public void clearData(boolean clearDatabaseFolder) {
projectDetails = null;
spectrumAnnotator = new SpectrumAnnotator();
try {
spectrumFactory.closeFiles();
} catch (Exception e) {
e.printStackTrace();
}
try {
sequenceFactory.closeFile();
} catch (Exception e) {
e.printStackTrace();
}
try {
GOFactory.getInstance().closeFiles();
} catch (Exception e) {
e.printStackTrace();
}
try {
spectrumFactory.clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
try {
sequenceFactory.clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
try {
GOFactory.getInstance().clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
identifiedModifications = null;
if (clearDatabaseFolder) {
clearDatabaseFolder();
}
resetFeatureGenerator();
// set up the tabs/panels
currentPSFile = null;
}
/**
* This dialog allows the user to resolve manually some protein inference issues.
*
* @author Marc Vaudel
* @author Harald Barsnes
*/
public class ProteinInferenceDialog extends javax.swing.JDialog {
/** The inspected protein match. */
private ProteinMatch inspectedMatch;
/** The protein accessions. */
private ArrayList<String> accessions;
/** The detected unique matches (if any). */
private ArrayList<String> uniqueMatches = new ArrayList<String>();
/** Associated matches presenting the same proteins or a share. */
private ArrayList<String> associatedMatches = new ArrayList<String>();
/** The sequence factory. */
private SequenceFactory sequenceFactory = SequenceFactory.getInstance();
/** The PeptideShaker parent frame. */
private PeptideShakerGUI peptideShakerGUI;
/** The candidate protein table column header tooltips. */
private ArrayList<String> candidateProteinsTableToolTips;
/** The unique hits table column header tooltips. */
private ArrayList<String> uniqueHitsTableToolTips;
/** The related hits table column header tooltips. */
private ArrayList<String> relatedHitsTableToolTips;
/** The identification. */
private Identification identification;
/** The selected main match. */
private String previousMainMatch;
/**
* Creates new form ProteinInferenceDialog.
*
* @param peptideShakerGUI
* @param inspectedMatch
* @param identification
*/
public ProteinInferenceDialog(
PeptideShakerGUI peptideShakerGUI, String inspectedMatch, Identification identification) {
super(peptideShakerGUI, true);
this.identification = identification;
this.peptideShakerGUI = peptideShakerGUI;
try {
this.inspectedMatch = identification.getProteinMatch(inspectedMatch);
previousMainMatch = this.inspectedMatch.getMainMatch();
} catch (Exception e) {
peptideShakerGUI.catchException(e);
this.dispose();
}
accessions = new ArrayList(Arrays.asList(ProteinMatch.getAccessions(inspectedMatch)));
for (String proteinAccession : accessions) {
if (identification.getProteinIdentification().contains(proteinAccession)) {
uniqueMatches.add(proteinAccession);
}
}
for (String proteinKey : identification.getProteinIdentification()) {
if (ProteinMatch.getNProteins(proteinKey) > 1
&& !associatedMatches.contains(proteinKey)
&& !proteinKey.equals(inspectedMatch)) {
for (String proteinAccession : accessions) {
if (proteinKey.contains(proteinAccession)) {
associatedMatches.add(proteinKey);
break;
}
}
}
}
initComponents();
// make sure that the scroll panes are see-through
proteinMatchJScrollPane.getViewport().setOpaque(false);
uniqueHitsJScrollPane.getViewport().setOpaque(false);
relatedHitsJScrollPane.getViewport().setOpaque(false);
groupClassJComboBox.setRenderer(new AlignedListCellRenderer(SwingConstants.CENTER));
PSParameter psParameter = new PSParameter();
try {
psParameter =
(PSParameter) identification.getProteinMatchParameter(inspectedMatch, psParameter);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
matchInfoLbl.setText(
"[Score: "
+ Util.roundDouble(psParameter.getProteinScore(), 2)
+ ", Confidence: "
+ Util.roundDouble(psParameter.getProteinConfidence(), 2)
+ "]");
// set up the table column properties
setColumnProperies();
// The index should be set in the design according to the PSParameter class static fields!
groupClassJComboBox.setSelectedIndex(psParameter.getGroupClass());
setLocationRelativeTo(peptideShakerGUI);
setVisible(true);
}
/** Set the properties for the columns in the results tables. */
private void setColumnProperies() {
proteinMatchTable.getTableHeader().setReorderingAllowed(false);
uniqueHitsTable.getTableHeader().setReorderingAllowed(false);
relatedHitsTable.getTableHeader().setReorderingAllowed(false);
proteinMatchTable.getColumn(" ").setMinWidth(30);
proteinMatchTable.getColumn(" ").setMaxWidth(30);
// set the preferred size of the accession column
Integer width =
peptideShakerGUI.getPreferredAccessionColumnWidth(
proteinMatchTable, proteinMatchTable.getColumn("Accession").getModelIndex(), 2);
if (width != null) {
proteinMatchTable.getColumn("Accession").setMinWidth(width);
proteinMatchTable.getColumn("Accession").setMaxWidth(width);
} else {
proteinMatchTable.getColumn("Accession").setMinWidth(15);
proteinMatchTable.getColumn("Accession").setMaxWidth(Integer.MAX_VALUE);
}
// the validated column
uniqueHitsTable.getColumn(" ").setMaxWidth(30);
relatedHitsTable.getColumn(" ").setMaxWidth(30);
uniqueHitsTable.getColumn(" ").setMinWidth(30);
relatedHitsTable.getColumn(" ").setMinWidth(30);
proteinMatchTable.getColumn("").setMaxWidth(30);
uniqueHitsTable.getColumn("").setMaxWidth(30);
relatedHitsTable.getColumn("").setMaxWidth(30);
proteinMatchTable.getColumn("").setMinWidth(30);
uniqueHitsTable.getColumn("").setMinWidth(30);
relatedHitsTable.getColumn("").setMinWidth(30);
// the score and confidence columns
uniqueHitsTable.getColumn("Confidence").setMaxWidth(90);
uniqueHitsTable.getColumn("Confidence").setMinWidth(90);
uniqueHitsTable.getColumn("Score").setMaxWidth(90);
uniqueHitsTable.getColumn("Score").setMinWidth(90);
relatedHitsTable.getColumn("Confidence").setMaxWidth(90);
relatedHitsTable.getColumn("Confidence").setMinWidth(90);
relatedHitsTable.getColumn("Score").setMaxWidth(90);
relatedHitsTable.getColumn("Score").setMinWidth(90);
// change the cell renderer to fix a problem in Nimbus and alternating row colors
proteinMatchTable.getColumn(" ").setCellRenderer(new NimbusCheckBoxRenderer());
proteinMatchTable
.getColumn("Accession")
.setCellRenderer(
new HtmlLinksRenderer(
peptideShakerGUI.getSelectedRowHtmlTagFontColor(),
peptideShakerGUI.getNotSelectedRowHtmlTagFontColor()));
uniqueHitsTable
.getColumn("Protein(s)")
.setCellRenderer(
new HtmlLinksRenderer(
peptideShakerGUI.getSelectedRowHtmlTagFontColor(),
peptideShakerGUI.getNotSelectedRowHtmlTagFontColor()));
uniqueHitsTable
.getColumn(" ")
.setCellRenderer(
new TrueFalseIconRenderer(
new ImageIcon(this.getClass().getResource("/icons/accept.png")),
new ImageIcon(this.getClass().getResource("/icons/Error_3.png")),
"Validated",
"Not Validated"));
uniqueHitsTable
.getColumn("Score")
.setCellRenderer(
new JSparklinesBarChartTableCellRenderer(
PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
uniqueHitsTable
.getColumn("Confidence")
.setCellRenderer(
new JSparklinesBarChartTableCellRenderer(
PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
