/** * Change the name of a qualifier * * @param qualifiers * @param oldName * @param newName */ private void changeQualifierName( QualifierVector qualifiers, final String oldName, final String newName) { QualifierVector tmpQualifiers = new QualifierVector(); for (int i = 0; i < qualifiers.size(); i++) { Qualifier qualifier = (Qualifier) qualifiers.elementAt(i); if (!qualifier.getName().equals(oldName)) { tmpQualifiers.addElement(qualifier); continue; } Qualifier newQualifier = new Qualifier(newName, qualifier.getValues()); tmpQualifiers.addQualifierValues(newQualifier); } qualifiers.removeAllElements(); for (int i = 0; i < tmpQualifiers.size(); i++) qualifiers.addElement(tmpQualifiers.elementAt(i)); }
/** * Merge qualifiers * * @param qualifiers * @param newQualifiers */ private void combineQualifiers( final QualifierVector qualifiers, final QualifierVector newQualifiers, final boolean isGene) { for (int i = 0; i < newQualifiers.size(); i++) { Qualifier newQualifier = (Qualifier) newQualifiers.get(i); if (newQualifier.getName().equals("ID") && !isGene) { continue; } // convert GO evidence to codes (e.g. ND=No biological Data available) if (newQualifier.getName().equals("GO")) { final StringVector newValues = newQualifier.getValues(); final StringVector tmpNewValues = new StringVector(); for (int j = 0; j < newValues.size(); j++) { String val = GoBox.getEvidenceCodeGoTextFromText((String) newValues.get(j)); tmpNewValues.add(val); } newQualifier = new Qualifier("GO", tmpNewValues); } if (newQualifier.getName().equals("product")) { final StringVector newValues = newQualifier.getValues(); final StringVector tmpNewValues = new StringVector(); for (int j = 0; j < newValues.size(); j++) { String val = (String) newValues.get(j); int ind = 0; if ((ind = val.indexOf(";db_xref=")) > -1) val = val.substring(0, ind); if ((ind = val.indexOf(";evidence=")) > -1) val = val.substring(0, ind); if (val.startsWith("term=")) val = val.substring(5, val.length()); if (val.endsWith(";")) val = val.substring(0, val.length() - 1); tmpNewValues.add(val); } newQualifier = new Qualifier("product", tmpNewValues); } if (newQualifier.getName().equals("orthologous_to") || newQualifier.getName().equals("paralogous_to")) { final StringVector newValues = newQualifier.getValues(); final StringVector tmpNewValues = new StringVector(); for (int j = 0; j < newValues.size(); j++) { if (!newValues.get(j).equals("")) tmpNewValues.add(newValues.get(j)); } if (tmpNewValues.size() == 0) continue; Pattern p = Pattern.compile("\\w+:link=\\w+"); for (int j = 0; j < tmpNewValues.size(); j++) { String valueStr = (String) tmpNewValues.get(j); String newValueStr; int indexEnd = valueStr.indexOf(';'); String endStr = ""; if (indexEnd > -1) endStr = valueStr.substring(indexEnd); Matcher m = p.matcher(valueStr); while (m.find()) { int index = valueStr.indexOf("link=", m.start()); newValueStr = valueStr.substring(m.start(), index) + valueStr.substring(index + 5, m.end()) + endStr; if (newQualifier.getName().equals("orthologous_to")) newQualifier = new Qualifier("orthologous_to", newValueStr); else newQualifier = new Qualifier("paralogous_to", newValueStr); qualifiers.addElement(newQualifier); } } continue; } addNewQualifier(qualifiers, newQualifier); } }