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Commit 0c95429e authored by Olivier Langella's avatar Olivier Langella
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labeling method and masschroqml tested ok

parent de117191
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Tags xtpcpp_0.1.11-1
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src/core/labeling/label.cpp
+ 25
− 0
View file @ 0c95429e
......@@ -28,6 +28,7 @@
******************************************************************************/
#include "label.h"
#include "../../utils/utils.h"
#include <pappsomspp/amino_acid/aamodification.h>
#include <pappsomspp/pappsoexception.h>
#include <QDebug>
......@@ -79,3 +80,27 @@ pappso::PeptideSp Label::getLabeledPeptideSp(const pappso::Peptide * p_peptide)
}
return (peptide.makePeptideSp());
}
const QString & Label::getXmlId() const {
return _xml_id;
}
void Label::writeMassChroqMl(QXmlStreamWriter* output_stream) const {
//<isotope_label id="iso1">
output_stream->writeStartElement("isotope_label");
output_stream->writeAttribute("id",_xml_id);
// <mod at="Nter" value="28.0" acc="MOD:00429"/>
// <mod at="K" value="28.0" acc="MOD:00429"/>
for (const LabelModification label_modification: _modification_list) {
output_stream->writeStartElement("mod");
output_stream->writeAttribute("at",label_modification.at);
output_stream->writeAttribute("value",Utils::getXmlDouble(label_modification.modification->getMass()));
output_stream->writeAttribute("acc",label_modification.modification->getAccession());
output_stream->writeEndElement();
output_stream->writeComment(label_modification.modification->getName());
}
// </isotope_label>
output_stream->writeEndElement();
}
src/core/labeling/label.h
+ 3
− 0
View file @ 0c95429e
......@@ -34,6 +34,7 @@
#include <QDomNode>
#include <pappsomspp/amino_acid/aamodification.h>
#include <pappsomspp/peptide/peptide.h>
#include <QXmlStreamWriter>
struct LabelModification {
......@@ -49,6 +50,8 @@ public:
Label( const Label & other);
bool containsAaModificationP(const std::list<pappso::AaModificationP> & modification_set) const;
pappso::PeptideSp getLabeledPeptideSp(const pappso::Peptide * p_peptide) const;
void writeMassChroqMl(QXmlStreamWriter* output_stream) const;
const QString & getXmlId() const;
private:
QString _xml_id;
std::vector<LabelModification> _modification_list;
......
src/core/labeling/labelingmethod.cpp
+ 27
− 0
View file @ 0c95429e
......@@ -71,6 +71,9 @@ Label * LabelingMethod::getLabel(const std::list<pappso::AaModificationP> & modi
return nullptr;
}
const QString & LabelingMethod::getXmlId() const {
return _xml_id;
}
LabelingMethod::LabelingMethod( const LabelingMethod & other):_xml_id(other._xml_id) {
for (Label * p_label: other._label_list) {
_label_list.push_back( new Label(*p_label));
......@@ -94,3 +97,27 @@ void LabelingMethod::parseMethod(QDomNode & method_node) {
child = child.nextSibling();
}
}
void LabelingMethod::writeMassChroqMl(QXmlStreamWriter* output_stream) const {
//<isotope_label_list>
output_stream->writeStartElement("isotope_label_list");
output_stream->writeComment(getXmlId());
/*
<isotope_label id="iso1">
<mod at="Nter" value="28.0" acc="MOD:00429"/>
<mod at="K" value="28.0" acc="MOD:00429"/>
</isotope_label>
<isotope_label id="iso2">
<mod at="Nter" value="32.0" />
<mod at="K" value="32.0" />
</isotope_label>*/
for (Label * p_label: _label_list) {
p_label->writeMassChroqMl(output_stream);
}
//</isotope_label_list>
output_stream->writeEndElement();
}
const std::vector<Label *> & LabelingMethod::getLabelList() const {
return _label_list;
}
src/core/labeling/labelingmethod.h
+ 4
− 0
View file @ 0c95429e
......@@ -33,6 +33,7 @@
#include <QDomNode>
#include <vector>
#include <memory>
#include <QXmlStreamWriter>
#include "label.h"
class LabelingMethod;
......@@ -46,6 +47,9 @@ public:
~LabelingMethod();
LabelingMethodSp makeLabelingMethodSp() const;
Label * getLabel(const std::list<pappso::AaModificationP> & modification_set) const;
const QString & getXmlId() const;
void writeMassChroqMl(QXmlStreamWriter* output_stream) const;
const std::vector<Label *> & getLabelList() const;
private :
void parseMethod(QDomNode & method_node);
void parseLabel(QDomNode & method_node);
......
