add(contextMenuPsmsBackgroundPanel);
contextMenuPsmsBackgroundPanel.setBounds(400, 0, 40, 19);
javax.swing.GroupLayout psmJPanelLayout = new javax.swing.GroupLayout(psmJPanel);
psmJPanel.setLayout(psmJPanelLayout);
psmJPanelLayout.setHorizontalGroup(psmJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(psmsLayeredPane, javax.swing.GroupLayout.DEFAULT_SIZE, 450, Short.MAX_VALUE));
psmJPanelLayout.setVerticalGroup(psmJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(psmsLayeredPane, javax.swing.GroupLayout.DEFAULT_SIZE, 175, Short.MAX_VALUE));
peptidesPsmJSplitPane.setRightComponent(psmJPanel);
peptidesPsmSpectrumFragmentIonsJSplitPane.setLeftComponent(peptidesPsmJSplitPane);
spectrumMainJPanel.setOpaque(false);
// NOI18N
spectrumMainPanel.setBorder(javax.swing.BorderFactory.createTitledBorder(null, "Spectrum & Fragment Ions", javax.swing.border.TitledBorder.DEFAULT_JUSTIFICATION, javax.swing.border.TitledBorder.DEFAULT_POSITION, new java.awt.Font("sansserif", 1, 14)));
spectrumMainPanel.setOpaque(false);
slidersSplitPane.setBackground(new java.awt.Color(51, 51, 51));
slidersSplitPane.setBorder(null);
slidersSplitPane.setDividerLocation(430);
slidersSplitPane.setDividerSize(0);
spectrumJTabbedPane.setBackground(new java.awt.Color(51, 51, 51));
spectrumJTabbedPane.setTabPlacement(javax.swing.JTabbedPane.BOTTOM);
spectrumJTabbedPane.addChangeListener(new javax.swing.event.ChangeListener() {
public void stateChanged(javax.swing.event.ChangeEvent evt) {
spectrumJTabbedPaneStateChanged(evt);
}
});
spectrumJTabbedPane.addMouseWheelListener(new java.awt.event.MouseWheelListener() {
public void mouseWheelMoved(java.awt.event.MouseWheelEvent evt) {
spectrumJTabbedPaneMouseWheelMoved(evt);
}
});
spectrumJTabbedPane.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
spectrumJTabbedPaneMouseEntered(evt);
}
});
fragmentIonJPanel.setOpaque(false);
fragmentIonsJScrollPane.addMouseWheelListener(new java.awt.event.MouseWheelListener() {
public void mouseWheelMoved(java.awt.event.MouseWheelEvent evt) {
fragmentIonsJScrollPaneMouseWheelMoved(evt);
}
});
ionTableJToolBar.setBackground(new java.awt.Color(255, 255, 255));
ionTableJToolBar.setBorder(null);
ionTableJToolBar.setFloatable(false);
ionTableJToolBar.setRollover(true);
ionTableJToolBar.setBorderPainted(false);
ionTableJToolBar.setOpaque(false);
ionTableAnnotationMenuPanel.setLayout(new javax.swing.BoxLayout(ionTableAnnotationMenuPanel, javax.swing.BoxLayout.LINE_AXIS));
ionTableJToolBar.add(ionTableAnnotationMenuPanel);
javax.swing.GroupLayout fragmentIonJPanelLayout = new javax.swing.GroupLayout(fragmentIonJPanel);
fragmentIonJPanel.setLayout(fragmentIonJPanelLayout);
fragmentIonJPanelLayout.setHorizontalGroup(fragmentIonJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(javax.swing.GroupLayout.Alignment.TRAILING, fragmentIonJPanelLayout.createSequentialGroup().addContainerGap().addGroup(fragmentIonJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING).addComponent(fragmentIonsJScrollPane, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 401, Short.MAX_VALUE).addComponent(ionTableJToolBar, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 405, Short.MAX_VALUE)).addContainerGap()));
fragmentIonJPanelLayout.setVerticalGroup(fragmentIonJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(javax.swing.GroupLayout.Alignment.TRAILING, fragmentIonJPanelLayout.createSequentialGroup().addContainerGap().addComponent(fragmentIonsJScrollPane, javax.swing.GroupLayout.DEFAULT_SIZE, 257, Short.MAX_VALUE).addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED).addComponent(ionTableJToolBar, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)));
spectrumJTabbedPane.addTab("Ion Table", fragmentIonJPanel);
bubblePlotTabJPanel.setBackground(new java.awt.Color(255, 255, 255));
bubblePlotTabJPanel.setOpaque(false);
bubbleJPanel.setOpaque(false);
bubbleJPanel.setLayout(new javax.swing.BoxLayout(bubbleJPanel, javax.swing.BoxLayout.LINE_AXIS));
bubblePlotJToolBar.setBackground(new java.awt.Color(255, 255, 255));
bubblePlotJToolBar.setBorder(null);
bubblePlotJToolBar.setFloatable(false);
bubblePlotJToolBar.setRollover(true);
bubblePlotJToolBar.setBorderPainted(false);
bubblePlotJToolBar.setOpaque(false);
bubbleAnnotationMenuPanel.setLayout(new javax.swing.BoxLayout(bubbleAnnotationMenuPanel, javax.swing.BoxLayout.LINE_AXIS));
bubblePlotJToolBar.add(bubbleAnnotationMenuPanel);
javax.swing.GroupLayout bubblePlotTabJPanelLayout = new javax.swing.GroupLayout(bubblePlotTabJPanel);
bubblePlotTabJPanel.setLayout(bubblePlotTabJPanelLayout);
bubblePlotTabJPanelLayout.setHorizontalGroup(bubblePlotTabJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(bubblePlotTabJPanelLayout.createSequentialGroup().addContainerGap().addComponent(bubblePlotJToolBar, javax.swing.GroupLayout.DEFAULT_SIZE, 405, Short.MAX_VALUE).addContainerGap()).addGroup(bubblePlotTabJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(bubbleJPanel, javax.swing.GroupLayout.DEFAULT_SIZE, 425, Short.MAX_VALUE)));
