package eu.isas.peptideshaker.gui.tabpanels;
import com.compomics.util.examples.BareBonesBrowserLaunch;
import com.compomics.util.experiment.annotation.gene.GeneFactory;
import com.compomics.util.experiment.identification.SequenceFactory;
import com.compomics.util.gui.JOptionEditorPane;
import eu.isas.peptideshaker.export.OutputGenerator;
import eu.isas.peptideshaker.gui.PeptideShakerGUI;
import java.io.IOException;
import javax.swing.JOptionPane;
/**
* This tab contains the basic protein annotation and links to other protein
* resources.
*
* @author Harald Barsnes
*/
public class AnnotationPanel extends javax.swing.JPanel {
/**
* The current protein accession number.
*/
private String currentAccessionNumber = "";
/**
* The PeptideShakerGUI parent.
*/
private PeptideShakerGUI peptideShakerGUI;
/**
* The sequence factory.
*/
private SequenceFactory sequenceFactory = SequenceFactory.getInstance();
/**
* The gene factory.
*/
private GeneFactory geneFactory = GeneFactory.getInstance();
/**
* Creates a new AnnotationPanel.
*
* @param peptideShakerGUI
*/
public AnnotationPanel(PeptideShakerGUI peptideShakerGUI) {
initComponents();
this.peptideShakerGUI = peptideShakerGUI;
}
/**
* Clears the old data.
*/
private void clearOldData() {
proteinDescriptionTextArea.setText("");
geneNameJTextField.setText("");
taxonomyJTextField.setText("");
}
/**
* 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() {
basicAnnotationJPanel = new javax.swing.JPanel();
accessionNumberLabel = new javax.swing.JLabel();
accessionNumberJTextField = new javax.swing.JTextField();
descriptionLabel = new javax.swing.JLabel();
geneNameLabel = new javax.swing.JLabel();
geneNameJTextField = new javax.swing.JTextField();
texonomyLabel = new javax.swing.JLabel();
taxonomyJTextField = new javax.swing.JTextField();
databaseLabel = new javax.swing.JLabel();
databaseJTextField = new javax.swing.JTextField();
proteinDescriptionScrollPane = new javax.swing.JScrollPane();
proteinDescriptionTextArea = new javax.swing.JTextArea();
chromosomeLabel = new javax.swing.JLabel();
chromosomeJTextField = new javax.swing.JTextField();
uniprotLinkJPanel = new javax.swing.JPanel();
uniprotLabel = new javax.swing.JLabel();
loadUniProtJButton = new javax.swing.JButton();
webUniProtLabel = new javax.swing.JLabel();
dastyLinkJPanel = new javax.swing.JPanel();
dastyLabel = new javax.swing.JLabel();
loadDastyJButton = new javax.swing.JButton();
webDastyLabel = new javax.swing.JLabel();
reactomeLinkJPanel = new javax.swing.JPanel();
reactomeLabel = new javax.swing.JLabel();
loadReactomeJButton = new javax.swing.JButton();
webReactomeLabel = new javax.swing.JLabel();
stringLinkJPanel = new javax.swing.JPanel();
stringLabel = new javax.swing.JLabel();
loadStringJButton = new javax.swing.JButton();
webStringLabel = new javax.swing.JLabel();
davidLinkJPanel = new javax.swing.JPanel();
davidLabel = new javax.swing.JLabel();
loadDavidJButton = new javax.swing.JButton();
webDavidLabel = new javax.swing.JLabel();
intActLinkJPanel = new javax.swing.JPanel();
intactLabel = new javax.swing.JLabel();
loadIntActJButton = new javax.swing.JButton();
webIntActLabel = new javax.swing.JLabel();
quickGOLinkJPanel = new javax.swing.JPanel();
quickGoLabel = new javax.swing.JLabel();
loadQuickGOJButton = new javax.swing.JButton();
webQuickGOLabel = new javax.swing.JLabel();
interProLinkJPanel = new javax.swing.JPanel();
interProLabel = new javax.swing.JLabel();
loadInterProJButton = new javax.swing.JButton();
webInterProLabel = new javax.swing.JLabel();
helpPanel = new javax.swing.JPanel();
helpScrollPane = new javax.swing.JScrollPane();
helpEditorPane = new javax.swing.JEditorPane();
picrLinkJLabel = new javax.swing.JLabel();
nextProtLinkJPanel = new javax.swing.JPanel();
nextProtLabel = new javax.swing.JLabel();
loadNextProtJButton = new javax.swing.JButton();
webNextProtLabel = new javax.swing.JLabel();
pdbLinkJPanel = new javax.swing.JPanel();
pdbLabel = new javax.swing.JLabel();
loadPdbJButton = new javax.swing.JButton();
webPdbLabel = new javax.swing.JLabel();
setBackground(new java.awt.Color(255, 255, 255));
basicAnnotationJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Basic Protein Annotation"));
basicAnnotationJPanel.setOpaque(false);
accessionNumberLabel.setText("Accession");
accessionNumberJTextField.setEditable(false);
descriptionLabel.setText("Description");
geneNameLabel.setText("Gene Name");
geneNameJTextField.setEditable(false);
texonomyLabel.setText("Taxonomy");
taxonomyJTextField.setEditable(false);
databaseLabel.setText("Database");
databaseJTextField.setEditable(false);
proteinDescriptionTextArea.setEditable(false);
proteinDescriptionTextArea.setColumns(20);
proteinDescriptionTextArea.setLineWrap(true);
proteinDescriptionTextArea.setRows(2);
proteinDescriptionTextArea.setTabSize(4);
proteinDescriptionTextArea.setWrapStyleWord(true);
proteinDescriptionScrollPane.setViewportView(proteinDescriptionTextArea);
chromosomeLabel.setText("Chromosome");
chromosomeJTextField.setEditable(false);
chromosomeJTextField.setHorizontalAlignment(javax.swing.JTextField.CENTER);
javax.swing.GroupLayout basicAnnotationJPanelLayout = new javax.swing.GroupLayout(basicAnnotationJPanel);
basicAnnotationJPanel.setLayout(basicAnnotationJPanelLayout);
basicAnnotationJPanelLayout.setHorizontalGroup(
basicAnnotationJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(basicAnnotationJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(basicAnnotationJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(accessionNumberLabel)
.addComponent(descriptionLabel)
.addComponent(geneNameLabel)
.addComponent(texonomyLabel)
.addComponent(databaseLabel))
.addGap(38, 38, 38)
.addGroup(basicAnnotationJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(accessionNumberJTextField, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.DEFAULT_SIZE, 494, Short.MAX_VALUE)
.addComponent(proteinDescriptionScrollPane)
.addComponent(taxonomyJTextField)
.addComponent(databaseJTextField)
.addGroup(basicAnnotationJPanelLayout.createSequentialGroup()
.addComponent(geneNameJTextField)
