/** * 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; }