ExitCodes main_(int, const char**) override
{
//-------------------------------------------------------------
// parsing parameters
//-------------------------------------------------------------
String in = getStringOption_("in");
String out = getStringOption_("out");
PeptideIndexing indexer;
Param param = getParam_().copy("", true);
Param param_pi = indexer.getParameters();
param_pi.update(param, false, Log_debug); // suppress param. update message
indexer.setParameters(param_pi);
indexer.setLogType(this->log_type_);
String db_name = getStringOption_("fasta");
if (!File::readable(db_name))
{
String full_db_name;
try
{
full_db_name = File::findDatabase(db_name);
}
catch (...)
{
printUsage_();
return ILLEGAL_PARAMETERS;
}
db_name = full_db_name;
}
//-------------------------------------------------------------
// reading input
//-------------------------------------------------------------
// we stream the Fasta file
std::vector<ProteinIdentification> prot_ids;
std::vector<PeptideIdentification> pep_ids;
IdXMLFile idxmlfile;
idxmlfile.setLogType(this->log_type_);
idxmlfile.load(in, prot_ids, pep_ids);
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
FASTAContainer<TFI_File> proteins(db_name);
PeptideIndexing::ExitCodes indexer_exit = indexer.run(proteins, prot_ids, pep_ids);
//-------------------------------------------------------------
// calculate protein coverage
//-------------------------------------------------------------
if (param.getValue("write_protein_sequence").toBool())
{
for (Size i = 0; i < prot_ids.size(); ++i)
{
prot_ids[i].computeCoverage(pep_ids);
}
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
idxmlfile.store(out, prot_ids, pep_ids);
if (indexer_exit == PeptideIndexing::DATABASE_EMPTY)
{
return INPUT_FILE_EMPTY;
}
else if (indexer_exit == PeptideIndexing::UNEXPECTED_RESULT)
{
return UNEXPECTED_RESULT;
}
else if ((indexer_exit != PeptideIndexing::EXECUTION_OK) &&
(indexer_exit != PeptideIndexing::PEPTIDE_IDS_EMPTY))
{
return UNKNOWN_ERROR;
}
return EXECUTION_OK;
}
END_SECTION
START_SECTION((ExitCodes run(std::vector<FASTAFile::FASTAEntry>& proteins, std::vector<ProteinIdentification>& prot_ids, std::vector<PeptideIdentification>& pep_ids)))
{
PeptideIndexing pi;
Param p = pi.getParameters();
PeptideIndexing::ExitCodes r;
// easy case:
std::vector<FASTAFile::FASTAEntry> proteins = toFASTAVec(QStringList() << "*MLT*EAXK"); // 1 X!! ; extra * chars (should be ignored)
std::vector<ProteinIdentification> prot_ids;
std::vector<PeptideIdentification> pep_ids = toPepVec(QStringList() << "MLTEAEK"); // requires 1 ambAA
p.setValue("aaa_max", 0);
pi.setParameters(p);
r = pi.run(proteins, prot_ids, pep_ids);
TEST_EQUAL(pep_ids[0].getHits()[0].extractProteinAccessions().size(), 0); // no hit or one hit!
p.setValue("aaa_max", 1);
pi.setParameters(p);
r = pi.run(proteins, prot_ids, pep_ids);
TEST_EQUAL(pep_ids[0].getHits()[0].extractProteinAccessions().size(), 1); // one hit! -- no ambAA's to spare
p.setValue("aaa_max", 10);
pi.setParameters(p);
r = pi.run(proteins, prot_ids, pep_ids);
TEST_EQUAL(pep_ids[0].getHits()[0].extractProteinAccessions().size(), 1); // one hit! -- plenty of ambAA's to spare
// 2 AmbAA's...
proteins = toFASTAVec(QStringList() << "B*EBE*"); // DB with 2 ambiguous AA's; and extra * chars (should be ignored)
pep_ids = toPepVec(QStringList() << "NENE" << "NEDE" << "DENE" << "DEDE"); // each is a hit, if >= 2 ambAA's are allowed;
for (int i_aa = 0; i_aa < 5; ++i_aa)