.addGap(18, 18, 18)
.addComponent(chromosomeLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(chromosomeJTextField, javax.swing.GroupLayout.PREFERRED_SIZE, 131, javax.swing.GroupLayout.PREFERRED_SIZE)))
.addContainerGap())
);
basicAnnotationJPanelLayout.linkSize(javax.swing.SwingConstants.HORIZONTAL, new java.awt.Component[] {accessionNumberLabel, descriptionLabel, texonomyLabel});
basicAnnotationJPanelLayout.setVerticalGroup(
basicAnnotationJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(basicAnnotationJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(basicAnnotationJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(accessionNumberJTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(accessionNumberLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(basicAnnotationJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(basicAnnotationJPanelLayout.createSequentialGroup()
.addGap(14, 14, 14)
.addComponent(descriptionLabel)
.addGap(25, 25, 25))
.addComponent(proteinDescriptionScrollPane, javax.swing.GroupLayout.Alignment.TRAILING, javax.swing.GroupLayout.PREFERRED_SIZE, 53, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(basicAnnotationJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(geneNameJTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(geneNameLabel)
.addComponent(chromosomeLabel)
.addComponent(chromosomeJTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(basicAnnotationJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(taxonomyJTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(texonomyLabel))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(basicAnnotationJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(databaseJTextField, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(databaseLabel))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
uniprotLinkJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("UniProt - protein knowledgebase"));
uniprotLinkJPanel.setOpaque(false);
uniprotLabel.setText("High-quality protein sequence and functional information.");
loadUniProtJButton.setText("Search UniProt");
loadUniProtJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
loadUniProtJButtonActionPerformed(evt);
}
});
webUniProtLabel.setText("<html> <a href=\\\"dummy_link\">web</a></html>");
webUniProtLabel.setToolTipText("Open the UniProt web page");
webUniProtLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
webUniProtLabelMouseClicked(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
webUniProtLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
webUniProtLabelMouseExited(evt);
}
});
javax.swing.GroupLayout uniprotLinkJPanelLayout = new javax.swing.GroupLayout(uniprotLinkJPanel);
uniprotLinkJPanel.setLayout(uniprotLinkJPanelLayout);
uniprotLinkJPanelLayout.setHorizontalGroup(
uniprotLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(uniprotLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(loadUniProtJButton, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(uniprotLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(webUniProtLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap())
);
uniprotLinkJPanelLayout.setVerticalGroup(
uniprotLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(uniprotLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(uniprotLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(loadUniProtJButton)
.addComponent(uniprotLabel)
.addComponent(webUniProtLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
dastyLinkJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("DASty - protein sequence features"));
dastyLinkJPanel.setOpaque(false);
dastyLabel.setText("Web client for visualizing protein sequence feature information.");
loadDastyJButton.setText("Search DASty");
loadDastyJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
loadDastyJButtonActionPerformed(evt);
}
});
webDastyLabel.setText("<html> <a href=\\\"dummy_link\">web</a></html>");
webDastyLabel.setToolTipText("Open the DASty web page");
webDastyLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
webDastyLabelMouseClicked(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
webDastyLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
webDastyLabelMouseExited(evt);
}
});
javax.swing.GroupLayout dastyLinkJPanelLayout = new javax.swing.GroupLayout(dastyLinkJPanel);
dastyLinkJPanel.setLayout(dastyLinkJPanelLayout);
dastyLinkJPanelLayout.setHorizontalGroup(
dastyLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(dastyLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(loadDastyJButton, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(dastyLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(webDastyLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap())
);
dastyLinkJPanelLayout.setVerticalGroup(
dastyLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(dastyLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(dastyLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(loadDastyJButton, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(dastyLabel)
.addComponent(webDastyLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap())
);
reactomeLinkJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Reactome - pathway database"));
reactomeLinkJPanel.setOpaque(false);
reactomeLabel.setText("Manually curated and peer-reviewed pathway database.");
loadReactomeJButton.setText("Search Reactome");
loadReactomeJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
loadReactomeJButtonActionPerformed(evt);
}
});
webReactomeLabel.setText("<html> <a href=\\\"dummy_link\">web</a></html>");
webReactomeLabel.setToolTipText("Open the Reactome web page");
webReactomeLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
webReactomeLabelMouseClicked(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
webReactomeLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
webReactomeLabelMouseExited(evt);
}
});
javax.swing.GroupLayout reactomeLinkJPanelLayout = new javax.swing.GroupLayout(reactomeLinkJPanel);
reactomeLinkJPanel.setLayout(reactomeLinkJPanelLayout);