((JSparklinesBarChartTableCellRenderer) uniqueHitsTable.getColumn("Score").getCellRenderer())
.showNumberAndChart(true, peptideShakerGUI.getLabelWidth() + 5);
((JSparklinesBarChartTableCellRenderer)
uniqueHitsTable.getColumn("Confidence").getCellRenderer())
.showNumberAndChart(true, peptideShakerGUI.getLabelWidth() + 5);
relatedHitsTable
.getColumn("Protein(s)")
.setCellRenderer(
new HtmlLinksRenderer(
peptideShakerGUI.getSelectedRowHtmlTagFontColor(),
peptideShakerGUI.getNotSelectedRowHtmlTagFontColor()));
relatedHitsTable
.getColumn(" ")
.setCellRenderer(
new TrueFalseIconRenderer(
new ImageIcon(this.getClass().getResource("/icons/accept.png")),
new ImageIcon(this.getClass().getResource("/icons/Error_3.png")),
"Validated",
"Not Validated"));
relatedHitsTable
.getColumn("Score")
.setCellRenderer(
new JSparklinesBarChartTableCellRenderer(
PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
relatedHitsTable
.getColumn("Confidence")
.setCellRenderer(
new JSparklinesBarChartTableCellRenderer(
PlotOrientation.HORIZONTAL, 100.0, peptideShakerGUI.getSparklineColor()));
((JSparklinesBarChartTableCellRenderer) relatedHitsTable.getColumn("Score").getCellRenderer())
.showNumberAndChart(true, peptideShakerGUI.getLabelWidth() + 5);
((JSparklinesBarChartTableCellRenderer)
relatedHitsTable.getColumn("Confidence").getCellRenderer())
.showNumberAndChart(true, peptideShakerGUI.getLabelWidth() + 5);
// set up the table header tooltips
candidateProteinsTableToolTips = new ArrayList<String>();
candidateProteinsTableToolTips.add(null);
candidateProteinsTableToolTips.add("Currently Selected Protein Match");
candidateProteinsTableToolTips.add("Protein Accession");
candidateProteinsTableToolTips.add("Protein Description");
uniqueHitsTableToolTips = new ArrayList<String>();
uniqueHitsTableToolTips.add(null);
uniqueHitsTableToolTips.add("Protein Accession(s)");
uniqueHitsTableToolTips.add("Protein Score");
uniqueHitsTableToolTips.add("Protein Confidence");
uniqueHitsTableToolTips.add("Validated");
relatedHitsTableToolTips = new ArrayList<String>();
relatedHitsTableToolTips.add(null);
relatedHitsTableToolTips.add("Protein Accession(s)");
relatedHitsTableToolTips.add("Protein Score");
relatedHitsTableToolTips.add("Protein Confidence");
relatedHitsTableToolTips.add("Validated");
}
/**
* 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")
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
private void initComponents() {
backgroundPanel = new javax.swing.JPanel();
okButton = new javax.swing.JButton();
relatedHitsJPanel = new javax.swing.JPanel();
relatedHitsJScrollPane = new javax.swing.JScrollPane();
relatedHitsTable =
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) relatedHitsTableToolTips.get(realIndex);
return tip;
}
};
}
};
uniqueHitsJPanel = new javax.swing.JPanel();
uniqueHitsJScrollPane = new javax.swing.JScrollPane();
uniqueHitsTable =
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) uniqueHitsTableToolTips.get(realIndex);
return tip;
}
};
}
};
proteinMatchJPanel = new javax.swing.JPanel();
proteinMatchJScrollPane = new javax.swing.JScrollPane();
proteinMatchTable =
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) candidateProteinsTableToolTips.get(realIndex);
return tip;
}
};
}
};
groupDetalsJPanel = new javax.swing.JPanel();
matchInfoLbl = new javax.swing.JLabel();
jLabel2 = new javax.swing.JLabel();
groupClassJComboBox = new javax.swing.JComboBox();
helpJButton = new javax.swing.JButton();
cancelButton = new javax.swing.JButton();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
setTitle("Protein Inference - Protein Level");
setResizable(false);
backgroundPanel.setBackground(new java.awt.Color(230, 230, 230));
okButton.setText("OK");
okButton.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
okButtonActionPerformed(evt);
}
});
relatedHitsJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Related Hits"));
relatedHitsJPanel.setOpaque(false);
relatedHitsTable.setModel(new AssociatedMatches());
relatedHitsTable.setOpaque(false);
relatedHitsTable.addMouseListener(
new java.awt.event.MouseAdapter() {
public void mouseExited(java.awt.event.MouseEvent evt) {
relatedHitsTableMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
relatedHitsTableMouseReleased(evt);
}
});
relatedHitsTable.addMouseMotionListener(
new java.awt.event.MouseMotionAdapter() {
public void mouseMoved(java.awt.event.MouseEvent evt) {
relatedHitsTableMouseMoved(evt);
}
});
relatedHitsJScrollPane.setViewportView(relatedHitsTable);
javax.swing.GroupLayout relatedHitsJPanelLayout =
new javax.swing.GroupLayout(relatedHitsJPanel);
relatedHitsJPanel.setLayout(relatedHitsJPanelLayout);
relatedHitsJPanelLayout.setHorizontalGroup(
relatedHitsJPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
relatedHitsJPanelLayout
.createSequentialGroup()
.addContainerGap()
.addComponent(
relatedHitsJScrollPane,
javax.swing.GroupLayout.DEFAULT_SIZE,
723,
Short.MAX_VALUE)
.addContainerGap()));
relatedHitsJPanelLayout.setVerticalGroup(
relatedHitsJPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
relatedHitsJPanelLayout
.createSequentialGroup()
.addContainerGap()
.addComponent(
relatedHitsJScrollPane,
javax.swing.GroupLayout.PREFERRED_SIZE,
73,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)));
uniqueHitsJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Unique Hits"));
uniqueHitsJPanel.setOpaque(false);
uniqueHitsTable.setModel(new UniqueMatches());
uniqueHitsTable.setOpaque(false);
uniqueHitsTable.addMouseListener(
new java.awt.event.MouseAdapter() {
public void mouseExited(java.awt.event.MouseEvent evt) {
uniqueHitsTableMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
uniqueHitsTableMouseReleased(evt);
}
});
uniqueHitsTable.addMouseMotionListener(
new java.awt.event.MouseMotionAdapter() {
public void mouseMoved(java.awt.event.MouseEvent evt) {
uniqueHitsTableMouseMoved(evt);
}
});
uniqueHitsJScrollPane.setViewportView(uniqueHitsTable);
javax.swing.GroupLayout uniqueHitsJPanelLayout = new javax.swing.GroupLayout(uniqueHitsJPanel);
uniqueHitsJPanel.setLayout(uniqueHitsJPanelLayout);
uniqueHitsJPanelLayout.setHorizontalGroup(
uniqueHitsJPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
uniqueHitsJPanelLayout
.createSequentialGroup()
.addContainerGap()
.addComponent(
uniqueHitsJScrollPane,
javax.swing.GroupLayout.DEFAULT_SIZE,
723,
Short.MAX_VALUE)
.addContainerGap()));
uniqueHitsJPanelLayout.setVerticalGroup(
uniqueHitsJPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
uniqueHitsJPanelLayout
.createSequentialGroup()
.addContainerGap()
.addComponent(
uniqueHitsJScrollPane,
javax.swing.GroupLayout.PREFERRED_SIZE,
70,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap(14, Short.MAX_VALUE)));
proteinMatchJPanel.setBorder(
javax.swing.BorderFactory.createTitledBorder("Candidate Proteins"));
proteinMatchJPanel.setOpaque(false);
proteinMatchTable.setModel(new MatchTable());
proteinMatchTable.setOpaque(false);
proteinMatchTable.addMouseListener(
new java.awt.event.MouseAdapter() {
public void mouseExited(java.awt.event.MouseEvent evt) {
