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;
}
private static String getGeneName(Feature feature) {
try {
return ((GFFStreamFeature) feature.getEmblFeature()).getChadoGene().getGeneUniqueName();
} catch (Exception e) {
}
return null;
}
/**
* Tool for transferring annotation from one feature to other feature(s)
*
* @param feature
* @param entryGroup
* @param geneNames
*/
public TransferAnnotationTool(
final Feature feature, final EntryGroup entryGroup, final MatchPanel matchPanel) {
super("Transfer Annotation Tool :: " + feature.getIDString());
this.matchPanel = matchPanel;
List<String> geneNames = null;
if (matchPanel != null) geneNames = matchPanel.getGeneNameList();
JPanel panel = new JPanel(new FlowLayout(FlowLayout.LEFT));
JPanel pane = new JPanel(new GridBagLayout());
JScrollPane jsp = new JScrollPane(panel);
panel.setBackground(Color.white);
pane.setBackground(Color.white);
panel.add(pane);
JPanel framePanel = (JPanel) getContentPane();
framePanel.add(jsp, BorderLayout.CENTER);
framePanel.setPreferredSize(new Dimension(600, 600));
final Vector<JCheckBox> geneNameCheckBoxes = new Vector<JCheckBox>();
final Vector<QualifierPanel> qualifierPanels = new Vector<QualifierPanel>();
addMainPanel(feature, pane, qualifierPanels, geneNameCheckBoxes, geneNames);
addBottomButtons(
qualifierPanels, geneNameCheckBoxes,
framePanel, entryGroup);
pack();
setVisible(true);
}
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");
}
/**
* 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;
}
/**
* @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;
}
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));
}
/**
* Change the stop_codon_redefined_as_selenocysteine SO qualifier to the transl_except EMBL
* qualifier.
*
* @param qualifiers
* @param feature
*/
private void handleSelenocysteine(QualifierVector qualifiers, Feature feature) {
if (!feature.getKey().getKeyString().equals(DatabaseDocument.EXONMODEL)) return;
qualifiers.removeQualifierByName("stop_codon_redefined_as_selenocysteine");
uk.ac.sanger.artemis.Feature f = ((uk.ac.sanger.artemis.Feature) feature.getUserData());
int translatedBasePosion = 0;
String aa = f.getTranslation().toString();
for (int i = 0; i < aa.length(); i++) {
if (AminoAcidSequence.isStopCodon(aa.charAt(i))) {
translatedBasePosion = i * 3;
break;
}
}
FeatureSegmentVector segments = f.getSegments();
int nbases = 0;
int sequenceloc = 0;
for (int i = 0; i < segments.size(); i++) {
int seglen = segments.elementAt(i).getBases().length();
if (nbases + seglen > translatedBasePosion) {
Bases bases = f.getStrand().getBases();
sequenceloc =
segments.elementAt(i).getStart().getPosition() + (translatedBasePosion - nbases);
if (!f.isForwardFeature()) sequenceloc = bases.getComplementPosition(sequenceloc);
}
nbases += seglen;
}
String pos = "";
if (f.isForwardFeature()) pos = sequenceloc + ".." + (sequenceloc + 2);
else pos = "complement(" + (sequenceloc - 2) + ".." + sequenceloc + ")";
qualifiers.add(new Qualifier("transl_except", "(pos:" + pos + ",aa:Sec)"));
}
/**
* 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;
}
/**
* 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);
}
}