reactomeLinkJPanelLayout.setHorizontalGroup(
reactomeLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(reactomeLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(loadReactomeJButton, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(reactomeLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(webReactomeLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap())
);
reactomeLinkJPanelLayout.setVerticalGroup(
reactomeLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(reactomeLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(reactomeLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(reactomeLabel)
.addComponent(loadReactomeJButton)
.addComponent(webReactomeLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
stringLinkJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("STRING - protein interaction"));
stringLinkJPanel.setOpaque(false);
stringLabel.setText("Known and Predicted Protein-Protein Interactions.");
loadStringJButton.setText("Search STRING");
loadStringJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
loadStringJButtonActionPerformed(evt);
}
});
webStringLabel.setText("<html> <a href=\\\"dummy_link\">web</a></html>");
webStringLabel.setToolTipText("Open the STRING web page");
webStringLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
webStringLabelMouseClicked(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
webStringLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
webStringLabelMouseExited(evt);
}
});
javax.swing.GroupLayout stringLinkJPanelLayout = new javax.swing.GroupLayout(stringLinkJPanel);
stringLinkJPanel.setLayout(stringLinkJPanelLayout);
stringLinkJPanelLayout.setHorizontalGroup(
stringLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(stringLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(loadStringJButton, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(stringLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 178, Short.MAX_VALUE)
.addComponent(webStringLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap())
);
stringLinkJPanelLayout.setVerticalGroup(
stringLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(stringLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(stringLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(stringLabel)
.addComponent(loadStringJButton)
.addComponent(webStringLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
davidLinkJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("DAVID - functional annotation"));
davidLinkJPanel.setOpaque(false);
davidLabel.setText("Database for Annotation, Visualization and Integrated Discovery.");
loadDavidJButton.setText("Search DAVID");
loadDavidJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
loadDavidJButtonActionPerformed(evt);
}
});
webDavidLabel.setText("<html> <a href=\\\"dummy_link\">web</a></html>");
webDavidLabel.setToolTipText("Open the DAVID web page");
webDavidLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
webDavidLabelMouseClicked(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
webDavidLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
webDavidLabelMouseExited(evt);
}
});
javax.swing.GroupLayout davidLinkJPanelLayout = new javax.swing.GroupLayout(davidLinkJPanel);
davidLinkJPanel.setLayout(davidLinkJPanelLayout);
davidLinkJPanelLayout.setHorizontalGroup(
davidLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(davidLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(loadDavidJButton, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(davidLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(webDavidLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap())
);
davidLinkJPanelLayout.setVerticalGroup(
davidLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(davidLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(davidLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(davidLabel)
.addComponent(loadDavidJButton)
.addComponent(webDavidLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
intActLinkJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("IntAct - protein interaction"));
intActLinkJPanel.setOpaque(false);
intactLabel.setText("Analysis tools for protein interaction data.");
loadIntActJButton.setText("Search IntAct");
loadIntActJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
loadIntActJButtonActionPerformed(evt);
}
});
webIntActLabel.setText("<html> <a href=\\\"dummy_link\">web</a></html>");
webIntActLabel.setToolTipText("Open the IntAct web page");
webIntActLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
webIntActLabelMouseClicked(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
webIntActLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
webIntActLabelMouseExited(evt);
}
});
javax.swing.GroupLayout intActLinkJPanelLayout = new javax.swing.GroupLayout(intActLinkJPanel);
intActLinkJPanel.setLayout(intActLinkJPanelLayout);
intActLinkJPanelLayout.setHorizontalGroup(
intActLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(intActLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(loadIntActJButton, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(intactLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(webIntActLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap())
);
intActLinkJPanelLayout.setVerticalGroup(
intActLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(intActLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(intActLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(intactLabel)
.addComponent(loadIntActJButton)
.addComponent(webIntActLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
quickGOLinkJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("QuickGO - gene ontology terms and annotations"));
quickGOLinkJPanel.setOpaque(false);
quickGoLabel.setText("Web-based browser for Gene Ontology terms.");
loadQuickGOJButton.setText("Search QuickGO");
loadQuickGOJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
loadQuickGOJButtonActionPerformed(evt);
}
});
webQuickGOLabel.setText("<html> <a href=\\\"dummy_link\">web</a></html>");
