void ToolDescriptionHandler::startElement(const XMLCh * const uri, const XMLCh * const local_name, const XMLCh * const qname, const xercesc::Attributes & attributes)
{
if (in_ini_section_)
{
ParamXMLHandler::startElement(uri, local_name, qname, attributes);
return;
}
tag_ = sm_.convert(qname);
open_tags_.push_back(tag_);
//std::cout << "starting tag " << tag_ << "\n";
if (tag_ == "tool")
{
String status = attributeAsString_(attributes, "status");
if (status == "external")
td_.is_internal = false;
else if (status == "internal")
td_.is_internal = true;
else
error(LOAD, "ToolDescriptionHandler::startElement: Element 'status' if tag 'tool' has unknown value " + status + "'.");
return;
}
if (tag_ == "mapping")
{
Int id = attributeAsInt_(attributes, "id");
String command = attributeAsString_(attributes, "cl");
tde_.tr_table.mapping[id] = command;
return;
}
if (tag_ == "file_post")
{
Internal::FileMapping fm;
fm.location = attributeAsString_(attributes, "location");
fm.target = attributeAsString_(attributes, "target");
tde_.tr_table.post_moves.push_back(fm);
return;
}
if (tag_ == "file_pre")
{
Internal::FileMapping fm;
fm.location = attributeAsString_(attributes, "location");
fm.target = attributeAsString_(attributes, "target");
tde_.tr_table.pre_moves.push_back(fm);
return;
}
if (tag_ == "ini_param")
{
in_ini_section_ = true;
p_ = Param(); // reset Param
return;
}
if (tag_ == "ttd" || tag_ == "category" || tag_ == "e_category" || tag_ == "type")
return;
if (td_.is_internal)
{
if (tag_ == "name")
{
return;
}
}
else if (!td_.is_internal)
{
if (tag_ == "external" || tag_ == "cloptions" || tag_ == "path" || tag_ == "mappings" || tag_ == "mapping" || tag_ == "ini_param" ||
tag_ == "text" || tag_ == "onstartup" || tag_ == "onfail" || tag_ == "onfinish" || tag_ == "workingdirectory")
return;
}
error(LOAD, "ToolDescriptionHandler::startElement(): Unkown element found: '" + tag_ + "', ignoring.");
}
void ProtXMLFile::startElement(const XMLCh* const /*uri*/, const XMLCh* const /*local_name*/, const XMLCh* const qname, const xercesc::Attributes& attributes)
{
String tag = sm_.convert(qname);
if (tag == "protein_summary_header")
{
String db = attributeAsString_(attributes, "reference_database");
String enzyme = attributeAsString_(attributes, "sample_enzyme");
ProteinIdentification::SearchParameters sp = prot_id_->getSearchParameters();
sp.db = db;
// find a matching enzyme name
sp.digestion_enzyme = *(ProteaseDB::getInstance()->getEnzyme(enzyme));
prot_id_->setSearchParameters(sp);
prot_id_->setScoreType("ProteinProphet probability");
prot_id_->setHigherScoreBetter(true);
pep_id_->setScoreType("ProteinProphet probability");
pep_id_->setHigherScoreBetter(true);
}
// identifier for Protein & PeptideIdentification
// <program_details analysis="proteinprophet" time="2009-11-29T18:30:03" ...
