// / The nucleotide sequence in the 'output' SAM file is compared
// with the amino acid sequence in the 'input' Mascot DAT or
// mzIdentML file.
if (DebuggingFlag.get_sbi_debug_flag() == 1) {
File translationTableFile = new File(line.getOptionValue("t"));
ResultAnalyserRunner analyser = new ResultAnalyserRunner(
searchResultsPaths, genomeFile, mapFile, outfile,
chromosomeDir, translationTableFile);
if (sqlQuery == null && repId == null) {
analyser.run();
} else if (sqlQuery != null
&& (repId != null || repListFile != null)) {
System.err.println("Only use either reportId or sqlQuery.");
} else if (sqlQuery != null) {
mainWithQuery(analyser, sqlQuery);
} else {
mainWithReportId(analyser, repId, repListFile);
}
} else {
ResultAnalyserRunner analyser = new ResultAnalyserRunner(
searchResultsPaths, genomeFile, mapFile, outfile,
chromosomeDir);
if (sqlQuery == null && repId == null) {
analyser.run();
} else if (sqlQuery != null
&& (repId != null || repListFile != null)) {
System.err.println("Only use either reportId or sqlQuery.");
} else if (sqlQuery != null) {
mainWithQuery(analyser, sqlQuery);