webQuickGOLabel.setToolTipText("Open the QuickGO web page");
webQuickGOLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
webQuickGOLabelMouseClicked(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
webQuickGOLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
webQuickGOLabelMouseExited(evt);
}
});
javax.swing.GroupLayout quickGOLinkJPanelLayout = new javax.swing.GroupLayout(quickGOLinkJPanel);
quickGOLinkJPanel.setLayout(quickGOLinkJPanelLayout);
quickGOLinkJPanelLayout.setHorizontalGroup(
quickGOLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(quickGOLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(loadQuickGOJButton, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(quickGoLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 196, Short.MAX_VALUE)
.addComponent(webQuickGOLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap())
);
quickGOLinkJPanelLayout.setVerticalGroup(
quickGOLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(quickGOLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(quickGOLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(quickGoLabel)
.addComponent(loadQuickGOJButton)
.addComponent(webQuickGOLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
interProLinkJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("InterPro - predictive protein signatures"));
interProLinkJPanel.setOpaque(false);
interProLabel.setText("Integrated database of predictive protein signatures.");
loadInterProJButton.setText("Search InterPro");
loadInterProJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
loadInterProJButtonActionPerformed(evt);
}
});
webInterProLabel.setText("<html> <a href=\\\"dummy_link\">web</a></html>");
webInterProLabel.setToolTipText("Open the InterPro web page");
webInterProLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
webInterProLabelMouseClicked(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
webInterProLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
webInterProLabelMouseExited(evt);
}
});
javax.swing.GroupLayout interProLinkJPanelLayout = new javax.swing.GroupLayout(interProLinkJPanel);
interProLinkJPanel.setLayout(interProLinkJPanelLayout);
interProLinkJPanelLayout.setHorizontalGroup(
interProLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(interProLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(loadInterProJButton, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(interProLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(webInterProLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap())
);
interProLinkJPanelLayout.setVerticalGroup(
interProLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(interProLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(interProLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(interProLabel)
.addComponent(loadInterProJButton)
.addComponent(webInterProLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
helpPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("Protein Annotation - Help"));
helpPanel.setOpaque(false);
helpScrollPane.setBorder(null);
helpScrollPane.setHorizontalScrollBarPolicy(javax.swing.ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
helpScrollPane.setVerticalScrollBarPolicy(javax.swing.ScrollPaneConstants.VERTICAL_SCROLLBAR_NEVER);
helpEditorPane.setEditable(false);
helpEditorPane.setContentType("text/html"); // NOI18N
helpEditorPane.setText("<html>\n<b>Single Protein</b><br>\nTo access the annotations for the currently selected protein, simply click the button corresponding to the \nwanted resource.\n<br><br>\n<b>Multiple Proteins</b><br>\nTo get the list of all validated proteins in your project click <a href=\"validated_proteins\">here</a>.<br>\nAdvanced export options: <i>Export</i> > <i>Identification Features</i>. \n<br><br>\nTo querry using multiple proteins, click the <a href=\"dummy_link\">web</a> link next to the resource and \nfollow the instructions provided at the resource web page.\n</html>");
helpEditorPane.addHyperlinkListener(new javax.swing.event.HyperlinkListener() {
public void hyperlinkUpdate(javax.swing.event.HyperlinkEvent evt) {
helpEditorPaneHyperlinkUpdate(evt);
}
});
helpScrollPane.setViewportView(helpEditorPane);
javax.swing.GroupLayout helpPanelLayout = new javax.swing.GroupLayout(helpPanel);
helpPanel.setLayout(helpPanelLayout);
helpPanelLayout.setHorizontalGroup(
helpPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(helpPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(helpScrollPane, javax.swing.GroupLayout.PREFERRED_SIZE, 481, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
helpPanelLayout.setVerticalGroup(
helpPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(helpPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(helpScrollPane)
.addContainerGap())
);
picrLinkJLabel.setText("<html><a href=\\\"dummy_link\\\">PICR - Protein Identifier Cross-Reference Service</a></html>");
picrLinkJLabel.setToolTipText("<html>\nMap protein identifiers across<br>\nmultiple source databases\n</html>");
picrLinkJLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
picrLinkJLabelMouseClicked(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
picrLinkJLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
picrLinkJLabelMouseExited(evt);
}
});
nextProtLinkJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("neXProt - human protein knowledgebase"));
nextProtLinkJPanel.setOpaque(false);
nextProtLabel.setText("High-quality human protein information and annotation.");
loadNextProtJButton.setText("Search neXtProt");
loadNextProtJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
loadNextProtJButtonActionPerformed(evt);
}
});
webNextProtLabel.setText("<html> <a href=\\\"dummy_link\">web</a></html>");
webNextProtLabel.setToolTipText("Open the neXtProt web page");
webNextProtLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
webNextProtLabelMouseClicked(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
webNextProtLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
webNextProtLabelMouseExited(evt);
}
});