bubblePlotTabJPanelLayout.setVerticalGroup(bubblePlotTabJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(bubblePlotTabJPanelLayout.createSequentialGroup().addContainerGap(269, Short.MAX_VALUE).addComponent(bubblePlotJToolBar, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)).addGroup(bubblePlotTabJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(bubblePlotTabJPanelLayout.createSequentialGroup().addComponent(bubbleJPanel, javax.swing.GroupLayout.DEFAULT_SIZE, 244, Short.MAX_VALUE).addGap(25, 25, 25))));
spectrumJTabbedPane.addTab("Bubble Plot", bubblePlotTabJPanel);
spectrumContainerJPanel.setOpaque(false);
spectrumJToolBar.setBackground(new java.awt.Color(255, 255, 255));
spectrumJToolBar.setBorder(null);
spectrumJToolBar.setFloatable(false);
spectrumJToolBar.setRollover(true);
spectrumJToolBar.setBorderPainted(false);
spectrumJToolBar.setOpaque(false);
spectrumAnnotationMenuPanel.setLayout(new javax.swing.BoxLayout(spectrumAnnotationMenuPanel, javax.swing.BoxLayout.LINE_AXIS));
spectrumJToolBar.add(spectrumAnnotationMenuPanel);
spectrumSplitPane.setBorder(null);
spectrumSplitPane.setDividerLocation(80);
spectrumSplitPane.setDividerSize(0);
spectrumSplitPane.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
secondarySpectrumPlotsJPanel.setMinimumSize(new java.awt.Dimension(0, 80));
secondarySpectrumPlotsJPanel.setOpaque(false);
secondarySpectrumPlotsJPanel.setLayout(new javax.swing.BoxLayout(secondarySpectrumPlotsJPanel, javax.swing.BoxLayout.LINE_AXIS));
spectrumSplitPane.setTopComponent(secondarySpectrumPlotsJPanel);
spectrumOuterJPanel.setOpaque(false);
spectrumPaddingPanel.setOpaque(false);
javax.swing.GroupLayout spectrumPaddingPanelLayout = new javax.swing.GroupLayout(spectrumPaddingPanel);
spectrumPaddingPanel.setLayout(spectrumPaddingPanelLayout);
spectrumPaddingPanelLayout.setHorizontalGroup(spectrumPaddingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 0, Short.MAX_VALUE));
spectrumPaddingPanelLayout.setVerticalGroup(spectrumPaddingPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 17, Short.MAX_VALUE));
spectrumJPanel.setOpaque(false);
spectrumJPanel.setLayout(new java.awt.BorderLayout());
javax.swing.GroupLayout spectrumOuterJPanelLayout = new javax.swing.GroupLayout(spectrumOuterJPanel);
spectrumOuterJPanel.setLayout(spectrumOuterJPanelLayout);
spectrumOuterJPanelLayout.setHorizontalGroup(spectrumOuterJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(spectrumPaddingPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE).addComponent(spectrumJPanel, javax.swing.GroupLayout.DEFAULT_SIZE, 425, Short.MAX_VALUE));
spectrumOuterJPanelLayout.setVerticalGroup(spectrumOuterJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(spectrumOuterJPanelLayout.createSequentialGroup().addComponent(spectrumPaddingPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE).addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED).addComponent(spectrumJPanel, javax.swing.GroupLayout.DEFAULT_SIZE, 160, Short.MAX_VALUE)));
spectrumSplitPane.setRightComponent(spectrumOuterJPanel);
javax.swing.GroupLayout spectrumContainerJPanelLayout = new javax.swing.GroupLayout(spectrumContainerJPanel);
spectrumContainerJPanel.setLayout(spectrumContainerJPanelLayout);
spectrumContainerJPanelLayout.setHorizontalGroup(spectrumContainerJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(spectrumContainerJPanelLayout.createSequentialGroup().addContainerGap().addComponent(spectrumJToolBar, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE).addContainerGap()).addComponent(spectrumSplitPane, javax.swing.GroupLayout.PREFERRED_SIZE, 0, Short.MAX_VALUE));
spectrumContainerJPanelLayout.setVerticalGroup(spectrumContainerJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(javax.swing.GroupLayout.Alignment.TRAILING, spectrumContainerJPanelLayout.createSequentialGroup().addComponent(spectrumSplitPane, javax.swing.GroupLayout.DEFAULT_SIZE, 263, Short.MAX_VALUE).addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED).addComponent(spectrumJToolBar, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)));
spectrumJTabbedPane.addTab("Spectrum", spectrumContainerJPanel);
spectrumJTabbedPane.setSelectedIndex(2);
slidersSplitPane.setLeftComponent(spectrumJTabbedPane);
slidersPanel.setOpaque(false);
accuracySlider.setOrientation(javax.swing.JSlider.VERTICAL);
accuracySlider.setPaintTicks(true);
accuracySlider.setToolTipText("Annotation Accuracy");
accuracySlider.setValue(100);
accuracySlider.addChangeListener(new javax.swing.event.ChangeListener() {
public void stateChanged(javax.swing.event.ChangeEvent evt) {
accuracySliderStateChanged(evt);
}
});
accuracySlider.addMouseWheelListener(new java.awt.event.MouseWheelListener() {
