diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 9d83c28381795063e2aaf2c1413a7bf8b640d8bf..42d4fb8ffd3688b5b44840562b52e09eea518787 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -29,8 +29,8 @@ SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${Qt5Xml_EXECUTABLE_COMPILE_FLAGS} ${Qt5
#sudo apt-get install libpappsomspp-dev
#FIND_PACKAGE( Pappsomspp REQUIRED )
- SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
-# SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
+# SET (PAPPSOMSPP_DIR "/home/olivier/eclipse/git/pappsomspp")
+ SET (PAPPSOMSPP_DIR "/home/langella/developpement/git/pappsomspp")
SET (PAPPSOMSPP_INCLUDE_DIR "${PAPPSOMSPP_DIR}/src")
SET (PAPPSOMSPP_QT4_LIBRARY "${PAPPSOMSPP_DIR}/cbuild/src/libpappsomspp-qt4.so")
diff --git a/src/core/identification_sources/identificationxtandemfile.cpp b/src/core/identification_sources/identificationxtandemfile.cpp
index 1f21279ea68f704d4b53a4b41a8ed1ee0215e937..3502835d87158b8de89bcdf77dcf0d4561bd6253 100644
--- a/src/core/identification_sources/identificationxtandemfile.cpp
+++ b/src/core/identification_sources/identificationxtandemfile.cpp
@@ -78,7 +78,7 @@ void IdentificationXtandemFile::parseTo(Project* p_project) {
}
}
- XtandemSaxHandler * parser = new XtandemSaxHandler(p_project, identification_group_p);
+ XtandemSaxHandler * parser = new XtandemSaxHandler(p_project, identification_group_p, this);
QXmlSimpleReader simplereader;
simplereader.setContentHandler(parser);
diff --git a/src/core/identificationgroup.cpp b/src/core/identificationgroup.cpp
index f85a149bceb40724962661b6cd653d491a050969..23eebfb3e05a4317cb4c674aebdce26978a6e42f 100644
--- a/src/core/identificationgroup.cpp
+++ b/src/core/identificationgroup.cpp
@@ -67,7 +67,7 @@ void IdentificationGroup::addProteinMatch(ProteinMatch * protein_match) {
throw pappso::PappsoException(QObject::tr("Error adding protein match : accession is empty"));
}
for (ProteinMatch * p_protein_match : _protein_match_list) {
- if (p_protein_match->getProteinXtpSp().get()->getAccession() == accession) {
+ if ((p_protein_match != protein_match) && (p_protein_match->getProteinXtpSp().get()->getAccession() == accession)) {
throw pappso::PappsoException(QObject::tr("Error adding protein match : accession %1 already registered").arg(accession));
}
}
diff --git a/src/gui/mainwindow.cpp b/src/gui/mainwindow.cpp
index 609e69950fcc1edb7de3b90cd804898a67bc1f15..8a03691f71654a48bdcbcca1cd7a84cbf85f2a4a 100644
--- a/src/gui/mainwindow.cpp
+++ b/src/gui/mainwindow.cpp
@@ -64,6 +64,7 @@ void XtpLoaderThread::doLoadingResults(bool is_individual, AutomaticFilterParame
project_sp.get()->readResultFile(filename);
}
+ project_sp.get()->updateAutomaticFilters(param);
emit projectReady(project_sp);
}
@@ -98,6 +99,7 @@ MainWindow::MainWindow(QWidget *parent):
//addDockWidget(Qt::RightDockWidgetArea, dock);
qRegisterMetaType<ProjectSp>("ProjectSp");
+ qRegisterMetaType<AutomaticFilterParameters>("AutomaticFilterParameters");
#if QT_VERSION >= 0x050000
// Qt5 code
/*
@@ -110,6 +112,7 @@ MainWindow::MainWindow(QWidget *parent):
connect(this, SIGNAL(operateXpipFile(QString)), worker,SLOT(doXpipFileLoad(QString)));
connect(worker, SIGNAL(projectReady(ProjectSp)), this,SLOT(doProjectReady(ProjectSp)));
+ connect(this, SIGNAL(operateLoadingResults(bool,AutomaticFilterParameters,QStringList)), worker,SLOT(doLoadingResults(bool,AutomaticFilterParameters,QStringList)));
connect(_p_load_results_dialog, SIGNAL(accepted()), this,SLOT(doAcceptedLoadResultDialog()));
/*
connect(&workerThread, SIGNAL(finished()), worker, SLOT(deleteLater()));
diff --git a/src/input/xpipsaxhandler.cpp b/src/input/xpipsaxhandler.cpp
index f494d5fd69a1b63a21a474b7d6629998e07cf711..bd719e399d2af7ffaad10b7f5e5ebae375bccad9 100644
--- a/src/input/xpipsaxhandler.cpp
+++ b/src/input/xpipsaxhandler.cpp
@@ -240,8 +240,6 @@ bool XpipSaxHandler::startElement_peptide(QXmlAttributes attributes) {
_p_peptide_match->setStart(attributes.value("start").simplified().toUInt()-1);
_p_peptide_match->setCharge(attributes.value("charge").simplified().toUInt());