proteinMatchTableMouseExited(evt);
}
public void mouseReleased(java.awt.event.MouseEvent evt) {
proteinMatchTableMouseReleased(evt);
}
});
proteinMatchTable.addMouseMotionListener(
new java.awt.event.MouseMotionAdapter() {
public void mouseMoved(java.awt.event.MouseEvent evt) {
proteinMatchTableMouseMoved(evt);
}
});
proteinMatchJScrollPane.setViewportView(proteinMatchTable);
javax.swing.GroupLayout proteinMatchJPanelLayout =
new javax.swing.GroupLayout(proteinMatchJPanel);
proteinMatchJPanel.setLayout(proteinMatchJPanelLayout);
proteinMatchJPanelLayout.setHorizontalGroup(
proteinMatchJPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
proteinMatchJPanelLayout
.createSequentialGroup()
.addContainerGap()
.addComponent(
proteinMatchJScrollPane,
javax.swing.GroupLayout.DEFAULT_SIZE,
723,
Short.MAX_VALUE)
.addContainerGap()));
proteinMatchJPanelLayout.setVerticalGroup(
proteinMatchJPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
proteinMatchJPanelLayout
.createSequentialGroup()
.addContainerGap()
.addComponent(
proteinMatchJScrollPane,
javax.swing.GroupLayout.DEFAULT_SIZE,
141,
Short.MAX_VALUE)
.addContainerGap()));
groupDetalsJPanel.setBorder(
javax.swing.BorderFactory.createTitledBorder("Protein Group Details"));
groupDetalsJPanel.setOpaque(false);
matchInfoLbl.setText("protein match information");
jLabel2.setText("Type:");
groupClassJComboBox.setModel(
new javax.swing.DefaultComboBoxModel(
new String[] {
"Single Protein", "Isoforms", "Unrelated Isoforms", "Unrelated Proteins"
}));
javax.swing.GroupLayout groupDetalsJPanelLayout =
new javax.swing.GroupLayout(groupDetalsJPanel);
groupDetalsJPanel.setLayout(groupDetalsJPanelLayout);
groupDetalsJPanelLayout.setHorizontalGroup(
groupDetalsJPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
groupDetalsJPanelLayout
.createSequentialGroup()
.addContainerGap()
.addComponent(jLabel2)
.addGap(20, 20, 20)
.addComponent(
groupClassJComboBox,
javax.swing.GroupLayout.PREFERRED_SIZE,
295,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(matchInfoLbl)
.addContainerGap(249, Short.MAX_VALUE)));
groupDetalsJPanelLayout.setVerticalGroup(
groupDetalsJPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
groupDetalsJPanelLayout
.createSequentialGroup()
.addContainerGap()
.addGroup(
groupDetalsJPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jLabel2)
.addComponent(
groupClassJComboBox,
javax.swing.GroupLayout.PREFERRED_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(matchInfoLbl))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)));
helpJButton.setIcon(
new javax.swing.ImageIcon(getClass().getResource("/icons/help.GIF"))); // NOI18N
helpJButton.setToolTipText("Help");
helpJButton.setBorder(null);
helpJButton.setBorderPainted(false);
helpJButton.setContentAreaFilled(false);
helpJButton.setFocusable(false);
helpJButton.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
helpJButton.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
helpJButton.addMouseListener(
new java.awt.event.MouseAdapter() {
public void mouseEntered(java.awt.event.MouseEvent evt) {
helpJButtonMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
helpJButtonMouseExited(evt);
}
});
helpJButton.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
helpJButtonActionPerformed(evt);
}
});
cancelButton.setText("Cancel");
cancelButton.addActionListener(
new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
cancelButtonActionPerformed(evt);
}
});
javax.swing.GroupLayout backgroundPanelLayout = new javax.swing.GroupLayout(backgroundPanel);
backgroundPanel.setLayout(backgroundPanelLayout);
backgroundPanelLayout.setHorizontalGroup(
backgroundPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
backgroundPanelLayout
.createSequentialGroup()
.addContainerGap()
.addGroup(
backgroundPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(
uniqueHitsJPanel,
javax.swing.GroupLayout.Alignment.TRAILING,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
Short.MAX_VALUE)
.addComponent(
groupDetalsJPanel,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
Short.MAX_VALUE)
.addComponent(
proteinMatchJPanel,
javax.swing.GroupLayout.Alignment.TRAILING,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
Short.MAX_VALUE)
.addComponent(
relatedHitsJPanel,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
Short.MAX_VALUE)
.addGroup(
backgroundPanelLayout
.createSequentialGroup()
.addGap(10, 10, 10)
.addComponent(helpJButton)
.addPreferredGap(
javax.swing.LayoutStyle.ComponentPlacement.RELATED,
586,
Short.MAX_VALUE)
.addComponent(
okButton,
javax.swing.GroupLayout.PREFERRED_SIZE,
71,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(
javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(cancelButton)))
.addContainerGap()));
backgroundPanelLayout.setVerticalGroup(
backgroundPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(
backgroundPanelLayout
.createSequentialGroup()
.addContainerGap()
.addComponent(
groupDetalsJPanel,
javax.swing.GroupLayout.PREFERRED_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(
proteinMatchJPanel,
javax.swing.GroupLayout.PREFERRED_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(
uniqueHitsJPanel,
javax.swing.GroupLayout.PREFERRED_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(
relatedHitsJPanel,
javax.swing.GroupLayout.PREFERRED_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(8, 8, 8)
.addGroup(
backgroundPanelLayout
.createParallelGroup(javax.swing.GroupLayout.Alignment.CENTER)
.addComponent(helpJButton)
.addComponent(okButton)
.addComponent(cancelButton))
.addContainerGap()));
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(
backgroundPanel,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
Short.MAX_VALUE));
layout.setVerticalGroup(
layout
.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(
backgroundPanel,
javax.swing.GroupLayout.DEFAULT_SIZE,
javax.swing.GroupLayout.DEFAULT_SIZE,
Short.MAX_VALUE));
pack();
} // </editor-fold>//GEN-END:initComponents
/**
* Update the protein table according to the protein inference selection.
*
* @param evt
*/
private void okButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_okButtonActionPerformed
PSParameter psParameter = new PSParameter();
try {
psParameter =
(PSParameter)
identification.getProteinMatchParameter(inspectedMatch.getKey(), psParameter);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
this.dispose();
return;
}
if (!inspectedMatch.getMainMatch().equals(previousMainMatch)
|| groupClassJComboBox.getSelectedIndex() != psParameter.getGroupClass()) {
try {
psParameter.setGroupClass(groupClassJComboBox.getSelectedIndex());
identification.updateProteinMatchParameter(inspectedMatch.getKey(), psParameter);
peptideShakerGUI.updateMainMatch(
inspectedMatch.getMainMatch(), groupClassJComboBox.getSelectedIndex());
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
peptideShakerGUI.setDataSaved(false);
}
this.dispose();
} // GEN-LAST:event_okButtonActionPerformed
/**
* Sets the main match if the main match column is selected, or opens the protein web link if the
* accession number column is selected.
