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;
}
/**
* Add a panel to display a given features qualifiers.
*
* @param f
* @param qualifierPanels
* @param c
* @param nrows
* @param pane
*/
private void addQualifierPanel(
Feature f,
Vector<QualifierPanel> qualifierPanels,
GridBagConstraints c,
int nrows,
JPanel pane) {
QualifierPanel qPanel = new QualifierPanel(f, f.getKey().getKeyString());
if (qPanel.nrows == 0) return;
c.fill = GridBagConstraints.HORIZONTAL;
c.anchor = GridBagConstraints.WEST;
c.weightx = 100;
qualifierPanels.add(qPanel);
c.gridy = ++nrows;
JLabel l = new JLabel(f.getIDString());
l.setFont(l.getFont().deriveFont(Font.BOLD));
l.setForeground(STEEL_BLUE);
pane.add(l, c);
c.gridy = ++nrows;
pane.add(qPanel, c);
c.weightx = 0.d;
}
/**
* Transfer selected qualifiers to the list of features defined by the selected names.
*
* @param qualifierCheckBoxes - list of qualifier check boxes
* @param geneNameTextArea - text with a list of feature names to transfer to
* @param feature - feature to copy from
* @param entryGroup
* @param sameKey
* @param overwrite
*/
protected static int transferAnnotation(
final Hashtable<JCheckBox, Vector<JCheckBox>> qualifierCheckBoxes,
final Vector<JCheckBox> geneNameCheckBoxes,
final Feature orginatingFeature,
final EntryGroup entryGroup,
final boolean sameKey,
final boolean overwrite,
final boolean setEvidenceAndWithFrom,
final StringBuffer buff,
final StringBuffer genesUpdated) {
// transfer selected annotation to genes
final QualifierVector qualifiers = orginatingFeature.getQualifiers();
final QualifierVector qualifiersToTransfer = new QualifierVector();
Enumeration<JCheckBox> enumQualifiers = qualifierCheckBoxes.keys();
while (enumQualifiers.hasMoreElements()) {
JCheckBox cb = enumQualifiers.nextElement();
if (cb.isSelected()) {
Vector<JCheckBox> qualifierValuesCheckBox = qualifierCheckBoxes.get(cb);
final StringVector values = qualifiers.getQualifierByName(cb.getText()).getValues();
StringVector valuesToTransfer = new StringVector(values);
logger4j.debug("TRANSFER " + cb.getText());
for (int i = 0; i < qualifierValuesCheckBox.size(); i++) {
JCheckBox valuesCb = qualifierValuesCheckBox.get(i);
if (!valuesCb.isSelected()) {
valuesToTransfer.remove(valuesCb.getText());
logger4j.debug("NOT TRANSFERING " + valuesCb.getText());
}
}
if (valuesToTransfer.size() < 1) continue;
valuesToTransfer =
new StringVector(
getTransferValues(
setEvidenceAndWithFrom, orginatingFeature, cb.getText(), valuesToTransfer));
qualifiersToTransfer.addElement(new Qualifier(cb.getText(), valuesToTransfer));
}
}
int count = 0;
for (int i = 0; i < geneNameCheckBoxes.size(); i++) {
if (geneNameCheckBoxes.get(i).isSelected()) count++;
}
if (count < 1) {
JOptionPane.showMessageDialog(
null, "No genes selected.", "Warning", JOptionPane.WARNING_MESSAGE);
return -1;
}
String geneNames[] = new String[count];
count = 0;
for (int i = 0; i < geneNameCheckBoxes.size(); i++) {
JCheckBox cb = geneNameCheckBoxes.get(i);
if (cb.isSelected()) {
geneNames[count] = cb.getText();
logger4j.debug("TRANSFER ANNOTATION TO " + geneNames[count]);
count++;
}
}
final String key = orginatingFeature.getKey().getKeyString();
final FeatureVector features = entryGroup.getAllFeatures();
// transfer selected annotation
entryGroup.getActionController().startAction();
geneNames =
transfer(
features,
qualifiersToTransfer,
key,
sameKey,
overwrite,
GeneUtils.isDatabaseEntry(entryGroup),
geneNames,
genesUpdated);
entryGroup.getActionController().endAction();
//
// Commit changes to genes not in Artemis but in the database
//
Vector<String> genesNotFound = null;
if (geneNames != null
&& orginatingFeature.getEntry().getEMBLEntry() instanceof DatabaseDocumentEntry) {
DatabaseDocumentEntry db_entry =
(DatabaseDocumentEntry) orginatingFeature.getEntry().getEMBLEntry();
DatabaseDocument doc = (DatabaseDocument) db_entry.getDocument();
for (int i = 0; i < geneNames.length; i++) {
DatabaseDocumentEntry newDbEntry = GeneEdit.makeGeneEntry(null, geneNames[i], doc, null);
if (newDbEntry == null) {
if (genesNotFound == null) genesNotFound = new Vector<String>();
genesNotFound.add(geneNames[i]);
continue;
}
char[] c = new char[1];
PartialSequence ps = new PartialSequence(c, 100, 0, null, null);
newDbEntry.setPartialSequence(ps);
Entry entry = null;
try {
entry = new Entry(newDbEntry);
} catch (Exception e) {
e.printStackTrace();
}
SimpleEntryGroup entry_group = new SimpleEntryGroup();
entry_group.addElement(entry);
ChadoTransactionManager ctm = new ChadoTransactionManager();
entry_group.addFeatureChangeListener(ctm);
entry_group.addEntryChangeListener(ctm);
ctm.setEntryGroup(entry_group);
transfer(
entry.getAllFeatures(),
qualifiersToTransfer,
key,
sameKey,
overwrite,
true,
geneNames,
genesUpdated);
for (int j = 0; j < ctm.getTransactionCount(); j++)
buff.append(ctm.getTransactionAt(j).getLogComment() + "\n");
ChadoTransactionManager.commit((DatabaseDocument) newDbEntry.getDocument(), false, ctm);
entry_group.removeFeatureChangeListener(ctm);
entry_group.removeEntryChangeListener(ctm);
// if(newDbEntry != null)
// GeneEdit.showGeneEditor(null, geneNames[i], newDbEntry);
}
}
if (genesNotFound != null)
JOptionPane.showMessageDialog(
null,
"Gene(s) Not Found:\n" + genesNotFound.toString(),
"Gene(s) Not Found",
JOptionPane.WARNING_MESSAGE);
return 0;
}