javax.swing.GroupLayout nextProtLinkJPanelLayout = new javax.swing.GroupLayout(nextProtLinkJPanel);
nextProtLinkJPanel.setLayout(nextProtLinkJPanelLayout);
nextProtLinkJPanelLayout.setHorizontalGroup(
nextProtLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(nextProtLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(loadNextProtJButton, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(nextProtLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(webNextProtLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap())
);
nextProtLinkJPanelLayout.setVerticalGroup(
nextProtLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(nextProtLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(nextProtLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(loadNextProtJButton)
.addComponent(nextProtLabel)
.addComponent(webNextProtLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
pdbLinkJPanel.setBorder(javax.swing.BorderFactory.createTitledBorder("PDB - protein data bank"));
pdbLinkJPanel.setOpaque(false);
pdbLabel.setText("Biological macromolecular resource.");
loadPdbJButton.setText("Search PDB");
loadPdbJButton.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
loadPdbJButtonActionPerformed(evt);
}
});
webPdbLabel.setText("<html> <a href=\\\"dummy_link\">web</a></html>");
webPdbLabel.setToolTipText("Open the PDB web page");
webPdbLabel.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
webPdbLabelMouseClicked(evt);
}
public void mouseEntered(java.awt.event.MouseEvent evt) {
webPdbLabelMouseEntered(evt);
}
public void mouseExited(java.awt.event.MouseEvent evt) {
webPdbLabelMouseExited(evt);
}
});
javax.swing.GroupLayout pdbLinkJPanelLayout = new javax.swing.GroupLayout(pdbLinkJPanel);
pdbLinkJPanel.setLayout(pdbLinkJPanelLayout);
pdbLinkJPanelLayout.setHorizontalGroup(
pdbLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(pdbLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addComponent(loadPdbJButton, javax.swing.GroupLayout.PREFERRED_SIZE, 130, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(18, 18, 18)
.addComponent(pdbLabel)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 240, Short.MAX_VALUE)
.addComponent(webPdbLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap())
);
pdbLinkJPanelLayout.setVerticalGroup(
pdbLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(pdbLinkJPanelLayout.createSequentialGroup()
.addContainerGap()
.addGroup(pdbLinkJPanelLayout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(pdbLabel)
.addComponent(loadPdbJButton)
.addComponent(webPdbLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
this.setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addContainerGap()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addGap(10, 10, 10)
.addComponent(picrLinkJLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(0, 0, Short.MAX_VALUE))
.addGroup(layout.createSequentialGroup()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
.addComponent(nextProtLinkJPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(uniprotLinkJPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(basicAnnotationJPanel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(quickGOLinkJPanel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(stringLinkJPanel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(dastyLinkJPanel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
.addComponent(helpPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addGap(10, 10, 10))
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
.addComponent(pdbLinkJPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addContainerGap())
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
.addComponent(reactomeLinkJPanel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(davidLinkJPanel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(intActLinkJPanel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(interProLinkJPanel, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
.addContainerGap())))))
);
layout.setVerticalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addContainerGap()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING, false)
.addComponent(basicAnnotationJPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addComponent(helpPanel, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addComponent(reactomeLinkJPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(davidLinkJPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGroup(layout.createSequentialGroup()
.addComponent(uniprotLinkJPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(nextProtLinkJPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addComponent(stringLinkJPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(quickGOLinkJPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addGroup(layout.createSequentialGroup()
.addComponent(intActLinkJPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(interProLinkJPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
.addComponent(dastyLinkJPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(pdbLinkJPanel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.UNRELATED)
.addComponent(picrLinkJLabel, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap(142, Short.MAX_VALUE))
);
}// </editor-fold>//GEN-END:initComponents
/**
* Open the protein accession in DASty.
*
* @param evt
*/
private void loadDastyJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_loadDastyJButtonActionPerformed
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.ebi.ac.uk/dasty/client/index.html?q=" + accessionNumberJTextField.getText());
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_loadDastyJButtonActionPerformed
/**
* Open the protein accession in UniProt.
*
* @param evt
*/
private void loadUniProtJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_loadUniProtJButtonActionPerformed
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.uniprot.org/uniprot/" + accessionNumberJTextField.getText());
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_loadUniProtJButtonActionPerformed
/**
* Open the protein accession in Reactome.