*
* @param evt
*/
private void proteinMatchTableMouseReleased(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_proteinMatchTableMouseReleased
int row = proteinMatchTable.rowAtPoint(evt.getPoint());
int column = proteinMatchTable.columnAtPoint(evt.getPoint());
if (row != -1) {
if (column == 1) {
try {
inspectedMatch.setMainMatch(accessions.get(row));
identification.updateProteinMatch(inspectedMatch);
peptideShakerGUI
.getIdentificationFeaturesGenerator()
.updateCoverableAA(inspectedMatch.getKey());
peptideShakerGUI
.getIdentificationFeaturesGenerator()
.updateSequenceCoverage(inspectedMatch.getKey());
peptideShakerGUI
.getIdentificationFeaturesGenerator()
.updateObservableCoverage(inspectedMatch.getKey());
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
proteinMatchTable.revalidate();
proteinMatchTable.repaint();
} else if (column == 2) {
// open protein link in web browser
if (evt.getButton() == MouseEvent.BUTTON1
&& ((String) proteinMatchTable.getValueAt(row, column)).lastIndexOf("<html>") != -1) {
String link = (String) proteinMatchTable.getValueAt(row, column);
link = link.substring(link.indexOf("\"") + 1);
link = link.substring(0, link.indexOf("\""));
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL(link);
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}
}
}
} // GEN-LAST:event_proteinMatchTableMouseReleased
/**
* Change the cursor to a hand cursor.
*
* @param evt
*/
private void helpJButtonMouseEntered(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_helpJButtonMouseEntered
setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
} // GEN-LAST:event_helpJButtonMouseEntered
/**
* Change the cursor back to the default cursor.
*
* @param evt
*/
private void helpJButtonMouseExited(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_helpJButtonMouseExited
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
} // GEN-LAST:event_helpJButtonMouseExited
/**
* Open the help dialog.
*
* @param evt
*/
private void helpJButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_helpJButtonActionPerformed
setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
new HelpDialog(peptideShakerGUI, getClass().getResource("/helpFiles/ProteinInference.html"));
setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
} // GEN-LAST:event_helpJButtonActionPerformed
/**
* Changes the cursor into a hand cursor if the table cell contains an HTML link.
*
* @param evt
*/
private void proteinMatchTableMouseMoved(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_proteinMatchTableMouseMoved
int row = proteinMatchTable.rowAtPoint(evt.getPoint());
int column = proteinMatchTable.columnAtPoint(evt.getPoint());
proteinMatchTable.setToolTipText(null);
if (column == 2 && proteinMatchTable.getValueAt(row, column) != null) {
String tempValue = (String) proteinMatchTable.getValueAt(row, column);
if (tempValue.lastIndexOf("<html>") != -1) {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
} else {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}
} else if (column == proteinMatchTable.getColumn("Description").getModelIndex()
&& proteinMatchTable.getValueAt(row, column) != null) {
if (GuiUtilities.getPreferredWidthOfCell(proteinMatchTable, row, column)
> proteinMatchTable.getColumn("Description").getWidth()) {
proteinMatchTable.setToolTipText("" + proteinMatchTable.getValueAt(row, column));
}
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
} else {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}
} // GEN-LAST:event_proteinMatchTableMouseMoved
/**
* Changes the cursor back to the default cursor a hand.
*
* @param evt
*/
private void proteinMatchTableMouseExited(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_proteinMatchTableMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
} // GEN-LAST:event_proteinMatchTableMouseExited
/**
* Changes the cursor back to the default cursor.
*
* @param evt
*/
private void uniqueHitsTableMouseExited(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_uniqueHitsTableMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
} // GEN-LAST:event_uniqueHitsTableMouseExited
/**
* Changes the cursor into a hand cursor if the table cell contains an HTML link.
*
* @param evt
*/
private void uniqueHitsTableMouseMoved(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_uniqueHitsTableMouseMoved
int row = uniqueHitsTable.rowAtPoint(evt.getPoint());
int column = uniqueHitsTable.columnAtPoint(evt.getPoint());
if (column == 1 && uniqueHitsTable.getValueAt(row, column) != null) {
String tempValue = (String) uniqueHitsTable.getValueAt(row, column);
if (tempValue.lastIndexOf("a href=") != -1) {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
} else {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}
} else {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}
} // GEN-LAST:event_uniqueHitsTableMouseMoved
/**
* Open the protein html links.
*
* @param evt
*/
private void uniqueHitsTableMouseReleased(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_uniqueHitsTableMouseReleased
int row = uniqueHitsTable.getSelectedRow();
int column = uniqueHitsTable.getSelectedColumn();
if (row != -1) {
if (column == 1) {
// open protein links in web browser
if (evt != null
&& evt.getButton() == MouseEvent.BUTTON1
&& ((String) uniqueHitsTable.getValueAt(row, column)).lastIndexOf("a href=") != -1) {
peptideShakerGUI.openProteinLinks((String) uniqueHitsTable.getValueAt(row, column));
}
}
}
} // GEN-LAST:event_uniqueHitsTableMouseReleased
/**
* Changes the cursor back to the default cursor.
*
* @param evt
*/
private void relatedHitsTableMouseExited(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_relatedHitsTableMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
} // GEN-LAST:event_relatedHitsTableMouseExited
/**
* Changes the cursor into a hand cursor if the table cell contains an HTML link.
*
* @param evt
*/
private void relatedHitsTableMouseMoved(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_relatedHitsTableMouseMoved
int row = relatedHitsTable.rowAtPoint(evt.getPoint());
int column = relatedHitsTable.columnAtPoint(evt.getPoint());
if (column == 1 && relatedHitsTable.getValueAt(row, column) != null) {
String tempValue = (String) relatedHitsTable.getValueAt(row, column);
if (tempValue.lastIndexOf("a href=") != -1) {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
} else {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}
} else {
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}
} // GEN-LAST:event_relatedHitsTableMouseMoved
/**
* Open the protein html links.
*
* @param evt
*/
private void relatedHitsTableMouseReleased(
java.awt.event.MouseEvent evt) { // GEN-FIRST:event_relatedHitsTableMouseReleased
int row = relatedHitsTable.getSelectedRow();
int column = relatedHitsTable.getSelectedColumn();
if (row != -1) {
if (column == 1) {
// open protein links in web browser
if (evt != null
&& evt.getButton() == MouseEvent.BUTTON1
&& ((String) relatedHitsTable.getValueAt(row, column)).lastIndexOf("a href=") != -1) {
peptideShakerGUI.openProteinLinks((String) relatedHitsTable.getValueAt(row, column));
}
}
}
} // GEN-LAST:event_relatedHitsTableMouseReleased
/**
* Closes the dialog.
