/** * @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; }