*
* @param evt
*/
private void loadReactomeJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_loadReactomeJButtonActionPerformed
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=" + accessionNumberJTextField.getText());
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_loadReactomeJButtonActionPerformed
/**
* Open the protein accession in STRING.
*
* @param evt
*/
private void loadStringJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_loadStringJButtonActionPerformed
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://string-db.org/newstring_cgi/show_input_page.pl?identifier=" + accessionNumberJTextField.getText());
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_loadStringJButtonActionPerformed
/**
* Open the protein accession in DAVID.
*
* @param evt
*/
private void loadDavidJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_loadDavidJButtonActionPerformed
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://david.abcc.ncifcrf.gov/api.jsp?type=UNIPROT_ACCESSION&ids=" + accessionNumberJTextField.getText() + "&tool=summary");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_loadDavidJButtonActionPerformed
/**
* Open the protein accession in IntAct.
*
* @param evt
*/
private void loadIntActJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_loadIntActJButtonActionPerformed
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.ebi.ac.uk/intact/pages/interactions/interactions.xhtml?query=" + accessionNumberJTextField.getText());
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_loadIntActJButtonActionPerformed
/**
* Open the protein accession in QuickGO.
*
* @param evt
*/
private void loadQuickGOJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_loadQuickGOJButtonActionPerformed
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.ebi.ac.uk/QuickGO/GSearch?q=" + accessionNumberJTextField.getText() + "&what=Protein");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_loadQuickGOJButtonActionPerformed
/**
* Open the protein accession in InterPro.
*
* @param evt
*/
private void loadInterProJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_loadInterProJButtonActionPerformed
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.ebi.ac.uk/interpro/ISearch?query=" + accessionNumberJTextField.getText());
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_loadInterProJButtonActionPerformed
/**
* Open the DASty web page.
*
* @param evt
*/
private void webDastyLabelMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webDastyLabelMouseClicked
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.ebi.ac.uk/dasty");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webDastyLabelMouseClicked
/**
* Change the cursor icon to a hand icon.
*
* @param evt
*/
private void webDastyLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webDastyLabelMouseEntered
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_webDastyLabelMouseEntered
/**
* Change the cursor back to the default icon.
*
* @param evt
*/
private void webDastyLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webDastyLabelMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webDastyLabelMouseExited
/**
* Open the UniProt web page.
*
* @param evt
*/
private void webUniProtLabelMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webUniProtLabelMouseClicked
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.uniprot.org");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webUniProtLabelMouseClicked
/**
* Change the cursor icon to a hand icon.
*
* @param evt
*/
private void webUniProtLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webUniProtLabelMouseEntered
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_webUniProtLabelMouseEntered
/**
* Change the cursor back to the default icon.
*
* @param evt
*/
private void webUniProtLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webUniProtLabelMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webUniProtLabelMouseExited
/**
* Open the Reactome web page.
*
* @param evt
*/
private void webReactomeLabelMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webReactomeLabelMouseClicked
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.reactome.org");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webReactomeLabelMouseClicked
/**
* Change the cursor icon to a hand icon.
*
* @param evt
*/
private void webReactomeLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webReactomeLabelMouseEntered
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_webReactomeLabelMouseEntered
/**
* Change the cursor back to the default icon.
*
* @param evt
*/
private void webReactomeLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webReactomeLabelMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webReactomeLabelMouseExited
/**
* Open the STRING web page.
*
* @param evt
*/
private void webStringLabelMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webStringLabelMouseClicked
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://string-db.org");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webStringLabelMouseClicked
/**
* Change the cursor icon to a hand icon.
*
* @param evt
*/
private void webStringLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webStringLabelMouseEntered
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_webStringLabelMouseEntered
/**
* Change the cursor back to the default icon.
*
* @param evt
*/
private void webStringLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webStringLabelMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webStringLabelMouseExited
/**
* Open the QuickGO web page.
*
* @param evt
*/
private void webQuickGOLabelMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webQuickGOLabelMouseClicked
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.ebi.ac.uk/QuickGO");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webQuickGOLabelMouseClicked
/**
* Change the cursor icon to a hand icon.
*
* @param evt
*/
private void webQuickGOLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webQuickGOLabelMouseEntered
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_webQuickGOLabelMouseEntered
/**
* Change the cursor back to the default icon.
*
* @param evt
*/
private void webQuickGOLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webQuickGOLabelMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webQuickGOLabelMouseExited
/**
* Open the InterPro web page.
*
* @param evt
*/
private void webInterProLabelMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webInterProLabelMouseClicked
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.ebi.ac.uk/interpro");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webInterProLabelMouseClicked
/**
* Change the cursor icon to a hand icon.
*
* @param evt
*/
private void webInterProLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webInterProLabelMouseEntered
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_webInterProLabelMouseEntered
/**
* Change the cursor back to the default icon.
*
* @param evt
*/
private void webInterProLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webInterProLabelMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webInterProLabelMouseExited
/**
* Open the IntAct web page.
*
* @param evt
*/
private void webIntActLabelMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webIntActLabelMouseClicked
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.ebi.ac.uk/intact");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webIntActLabelMouseClicked
/**
* Change the cursor icon to a hand icon.