*
* @param evt
*/
private void cancelButtonActionPerformed(
java.awt.event.ActionEvent evt) { // GEN-FIRST:event_cancelButtonActionPerformed
this.setVisible(false);
this.dispose();
} // GEN-LAST:event_cancelButtonActionPerformed
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JPanel backgroundPanel;
private javax.swing.JButton cancelButton;
private javax.swing.JComboBox groupClassJComboBox;
private javax.swing.JPanel groupDetalsJPanel;
private javax.swing.JButton helpJButton;
private javax.swing.JLabel jLabel2;
private javax.swing.JLabel matchInfoLbl;
private javax.swing.JButton okButton;
private javax.swing.JPanel proteinMatchJPanel;
private javax.swing.JScrollPane proteinMatchJScrollPane;
private javax.swing.JTable proteinMatchTable;
private javax.swing.JPanel relatedHitsJPanel;
private javax.swing.JScrollPane relatedHitsJScrollPane;
private javax.swing.JTable relatedHitsTable;
private javax.swing.JPanel uniqueHitsJPanel;
private javax.swing.JScrollPane uniqueHitsJScrollPane;
private javax.swing.JTable uniqueHitsTable;
// End of variables declaration//GEN-END:variables
/** Table model for the protein match table. */
private class MatchTable extends DefaultTableModel {
@Override
public int getRowCount() {
return accessions.size();
}
@Override
public int getColumnCount() {
return 4;
}
@Override
public String getColumnName(int column) {
switch (column) {
case 0:
return "";
case 1:
return " ";
case 2:
return "Accession";
case 3:
return "Description";
default:
return " ";
}
}
@Override
public Object getValueAt(int row, int column) {
switch (column) {
case 0:
return (row + 1);
case 1:
return inspectedMatch.getMainMatch().equals(accessions.get(row));
case 2:
return peptideShakerGUI
.getIdentificationFeaturesGenerator()
.addDatabaseLink(accessions.get(row));
case 3:
try {
return sequenceFactory.getHeader(accessions.get(row)).getDescription();
} catch (Exception e) {
peptideShakerGUI.catchException(e);
return "Database Error";
}
default:
return " ";
}
}
@Override
public Class getColumnClass(int columnIndex) {
return getValueAt(0, columnIndex).getClass();
}
@Override
public boolean isCellEditable(int rowIndex, int columnIndex) {
return columnIndex == 1;
}
}
/** Table model for the unique matches table. */
private class UniqueMatches extends DefaultTableModel {
@Override
public int getRowCount() {
return uniqueMatches.size();
}
@Override
public int getColumnCount() {
return 5;
}
@Override
public String getColumnName(int column) {
switch (column) {
case 0:
return "";
case 1:
return "Protein(s)";
case 2:
return "Score";
case 3:
return "Confidence";
case 4:
return " ";
default:
return "";
}
}
@Override
public Object getValueAt(int row, int column) {
PSParameter pSParameter = new PSParameter();
try {
pSParameter =
(PSParameter)
identification.getProteinMatchParameter(uniqueMatches.get(row), pSParameter);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
switch (column) {
case 0:
return (row + 1);
case 1:
return peptideShakerGUI
.getIdentificationFeaturesGenerator()
.addDatabaseLinks(
new ArrayList<String>(
Arrays.asList(ProteinMatch.getAccessions(uniqueMatches.get(row)))));
case 2:
return pSParameter.getProteinScore();
case 3:
return pSParameter.getProteinConfidence();
case 4:
return pSParameter.isValidated();
default:
return "";
}
}
@Override
public Class getColumnClass(int columnIndex) {
return getValueAt(0, columnIndex).getClass();
}
@Override
public boolean isCellEditable(int rowIndex, int columnIndex) {
return false;
}
}
/** Table model for the associated matches table. */
private class AssociatedMatches extends DefaultTableModel {
@Override
public int getRowCount() {
return associatedMatches.size();
}
@Override
public int getColumnCount() {
return 5;
}
@Override
public String getColumnName(int column) {
switch (column) {
case 0:
return "";
case 1:
return "Protein(s)";
case 2:
return "Score";
case 3:
return "Confidence";
case 4:
return " ";
default:
return "";
}
}
@Override
public Object getValueAt(int row, int column) {
PSParameter pSParameter = new PSParameter();
try {
pSParameter =
(PSParameter)
identification.getProteinMatchParameter(associatedMatches.get(row), pSParameter);
} catch (Exception e) {
peptideShakerGUI.catchException(e);
}
switch (column) {
case 0:
return (row + 1);
case 1:
return peptideShakerGUI
.getIdentificationFeaturesGenerator()
.addDatabaseLinks(
new ArrayList<String>(
Arrays.asList(ProteinMatch.getAccessions(associatedMatches.get(row)))));
case 2:
return pSParameter.getProteinScore();
case 3:
return pSParameter.getProteinConfidence();
case 4:
return pSParameter.isValidated();
default:
return "";
}
}
@Override
public Class getColumnClass(int columnIndex) {
return getValueAt(0, columnIndex).getClass();
}
@Override
public boolean isCellEditable(int rowIndex, int columnIndex) {
return false;
}
}
}
public class PSFileImporter {
private File currentPSFile;
private EnzymeFactory enzymeFactory = EnzymeFactory.getInstance();
private String resource;
/** The spectrum annotator. */
private SpectrumAnnotator spectrumAnnotator = new SpectrumAnnotator();
/** The project details. */
private ProjectDetails projectDetails = null;
/** The spectrum factory. */
private SpectrumFactory spectrumFactory = SpectrumFactory.getInstance(100);
/** The identification to display. */
private Identification identification;
/** The compomics PTM factory. */
private PTMFactory ptmFactory = PTMFactory.getInstance();
/** The parameters of the search. */
private SearchParameters searchParameters = new SearchParameters();
/** The initial processing preferences */
private ProcessingPreferences processingPreferences = new ProcessingPreferences();
/** The annotation preferences. */
private AnnotationPreferences annotationPreferences = new AnnotationPreferences();
/** The spectrum counting preferences. */
private SpectrumCountingPreferences spectrumCountingPreferences =
new SpectrumCountingPreferences();
/** The PTM scoring preferences */
private PTMScoringPreferences ptmScoringPreferences = new PTMScoringPreferences();
/** The identification filter used for this project. */
private IdFilter idFilter = new IdFilter();
/** The actually identified modifications. */
/**
* Returns the modifications found in this project.
