/**
* @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");
}
public QualifierPanel(Feature feature, String title) {
super(new GridBagLayout());
this.feature = feature;
TitledBorder titleBorder =
BorderFactory.createTitledBorder(
BorderFactory.createEtchedBorder(EtchedBorder.LOWERED), title);
titleBorder.setTitleJustification(TitledBorder.LEFT);
titleBorder.setTitleColor(TransferAnnotationTool.STEEL_BLUE);
setBorder(titleBorder);
GridBagConstraints c = new GridBagConstraints();
c.anchor = GridBagConstraints.WEST;
c.ipadx = 0;
final QualifierVector qualifiers = feature.getQualifiers();
for (int i = 0; i < qualifiers.size(); i++) {
nrows = addQualifierComponents(qualifiers.get(i), qualifierCheckBoxes, c, nrows);
}
setMinimumSize(new Dimension(titleBorder.getMinimumSize(this).width, getMinimumSize().height));
}
/**
* Get the latest (edited) literature/dbxref qualifiers
*
* @return
*/
public QualifierVector getQualifiers() {
QualifierVector referenceQualifier = null;
String literatureTxt = literatureTextArea.getText().trim();
if (!literatureTxt.equals("")) {
referenceQualifier = new QualifierVector();
String[] lits = getValues(literatureTxt);
StringVector litValues = new StringVector(lits);
Qualifier literature = new Qualifier("literature", litValues);
referenceQualifier.setQualifier(literature);
}
String dbxrefTxt = dbxrefTextArea.getText().trim();
if (!dbxrefTxt.equals("")) {
if (referenceQualifier == null) referenceQualifier = new QualifierVector();
String[] dbxrefs = getValues(dbxrefTxt);
StringVector dbxrefsValues = new StringVector(dbxrefs);
Qualifier dbxrefsQualifier = new Qualifier("Dbxref", dbxrefsValues);
referenceQualifier.setQualifier(dbxrefsQualifier);
}
return referenceQualifier;
}
/**
* 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;
}