From d9b07c79783ac146600799a392cd2d005735bef3 Mon Sep 17 00:00:00 2001
From: Olivier Langella <Olivier.Langella@moulon.inra.fr>
Date: Thu, 23 Mar 2017 23:01:16 +0100
Subject: [PATCH] protein coverage OK
---
src/core/proteinmatch.cpp | 42 ++++++++++---------
.../protein_list_view/proteintablemodel.cpp | 9 +++-
src/input/xpipsaxhandler.cpp | 14 +++----
src/utils/proteinstore.cpp | 6 +--
4 files changed, 40 insertions(+), 31 deletions(-)
diff --git a/src/core/proteinmatch.cpp b/src/core/proteinmatch.cpp
index e750622d..f035edbc 100644
--- a/src/core/proteinmatch.cpp
+++ b/src/core/proteinmatch.cpp
@@ -116,15 +116,15 @@ void ProteinMatch::setGroupingExperiment(GroupingExperiment * p_grp_experiment)
_sp_grp_protein = nullptr;
if (isValidAndChecked()) {
_sp_grp_protein = p_grp_experiment->getGrpProteinSp(this);
-
+
for (auto & p_peptide_match : _peptide_match_list) {
p_peptide_match->setGrpPeptideSp(nullptr);
if (p_peptide_match->isValidAndChecked()) {
p_peptide_match->setGrpPeptideSp(p_grp_experiment->setGrpPeptide(_sp_grp_protein, p_peptide_match));
}
}
-
-
+
+
if (_protein_sp.get()->isContaminant()) {
p_grp_experiment->addPostGroupingGrpProteinSpRemoval(_sp_grp_protein);
}
@@ -137,24 +137,26 @@ const pappso::GrpProteinSp & ProteinMatch::getGrpProteinSp() const {
}
- pappso::pappso_double ProteinMatch::getCoverage() const {
- size_t prot_size = _protein_sp.get()->size();
- if (prot_size == 0) return 0;
- bool cover_bool[prot_size] = {false};
- for (auto & p_peptide_match : _peptide_match_list) {
- if (p_peptide_match->isValidAndChecked()) {
- size_t size = p_peptide_match->getPeptideSp().get()->size();
- size_t offset = p_peptide_match->getStart();
- if (offset >= 0) {
- for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
- cover_bool[offset] = true;
- }
+pappso::pappso_double ProteinMatch::getCoverage() const {
+ size_t prot_size = _protein_sp.get()->size();
+ //qDebug() << "ProteinMatch::getCoverage begin prot_size=" << prot_size << " " << _protein_sp.get()-//>getSequence();
+ if (prot_size == 0) return 0;
+ bool cover_bool[prot_size] = {false};
+ for (auto & p_peptide_match : _peptide_match_list) {
+ if (p_peptide_match->isValidAndChecked()) {
+ size_t size = p_peptide_match->getPeptideSp().get()->size();
+ size_t offset = p_peptide_match->getStart();
+ if (offset >= 0) {
+ for (size_t i=0; (i < size) && (offset < prot_size) ; i++,offset++) {
+ cover_bool[offset] = true;
}
}
}
- size_t count = 0;
- for (size_t i=0; i < prot_size; i++) {
- if(cover_bool[i]) count++;
- }
- return ((pappso::pappso_double)count/ (pappso::pappso_double)prot_size);
}
+ size_t count = 0;
+ for (size_t i=0; i < prot_size; i++) {
+ if(cover_bool[i]) count++;
+ }
+ //qDebug() << "ProteinMatch::getCoverage count=" << count << " prot_size=" << prot_size;
+ return (((pappso::pappso_double)count)/ ((pappso::pappso_double)prot_size));
+}
diff --git a/src/gui/protein_list_view/proteintablemodel.cpp b/src/gui/protein_list_view/proteintablemodel.cpp
index 341b67d8..711528c8 100644
--- a/src/gui/protein_list_view/proteintablemodel.cpp
+++ b/src/gui/protein_list_view/proteintablemodel.cpp
@@ -127,7 +127,7 @@ int ProteinTableModel::rowCount(const QModelIndex &parent ) const {
return 0;
}
int ProteinTableModel::columnCount(const QModelIndex &parent ) const {
- return 5;
+ return 7;
}
QVariant ProteinTableModel::headerData(int section, Qt::Orientation orientation, int role) const
{
@@ -146,6 +146,10 @@ QVariant ProteinTableModel::headerData(int section, Qt::Orientation orientation,
return QString("protein description");
case 4:
return QString("Evalue");
+ case 5:
+ return QString("spectrum");
+ case 6:
+ return QString("coverage");
}
}
}
@@ -201,6 +205,9 @@ QVariant ProteinTableModel::data(const QModelIndex &index, int role ) const {
if (col == 5) {
return QVariant ((quint16) _p_identification_group->getProteinMatchList().at(row)->getPeptideMatchList().size());
}
+ if (col == 6) {
+ return QVariant ((qreal)_p_identification_group->getProteinMatchList().at(row)->getCoverage());
+ }
return QString("Row%1, Column%2")
.arg(index.row() + 1)
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index 921d4262..1d42b8ca 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -285,17 +285,17 @@ bool XpipSaxHandler::endElement_peptide() {
}
bool XpipSaxHandler::endElement_sequence() {
- if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 1] == "protein")) {
- _current_protein.setSequence(_current_text);
- }
- else {
- // XtandemHyperscore hyperscore(_curent_spectrum, _current_peptide_sp, _precision, _ion_list, _max_charge,_refine_spectrum_synthesis);
- }
+ //if ((_tag_stack.size() > 1) && (_tag_stack[_tag_stack.size() - 1] == "protein")) {
+ _current_protein.setSequence(_current_text);
+ //}
+ //else {
+ // XtandemHyperscore hyperscore(_curent_spectrum, _current_peptide_sp, _precision, _ion_list, _max_charge,_refine_spectrum_synthesis);
+ //}
return true;
}
bool XpipSaxHandler::endElement_protein() {
ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
-
+
_p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
return true;
diff --git a/src/utils/proteinstore.cpp b/src/utils/proteinstore.cpp
index acb0a876..7eab25a1 100644
--- a/src/utils/proteinstore.cpp
+++ b/src/utils/proteinstore.cpp
@@ -55,14 +55,14 @@ ProteinXtpSp & ProteinStore::getInstance(ProteinXtpSp & peptide_in) {
}
void ProteinStore::setProteinInformations(ProteinXtpSp & peptide_in) {
- qDebug() << "ProteinStore::setProteinInformations begin";
+ //qDebug() << "ProteinStore::setProteinInformations begin" << peptide_in.get()->getSequence();
QString accession = peptide_in.get()->getAccession();
if (_regexp_contaminant.indexIn(accession, 0)>-1) {
- qDebug() << "ProteinStore::setProteinInformations is contaminant " << accession;
+ //qDebug() << "ProteinStore::setProteinInformations is contaminant " << accession;
peptide_in.get()->setIsContaminant(true);
}
if (_regexp_decoy.indexIn(accession, 0)>-1) {
peptide_in.get()->setIsDecoy(true);
}
- qDebug() << "ProteinStore::setProteinInformations end";
+ //qDebug() << "ProteinStore::setProteinInformations end";
}
--
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