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Commit 73cf8585 authored by Olivier Langella's avatar Olivier Langella
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WIP : writing MassChroqML

parent de411c62
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src/grouping/groupinggroup.cpp
+ 22
− 15
View file @ 73cf8585
......@@ -37,26 +37,33 @@ GroupingGroup::~GroupingGroup()
{
}
const std::vector<std::pair<unsigned int, const PeptideMatch *>> & GroupingGroup::getPairSgNumberPeptideMatchList() const {
return _pair_sg_number_peptide_match_list;
}
unsigned int GroupingGroup::getGroupNumber() const {
return _group_number;
}
unsigned int GroupingGroup::getNumberOfSubgroups() const {
return _number_of_subgroup;
}
const QStringList GroupingGroup::getSubgroupIdList(const PeptideMatch * p_peptide_match) const {
std::set<unsigned int> subgroup_list;
std::set<unsigned int> subgroup_list;
pappso::GrpPeptide * p_grp_peptide = p_peptide_match->getGrpPeptideSp().get();
if (p_grp_peptide != nullptr) {
for (auto && pair_peptide_match :_pair_sg_number_peptide_match_list) {
if(pair_peptide_match.second->getGrpPeptideSp().get() == p_grp_peptide) {
subgroup_list.insert(pair_peptide_match.first);
for (auto && pair_peptide_match :_pair_sg_number_peptide_match_list) {
if(pair_peptide_match.second->getGrpPeptideSp().get() == p_grp_peptide) {
subgroup_list.insert(pair_peptide_match.first);
}
}
}
QStringList sg_str_list;
for (unsigned int sgnum : subgroup_list) {
sg_str_list << QString("%1%2").arg(pappso::Utils::getLexicalOrderedString(_group_number)).arg(pappso::Utils::getLexicalOrderedString(sgnum));
}
QStringList sg_str_list;
for (unsigned int sgnum : subgroup_list) {
sg_str_list << QString("%1%2").arg(pappso::Utils::getLexicalOrderedString(_group_number)).arg(pappso::Utils::getLexicalOrderedString(sgnum));
}
return sg_str_list;
}
......@@ -65,12 +72,12 @@ unsigned int GroupingGroup::countSubgroupPresence(const PeptideMatch * p_peptide
std::set<unsigned int> subgroup_list;
pappso::GrpPeptide * p_grp_peptide = p_peptide_match->getGrpPeptideSp().get();
if (p_grp_peptide != nullptr) {
for (auto && pair_peptide_match :_pair_sg_number_peptide_match_list) {
if(pair_peptide_match.second->getGrpPeptideSp().get() == p_grp_peptide) {
subgroup_list.insert(pair_peptide_match.first);
for (auto && pair_peptide_match :_pair_sg_number_peptide_match_list) {
if(pair_peptide_match.second->getGrpPeptideSp().get() == p_grp_peptide) {
subgroup_list.insert(pair_peptide_match.first);
}
}
}
}
return subgroup_list.size();
}
......@@ -131,7 +138,7 @@ std::size_t GroupingGroup::countSpecificSequence(const ProteinMatch * p_protein_
}
void GroupingGroup::add(const ProteinMatch * p_protein_match) {
_group_number = p_protein_match->getGrpProteinSp().get()->getGroupNumber();
_group_number = p_protein_match->getGrpProteinSp().get()->getGroupNumber();
if (p_protein_match->getGrpProteinSp().get()->getRank() == 1) {
_number_of_subgroup++;
unsigned int sg_number = p_protein_match->getGrpProteinSp().get()->getSubGroupNumber();
......
src/grouping/groupinggroup.h
+ 4
− 0
View file @ 73cf8585
......@@ -40,6 +40,8 @@ public:
GroupingGroup();
~GroupingGroup();
unsigned int getGroupNumber() const ;
void add(const ProteinMatch * p_protein_match);
std::size_t countSpecificSpectrum(const ProteinMatch * p_protein_match) const;
......@@ -55,6 +57,8 @@ public:
* */
const QStringList getSubgroupIdList(const PeptideMatch * p_peptide_match) const;
const std::vector<std::pair<unsigned int, const PeptideMatch *>> & getPairSgNumberPeptideMatchList() const;
private :
unsigned int _group_number=0;
......
