/** * 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); } } } } }