/**
* @param features
* @param qualifiersToTransfer
* @param key
* @param sameKey
* @param isDatabaseEntry
* @param geneNames
* @return
*/
private static String[] transfer(
final FeatureVector features,
final QualifierVector qualifiersToTransfer,
final String key,
final boolean sameKey,
final boolean overwrite,
final boolean isDatabaseEntry,
String[] geneNames,
final StringBuffer genesUpdated) {
final TransferFeaturePredicate predicate =
new TransferFeaturePredicate(key, sameKey, isDatabaseEntry, geneNames);
for (int i = 0; i < features.size(); i++) {
Feature thisFeature = features.elementAt(i);
if (predicate.testPredicate(thisFeature)) {
StringBuffer qualifierBuffer = new StringBuffer();
for (int j = 0; j < qualifiersToTransfer.size(); j++) {
Qualifier newQualifier = qualifiersToTransfer.elementAt(j);
String qualifierName = newQualifier.getName();
try {
if (overwrite) {
thisFeature.setQualifier(newQualifier);
qualifierBuffer.append(
" "
+ qualifierName
+ " (overwritten)\n"
+ parseStringVector(newQualifier.getValues()));
} else {
final StringVector oldValues;
if (thisFeature.getQualifierByName(newQualifier.getName()) == null) oldValues = null;
else oldValues = thisFeature.getQualifierByName(newQualifier.getName()).getValues();
final Qualifier newQualifierTmp =
getQualifierWithoutDuplicateValues(newQualifier, oldValues);
if (newQualifierTmp == null) continue;
thisFeature.addQualifierValues(newQualifierTmp);
qualifierBuffer.append(
" "
+ qualifierName
+ " (added)\n"
+ parseStringVector(newQualifier.getValues()));
}
} catch (Exception e1) {
e1.printStackTrace();
}
}
geneNames = removeArrayElement(geneNames, predicate.getGeneName());
if (qualifierBuffer.length() > 0)
genesUpdated.append(
thisFeature.getSystematicName() + " (" + key + ")\n" + qualifierBuffer);
}
}
return geneNames;
}
private void updateFromFeature(Feature feature) {
GridBagConstraints c = new GridBagConstraints();
JPanel gridPanel = new JPanel(new GridBagLayout());
gridPanel.setBackground(Color.white);
//
// literature & dbxref
literatureTextArea = new QualifierTextArea();
literatureTextArea.setBorder(BorderFactory.createLineBorder(Color.gray));
dbxrefTextArea = new QualifierTextArea();
dbxrefTextArea.setBorder(BorderFactory.createLineBorder(Color.gray));
literatureTextArea
.getDocument()
.addDocumentListener(new TextAreaDocumentListener(literatureTextArea));
dbxrefTextArea.getDocument().addDocumentListener(new TextAreaDocumentListener(dbxrefTextArea));
final QualifierVector qualifiers = feature.getQualifiers().copy();
final StringBuffer litBuffer = new StringBuffer();
final StringBuffer dbxrefBuffer = new StringBuffer();
for (int i = 0; i < qualifiers.size(); ++i) {
Qualifier this_qualifier = (Qualifier) qualifiers.elementAt(i);
if (this_qualifier.getName().equals("literature"))
appendToBuffer(this_qualifier.getValues(), litBuffer);
else if (this_qualifier.getName().equalsIgnoreCase("Dbxref"))
appendToBuffer(this_qualifier.getValues(), dbxrefBuffer);
}
c.gridx = 0;
c.gridy = 0;
c.ipadx = 5;
c.ipady = 5;
c.anchor = GridBagConstraints.NORTHWEST;
c.fill = GridBagConstraints.NONE;
gridPanel.add(new JLabel("Literature"), c);
c.gridx = 1;
gridPanel.add(literatureTextArea, c);
c.gridx = 0;
c.gridy = 1;
gridPanel.add(new JLabel("Dbxref"), c);
c.gridx = 1;
gridPanel.add(dbxrefTextArea, c);
add(gridPanel);
literatureTextArea.setText(litBuffer.toString() + "\n");
dbxrefTextArea.setText(dbxrefBuffer.toString() + "\n");
}