src/output/masschroqml.cpp
+ 51
− 33
View file @ 73cf8585
......@@ -72,7 +72,7 @@ void MassChroQml::write(ProjectSp sp_project) {
if (_sp_project.get() == nullptr) {
throw pappso::PappsoException(QObject::tr("Error writing MassChroqML file :\n project is empty"));
}
//<masschroq>
_output_stream->writeStartElement("masschroq");
_output_stream->writeAttribute("type","input");
......@@ -116,27 +116,44 @@ void MassChroQml::write(ProjectSp sp_project) {
void MassChroQml::writePeptideList() {
//<peptide_list>
_output_stream->writeStartElement("peptide_list");
/*
<peptide id="pep0" mh="1463.626" mods="114.08" prot_ids="P1.1"
seq="TCVADESHAGCEK">
<modifications><!-- this tag is optional but gives an exact mass computation -->
<psimod at="2" acc="MOD:00397"></psimod>
<psimod at="11" acc="MOD:00397"></psimod>
</modifications>
<observed_in data="samp0" scan="655" z="2" />
<observed_in data="samp1" scan="798" z="2" />
</peptide>
<peptide id="pep1" mh="1103.461" mods="57.04" prot_ids="P1.1"
seq="ADESHAGCEK">
<modifications><!-- this tag is optional but gives an exact mass computation -->
<psimod at="8" acc="MOD:00397"></psimod>
</modifications>
<observed_in data="samp3" scan="663" z="2" />
</peptide>*/
//</peptide_list>
QStringList empty;
for (const GroupingGroupSp & group:_group_list) {
std::map<const PeptideMatch *, QStringList> peptide_sg_map;
unsigned int group_number = group.get()->getGroupNumber();
for (auto && pair_peptide_match :group.get()->getPairSgNumberPeptideMatchList()) {
unsigned int sg_number = pair_peptide_match.first;
const PeptideMatch * p_peptide_match = pair_peptide_match.second;
if (!p_peptide_match->isGrouped()) continue;
std::pair<std::map< const PeptideMatch *, QStringList>::iterator,bool> ret = peptide_sg_map.insert(std::pair<const PeptideMatch *, QStringList>(p_peptide_match, empty));
QString sg_str = QString("%1.%2.a1").arg(pappso::Utils::getLexicalOrderedString(group_number)).arg(pappso::Utils::getLexicalOrderedString(sg_number));
if (!ret.first->second.contains(sg_str)) {
ret.first->second << sg_str;
}
}
for (auto && pair_peptide_sgid : peptide_sg_map) {
//<peptide id="pep0" mh="1463.626" mods="114.08" prot_ids="P1.1"
// seq="TCVADESHAGCEK">
_output_stream->writeStartElement("peptide");
_output_stream->writeAttribute("id",pair_peptide_sgid.first->getGrpPeptideSp().get()->getGroupingId());
_output_stream->writeAttribute("prot_ids",pair_peptide_sgid.second.join(" "));
/*
<modifications><!-- this tag is optional but gives an exact mass computation -->
<psimod at="2" acc="MOD:00397"></psimod>
<psimod at="11" acc="MOD:00397"></psimod>
</modifications>
<observed_in data="samp0" scan="655" z="2" />
<observed_in data="samp1" scan="798" z="2" />*/
//</peptide>
_output_stream->writeEndElement();
}
}
//</peptide_list>
_output_stream->writeEndElement();
}
void MassChroQml::writeGroups() {
//<groups>
_output_stream->writeStartElement("groups");
......@@ -168,21 +185,22 @@ void MassChroQml::writeProteinList() {
_p_identification_group = identification_list[0];
for (ProteinMatch * p_protein_match :_p_identification_group->getProteinMatchList()) {
if (!p_protein_match->isGrouped()) continue;
//<protein desc="conta|P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
// id="P1.1" />
//<protein desc="conta|P02769|ALBU_BOVIN SERUM ALBUMIN PRECURSOR."
// id="P1.1" />
_group_list.insert(p_protein_match->getGroupingGroupSp());
pappso::GrpProteinSp grp_protein = p_protein_match->getGrpProteinSp();
if (grp_protein.get()->getRank() == 1) {
_output_stream->writeStartElement("protein");
_output_stream->writeAttribute("id",grp_protein.get()->getGroupingId());
QStringList list;
list << p_protein_match->getProteinXtpSp().get()->getAccession();
list << p_protein_match->getProteinXtpSp().get()->getDescription();
_output_stream->writeAttribute("desc",list.join(" "));
//<protein desc="conta|P02770|ALBU_RAT SERUM ALBUMIN PRECURSOR."
// id="P1.2" />
_output_stream->writeEndElement();
_output_stream->writeStartElement("protein");
_output_stream->writeAttribute("id",grp_protein.get()->getGroupingId());
QStringList list;
list << p_protein_match->getProteinXtpSp().get()->getAccession();
list << p_protein_match->getProteinXtpSp().get()->getDescription();
_output_stream->writeAttribute("desc",list.join(" "));
//<protein desc="conta|P02770|ALBU_RAT SERUM ALBUMIN PRECURSOR."
// id="P1.2" />
_output_stream->writeEndElement();
}
}
//</protein_list>
_output_stream->writeEndElement();
//</protein_list>
_output_stream->writeEndElement();
}
src/output/masschroqml.h
+ 2
− 0
View file @ 73cf8585
......@@ -34,6 +34,7 @@
#include <QFile>
#include <QString>
#include "../core/project.h"
#include "../grouping/groupinggroup.h"
class MassChroQml
{
......@@ -52,6 +53,7 @@ private :
QXmlStreamWriter * _output_stream;
ProjectSp _sp_project;
IdentificationGroup * _p_identification_group;
std::set<GroupingGroupSp> _group_list;
};
#endif // MASSCHROQML_H
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