*
* @return the modifications found in this project
*/
public ArrayList<String> getFoundModifications() {
if (identifiedModifications == null) {
identifiedModifications = new ArrayList<String>();
for (String peptideKey : identification.getPeptideIdentification()) {
boolean modified = false;
for (String modificationName : Peptide.getModificationFamily(peptideKey)) {
if (!identifiedModifications.contains(modificationName)) {
identifiedModifications.add(modificationName);
modified = true;
}
}
if (!modified && !identifiedModifications.contains(PtmPanel.NO_MODIFICATION)) {
identifiedModifications.add(PtmPanel.NO_MODIFICATION);
}
}
}
return identifiedModifications;
}
private ArrayList<String> identifiedModifications = null;
/** Metrics picked-up while loading the files. */
private Metrics metrics;
/** The display preferences. */
private DisplayPreferences displayPreferences = new DisplayPreferences();
/** The sequence factory. */
private SequenceFactory sequenceFactory = SequenceFactory.getInstance(30000);
/** The filter preferences. */
private FilterPreferences filterPreferences = new FilterPreferences();
/** The compomics experiment. */
private MsExperiment experiment = null;
/** The investigated sample. */
private Sample sample;
/** The replicate number. */
private int replicateNumber;
/** The class used to provide sexy features out of the identification. */
private IdentificationFeaturesGenerator identificationFeaturesGenerator;
/** The last folder opened by the user. Defaults to user.home. */
private String lastSelectedFolder = "user.home";
/** The object cache used for the identification database. */
private ObjectsCache objectsCache;
private com.compomics.util.experiment.ProteomicAnalysis proteomicAnalysis;
private ProgressDialogX progressDialog;
private javax.swing.JProgressBar jprog;
public PSFileImporter(javax.swing.JProgressBar jprog) {
this.progressDialog = new ProgressDialogX(false);
this.jprog = jprog;
}
public void importPeptideShakerFile(File aPsFile, final String resource) {
this.resource = resource;
this.currentPSFile = aPsFile;
loadGeneMapping();
loadEnzymes();
resetPtmFactory();
// setDefaultPreferences(); // @TODO: i tried re-adding this but then we get a null pointer, but
// the two below have to be added or the default neutral losses won't appear
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.H2O);
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.NH3);
// exceptionHandler = new ExceptionHandler(this);
new Thread("ProgressThread") {
@Override
public void run() {
jprog.setValue(10);
}
}.start();
Thread importThread =
new Thread("ImportThread") {
@Override
public void run() {
try {
// reset enzymes, ptms and preferences
loadEnzymes();
resetPtmFactory();
setDefaultPreferences();
try {
// close any open connection to an identification database
if (identification != null) {
identification.close();
}
} catch (Exception e) {
e.printStackTrace();
}
File experimentFile =
new File(
PeptideShaker.SERIALIZATION_DIRECTORY, PeptideShaker.experimentObjectName);
File matchFolder = new File(PeptideShaker.SERIALIZATION_DIRECTORY);
// empty the existing files in the matches folder
if (matchFolder.exists()) {
for (File file : matchFolder.listFiles()) {
if (file.isDirectory()) {
boolean deleted = Util.deleteDir(file);
if (!deleted) {
System.out.println("Failed to delete folder: " + file.getPath());
}
} else {
boolean deleted = file.delete();
if (!deleted) {
System.out.println("Failed to delete file: " + file.getPath());
}
}
}
}
final int BUFFER = 2048;
byte data[] = new byte[BUFFER];
FileInputStream fi = new FileInputStream(currentPSFile);
BufferedInputStream bis = new BufferedInputStream(fi, BUFFER);
try {
ArchiveInputStream tarInput =
new ArchiveStreamFactory().createArchiveInputStream(bis);
ArchiveEntry archiveEntry;
while ((archiveEntry = tarInput.getNextEntry()) != null) {
File destinationFile = new File(archiveEntry.getName());
File destinationFolder = destinationFile.getParentFile();
boolean destFolderExists = true;
if (!destinationFolder.exists()) {
destFolderExists = destinationFolder.mkdirs();
}
if (destFolderExists) {
FileOutputStream fos = new FileOutputStream(destinationFile);
BufferedOutputStream bos = new BufferedOutputStream(fos);
int count;
while ((count = tarInput.read(data, 0, BUFFER)) != -1
&& !progressDialog.isRunCanceled()) {
bos.write(data, 0, count);
}
bos.close();
fos.close();
// int progress = (int) (100 *
// tarInput.getBytesRead() / fileLength);
// progressDialog.setValue(progress);
} else {
System.out.println(
"Folder does not exist: \'"
+ destinationFolder.getAbsolutePath()
+ "\'. User preferences not saved.");
}
}
tarInput.close();
} catch (ArchiveException e) {
// Most likely an old project
experimentFile = currentPSFile;
e.printStackTrace();
}
fi.close();
bis.close();
fi.close();
MsExperiment tempExperiment = ExperimentIO.loadExperiment(experimentFile);
Sample tempSample = null;
PeptideShakerSettings experimentSettings = new PeptideShakerSettings();
if (tempExperiment.getUrParam(experimentSettings) instanceof PSSettings) {
// convert old settings files using utilities version 3.10.68 or older
// convert the old ProcessingPreferences object
PSSettings tempSettings =
(PSSettings) tempExperiment.getUrParam(experimentSettings);
ProcessingPreferences tempProcessingPreferences = new ProcessingPreferences();
tempProcessingPreferences.setProteinFDR(
tempSettings.getProcessingPreferences().getProteinFDR());
tempProcessingPreferences.setPeptideFDR(
tempSettings.getProcessingPreferences().getPeptideFDR());
tempProcessingPreferences.setPsmFDR(
tempSettings.getProcessingPreferences().getPsmFDR());
// convert the old PTMScoringPreferences object
PTMScoringPreferences tempPTMScoringPreferences = new PTMScoringPreferences();
tempPTMScoringPreferences.setaScoreCalculation(
tempSettings.getPTMScoringPreferences().aScoreCalculation());
tempPTMScoringPreferences.setaScoreNeutralLosses(
tempSettings.getPTMScoringPreferences().isaScoreNeutralLosses());
tempPTMScoringPreferences.setFlrThreshold(
tempSettings.getPTMScoringPreferences().getFlrThreshold());
// missing gene refrences
GenePreferences genePreferences = getGenePreferences();
// String selectedSpecies = genePreferences.getCurrentSpecies();
// String speciesDatabase =
// genePreferences.getEnsemblDatabaseName(selectedSpecies);
experimentSettings =
new PeptideShakerSettings(
tempSettings.getSearchParameters(),
tempSettings.getAnnotationPreferences(),
tempSettings.getSpectrumCountingPreferences(),
tempSettings.getProjectDetails(),
tempSettings.getFilterPreferences(),
tempSettings.getDisplayPreferences(),
tempSettings.getMetrics(),
tempProcessingPreferences,
tempSettings.getIdentificationFeaturesCache(),
tempPTMScoringPreferences,
genePreferences,
new IdFilter());
;
} else {
experimentSettings =
(PeptideShakerSettings) tempExperiment.getUrParam(experimentSettings);
}
idFilter = experimentSettings.getIdFilter();
setAnnotationPreferences(experimentSettings.getAnnotationPreferences());
setSpectrumCountingPreferences(experimentSettings.getSpectrumCountingPreferences());
setPtmScoringPreferences(experimentSettings.getPTMScoringPreferences());
setProjectDetails(experimentSettings.getProjectDetails());
setSearchParameters(experimentSettings.getSearchParameters());
setProcessingPreferences(experimentSettings.getProcessingPreferences());
setMetrics(experimentSettings.getMetrics());
setDisplayPreferences(experimentSettings.getDisplayPreferences());
if (experimentSettings.getFilterPreferences() != null) {
setFilterPreferences(experimentSettings.getFilterPreferences());
} else {
setFilterPreferences(new FilterPreferences());
}
if (experimentSettings.getDisplayPreferences() != null) {
setDisplayPreferences(experimentSettings.getDisplayPreferences());
displayPreferences.compatibilityCheck(searchParameters.getModificationProfile());
} else {
setDisplayPreferences(new DisplayPreferences());
displayPreferences.setDefaultSelection(searchParameters.getModificationProfile());
}
ArrayList<Sample> samples = new ArrayList(tempExperiment.getSamples().values());
if (samples.size() == 1) {
tempSample = samples.get(0);
} else {