public void mouseWheelMoved(java.awt.event.MouseWheelEvent evt) {
accuracySliderMouseWheelMoved(evt);
}
});
intensitySlider.setOrientation(javax.swing.JSlider.VERTICAL);
intensitySlider.setPaintTicks(true);
intensitySlider.setToolTipText("Annotation Level");
intensitySlider.setValue(75);
intensitySlider.addChangeListener(new javax.swing.event.ChangeListener() {
public void stateChanged(javax.swing.event.ChangeEvent evt) {
intensitySliderStateChanged(evt);
}
});
intensitySlider.addMouseWheelListener(new java.awt.event.MouseWheelListener() {
public void mouseWheelMoved(java.awt.event.MouseWheelEvent evt) {
intensitySliderMouseWheelMoved(evt);
}
});
javax.swing.GroupLayout slidersPanelLayout = new javax.swing.GroupLayout(slidersPanel);
slidersPanel.setLayout(slidersPanelLayout);
slidersPanelLayout.setHorizontalGroup(slidersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(javax.swing.GroupLayout.Alignment.TRAILING, slidersPanelLayout.createSequentialGroup().addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE).addGroup(slidersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING).addComponent(accuracySlider, javax.swing.GroupLayout.PREFERRED_SIZE, 26, javax.swing.GroupLayout.PREFERRED_SIZE).addComponent(intensitySlider, javax.swing.GroupLayout.PREFERRED_SIZE, 26, javax.swing.GroupLayout.PREFERRED_SIZE)).addGap(0, 0, 0)));
slidersPanelLayout.setVerticalGroup(slidersPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(slidersPanelLayout.createSequentialGroup().addGap(29, 29, 29).addComponent(accuracySlider, javax.swing.GroupLayout.DEFAULT_SIZE, 86, Short.MAX_VALUE).addGap(29, 29, 29).addComponent(intensitySlider, javax.swing.GroupLayout.DEFAULT_SIZE, 89, Short.MAX_VALUE).addGap(66, 66, 66)));
slidersSplitPane.setRightComponent(slidersPanel);
javax.swing.GroupLayout spectrumMainPanelLayout = new javax.swing.GroupLayout(spectrumMainPanel);
spectrumMainPanel.setLayout(spectrumMainPanelLayout);
spectrumMainPanelLayout.setHorizontalGroup(spectrumMainPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(spectrumMainPanelLayout.createSequentialGroup().addContainerGap().addComponent(slidersSplitPane, javax.swing.GroupLayout.DEFAULT_SIZE, 458, Short.MAX_VALUE).addContainerGap()));
spectrumMainPanelLayout.setVerticalGroup(spectrumMainPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(spectrumMainPanelLayout.createSequentialGroup().addComponent(slidersSplitPane).addContainerGap()));
spectrumLayeredPane.add(spectrumMainPanel);
spectrumMainPanel.setBounds(0, 0, 490, 350);
// NOI18N
spectrumHelpJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help_no_frame_grey.png")));
spectrumHelpJButton.setToolTipText("Help");
spectrumHelpJButton.setBorder(null);
spectrumHelpJButton.setBorderPainted(false);
spectrumHelpJButton.setContentAreaFilled(false);
// NOI18N
spectrumHelpJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/help_no_frame.png")));
spectrumHelpJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
spectrumHelpJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
spectrumHelpJButtonMouseExited(evt);
}
});
spectrumHelpJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
spectrumHelpJButtonActionPerformed(evt);
}
});
spectrumLayeredPane.setLayer(spectrumHelpJButton, javax.swing.JLayeredPane.POPUP_LAYER);
spectrumLayeredPane.add(spectrumHelpJButton);
spectrumHelpJButton.setBounds(460, 0, 10, 19);
// NOI18N
exportSpectrumJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame_grey.png")));
exportSpectrumJButton.setToolTipText("Export");
exportSpectrumJButton.setBorder(null);
exportSpectrumJButton.setBorderPainted(false);
exportSpectrumJButton.setContentAreaFilled(false);
// NOI18N
exportSpectrumJButton.setDisabledIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame_grey.png")));
exportSpectrumJButton.setEnabled(false);
// NOI18N
exportSpectrumJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/export_no_frame.png")));
exportSpectrumJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
exportSpectrumJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
exportSpectrumJButtonMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
exportSpectrumJButtonMouseReleased(evt);
}
});
spectrumLayeredPane.setLayer(exportSpectrumJButton, javax.swing.JLayeredPane.POPUP_LAYER);
spectrumLayeredPane.add(exportSpectrumJButton);
exportSpectrumJButton.setBounds(450, 0, 10, 19);
// NOI18N
hideSpectrumPanelJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/hide_grey.png")));
hideSpectrumPanelJButton.setToolTipText("Hide Spectrum (Shift+Ctrl+E)");
hideSpectrumPanelJButton.setBorder(null);
hideSpectrumPanelJButton.setBorderPainted(false);
hideSpectrumPanelJButton.setContentAreaFilled(false);
// NOI18N
hideSpectrumPanelJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/hide.png")));
hideSpectrumPanelJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
hideSpectrumPanelJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
hideSpectrumPanelJButtonMouseExited(evt);
}
});
hideSpectrumPanelJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
hideSpectrumPanelJButtonActionPerformed(evt);
}
});
spectrumLayeredPane.setLayer(hideSpectrumPanelJButton, javax.swing.JLayeredPane.POPUP_LAYER);
spectrumLayeredPane.add(hideSpectrumPanelJButton);
hideSpectrumPanelJButton.setBounds(440, 0, 10, 19);
// NOI18N
maximizeSpectrumPanelJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/maximize_grey.png")));
maximizeSpectrumPanelJButton.setToolTipText("Maximize Spectrum");
maximizeSpectrumPanelJButton.setBorder(null);
maximizeSpectrumPanelJButton.setBorderPainted(false);
maximizeSpectrumPanelJButton.setContentAreaFilled(false);
// NOI18N
maximizeSpectrumPanelJButton.setRolloverIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/maximize.png")));
maximizeSpectrumPanelJButton.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
maximizeSpectrumPanelJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
maximizeSpectrumPanelJButtonMouseExited(evt);
}
});
maximizeSpectrumPanelJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
maximizeSpectrumPanelJButtonActionPerformed(evt);
}
});
spectrumLayeredPane.setLayer(maximizeSpectrumPanelJButton, javax.swing.JLayeredPane.POPUP_LAYER);
spectrumLayeredPane.add(maximizeSpectrumPanelJButton);
maximizeSpectrumPanelJButton.setBounds(425, 5, 10, 19);
contextMenuSpectrumBackgroundPanel.setOpaque(false);
javax.swing.GroupLayout contextMenuSpectrumBackgroundPanelLayout = new javax.swing.GroupLayout(contextMenuSpectrumBackgroundPanel);
contextMenuSpectrumBackgroundPanel.setLayout(contextMenuSpectrumBackgroundPanelLayout);
contextMenuSpectrumBackgroundPanelLayout.setHorizontalGroup(contextMenuSpectrumBackgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 60, Short.MAX_VALUE));
contextMenuSpectrumBackgroundPanelLayout.setVerticalGroup(contextMenuSpectrumBackgroundPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 19, Short.MAX_VALUE));
spectrumLayeredPane.setLayer(contextMenuSpectrumBackgroundPanel, javax.swing.JLayeredPane.POPUP_LAYER);
spectrumLayeredPane.add(contextMenuSpectrumBackgroundPanel);
contextMenuSpectrumBackgroundPanel.setBounds(420, 0, 60, 19);
javax.swing.GroupLayout spectrumMainJPanelLayout = new javax.swing.GroupLayout(spectrumMainJPanel);
spectrumMainJPanel.setLayout(spectrumMainJPanelLayout);
spectrumMainJPanelLayout.setHorizontalGroup(spectrumMainJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(spectrumLayeredPane, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 510, Short.MAX_VALUE));
spectrumMainJPanelLayout.setVerticalGroup(spectrumMainJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(spectrumLayeredPane, javax.swing.GroupLayout.DEFAULT_SIZE, 350, Short.MAX_VALUE));
peptidesPsmSpectrumFragmentIonsJSplitPane.setRightComponent(spectrumMainJPanel);
coverageJSplitPane.setLeftComponent(peptidesPsmSpectrumFragmentIonsJSplitPane);
overviewJSplitPane.setRightComponent(coverageJSplitPane);
javax.swing.GroupLayout overviewJPanelLayout = new javax.swing.GroupLayout(overviewJPanel);
overviewJPanel.setLayout(overviewJPanelLayout);
overviewJPanelLayout.setHorizontalGroup(overviewJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(overviewJPanelLayout.createSequentialGroup().addContainerGap().addComponent(overviewJSplitPane).addContainerGap()));
overviewJPanelLayout.setVerticalGroup(overviewJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGroup(overviewJPanelLayout.createSequentialGroup().addContainerGap().addComponent(overviewJSplitPane).addContainerGap()));
backgroundLayeredPane.add(overviewJPanel);
overviewJPanel.setBounds(0, 0, 980, 720);
toolBar.setBackground(new java.awt.Color(255, 255, 255));
toolBar.setBorder(null);
toolBar.setFloatable(false);
toolBar.setRollover(true);
toolBar.setOpaque(false);
showProteinsBeforeSeparator.setOrientation(javax.swing.SwingConstants.VERTICAL);
showProteinsBeforeSeparator.setOpaque(true);
toolBar.add(showProteinsBeforeSeparator);
// NOI18N
showProteinsJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/list2.gif")));
showProteinsJButton.setText("Proteins");
showProteinsJButton.setToolTipText("Click to Show (Shift+Ctrl+P)");
showProteinsJButton.setFocusable(false);
showProteinsJButton.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
showProteinsJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
showProteinsJButtonActionPerformed(evt);
}
});
toolBar.add(showProteinsJButton);
showProteinsAfterSeparator.setOrientation(javax.swing.SwingConstants.VERTICAL);
showProteinsAfterSeparator.setOpaque(true);
toolBar.add(showProteinsAfterSeparator);
// NOI18N
showPeptidesAndPsmsJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/list2.gif")));