if (tag == "program_details")
{
String analysis = attributeAsString_(attributes, "analysis");
String time = attributeAsString_(attributes, "time");
String version = attributeAsString_(attributes, "version");
QDateTime date = QDateTime::fromString(time.toQString());
if (!date.isValid())
date = QDateTime::fromString(time.toQString(), Qt::ISODate);
if (!date.isValid())
LOG_WARN << "Warning: Cannot parse 'time'='" << time << "'.\n";
prot_id_->setDateTime(date);
prot_id_->setSearchEngine(analysis);
prot_id_->setSearchEngineVersion(version);
String id = String(UniqueIdGenerator::getUniqueId()); // was: analysis + "_" + time;
prot_id_->setIdentifier(id);
pep_id_->setIdentifier(id);
}
if (tag == "protein_group")
{
// we group all <protein>'s and <indistinguishable_protein>'s in our
// internal group structure
protein_group_ = ProteinGroup();
protein_group_.probability = attributeAsDouble_(attributes, "probability");
}
else if (tag == "protein")
{
// usually there will be just one <protein> per <protein_group>, but more
// are possible; each <protein> is distinguishable from the other, we
// nevertheless group them
String protein_name = attributeAsString_(attributes, "protein_name");
// open new "indistinguishable" group:
prot_id_->insertIndistinguishableProteins(ProteinGroup());
registerProtein_(protein_name); // create new protein
// fill protein with life
double pc_coverage;
if (optionalAttributeAsDouble_(pc_coverage, attributes, "percent_coverage"))
{
prot_id_->getHits().back().setCoverage(pc_coverage);
}
else
{
LOG_WARN << "Required attribute 'percent_coverage' missing\n";
}
prot_id_->getHits().back().setScore(attributeAsDouble_(attributes, "probability"));
}
else if (tag == "indistinguishable_protein")
{
String protein_name = attributeAsString_(attributes, "protein_name");
// current last protein is from the same "indistinguishable" group:
double score = prot_id_->getHits().back().getScore();
registerProtein_(protein_name);
// score of group leader might technically not be transferable (due to
// protein length etc.), but we still transfer it to allow filtering of
// proteins by score without disrupting the groups:
prot_id_->getHits().back().setScore(score);
}
else if (tag == "peptide")
{
// If a peptide is degenerate it will show in multiple groups, but have different statistics (e.g. 'nsp_adjusted_probability')
// We thus treat each instance as a separate peptide
// todo/improvement: link them by a group in PeptideIdentification?!
pep_hit_ = new PeptideHit;
pep_hit_->setSequence(AASequence::fromString(String(attributeAsString_(attributes, "peptide_sequence"))));
pep_hit_->setScore(attributeAsDouble_(attributes, "nsp_adjusted_probability"));
Int charge;
if (optionalAttributeAsInt_(charge, attributes, "charge"))
{
pep_hit_->setCharge(charge);
}
else
{
LOG_WARN << "Required attribute 'charge' missing\n";
}
// add accessions of all indistinguishable proteins the peptide belongs to
ProteinIdentification::ProteinGroup& indist = prot_id_->getIndistinguishableProteins().back();
for (StringList::const_iterator accession = indist.accessions.begin(); accession != indist.accessions.end(); ++accession)
{
PeptideEvidence pe;
pe.setProteinAccession(*accession);
pep_hit_->addPeptideEvidence(pe);
}
pep_hit_->setMetaValue("is_unique", String(attributeAsString_(attributes, "is_nondegenerate_evidence")) == "Y" ? 1 : 0);
pep_hit_->setMetaValue("is_contributing", String(attributeAsString_(attributes, "is_contributing_evidence")) == "Y" ? 1 : 0);
}
else if (tag == "mod_aminoacid_mass")
{
// relates to the last seen peptide (we hope)
Size position = attributeAsInt_(attributes, "position");
double mass = attributeAsDouble_(attributes, "mass");
AASequence temp_aa_sequence(pep_hit_->getSequence());
String temp_description = "";
String origin = temp_aa_sequence[position - 1].getOneLetterCode();
matchModification_(mass, origin, temp_description);
if (temp_description.size() > 0) // only if a mod was found
{
// e.g. Carboxymethyl (C)
vector<String> mod_split;
temp_description.split(' ', mod_split);
if (mod_split.size() == 2)
{
if (mod_split[1] == "(C-term)" || ModificationsDB::getInstance()->getModification(temp_description).getTermSpecificity() == ResidueModification::C_TERM)
{
temp_aa_sequence.setCTerminalModification(mod_split[0]);
}
else
{
if (mod_split[1] == "(N-term)" || ModificationsDB::getInstance()->getModification(temp_description).getTermSpecificity() == ResidueModification::N_TERM)
{
temp_aa_sequence.setNTerminalModification(mod_split[0]);
}
else
{
// search this mod, if not directly use a general one
temp_aa_sequence.setModification(position - 1, mod_split[0]);
}
}
}
else
{
error(LOAD, String("Cannot parse modification '") + temp_description + "@" + position + "'");
}
}
else
{
error(LOAD, String("Cannot find modification '") + String(mass) + " " + String(origin) + "' @" + String(position));
}
pep_hit_->setSequence(temp_aa_sequence);
}
}