tempSample = samples.get(0);
String[] sampleNames = new String[samples.size()];
for (int cpt = 0; cpt < sampleNames.length; cpt++) {
sampleNames[cpt] = samples.get(cpt).getReference();
System.out.println(sampleNames[cpt]);
}
SampleSelection sampleSelection =
new SampleSelection(null, true, sampleNames, "sample");
sampleSelection.setVisible(false);
String choice = sampleSelection.getChoice();
for (Sample sampleTemp : samples) {
if (sampleTemp.getReference().equals(choice)) {
tempSample = sampleTemp;
break;
}
}
}
ArrayList<Integer> replicates =
new ArrayList(tempExperiment.getAnalysisSet(tempSample).getReplicateNumberList());
System.out.println(replicates);
int tempReplicate;
if (replicates.size() == 1) {
tempReplicate = replicates.get(0);
} else {
String[] replicateNames = new String[replicates.size()];
for (int cpt = 0; cpt < replicateNames.length; cpt++) {
replicateNames[cpt] = samples.get(cpt).getReference();
}
SampleSelection sampleSelection =
new SampleSelection(null, true, replicateNames, "replicate");
sampleSelection.setVisible(false);
Integer choice = new Integer(sampleSelection.getChoice());
tempReplicate = 0;
}
setProject(tempExperiment, tempSample, tempReplicate);
identificationFeaturesGenerator =
new IdentificationFeaturesGenerator(
identification,
searchParameters,
idFilter,
metrics,
spectrumCountingPreferences);
if (experimentSettings.getIdentificationFeaturesCache() != null) {
identificationFeaturesGenerator.setIdentificationFeaturesCache(
experimentSettings.getIdentificationFeaturesCache());
}
// mainProgressDialog.setTitle("Loading FASTA File. Please
// Wait...");
try {
File providedFastaLocation =
experimentSettings.getSearchParameters().getFastaFile();
String fileName = providedFastaLocation.getName();
File projectFolder = currentPSFile.getParentFile();
File dataFolder = new File(projectFolder, "data");
// try to locate the FASTA file
if (providedFastaLocation.exists()) {
SequenceFactory.getInstance().loadFastaFile(providedFastaLocation);
} else if (new File(projectFolder, fileName).exists()) {
SequenceFactory.getInstance().loadFastaFile(new File(projectFolder, fileName));
experimentSettings
.getSearchParameters()
.setFastaFile(new File(projectFolder, fileName));
} else if (new File(dataFolder, fileName).exists()) {
SequenceFactory.getInstance().loadFastaFile(new File(dataFolder, fileName));
experimentSettings
.getSearchParameters()
.setFastaFile(new File(dataFolder, fileName));
} else {
// return error
System.out.println("fastafile is missing");
}
} catch (Exception e) {
e.printStackTrace();
System.out.println("fastafile is missing");
}
// mainProgressDialog.setTitle("Locating Spectrum Files. Please
// Wait...");
for (String spectrumFileName : identification.getSpectrumFiles()) {
try {
File providedSpectrumLocation = projectDetails.getSpectrumFile(spectrumFileName);
// try to locate the spectrum file
if (providedSpectrumLocation == null || !providedSpectrumLocation.exists()) {
File projectFolder = currentPSFile.getParentFile();
File fileInProjectFolder = new File(projectFolder, spectrumFileName);
File dataFolder = new File(projectFolder, "data");
File fileInDataFolder = new File(dataFolder, spectrumFileName);
File fileInLastSelectedFolder =
new File(getLastSelectedFolder(), spectrumFileName);
if (fileInProjectFolder.exists()) {
projectDetails.addSpectrumFile(fileInProjectFolder);
} else if (fileInDataFolder.exists()) {
projectDetails.addSpectrumFile(fileInDataFolder);
} else if (fileInLastSelectedFolder.exists()) {
projectDetails.addSpectrumFile(fileInLastSelectedFolder);
} else {
System.out.println("error no file");
}
}
} catch (Exception e) {
clearData(true);
// clearPreferences();
e.printStackTrace();
System.out.println("error no file");
return;
}
}
objectsCache = new ObjectsCache();
objectsCache.setAutomatedMemoryManagement(true);
if (identification.isDB()) {
try {
String dbFolder =
new File(resource, PeptideShaker.SERIALIZATION_DIRECTORY).getAbsolutePath();
identification.establishConnection(dbFolder, false, objectsCache);
} catch (Exception e) {
e.printStackTrace();
}
} else {
updateAnnotationPreferencesFromSearchSettings();
annotationPreferences.useAutomaticAnnotation(true);
}
int cpt = 1, nfiles = identification.getSpectrumFiles().size();
for (String fileName : identification.getSpectrumFiles()) {
// mainProgressDialog.setTitle("Importing Spectrum
// Files. Please Wait...");
try {
File mgfFile = projectDetails.getSpectrumFile(fileName);
spectrumFactory.addSpectra(mgfFile, progressDialog);
} catch (Exception e) {
clearData(true);
e.printStackTrace();
return;
}
}
boolean compatibilityIssue =
getSearchParameters().getIonSearched1() == null
|| getSearchParameters().getIonSearched2() == null;
if (compatibilityIssue) {
JOptionPane.showMessageDialog(
null,
"The annotation preferences for this project may have changed.\n\n"
+ "Note that PeptideShaker has substancially improved, we strongly\n"
+ "recommend reprocessing your identification files.",
"Annotation Preferences",
JOptionPane.INFORMATION_MESSAGE);
updateAnnotationPreferencesFromSearchSettings();
}
if (identification.getSpectrumIdentificationMap() == null) {
// 0.18 version, needs update of the spectrum mapping
identification.updateSpectrumMapping();
}
} catch (OutOfMemoryError error) {
System.out.println(
"Ran out of memory! (runtime.maxMemory(): "
+ Runtime.getRuntime().maxMemory()
+ ")");
Runtime.getRuntime().gc();
JOptionPane.showMessageDialog(
null,
"The task used up all the available memory and had to be stopped.\n"
+ "Memory boundaries are set in ../resources/conf/JavaOptions.txt.",
"Out Of Memory Error",
JOptionPane.ERROR_MESSAGE);
error.printStackTrace();
} catch (Exception exp) {
exp.printStackTrace();
}
}
};
importThread.setPriority(Thread.MAX_PRIORITY);
// importThread.start();
// while (importThread.isAlive()) {
// try {
// Thread.currentThread().sleep(100);
//
// } catch (Exception e) {
// e.printStackTrace();
// }
// }
ExecutorService es = Executors.newCachedThreadPool();
es.execute(importThread);
es.shutdown();
try {
boolean finshed = es.awaitTermination(1, TimeUnit.DAYS);
System.gc();
return;
// t.start();
} catch (InterruptedException ex) {
System.err.println(ex.getMessage());
// Logger.getLogger(UpdatedOutputGenerator.class.getName()).log(Level.SEVERE, null, ex);
}
System.gc();
// return;
}
/** Loads the enzymes from the enzyme file into the enzyme factory. */
private void loadEnzymes() {
try {
enzymeFactory.importEnzymes(new File(resource, PeptideShaker.ENZYME_FILE));
} catch (Exception e) {
System.out.println("Not able to load the enzyme file." + "Wrong enzyme file.");
e.printStackTrace();
}
}
/** Loads the modifications from the modification file. */
public void resetPtmFactory() {
// reset ptm factory
ptmFactory.reloadFactory();
ptmFactory = PTMFactory.getInstance();
try {
ptmFactory.importModifications(new File(resource, PeptideShaker.MODIFICATIONS_FILE), false);
} catch (Exception e) {
e.printStackTrace();
}
try {
ptmFactory.importModifications(
new File(resource, PeptideShaker.USER_MODIFICATIONS_FILE), true);
} catch (Exception e) {
e.printStackTrace();
}
}
/** Set the default preferences. */
private void setDefaultPreferences() {
searchParameters = new SearchParameters();
annotationPreferences.setAnnotationLevel(0.75);
annotationPreferences.useAutomaticAnnotation(true);
spectrumCountingPreferences.setSelectedMethod(SpectralCountingMethod.NSAF);
spectrumCountingPreferences.setValidatedHits(true);
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.NH3);
IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.H2O);
processingPreferences = new ProcessingPreferences();
ptmScoringPreferences = new PTMScoringPreferences();
}
/** Imports the gene mapping. */
private void loadGeneMapping() {
try {
geneFactory.initialize(new File(resource, GENE_MAPPING_PATH), null);
} catch (Exception e) {
e.printStackTrace();
}
}
/** The path to the gene mapping file. */
private final String GENE_MAPPING_PATH = "/resources/conf/gene_ontology/gene_details_human";
/** The gene factory. */
private GeneFactory geneFactory = GeneFactory.getInstance();
/**
* Updates the new annotation preferences.