showPeptidesAndPsmsJButton.setText("Peptides & PSMs");
showPeptidesAndPsmsJButton.setToolTipText("Click to Show (Shift+Ctrl+E)");
showPeptidesAndPsmsJButton.setFocusable(false);
showPeptidesAndPsmsJButton.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
showPeptidesAndPsmsJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
showPeptidesAndPsmsJButtonActionPerformed(evt);
}
});
toolBar.add(showPeptidesAndPsmsJButton);
showPeptidesAfterSeparator.setOrientation(javax.swing.SwingConstants.VERTICAL);
showPeptidesAfterSeparator.setOpaque(true);
toolBar.add(showPeptidesAfterSeparator);
// NOI18N
showSpectrumJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/spectrum.GIF")));
showSpectrumJButton.setText("Spectrum & Fragment Ions");
showSpectrumJButton.setToolTipText("Click to Show (Shift+Ctrl+S)");
showSpectrumJButton.setFocusable(false);
showSpectrumJButton.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
showSpectrumJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
showSpectrumJButtonActionPerformed(evt);
}
});
toolBar.add(showSpectrumJButton);
showSpectrumAfterSeparator.setOrientation(javax.swing.SwingConstants.VERTICAL);
showSpectrumAfterSeparator.setOpaque(true);
toolBar.add(showSpectrumAfterSeparator);
// NOI18N
showCoverageJButton.setIcon(new javax.swing.ImageIcon(getClass().getResource("/icons/coverage3.gif")));
showCoverageJButton.setText("Protein Sequence Coverage");
showCoverageJButton.setToolTipText("Click to Show (Shift+Ctrl+C)");
showCoverageJButton.setFocusable(false);
showCoverageJButton.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
showCoverageJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
showCoverageJButtonActionPerformed(evt);
}
});
toolBar.add(showCoverageJButton);
showCoverageAfterSeparator.setOrientation(javax.swing.SwingConstants.VERTICAL);
showCoverageAfterSeparator.setOpaque(true);
toolBar.add(showCoverageAfterSeparator);
backgroundLayeredPane.add(toolBar);
toolBar.setBounds(0, 720, 980, 20);
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
this.setLayout(layout);
layout.setHorizontalGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 977, Short.MAX_VALUE).addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(backgroundLayeredPane, javax.swing.GroupLayout.DEFAULT_SIZE, 977, Short.MAX_VALUE)));
layout.setVerticalGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addGap(0, 742, Short.MAX_VALUE).addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING).addComponent(backgroundLayeredPane, javax.swing.GroupLayout.DEFAULT_SIZE, 742, Short.MAX_VALUE)));
}
Also used :
PsmTableModel(eu.isas.peptideshaker.gui.tablemodels.PsmTableModel)
JTableHeader(javax.swing.table.JTableHeader)
MouseAdapter(java.awt.event.MouseAdapter)
ProteinTableModel(eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel)
KeyEvent(java.awt.event.KeyEvent)
PeptideTableModel(eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel)
MouseEvent(java.awt.event.MouseEvent)
MouseEvent(java.awt.event.MouseEvent)
javax.swing(javax.swing)
java.awt(java.awt)
Example 3 with PsmTableModel
use of eu.isas.peptideshaker.gui.tablemodels.PsmTableModel in project peptide-shaker by compomics.
the class OverviewPanel method updateSpectrumPanelBorderTitle.
/**
* Update the spectrum and fragment ions panel border title with information
* about the currently selected PSM.
*
* @param currentPeptide the current peptide
* @param currentSpectrum the current spectrum
*/
private void updateSpectrumPanelBorderTitle(Spectrum currentSpectrum) {
if (peptideTable.getSelectedRow() != -1 && proteinTable.getSelectedRow() != -1 && psmTable.getSelectedRow() != -1) {
Identification identification = peptideShakerGUI.getIdentification();
int nAA = peptideShakerGUI.getDisplayParameters().getnAASurroundingPeptides();
SequenceProvider sequenceProvider = peptideShakerGUI.getSequenceProvider();
SelfUpdatingTableModel psmTableModel = (SelfUpdatingTableModel) psmTable.getModel();
int psmIndex = psmTableModel.getViewIndex(psmTable.getSelectedRow());
long spectrumMatchKey = psmKeys[psmIndex];
SpectrumMatch spectrumMatch = identification.getSpectrumMatch(spectrumMatchKey);
PeptideAssumption peptideAssumption = spectrumMatch.getBestPeptideAssumption();
SelfUpdatingTableModel peptideTableModel = (SelfUpdatingTableModel) peptideTable.getModel();
int peptideIndex = peptideTableModel.getViewIndex(peptideTable.getSelectedRow());
long peptideKey = peptideKeys[peptideIndex];
PeptideMatch peptideMatch = identification.getPeptideMatch(peptideKey);
Peptide peptide = peptideMatch.getPeptide();
SelfUpdatingTableModel proteinTableModel = (SelfUpdatingTableModel) proteinTable.getModel();
long proteinKey = proteinKeys[proteinTableModel.getViewIndex(proteinTable.getSelectedRow())];
ProteinMatch proteinMatch = identification.getProteinMatch(proteinKey);
String leadingAccession = proteinMatch.getLeadingAccession();
