private static String getGeneName(Feature feature) {
try {
return ((GFFStreamFeature) feature.getEmblFeature()).getChadoGene().getGeneUniqueName();
} catch (Exception e) {
}
return null;
}
public boolean testPredicate(Feature targetFeature) {
String targetKey = targetFeature.getKey().getKeyString();
if (sameKey && !targetKey.equals(key)) return false;
Vector<String> chadoNames = null;
if (isDatabaseEntry) {
GFFStreamFeature gffFeature = ((GFFStreamFeature) targetFeature.getEmblFeature());
if (gffFeature.getChadoGene() != null) {
chadoNames = new Vector<String>();
ChadoCanonicalGene chadoGene = gffFeature.getChadoGene();
chadoNames.add(chadoGene.getGeneUniqueName());
List<uk.ac.sanger.artemis.io.Feature> transcripts = chadoGene.getTranscripts();
for (int i = 0; i < transcripts.size(); i++) {
GFFStreamFeature feature = (GFFStreamFeature) transcripts.get(i);
chadoNames.add(GeneUtils.getUniqueName(feature));
}
}
}
String thisFeatureSystematicName = targetFeature.getSystematicName();
for (int i = 0; i < geneNames.length; i++) {
if (geneNames[i].equals(thisFeatureSystematicName)
|| (chadoNames != null && chadoNames.contains(geneNames[i]))) {
geneName = geneNames[i];
return true;
}
}
return false;
}
/**
* Construct the panel for setting up the gene list and the list of qualifiers to transfer.
*
* @param feature
* @param pane
* @param qualifierCheckBoxes
* @param geneNameCheckBoxes
* @param geneNames
*/
private void addMainPanel(
final Feature feature,
final JPanel pane,
final Vector<QualifierPanel> qualifierPanels,
final Vector<JCheckBox> geneNameCheckBoxes,
final List<String> geneNames) {
GridBagConstraints c = new GridBagConstraints();
int nrows = 0;
c.anchor = GridBagConstraints.NORTHWEST;
c.gridx = 2;
c.gridy = 0;
c.ipadx = 50;
JLabel geneLabel = new JLabel("Qualifier(s)");
geneLabel.setFont(geneLabel.getFont().deriveFont(Font.BOLD));
pane.add(geneLabel, c);
c.gridy = 0;
c.gridx = 0;
JLabel label = new JLabel("Gene List");
label.setFont(label.getFont().deriveFont(Font.BOLD));
pane.add(label, c);
nrows += 3;
c.gridx = 2;
c.gridy = nrows;
c.anchor = GridBagConstraints.WEST;
addQualifierPanel(feature, qualifierPanels, c, nrows, pane);
nrows += 2;
if (feature.getEmblFeature() instanceof GFFStreamFeature) {
GFFStreamFeature gffFeature = ((GFFStreamFeature) feature.getEmblFeature());
if (gffFeature.getChadoGene() != null) {
String id = GeneUtils.getUniqueName(gffFeature);
ChadoCanonicalGene chadoGene = gffFeature.getChadoGene();
Feature gene = (Feature) chadoGene.getGene().getUserData();
if (!id.equals(GeneUtils.getUniqueName(((GFFStreamFeature) chadoGene.getGene()))))
addQualifierPanel(gene, qualifierPanels, c, nrows, pane);
nrows += 2;
String transcriptName =
chadoGene.getTranscriptFromName(GeneUtils.getUniqueName(gffFeature));
if (transcriptName != null) {
GFFStreamFeature transcript =
(GFFStreamFeature) chadoGene.getFeatureFromId(transcriptName);
addQualifierPanel((Feature) transcript.getUserData(), qualifierPanels, c, nrows, pane);
nrows += 2;
Set<uk.ac.sanger.artemis.io.Feature> children = chadoGene.getChildren(transcript);
Iterator<uk.ac.sanger.artemis.io.Feature> it = children.iterator();
while (it.hasNext()) {
GFFStreamFeature kid = (GFFStreamFeature) it.next();
if (id.equals(GeneUtils.getUniqueName(((GFFStreamFeature) kid)))) continue;
addQualifierPanel((Feature) kid.getUserData(), qualifierPanels, c, nrows, pane);
nrows += 2;
}
}
}
}
c.gridx = 0;
c.gridy = 3;
c.gridheight = nrows;
c.fill = GridBagConstraints.BOTH;
final Box geneNameBox = Box.createVerticalBox();
pane.add(geneNameBox, c);
if (geneNames != null) {
for (int i = 0; i < geneNames.size(); i++) {
JCheckBox cb = new JCheckBox((String) geneNames.get(i), true);
geneNameBox.add(cb);
geneNameCheckBoxes.add(cb);
}
}
c.gridy = 1;
c.gridheight = 1;
c.fill = GridBagConstraints.NONE;
c.gridx = 2;
final JButton toggle = new JButton("Toggle");
toggle.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
for (int i = 0; i < qualifierPanels.size(); i++) {
QualifierPanel qP = qualifierPanels.get(i);
Enumeration<JCheckBox> enumQualifiers = qP.getQualifierCheckBoxes().keys();
while (enumQualifiers.hasMoreElements()) {
JCheckBox cb = enumQualifiers.nextElement();
cb.setSelected(!cb.isSelected());
}
}
}
});
pane.add(toggle, c);
Box xBox = Box.createHorizontalBox();
final JButton toggleGeneList = new JButton("Toggle");
toggleGeneList.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
for (int i = 0; i < geneNameCheckBoxes.size(); i++) {
JCheckBox cb = geneNameCheckBoxes.get(i);
cb.setSelected(!cb.isSelected());
}
geneNameBox.repaint();
}
});
xBox.add(toggleGeneList);
final JButton addGenes = new JButton("Add");
addGenes.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
JTextArea geneNameTextArea = new JTextArea();
geneNameTextArea.setEditable(true);
JScrollPane jsp = new JScrollPane(geneNameTextArea);
int res =
JOptionPane.showConfirmDialog(
TransferAnnotationTool.this,
jsp,
"Paste Feature Names to Add",
JOptionPane.OK_CANCEL_OPTION);
if (res == JOptionPane.CANCEL_OPTION) return;
String geneNames[] = geneNameTextArea.getText().split("\\s");
for (int i = 0; i < geneNames.length; i++) {
if (geneNames[i] == null || geneNames[i].equals("")) continue;
JCheckBox cb = new JCheckBox(geneNames[i], true);
geneNameBox.add(cb);
geneNameCheckBoxes.add(cb);
}
pane.revalidate();
}
});
xBox.add(addGenes);
c.gridx = 0;
pane.add(xBox, c);
final List<String> clusterList = (matchPanel == null ? null : matchPanel.getGeneNameList(true));
if (clusterList != null && !geneNames.contains(clusterList.get(0))) {
final JButton importCluster = new JButton("Import Cluster Names");
importCluster.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
for (String n : clusterList) {
if (n == null || n.equals("")) continue;
JCheckBox cb = new JCheckBox(n, true);
geneNameBox.add(cb);
geneNameCheckBoxes.add(cb);
}
importCluster.setEnabled(false);
pane.revalidate();
}
});
c.gridy = 2;
pane.add(importCluster, c);
}
}