*
* @param annotationPreferences the new annotation preferences
*/
public void setAnnotationPreferences(AnnotationPreferences annotationPreferences) {
this.annotationPreferences = annotationPreferences;
}
/**
* Sets new spectrum counting preferences.
*
* @param spectrumCountingPreferences new spectrum counting preferences
*/
public void setSpectrumCountingPreferences(
SpectrumCountingPreferences spectrumCountingPreferences) {
this.spectrumCountingPreferences = spectrumCountingPreferences;
}
/**
* Sets the PTM scoring preferences
*
* @param ptmScoringPreferences the PTM scoring preferences
*/
public void setPtmScoringPreferences(PTMScoringPreferences ptmScoringPreferences) {
this.ptmScoringPreferences = ptmScoringPreferences;
}
/**
* Sets the project details.
*
* @param projectDetails the project details
*/
public void setProjectDetails(ProjectDetails projectDetails) {
this.projectDetails = projectDetails;
}
/**
* Updates the search parameters.
*
* @param searchParameters the new search parameters
*/
public void setSearchParameters(SearchParameters searchParameters) {
this.searchParameters = searchParameters;
PeptideShaker.loadModifications(searchParameters);
}
/**
* Sets the initial processing preferences.
*
* @param processingPreferences the initial processing preferences
*/
public void setProcessingPreferences(ProcessingPreferences processingPreferences) {
this.processingPreferences = processingPreferences;
}
/**
* Sets the metrics saved while loading the files.
*
* @param metrics the metrics saved while loading the files
*/
public void setMetrics(Metrics metrics) {
this.metrics = metrics;
}
/**
* Sets the display preferences to use.
*
* @param displayPreferences the display preferences to use
*/
public void setDisplayPreferences(DisplayPreferences displayPreferences) {
this.displayPreferences = displayPreferences;
}
/**
* Sets the gui filter preferences to use. .\
*
* @param filterPreferences the gui filter preferences to use
*/
public void setFilterPreferences(FilterPreferences filterPreferences) {
this.filterPreferences = filterPreferences;
}
/**
* This method sets the information of the project when opened.
*
* @param experiment the experiment conducted
* @param sample The sample analyzed
* @param replicateNumber The replicate number
*/
public void setProject(MsExperiment experiment, Sample sample, int replicateNumber) {
this.experiment = experiment;
this.sample = sample;
this.replicateNumber = replicateNumber;
ProteomicAnalysis proteomic_Analysis =
experiment.getAnalysisSet(sample).getProteomicAnalysis(replicateNumber);
identification = proteomic_Analysis.getIdentification(IdentificationMethod.MS2_IDENTIFICATION);
}
/**
* Returns the last selected folder.
*
* @return the last selected folder
*/
public String getLastSelectedFolder() {
return lastSelectedFolder;
}
/**
* Set the last selected folder.
*
* @param lastSelectedFolder the folder to set
*/
public void setLastSelectedFolder(String lastSelectedFolder) {
this.lastSelectedFolder = lastSelectedFolder;
}
/**
* Returns the identification displayed.
*
* @return the identification displayed
*/
public com.compomics.util.experiment.identification.Identification getIdentification() {
return identification;
}
/**
* Returns the identification features generator.
*
* @return the identification features generator
*/
public IdentificationFeaturesGenerator getIdentificationFeaturesGenerator() {
return identificationFeaturesGenerator;
}
/**
* Returns the search parameters.
*
* @return the search parameters
*/
public SearchParameters getSearchParameters() {
return searchParameters;
}
/**
* Return the display preferences to use.
*
* @return the display preferences to use
*/
public DisplayPreferences getDisplayPreferences() {
return displayPreferences;
}
public ArrayList<IonMatch> getIonsCurrentlyMatched() throws MzMLUnmarshallerException {
return spectrumAnnotator.getCurrentAnnotation(
annotationPreferences.getIonTypes(),
annotationPreferences.getNeutralLosses(),
annotationPreferences.getValidatedCharges());
}
public SpectrumAnnotator getSpectrumAnnorator() {
return spectrumAnnotator;
}
public void clearData(boolean clearDatabaseFolder) {
projectDetails = null;
spectrumAnnotator = new SpectrumAnnotator();
try {
spectrumFactory.closeFiles();
} catch (Exception e) {
e.printStackTrace();
}
try {
sequenceFactory.closeFile();
} catch (Exception e) {
e.printStackTrace();
}
try {
GOFactory.getInstance().closeFiles();
} catch (Exception e) {
e.printStackTrace();
}
try {
spectrumFactory.clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
try {
sequenceFactory.clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
try {
GOFactory.getInstance().clearFactory();
} catch (Exception e) {
e.printStackTrace();
}
identifiedModifications = null;
if (clearDatabaseFolder) {
clearDatabaseFolder();
}
resetFeatureGenerator();
// set up the tabs/panels
currentPSFile = null;
}
/** Resets the feature generator. */
public void resetFeatureGenerator() {
identificationFeaturesGenerator =
new IdentificationFeaturesGenerator(
identification, searchParameters, idFilter, metrics, spectrumCountingPreferences);
}
/** Clears the database folder. */
private void clearDatabaseFolder() {
boolean databaseClosed = true;
// close the database connection
if (identification != null) {
try {
identification.close();
identification = null;
} catch (SQLException e) {
databaseClosed = false;
e.printStackTrace();
JOptionPane.showMessageDialog(
null, "Failed to close the database.", "Database Error", JOptionPane.WARNING_MESSAGE);
}
}
// empty the matches folder
if (databaseClosed) {
File matchFolder = new File(resource, PeptideShaker.SERIALIZATION_DIRECTORY);
if (matchFolder.exists()) {
File[] tempFiles = matchFolder.listFiles();
if (tempFiles != null) {
for (File currentFile : tempFiles) {
Util.deleteDir(currentFile);
}
}
if (matchFolder.listFiles() != null && matchFolder.listFiles().length > 0) {
JOptionPane.showMessageDialog(
null,
"Failed to empty the database folder:\n" + matchFolder.getPath() + ".",
"Database Cleanup Failed",
JOptionPane.WARNING_MESSAGE);
}
}
}
}
/** Updates the ions used for fragment annotation. */
public void updateAnnotationPreferencesFromSearchSettings() {
annotationPreferences.setPreferencesFromSearchParamaers(searchParameters);
}
/**
* Returns the gene preferences.
*
* @return the gene preferences
*/
public GenePreferences getGenePreferences() {
return genePreferences;
}
private GenePreferences genePreferences = new GenePreferences();
/**
* Returns the experiment.
*
* @return the experiment
*/
public MsExperiment getExperiment() {
return experiment;
}
/*
* Returns the sample.
* @return the sample
*/
public Sample getSample() {
return sample;
}
/**
* Returns the replicate number.
*
* @return the replicateNumber
*/
public int getReplicateNumber() {
return this.replicateNumber;
}
/**
* Returns the desired spectrum.
*
* @param spectrumKey the key of the spectrum
* @return the desired spectrum
*/
public MSnSpectrum getSpectrum(String spectrumKey) {
String spectrumFile = Spectrum.getSpectrumFile(spectrumKey);
String spectrumTitle = Spectrum.getSpectrumTitle(spectrumKey);
try {
return (MSnSpectrum) spectrumFactory.getSpectrum(spectrumFile, spectrumTitle);
} catch (Exception e) {
System.out.println(e.getMessage());
return null;
}
}
}