String aaBefore = Arrays.stream(peptide.getProteinMapping().get(leadingAccession)).mapToObj(index -> PeptideUtils.getAaBefore(peptide, leadingAccession, index, nAA, sequenceProvider)).collect(Collectors.joining("|"));
String aaAfter = Arrays.stream(peptide.getProteinMapping().get(leadingAccession)).mapToObj(index -> PeptideUtils.getAaAfter(peptide, leadingAccession, index, nAA, sequenceProvider)).collect(Collectors.joining("|"));
if (!aaBefore.equals("")) {
aaBefore += " - ";
}
if (!aaAfter.equals("")) {
aaAfter = " - " + aaAfter;
}
if (psmTable.getSelectedRowCount() == 1) {
String modifiedSequence = peptideShakerGUI.getDisplayFeaturesGenerator().getTaggedPeptideSequence(spectrumMatch, false, false, true);
((TitledBorder) spectrumMainPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions (" + aaBefore + modifiedSequence + aaAfter + " " + Charge.toString(peptideAssumption.getIdentificationCharge()) + " " + Util.roundDouble(currentSpectrum.getPrecursor().mz, 2) + " m/z)" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
} else if (psmTable.getSelectedRowCount() == 2) {
int[] selectedRows = psmTable.getSelectedRows();
psmIndex = psmTableModel.getViewIndex(selectedRows[0]);
spectrumMatchKey = psmKeys[psmIndex];
SpectrumMatch firstSpectrumMatch = identification.getSpectrumMatch(spectrumMatchKey);
String firstModifiedSequence = peptideShakerGUI.getDisplayFeaturesGenerator().getTaggedPeptideSequence(firstSpectrumMatch, false, false, true);
psmIndex = psmTableModel.getViewIndex(selectedRows[1]);
spectrumMatchKey = psmKeys[psmIndex];
SpectrumMatch secondSpectrumMatch = identification.getSpectrumMatch(spectrumMatchKey);
String secondModifiedSequence = peptideShakerGUI.getDisplayFeaturesGenerator().getTaggedPeptideSequence(secondSpectrumMatch, false, false, true);
((TitledBorder) spectrumMainPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions (" + firstModifiedSequence + " vs. " + secondModifiedSequence + ")" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
} else {
PeptideMatch currentPeptideMatch = (PeptideMatch) peptideShakerGUI.getIdentification().retrieveObject(peptideKey);
String peptideSequence = peptideShakerGUI.getDisplayFeaturesGenerator().getTaggedPeptideSequence(currentPeptideMatch, false, false, true);
((TitledBorder) spectrumMainPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions (" + peptideSequence + " " + psmTable.getSelectedRowCount() + " PSMs)" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
}
spectrumMainPanel.repaint();
} else {
((TitledBorder) spectrumMainPanel.getBorder()).setTitle(PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Spectrum & Fragment Ions" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING);
spectrumMainPanel.repaint();
}
}
Also used :
MatchType(eu.isas.peptideshaker.gui.MatchValidationDialog.MatchType)
PsPeptideFeature(com.compomics.util.io.export.features.peptideshaker.PsPeptideFeature)
PsProteinFeature(com.compomics.util.io.export.features.peptideshaker.PsProteinFeature)
NO_KEY(com.compomics.util.experiment.personalization.ExperimentObject.NO_KEY)
IdentificationFeaturesGenerator(com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator)
JSparklinesDataSeries(no.uib.jsparklines.data.JSparklinesDataSeries)
FileAndFileFilter(com.compomics.util.gui.file_handling.FileAndFileFilter)
BareBonesBrowserLaunch(com.compomics.util.examples.BareBonesBrowserLaunch)
FileChooserUtil(com.compomics.util.gui.file_handling.FileChooserUtil)
JTableHeader(javax.swing.table.JTableHeader)
ProteinInferencePeptideLevelDialog(eu.isas.peptideshaker.gui.protein_inference.ProteinInferencePeptideLevelDialog)
PeptideShakerGUI(eu.isas.peptideshaker.gui.PeptideShakerGUI)
SpecificAnnotationParameters(com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters)
SpectrumAnnotator(com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator)
MouseAdapter(java.awt.event.MouseAdapter)
TitledBorder(javax.swing.border.TitledBorder)
JSparklinesDataset(no.uib.jsparklines.data.JSparklinesDataset)
SpectrumProvider(com.compomics.util.experiment.mass_spectrometry.SpectrumProvider)
PeptideTableModel(eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel)
Variant(com.compomics.util.experiment.biology.variants.Variant)
TableProperties(com.compomics.util.gui.TableProperties)
SpectrumCountingMethod(com.compomics.util.experiment.quantification.spectrumcounting.SpectrumCountingMethod)
ModificationParameters(com.compomics.util.parameters.identification.search.ModificationParameters)
ProteinSequencePanelParent(eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanelParent)
PSModificationScores(com.compomics.util.experiment.identification.peptide_shaker.PSModificationScores)
Clipboard(java.awt.datatransfer.Clipboard)
TableModelEvent(javax.swing.event.TableModelEvent)
ExportScheme(com.compomics.util.io.export.ExportScheme)