*
* @param evt
*/
private void webIntActLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webIntActLabelMouseEntered
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_webIntActLabelMouseEntered
/**
* Change the cursor back to the default icon.
*
* @param evt
*/
private void webIntActLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webIntActLabelMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webIntActLabelMouseExited
/**
* Enable the hyperlinks in the help panel.
*
* @param evt
*/
private void helpEditorPaneHyperlinkUpdate(javax.swing.event.HyperlinkEvent evt) {//GEN-FIRST:event_helpEditorPaneHyperlinkUpdate
if (evt.getEventType().toString().equalsIgnoreCase(
javax.swing.event.HyperlinkEvent.EventType.ACTIVATED.toString())) {
if (evt.getDescription().equalsIgnoreCase("validated_proteins")) {
if (peptideShakerGUI.getIdentification() != null) {
OutputGenerator outputGenerator = new OutputGenerator(peptideShakerGUI);
try {
outputGenerator.getProteinsOutput(
null, null, false, true, true, false, false, false,
false, false, false, false, false, false,
false, false, false, false, false, false,
false, false, false, false, false);
} catch (Exception e) {
JOptionPane.showMessageDialog(this, "An error occurred while generating the output.", "Output Error.", JOptionPane.ERROR_MESSAGE);
e.printStackTrace();
}
} else {
JOptionPane.showMessageDialog(peptideShakerGUI, "You have to load a project first!", "No Project", JOptionPane.WARNING_MESSAGE);
}
}
}
}//GEN-LAST:event_helpEditorPaneHyperlinkUpdate
/**
* Change the cursor back to the default icon.
*
* @param evt
*/
private void webDavidLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webDavidLabelMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webDavidLabelMouseExited
/**
* Change the cursor back to a hand icon.
*
* @param evt
*/
private void webDavidLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webDavidLabelMouseEntered
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_webDavidLabelMouseEntered
/**
* Open the DAVID web page.
*
* @param evt
*/
private void webDavidLabelMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webDavidLabelMouseClicked
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://david.abcc.ncifcrf.gov");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webDavidLabelMouseClicked
/**
* Change the cursor back to a hand icon.
*
* @param evt
*/
private void picrLinkJLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_picrLinkJLabelMouseEntered
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_picrLinkJLabelMouseEntered
/**
* Change the cursor back to the default icon.
*
* @param evt
*/
private void picrLinkJLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_picrLinkJLabelMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_picrLinkJLabelMouseExited
/**
* Open the PICR web page.
*
* @param evt
*/
private void picrLinkJLabelMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_picrLinkJLabelMouseClicked
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.ebi.ac.uk/Tools/picr/");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_picrLinkJLabelMouseClicked
/**
* Open the protein accession in neXtProt.
*
* @param evt
*/
private void loadNextProtJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_loadNextProtJButtonActionPerformed
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.nextprot.org/db/entry/NX_" + accessionNumberJTextField.getText());
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_loadNextProtJButtonActionPerformed
/**
* Open the neXtProt web page.
*
* @param evt
*/
private void webNextProtLabelMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webNextProtLabelMouseClicked
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.nextprot.org/db/");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webNextProtLabelMouseClicked
/**
* Change the cursor back to a hand icon.
*
* @param evt
*/
private void webNextProtLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webNextProtLabelMouseEntered
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_webNextProtLabelMouseEntered
/**
* Change the cursor back to the default icon.
*
* @param evt
*/
private void webNextProtLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webNextProtLabelMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webNextProtLabelMouseExited
/**
* Open the protein accession in PDB.
*
* @param evt
*/
private void loadPdbJButtonActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_loadPdbJButtonActionPerformed
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.rcsb.org/pdb/protein/" + accessionNumberJTextField.getText());
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_loadPdbJButtonActionPerformed
/**
* Open the PDB web page.
*
* @param evt
*/
private void webPdbLabelMouseClicked(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webPdbLabelMouseClicked
this.setCursor(new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR));
BareBonesBrowserLaunch.openURL("http://www.rcsb.org/pdb/");
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webPdbLabelMouseClicked
/**
* Change the cursor back to a hand icon.
*
* @param evt
*/
private void webPdbLabelMouseEntered(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webPdbLabelMouseEntered
this.setCursor(new java.awt.Cursor(java.awt.Cursor.HAND_CURSOR));
}//GEN-LAST:event_webPdbLabelMouseEntered
/**
* Change the cursor back to the default icon.