src/core/project.cpp
+ 5
− 1
View file @ 0c95429e
......@@ -85,7 +85,7 @@ ProteinStore & Project::getProteinStore() {
IdentificationDataSourceStore & Project::getIdentificationDataSourceStore() {
return _identification_data_source_store;
}
const IdentificationDataSourceStore & Project::getIdentificationDataSourceStore() const{
const IdentificationDataSourceStore & Project::getIdentificationDataSourceStore() const {
return _identification_data_source_store;
}
const AutomaticFilterParameters & Project::getAutomaticFilterParameters() const {
......@@ -147,3 +147,7 @@ void Project::setLabelingMethodSp(LabelingMethodSp labeling_method_sp) {
_labeling_method_sp = labeling_method_sp;
_peptide_store.setLabelingMethodSp(labeling_method_sp);
}
LabelingMethodSp Project::getLabelingMethodSp() const {
return _labeling_method_sp;
}
src/core/project.h
+ 4
− 0
View file @ 0c95429e
......@@ -78,6 +78,10 @@ public:
* */
void setLabelingMethodSp(LabelingMethodSp labeling_method_sp);
/** @brief get labeling method shared pointer
* */
LabelingMethodSp getLabelingMethodSp() const;
private :
LabelingMethodSp _labeling_method_sp;
bool _is_combine_mode =true;
......
src/output/masschroqml.cpp
+ 38
− 38
View file @ 0c95429e
......@@ -32,6 +32,7 @@
#include <pappsomspp/utils.h>
#include <pappsomspp/grouping/grpprotein.h>
#include <pappsomspp/amino_acid/Aa.h>
#include <QStringList>
struct McqObserved {
......@@ -144,8 +145,8 @@ void MassChroQml::write(ProjectSp sp_project) {
writeQuantificationTraces();
writeQuantify();
_output_stream->writeEndElement();
_output_stream->writeEndDocument();
}
......@@ -210,6 +211,13 @@ void MassChroQml::writeQuantify() {
_output_stream->writeStartElement("peptides_in_peptide_list");
_output_stream->writeAttribute("mode","post_matching");
_output_stream->writeAttribute("ni_min_abundance","0.8");
if (_sp_project.get()->getLabelingMethodSp().get() != nullptr) {
QStringList isotope_label_ref;
for (const Label * p_label :_sp_project.get()->getLabelingMethodSp().get()->getLabelList()) {
isotope_label_ref << p_label->getXmlId();
}
_output_stream->writeAttribute("isotope_label_refs",isotope_label_ref.join(" "));
}
_output_stream->writeEndElement();
_output_stream->writeComment("<mz_list>732.317 449.754 552.234 464.251 381.577 569.771 575.256</mz_list>");
......@@ -231,7 +239,7 @@ void MassChroQml::writeQuantificationMethods() {
_output_stream->writeComment("max : XIC on BasePeak; sum : XIC on TIC");
//<ppm_range min="10" max="10"/><!--For XIC extraction on Da use: mz_range-->
_output_stream->writeComment("For XIC extraction on Da use: mz_range");
_output_stream->writeStartElement("ppm_range");
_output_stream->writeAttribute("min","10");
......@@ -330,53 +338,45 @@ void MassChroQml::writeAlignments() {
}
void MassChroQml::writeIsotopeLabelList() {
//<isotope_label_list>
//_output_stream->writeStartElement("isotope_label_list");
/*
<isotope_label id="iso1">
<mod at="Nter" value="28.0" acc="MOD:00429"/>
<mod at="K" value="28.0" acc="MOD:00429"/>
</isotope_label>
<isotope_label id="iso2">
<mod at="Nter" value="32.0" />
<mod at="K" value="32.0" />
</isotope_label>*/
//</isotope_label_list>
//_output_stream->writeEndElement();
LabelingMethod * p_labeling_method = _sp_project.get()->getLabelingMethodSp().get();
if (p_labeling_method != nullptr) {
//<isotope_label_list>
p_labeling_method->writeMassChroqMl(_output_stream);