PeptideAssumption(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption)
DefaultTableModel(javax.swing.table.DefaultTableModel)
TrueFalseIconRenderer(no.uib.jsparklines.extra.TrueFalseIconRenderer)
SequenceMatchingParameters(com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters)
PSExportFactory(eu.isas.peptideshaker.export.PSExportFactory)
SelfUpdatingTableModel(com.compomics.util.gui.tablemodels.SelfUpdatingTableModel)
Util(com.compomics.util.Util)
KeyEvent(java.awt.event.KeyEvent)
Collectors(java.util.stream.Collectors)
FileNotFoundException(java.io.FileNotFoundException)
SearchParameters(com.compomics.util.parameters.identification.search.SearchParameters)
com.compomics.util.experiment.identification.matches(com.compomics.util.experiment.identification.matches)
GuiUtilities(com.compomics.util.gui.GuiUtilities)
DisplayParameters(eu.isas.peptideshaker.preferences.DisplayParameters)
IdentificationParameters(com.compomics.util.parameters.identification.IdentificationParameters)
ProteinSequencePanel(eu.isas.peptideshaker.gui.protein_sequence.ProteinSequencePanel)
PSParameter(com.compomics.util.experiment.identification.peptide_shaker.PSParameter)
CategoryPlot(org.jfree.chart.plot.CategoryPlot)
ArrayUtil(com.compomics.util.ArrayUtil)
Precursor(com.compomics.util.experiment.mass_spectrometry.spectra.Precursor)
MatchValidationDialog(eu.isas.peptideshaker.gui.MatchValidationDialog)
IntStream(java.util.stream.IntStream)
java.util(java.util)
SpectrumIdentificationAssumption(com.compomics.util.experiment.identification.SpectrumIdentificationAssumption)
HelpDialog(com.compomics.util.gui.error_handlers.HelpDialog)
ChromosomeTableCellRenderer(no.uib.jsparklines.extra.ChromosomeTableCellRenderer)
PeptideUtils(com.compomics.util.experiment.identification.utils.PeptideUtils)
NonSymmetricalNormalDistribution(com.compomics.util.math.statistics.distributions.NonSymmetricalNormalDistribution)
PlotOrientation(org.jfree.chart.plot.PlotOrientation)
TableModelListener(javax.swing.event.TableModelListener)
XYPlottingDialog(com.compomics.util.gui.XYPlottingDialog)
ModificationUtils(com.compomics.util.experiment.identification.utils.ModificationUtils)
ProteinTableModel(eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel)
StringSelection(java.awt.datatransfer.StringSelection)
PsmTableModel(eu.isas.peptideshaker.gui.tablemodels.PsmTableModel)
Spectrum(com.compomics.util.experiment.mass_spectrometry.spectra.Spectrum)
ProteinInferenceDialog(eu.isas.peptideshaker.gui.protein_inference.ProteinInferenceDialog)
MatchValidationLevel(com.compomics.util.experiment.identification.validation.MatchValidationLevel)
BufferedWriter(java.io.BufferedWriter)
FileWriter(java.io.FileWriter)
DecimalFormat(java.text.DecimalFormat)
SequenceProvider(com.compomics.util.experiment.io.biology.protein.SequenceProvider)
ExportFeature(com.compomics.util.io.export.ExportFeature)
Identification(com.compomics.util.experiment.identification.Identification)
ResidueAnnotation(eu.isas.peptideshaker.gui.protein_sequence.ResidueAnnotation)
Peptide(com.compomics.util.experiment.biology.proteins.Peptide)
ExportGraphicsDialog(com.compomics.util.gui.export.graphics.ExportGraphicsDialog)
PSMaps(eu.isas.peptideshaker.scoring.PSMaps)
AnnotationParameters(com.compomics.util.experiment.identification.spectrum_annotation.AnnotationParameters)
MouseEvent(java.awt.event.MouseEvent)
File(java.io.File)
ChartChangeEvent(org.jfree.chart.event.ChartChangeEvent)
PeptideSpectrumAnnotator(com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator)
ExportFormat(com.compomics.util.io.export.ExportFormat)
java.awt(java.awt)
Charge(com.compomics.util.experiment.biology.ions.Charge)
HtmlLinksRenderer(no.uib.jsparklines.extra.HtmlLinksRenderer)
com.compomics.util.gui.spectrum(com.compomics.util.gui.spectrum)
GeneDetailsDialog(com.compomics.util.gui.genes.GeneDetailsDialog)
no.uib.jsparklines.renderers(no.uib.jsparklines.renderers)
Range(org.jfree.data.Range)
org.jfree.chart(org.jfree.chart)
ChartChangeListener(org.jfree.chart.event.ChartChangeListener)
ProgressDialogX(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX)
javax.swing(javax.swing)
Identification(com.compomics.util.experiment.identification.Identification)
TitledBorder(javax.swing.border.TitledBorder)
SequenceProvider(com.compomics.util.experiment.io.biology.protein.SequenceProvider)
SelfUpdatingTableModel(com.compomics.util.gui.tablemodels.SelfUpdatingTableModel)
PeptideAssumption(com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption)
Peptide(com.compomics.util.experiment.biology.proteins.Peptide)
Example 4 with PsmTableModel
use of eu.isas.peptideshaker.gui.tablemodels.PsmTableModel in project peptide-shaker by compomics.
the class OverviewPanel method updatePsmSelection.
/**
* Update the PSM selection according to the currently selected peptide.
