From 29e9d01b0de84a0883fa548dc13af8596c536b4c Mon Sep 17 00:00:00 2001
From: Olivier Langella <olivier.langella@u-psud.fr>
Date: Sun, 4 Mar 2018 23:15:55 +0100
Subject: [PATCH] WIP: Mascot parser
---
src/input/mascot/mascotdatparser.cpp | 28 ++++++++++++++++++++++++++--
src/input/mascot/mascotdatparser.h | 2 ++
2 files changed, 28 insertions(+), 2 deletions(-)
diff --git a/src/input/mascot/mascotdatparser.cpp b/src/input/mascot/mascotdatparser.cpp
index 21ed9da84..1ef92308c 100644
--- a/src/input/mascot/mascotdatparser.cpp
+++ b/src/input/mascot/mascotdatparser.cpp
@@ -31,7 +31,8 @@
#include "mimeparser.h"
#include <QDebug>
#include <pappsomspp/pappsoexception.h>
-#include <pappsomspp/peptide/peptide.h>
+#include "../../core/peptidextp.h"
+#include "../../core/proteinmatch.h"
MascotDatParser::MascotDatParser(Project * p_project, IdentificationGroup * p_identification_group,
IdentificationDataSource * p_identification_data_source) {
@@ -120,6 +121,7 @@ void MascotDatParser::parseHeaderLine(const QString & header_line) {
else if (header_list[1].startsWith("queries")) {
qDebug() << "queries=" << header_list[2];
_number_of_queries = header_list[2].toUInt();
+ _query_peptide_results.resize(_number_of_queries);
}
//min_peaks_for_homology=6
//max_hits=50
@@ -150,6 +152,8 @@ void MascotDatParser::parseHeaderLine(const QString & header_line) {
void MascotDatParser::saveAndClearPeptide() {
qDebug() << "MascotDatParser::saveAndClearPeptide begin";
if (_current_peptide.query_index > 0) {
+ // save
+ _query_peptide_results[_current_peptide.query_index-1].push_back(_current_peptide);
//parse and save
QString peptide_str =_current_peptide.peptide_string_list.at(4);
@@ -161,7 +165,9 @@ void MascotDatParser::saveAndClearPeptide() {
peptide_str = peptide_str.replace(subst_list.at(0+i).toInt()-1,1,subst_list.at(2+i));
}
}
- pappso::Peptide peptide(peptide_str);
+ PeptideXtpSp peptide_sp;
+ peptide_sp = PeptideXtp(peptide_str).makePeptideXtpSp();
+ peptide_sp = _p_project->getPeptideStore().getInstance(peptide_sp);
if (_current_peptide.protein_string_list.size() != _current_peptide.fasta_file_list.size()) {
throw pappso::PappsoException(QObject::tr("ERROR (_current_peptide.protein_string_list.size() != _current_peptide.fasta_file_list.size()) %1").arg(_current_peptide.protein_string_list.join(",\"")));
@@ -178,6 +184,24 @@ void MascotDatParser::saveAndClearPeptide() {
}
unsigned int start = position_list.at(1).toUInt();
unsigned int stop = position_list.at(2).toUInt();
+
+ ProteinXtp protein;
+ protein.setAccession(accession);
+
+ ProteinMatch * p_protein_match = _p_identification_group->getProteinMatchInstance(protein.getAccession());
+ if (p_protein_match == nullptr) {
+ throw pappso::PappsoException(QObject::tr("ERROR (p_protein_match == nullptr) %1").arg(str));
+ }
+
+ ProteinXtpSp sp_xtp_protein = protein.makeProteinXtpSp();
+ p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
+ p_protein_match->setChecked(true);
+
+ PeptideMatch peptide_match;
+ peptide_match.setStart(start);
+ //peptide_match.setPeptideEvidenceSp();
+
+ p_protein_match->addPeptideMatch(peptide_match);
}
}
diff --git a/src/input/mascot/mascotdatparser.h b/src/input/mascot/mascotdatparser.h
index c349ff68c..23f387754 100644
--- a/src/input/mascot/mascotdatparser.h
+++ b/src/input/mascot/mascotdatparser.h
@@ -71,6 +71,8 @@ private:
PeptideLine _current_peptide;
+ std::vector<std::vector<PeptideLine>> _query_peptide_results;
+
};
--
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