/**
* Maps database (SO) keys to EMBl keys. It will add any extra qualifiers found in the 3rd column
* of DATABASE_MAP_KEYS.
*
* @param key
* @return
*/
private Key map(final Key key, final QualifierVector qualifiers) {
if (DATABASE_MAP_KEYS == null) initDatabaseMappings();
for (int i = 0; i < DATABASE_MAP_KEYS.length; i++) {
if (key.getKeyString().equals(DATABASE_MAP_KEYS[i][0])) {
Key mappedKey = new Key((String) DATABASE_MAP_KEYS[i][1]);
if (DATABASE_MAP_KEYS[i][2] != null) {
Qualifier newQualifier = (Qualifier) DATABASE_MAP_KEYS[i][2];
if (!getEntryInformation().isValidQualifier(mappedKey, newQualifier.getName())) {
try {
final int nvalues;
if (newQualifier.getValues() == null) nvalues = 0;
else nvalues = newQualifier.getValues().size();
final int type;
if (nvalues == 0) type = QualifierInfo.NO_VALUE;
else type = QualifierInfo.QUOTED_TEXT;
getEntryInformation()
.addQualifierInfo(
new QualifierInfo(newQualifier.getName(), type, null, null, false));
} catch (QualifierInfoException e) {
}
}
qualifiers.addQualifierValues(newQualifier);
}
return mappedKey;
}
}
return key;
}
/**
* Add a new qualifier to a list of qualifiers
*
* @param qualifiers
* @param newQualifier
*/
private void addNewQualifier(QualifierVector qualifiers, Qualifier newQualifier) {
Qualifier qualifier;
if ((qualifier = qualifiers.getQualifierByName(newQualifier.getName())) != null) {
final StringVector newValues = newQualifier.getValues();
final StringVector values = qualifier.getValues();
if (newValues == null) return;
for (int j = 0; j < newValues.size(); j++) {
String newValue = (String) newValues.get(j);
if (!values.contains(newValue)) qualifier.addValue(newValue);
}
} else qualifiers.addElement(newQualifier);
}
/**
* 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);
}
}