/**
* reset the various unigene records
*
* @param alias boolean to show whether file is uniSTS.alias
*/
private void resetRecords(boolean noAlias) {
if (true == noAlias) {
uniStsRecord.resetAllFields();
uniStsAccNoRecord.resetAllFields();
} else {
uniStsAliasRecord.resetAllFields();
}
}
/**
* Parsing of the Unigene record for 1st,5th,7th and 8th token. The first field indicates STS id.
* The fifth (NAME) coresponds to STSNAME. The seventh(ACCESSION NUMBER) & eighth(ORGANISM). For
* the UniStsAlias Record we use 1st and 2nd token The first field indicates STS id. The first
* field indicates Aliases.
*
* @param alias boolean to indicate if file being parsed in unSTS.alias
*/
private void parseLine(boolean noAlias) throws FatalException {
m_tokenizer = new StringTokenizer(m_line, m_fieldDelimiter);
if (true == noAlias) {
/** noAlias = true ---> filename = UNISTS.STS */
if (m_tokenizer.countTokens() >= Constants.uniStsTableCols) {
String uniStsElement = null;
int count = 0;
while (m_tokenizer.hasMoreTokens()) {
uniStsElement = m_tokenizer.nextToken();
uniStsElement = uniStsElement.trim();
count++; // ith term
if (count == 1) {
uniStsRecord.fields[0].append(uniStsElement);
uniStsAccNoRecord.fields[0].append(uniStsElement);
} else if (count == 5) {
uniStsRecord.fields[1].append(uniStsElement);
} else if (count == 7) {
uniStsAccNoRecord.fields[2].append(uniStsElement);
} else if (count == 8) {
String localTaxid = (String) Variables.hmOrganismLocalId.get(uniStsElement);
uniStsRecord.fields[2].append(localTaxid);
uniStsAccNoRecord.fields[1].append(localTaxid);
}
}
}
} else {
/** noAlias = false ---> filename = UNISTSalias file */
if (m_tokenizer.countTokens() >= Constants.uniStsAliasTableCols) {
String uniStsAliasElement = null;
int count = 0;
/** here we have to add the records with same locus id,different alias. */
while (m_tokenizer.hasMoreTokens()) {
uniStsAliasElement = m_tokenizer.nextToken();
uniStsAliasElement = uniStsAliasElement.trim();
count++; // ith term
if (count == 1) uniStsAliasRecord.fields[0].append(uniStsAliasElement);
else if (count == 2) {
StringTokenizer token = new StringTokenizer(uniStsAliasElement, semiColonSeperator);
int counttoken = token.countTokens();
if (counttoken != 0) {
StringBuffer id = new StringBuffer(uniStsAliasRecord.fields[0].toString());
uniStsAliasRecord.resetAllFields();
while (token.hasMoreElements()) {
uniStsAliasRecord.fields[0].append(id.toString());
uniStsAliasRecord.fields[1].append(token.nextElement());
try {
writeRecordToDb(Variables.uniStsAliasTableName, uniStsAliasRecord);
} catch (InsertException ie) {
Logger.log("Exception in UniSTS parser :" + ie.getMessage(), Logger.DEBUG);
}
uniStsAliasRecord.resetAllFields();
}
} else {
uniStsAliasRecord.fields[1].append(uniStsAliasElement);
try {
writeRecordToDb(Variables.uniStsAliasTableName, uniStsAliasRecord);
} catch (InsertException ie) {
Logger.log("Exception in UniSTS parser :" + ie.getMessage(), Logger.DEBUG);
}
}
resetRecords(false);
}
}
}
}
}