*
* @param evt
*/
private void webPdbLabelMouseExited(java.awt.event.MouseEvent evt) {//GEN-FIRST:event_webPdbLabelMouseExited
this.setCursor(new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR));
}//GEN-LAST:event_webPdbLabelMouseExited
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JTextField accessionNumberJTextField;
private javax.swing.JLabel accessionNumberLabel;
private javax.swing.JPanel basicAnnotationJPanel;
private javax.swing.JTextField chromosomeJTextField;
private javax.swing.JLabel chromosomeLabel;
private javax.swing.JLabel dastyLabel;
private javax.swing.JPanel dastyLinkJPanel;
private javax.swing.JTextField databaseJTextField;
private javax.swing.JLabel databaseLabel;
private javax.swing.JLabel davidLabel;
private javax.swing.JPanel davidLinkJPanel;
private javax.swing.JLabel descriptionLabel;
private javax.swing.JTextField geneNameJTextField;
private javax.swing.JLabel geneNameLabel;
private javax.swing.JEditorPane helpEditorPane;
private javax.swing.JPanel helpPanel;
private javax.swing.JScrollPane helpScrollPane;
private javax.swing.JPanel intActLinkJPanel;
private javax.swing.JLabel intactLabel;
private javax.swing.JLabel interProLabel;
private javax.swing.JPanel interProLinkJPanel;
private javax.swing.JButton loadDastyJButton;
private javax.swing.JButton loadDavidJButton;
private javax.swing.JButton loadIntActJButton;
private javax.swing.JButton loadInterProJButton;
private javax.swing.JButton loadNextProtJButton;
private javax.swing.JButton loadPdbJButton;
private javax.swing.JButton loadQuickGOJButton;
private javax.swing.JButton loadReactomeJButton;
private javax.swing.JButton loadStringJButton;
private javax.swing.JButton loadUniProtJButton;
private javax.swing.JLabel nextProtLabel;
private javax.swing.JPanel nextProtLinkJPanel;
private javax.swing.JLabel pdbLabel;
private javax.swing.JPanel pdbLinkJPanel;
private javax.swing.JLabel picrLinkJLabel;
private javax.swing.JScrollPane proteinDescriptionScrollPane;
private javax.swing.JTextArea proteinDescriptionTextArea;
private javax.swing.JPanel quickGOLinkJPanel;
private javax.swing.JLabel quickGoLabel;
private javax.swing.JLabel reactomeLabel;
private javax.swing.JPanel reactomeLinkJPanel;
private javax.swing.JLabel stringLabel;
private javax.swing.JPanel stringLinkJPanel;
private javax.swing.JTextField taxonomyJTextField;
private javax.swing.JLabel texonomyLabel;
private javax.swing.JLabel uniprotLabel;
private javax.swing.JPanel uniprotLinkJPanel;
private javax.swing.JLabel webDastyLabel;
private javax.swing.JLabel webDavidLabel;
private javax.swing.JLabel webIntActLabel;
private javax.swing.JLabel webInterProLabel;
private javax.swing.JLabel webNextProtLabel;
private javax.swing.JLabel webPdbLabel;
private javax.swing.JLabel webQuickGOLabel;
private javax.swing.JLabel webReactomeLabel;
private javax.swing.JLabel webStringLabel;
private javax.swing.JLabel webUniProtLabel;
// End of variables declaration//GEN-END:variables
/**
* Updates the basic protein annotation information.
*
* @param aAccessionNumber the new accession number
*/
public void updateBasicProteinAnnotation(String aAccessionNumber) {
// only update if new accession number
if (aAccessionNumber != null
&& !aAccessionNumber.equals(PeptideShakerGUI.NO_SELECTION)
&& !currentAccessionNumber.equalsIgnoreCase(aAccessionNumber)) {
currentAccessionNumber = aAccessionNumber;
accessionNumberJTextField.setText(currentAccessionNumber);
try {
proteinDescriptionTextArea.setText(sequenceFactory.getHeader(aAccessionNumber).getSimpleProteinDescription());
String geneName = sequenceFactory.getHeader(aAccessionNumber).getGeneName();
geneNameJTextField.setText(geneName);
if (geneName != null) {
chromosomeJTextField.setText(geneFactory.getChromosomeForGeneName(geneName));
} else {
chromosomeJTextField.setText(null);
}
taxonomyJTextField.setText(sequenceFactory.getHeader(aAccessionNumber).getTaxonomy());
databaseJTextField.setText("" + sequenceFactory.getProtein(aAccessionNumber).getDatabaseType());
} catch (IOException e) {
JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while loading the protein information.", "File Error", JOptionPane.ERROR_MESSAGE);
e.printStackTrace();
} catch (InterruptedException e) {
JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while loading the protein information.", "File Error", JOptionPane.ERROR_MESSAGE);
e.printStackTrace();
} catch (ClassNotFoundException e) {
JOptionPane.showMessageDialog(peptideShakerGUI, "An error occurred while loading the protein information.", "File Error", JOptionPane.ERROR_MESSAGE);
e.printStackTrace();
} catch (IllegalArgumentException e) {
JOptionPane.showMessageDialog(peptideShakerGUI, JOptionEditorPane.getJOptionEditorPane(
e.getLocalizedMessage() + "<br>"
+ "Please see the <a href=\"http://code.google.com/p/peptide-shaker/#Troubleshooting\">troubleshooting section</a>."),
"File Error", JOptionPane.ERROR_MESSAGE);
e.printStackTrace();
}
}
}
}