void MapAlignmentAlgorithmIdentification::setReference(Size reference_index,
const String & reference_file)
{
reference_.clear();
reference_index_ = reference_index;
// reference is one of the input files, or no reference given:
if (reference_index_ || reference_file.empty())
return;
// reference is external file:
LOG_DEBUG << "Extracting reference RT data..." << endl;
SeqToList rt_data;
bool sorted = true;
FileTypes::Type filetype = FileHandler::getType(reference_file);
if (filetype == FileTypes::MZML)
{
MSExperiment<> experiment;
MzMLFile().load(reference_file, experiment);
getRetentionTimes_(experiment, rt_data);
sorted = false;
}
else if (filetype == FileTypes::FEATUREXML)
{
FeatureMap<> features;
FeatureXMLFile().load(reference_file, features);
getRetentionTimes_(features, rt_data);
}
else if (filetype == FileTypes::CONSENSUSXML)
{
ConsensusMap features;
ConsensusXMLFile().load(reference_file, features);
getRetentionTimes_(features, rt_data);
}
else if (filetype == FileTypes::IDXML)
{
vector<ProteinIdentification> proteins;
vector<PeptideIdentification> peptides;
IdXMLFile().load(reference_file, proteins, peptides);
getRetentionTimes_(peptides, rt_data);
}
computeMedians_(rt_data, reference_, sorted);
if (reference_.empty())
{
throw Exception::MissingInformation(
__FILE__, __LINE__, __PRETTY_FUNCTION__,
"Could not extract retention time information from the reference file");
}
}
bool
validate(const std::vector<std::string>& file_names)
{
std::cout << "checking (created temporary files)..." << std::endl;
bool passed_all = true;
for (Size i = 0; i < file_names.size(); ++i)
{
if (File::exists(file_names[i]))
{
FileTypes::Type type = FileHandler::getType(file_names[i]);
bool passed_single = true;
bool skipped = false;
switch (type)
{
case FileTypes::MZML:
{
if (!MzMLFile().isValid(file_names[i]))
{
std::cout << " - Error: mzML file does not validate against XML schema '" << file_names[i] << "'" << std::endl;
passed_single = false;
}
StringList errors, warnings;
if (!MzMLFile().isSemanticallyValid(file_names[i], errors,
warnings))
{
std::cout << " - Error: mzML file semantically invalid '" << file_names[i] << "'" << std::endl;
for (Size j = 0; j < errors.size(); ++j)
{
std::cout << "Error - " << errors[j] << std::endl;
}
passed_single = false;
}
}
break;
case FileTypes::MZDATA:
if (!MzDataFile().isValid(file_names[i], std::cerr))
{
std::cout << " - Error: Invalid mzData file '" << file_names[i] << "'" << std::endl;
passed_single = false;
}
break;
case FileTypes::MZXML:
if (!MzXMLFile().isValid(file_names[i], std::cerr))
{
std::cout << " - Error: Invalid mzXML file '" << file_names[i] << "'" << std::endl;
passed_single = false;
}
break;
case FileTypes::FEATUREXML:
if (!FeatureXMLFile().isValid(file_names[i], std::cerr))
{
std::cout << " - Error: Invalid featureXML file '" << file_names[i] << "'" << std::endl;
passed_single = false;
}
break;
case FileTypes::IDXML:
if (!IdXMLFile().isValid(file_names[i], std::cerr))
{
std::cout << " - Error: Invalid idXML file '" << file_names[i] << "'" << std::endl;
passed_single = false;
}
break;
case FileTypes::CONSENSUSXML:
if (!ConsensusXMLFile().isValid(file_names[i], std::cerr))
{
std::cout << " - Error: Invalid consensusXML file '" << file_names[i] << "'" << std::endl;
passed_single = false;
}
break;
case FileTypes::INI:
if (!ParamXMLFile().isValid(file_names[i], std::cerr))
{
std::cout << " - Error: Invalid Param file '" << file_names[i] << "'" << std::endl;
passed_single = false;
}
break;
case FileTypes::TRANSFORMATIONXML:
if (!TransformationXMLFile().isValid(file_names[i], std::cerr))
{
passed_single = false;
}
break;
default:
skipped = true;
break;
}
//output for single file
if (skipped)
{
std::cout << " + skipped file '" << file_names[i] << "' (type: " << FileTypes::typeToName(type) << ")" << std::endl;
}
else if (passed_single)
{
std::cout << " + valid file '" << file_names[i] << "' (type: " << FileTypes::typeToName(type) << ")" << std::endl;
}
else
{
passed_all = false;
std::cout << " - invalid file '" << file_names[i] << "' (type: " << FileTypes::typeToName(type) << ")" << std::endl;
}
}
}
//output for all files
if (passed_all)
{
std::cout << ": passed" << std::endl << std::endl;
}
else
{
std::cout << ": failed" << std::endl << std::endl;
}
return passed_all;
}
ExitCodes main_(int, const char **)
{
String in = getStringOption_("in");
StringList out = getStringList_("out");
SeedListGenerator seed_gen;
// results (actually just one result, except for consensusXML input):
Map<UInt64, SeedListGenerator::SeedList> seed_lists;
Size num_maps = 0;
FileTypes::Type in_type = FileHandler::getType(in);
if (in_type == FileTypes::CONSENSUSXML)
{
ConsensusMap consensus;
ConsensusXMLFile().load(in, consensus);
num_maps = consensus.getFileDescriptions().size();
if (out.size() != num_maps)
{
writeLog_("Error: expected " + String(num_maps) +
" output filenames");
return ILLEGAL_PARAMETERS;
}
seed_gen.generateSeedLists(consensus, seed_lists);
}
else if (out.size() > 1)
{
writeLog_("Error: expected only one output filename");
return ILLEGAL_PARAMETERS;
}
else if (in_type == FileTypes::MZML)
{
MSExperiment<> experiment;
MzMLFile().load(in, experiment);
seed_gen.generateSeedList(experiment, seed_lists[0]);
}
else if (in_type == FileTypes::IDXML)
{
vector<ProteinIdentification> proteins;
vector<PeptideIdentification> peptides;
IdXMLFile().load(in, proteins, peptides);
seed_gen.generateSeedList(peptides, seed_lists[0],
getFlag_("use_peptide_mass"));
}
else if (in_type == FileTypes::FEATUREXML)
{
FeatureMap features;
FeatureXMLFile().load(in, features);
seed_gen.generateSeedList(
features.getUnassignedPeptideIdentifications(), seed_lists[0]);
}
// output:
num_maps = 0;
for (Map<UInt64, SeedListGenerator::SeedList>::Iterator it =
seed_lists.begin(); it != seed_lists.end(); ++it, ++num_maps)
{
FeatureMap features;
seed_gen.convertSeedList(it->second, features);
//annotate output with data processing info:
addDataProcessing_(features, getProcessingInfo_(
DataProcessing::DATA_PROCESSING));
FeatureXMLFile().store(out[num_maps], features);
}
return EXECUTION_OK;
}