*
* @param row the row index of the selected peptide
* @param forcePsmOrderUpdate if true, the sorted listed is recreated even
* if not needed
*/
private void updatePsmSelection(int row, boolean forcePsmOrderUpdate) {
if (row != -1) {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
Identification identification = peptideShakerGUI.getIdentification();
IdentificationFeaturesGenerator identificationFeaturesGenerator = peptideShakerGUI.getIdentificationFeaturesGenerator();
SelfUpdatingTableModel tableModel = (SelfUpdatingTableModel) peptideTable.getModel();
int peptideIndex = tableModel.getViewIndex(row);
long peptideKey = peptideKeys[peptideIndex];
psmKeys = identificationFeaturesGenerator.getSortedPsmKeys(peptideKey, peptideShakerGUI.getUtilitiesUserParameters().getSortPsmsOnRt(), forcePsmOrderUpdate);
// clear the selection in case more than one row was selected for the last peptide
psmTable.clearSelection();
// update the table model
if (psmTable.getModel() instanceof PsmTableModel && ((PsmTableModel) psmTable.getModel()).isInstantiated()) {
((PsmTableModel) psmTable.getModel()).updateDataModel(identification, peptideShakerGUI.getDisplayFeaturesGenerator(), peptideShakerGUI.getIdentificationParameters(), psmKeys);
((PsmTableModel) psmTable.getModel()).setSelfUpdating(true);
((PsmTableModel) psmTable.getModel()).resetSorting(new ProgressDialogX(peptideShakerGUI, Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker.gif")), Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/peptide-shaker-orange.gif")), true));
} else {
PsmTableModel psmTableModel = new PsmTableModel(identification, peptideShakerGUI.getDisplayFeaturesGenerator(), peptideShakerGUI.getSpectrumProvider(), peptideShakerGUI.getIdentificationParameters(), psmKeys, peptideShakerGUI.getDisplayParameters().showScores(), peptideShakerGUI.getExceptionHandler());
psmTable.setModel(psmTableModel);
}
setPsmTableProperties();
showSparkLines(peptideShakerGUI.showSparklines());
int nValidatedPsms = identificationFeaturesGenerator.getNValidatedSpectraForPeptide(peptideKey);
int nConfidentPsms = identificationFeaturesGenerator.getNConfidentSpectraForPeptide(peptideKey);
int nPsms = psmTable.getRowCount();
String title = PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING + "Peptide Spectrum Matches (";
if (nConfidentPsms > 0) {
title += nValidatedPsms + "/" + nPsms + " - " + nConfidentPsms + " confident, " + (nValidatedPsms - nConfidentPsms) + " doubtful";
} else {
title += nValidatedPsms + "/" + nPsms;
}
title += ")" + PeptideShakerGUI.TITLED_BORDER_HORIZONTAL_PADDING;
((TitledBorder) psmsPanel.getBorder()).setTitle(title);
psmsPanel.repaint();
updateSelection(true);
newItemSelection();
// update the sequence coverage map
SwingUtilities.invokeLater(new Runnable() {
public void run() {
try {
int proteinIndex, selectedProteinRow = proteinTable.getSelectedRow();
if (selectedProteinRow != -1) {
SelfUpdatingTableModel proteinTableModel = (SelfUpdatingTableModel) proteinTable.getModel();
proteinIndex = proteinTableModel.getViewIndex(selectedProteinRow);
} else {
proteinIndex = 0;
}
long proteinKey = proteinKeys[proteinIndex];
ProteinMatch proteinMatch = peptideShakerGUI.getIdentification().getProteinMatch(proteinKey);
updateSequenceCoverage(proteinKey, proteinMatch.getLeadingAccession());
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
}
});
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}
}
Also used :
PsmTableModel(eu.isas.peptideshaker.gui.tablemodels.PsmTableModel)
IdentificationFeaturesGenerator(com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator)
Identification(com.compomics.util.experiment.identification.Identification)
TitledBorder(javax.swing.border.TitledBorder)
FileNotFoundException(java.io.FileNotFoundException)
ProgressDialogX(com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX)
SelfUpdatingTableModel(com.compomics.util.gui.tablemodels.SelfUpdatingTableModel)
java.awt(java.awt)
Aggregations
PsmTableModel (eu.isas.peptideshaker.gui.tablemodels.PsmTableModel)4
PeptideTableModel (eu.isas.peptideshaker.gui.tablemodels.PeptideTableModel)3
ProteinTableModel (eu.isas.peptideshaker.gui.tablemodels.ProteinTableModel)3
java.awt (java.awt)3
TitledBorder (javax.swing.border.TitledBorder)3
Identification (com.compomics.util.experiment.identification.Identification)2
IdentificationFeaturesGenerator (com.compomics.util.experiment.identification.features.IdentificationFeaturesGenerator)2
SelfUpdatingTableModel (com.compomics.util.gui.tablemodels.SelfUpdatingTableModel)2
ProgressDialogX (com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX)2
KeyEvent (java.awt.event.KeyEvent)2
MouseAdapter (java.awt.event.MouseAdapter)2
MouseEvent (java.awt.event.MouseEvent)2
FileNotFoundException (java.io.FileNotFoundException)2
javax.swing (javax.swing)2
JTableHeader (javax.swing.table.JTableHeader)2
ArrayUtil (com.compomics.util.ArrayUtil)1
Util (com.compomics.util.Util)1
BareBonesBrowserLaunch (com.compomics.util.examples.BareBonesBrowserLaunch)1
Charge (com.compomics.util.experiment.biology.ions.Charge)1
Peptide (com.compomics.util.experiment.biology.proteins.Peptide)1