}
}
void MassChroQml::writePeptideList() {
//<peptide_list>
_output_stream->writeStartElement("peptide_list");
const std::map<unsigned int, GroupingGroupSp> & group_store = _p_identification_group->getGroupStore().getGroupMap();
for (auto & group_pair :group_store) {
writePeptideListInGroup(group_pair.second.get());
}
//</peptide_list>
_output_stream->writeEndElement();
}
}
void MassChroQml::writePeptideListInGroup(const GroupingGroup * p_group) {
const std::vector<std::pair<unsigned int, const PeptideMatch *>> & sg_peptide_match_list = p_group->getPairSgNumberPeptideMatchList();
std::vector<McqPeptide> mcq_peptide_list;
for (auto & sg_peptide_pair :sg_peptide_match_list) {
unsigned int sg_number = sg_peptide_pair.first;
const PeptideMatch * peptide_match = sg_peptide_pair.second;
McqPeptide mcq_peptide;
mcq_peptide.id = peptide_match->getGrpPeptideSp().get()->getGroupingId();
mcq_peptide.mods << peptide_match->getPeptideXtpSp().get()->getModifString();
mcq_peptide.prot_ids << p_group->getProteinGroupingIdOfSubgroup(sg_number);
mcq_peptide.seq = peptide_match->getPeptideXtpSp().get()->getSequence();
mcq_peptide.native_peptide = peptide_match->getPeptideXtpSp().get()->getNativePeptideP();
McqObserved observed = {peptide_match->getMsRunP(),peptide_match->getScan(),peptide_match->getCharge() };
mcq_peptide.observed_in.push_back(observed);
mcq_peptide_list.push_back(mcq_peptide);
McqPeptide mcq_peptide;
mcq_peptide.id = peptide_match->getGrpPeptideSp().get()->getGroupingId();
mcq_peptide.mods << peptide_match->getPeptideXtpSp().get()->getModifString();
mcq_peptide.prot_ids << p_group->getProteinGroupingIdOfSubgroup(sg_number);
mcq_peptide.seq = peptide_match->getPeptideXtpSp().get()->getSequence();
mcq_peptide.native_peptide = peptide_match->getPeptideXtpSp().get()->getNativePeptideP();
McqObserved observed = {peptide_match->getMsRunP(),peptide_match->getScan(),peptide_match->getCharge() };
mcq_peptide.observed_in.push_back(observed);
mcq_peptide_list.push_back(mcq_peptide);
}
......@@ -390,9 +390,9 @@ void MassChroQml::writePeptideListInGroup(const GroupingGroup * p_group) {
McqPeptide cumul = mcq_peptide_list[0];
for (McqPeptide & mcq_peptide : mcq_peptide_list) {
if (cumul.id == mcq_peptide.id) {
cumul.observed_in.push_back(mcq_peptide.observed_in[0]);
if (!cumul.prot_ids.contains(mcq_peptide.prot_ids[0])) {
cumul.prot_ids << mcq_peptide.prot_ids[0];
}
......@@ -450,11 +450,11 @@ void MassChroQml::writePeptideListInGroup(const GroupingGroup * p_group) {
//<observed_in data="samp0" scan="655" z="2" />
std::sort(mcq_peptide.observed_in.begin(), mcq_peptide.observed_in.end(),[](const McqObserved & first, const McqObserved & second) {
return std::tie(first.charge, first.scan, first.msrun) < std::tie(second.charge, second.scan, second.msrun);
});
return std::tie(first.charge, first.scan, first.msrun) < std::tie(second.charge, second.scan, second.msrun);
});
auto last = std::unique(mcq_peptide.observed_in.begin(), mcq_peptide.observed_in.end());
mcq_peptide.observed_in.erase(last, mcq_peptide.observed_in.end());
mcq_peptide.observed_in.erase(last, mcq_peptide.observed_in.end());
for (McqObserved observed_in : mcq_peptide.observed_in) {
_output_stream->writeStartElement("observed_in");
_output_stream->writeAttribute("data",observed_in.msrun->getXmlId());
......
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