- _p_peptide_match->setCharge(attributes.value("charge").simplified().toUInt());
-
IdentificationDataSource* p_identification_data_source = _p_project->getIdentificationDataSourceStore().getInstance(attributes.value("sample_file").simplified()).get();
_p_peptide_match->setIdentificationDataSource( p_identification_data_source);
if (p_identification_data_source->getMsRunSp().get() == nullptr) {
diff --git a/src/input/xtandemsaxhandler.cpp b/src/input/xtandemsaxhandler.cpp
index a720f5839c82e96eededa46f7ab35f5b2be73532..8e7b258b143004f204a6d008029b0391ba243f0f 100644
--- a/src/input/xtandemsaxhandler.cpp
+++ b/src/input/xtandemsaxhandler.cpp
@@ -35,9 +35,13 @@
#include "../utils/peptidestore.h"
#include "../utils/proteinstore.h"
-XtandemSaxHandler::XtandemSaxHandler(Project * p_project, IdentificationGroup * p_identification_group):_p_project(p_project)
+XtandemSaxHandler::XtandemSaxHandler(Project * p_project, IdentificationGroup * p_identification_group,
+ IdentificationDataSource * p_identification_data_source):_p_project(p_project)
{
_p_identification_group = p_identification_group;
+
+ _p_identification_data_source =p_identification_data_source;
+ _sp_msrun = p_identification_data_source->getMsRunSp();
}
XtandemSaxHandler::~XtandemSaxHandler()
@@ -63,8 +67,7 @@ bool XtandemSaxHandler::startElement(const QString & namespaceURI, const QString
}
else if (qName == "file") {
is_ok = startElement_file(attributes);
- } else if (qName == "peptide") {
- is_ok = startElement_peptide(attributes);
+
} else if (qName == "aa") {
is_ok = startElement_aa(attributes);
} else if (qName == "domain") {
@@ -117,7 +120,7 @@ bool XtandemSaxHandler::endElement(const QString & namespaceURI, const QString &
bool XtandemSaxHandler::startElement_group(QXmlAttributes attrs) {
//<group id="1976" mh="1120.529471" z="2" rt="PT667.022S" expect="9.7e-04" label="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC..." type="model" sumI="5.34" maxI="35986.9" fI="359.869" act="0" >
-
+ bool is_ok = true;
// logger.debug("startElementgroup begin");
// <group label="performance parameters" type="parameters">
_current_group_label = attrs.value("label");
@@ -128,118 +131,127 @@ bool XtandemSaxHandler::startElement_group(QXmlAttributes attrs) {
_charge = attrs.value("z").toUInt();
//_retention_time = attrs.value("rt");
}
+ return is_ok;
}
bool XtandemSaxHandler::startElement_note(QXmlAttributes attributes) {
//<note label="description">GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC //4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01;
////parent_gene=GRMZM2G083841</note>
+ bool is_ok = true;
_is_protein_description = false;
if (attributes.value("label") == "description") {
if (_tag_stack[_tag_stack.size() - 2] == "protein") {
_is_protein_description = true;
}
}
+ return is_ok;
}
bool XtandemSaxHandler::startElement_protein(QXmlAttributes attributes) {
//<protein expect="-704.6" id="1976.1" uid="195701" label="GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC..." sumI="9.36" >
-
- qDebug() << "startElement_protein ";
+ bool is_ok = true;
+ //qDebug() << "startElement_protein begin";
QString accession = attributes.value("label").simplified().split(" ", QString::SkipEmptyParts).at(0);
- ProteinMatch * p_protein_match = _p_identification_group->getProteinMatch(accession);
+ //qDebug() << "startElement_protein accession" << accession;
+ _p_protein_match = _p_identification_group->getProteinMatch(accession);
+ //qDebug() << "startElement_protein p_protein_match 1 " << _p_protein_match;
_current_protein.setAccession(accession);
- if (p_protein_match == nullptr) {
+ if (_p_protein_match == nullptr) {
_p_protein_match = new ProteinMatch();
+ //qDebug() << "startElement_protein p_protein_match 2 " << _p_protein_match;
_p_protein_match->setChecked(false);
}
+ //qDebug() << "startElement_protein p_protein_match 3 " << _p_protein_match;
ProteinXtpSp sp_xtp_protein = _current_protein.makeProteinXtpSp();
- p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
- qDebug() << "startElement_protein end" ;
- return true;
+ _p_protein_match->setProteinXtpSp(_p_project->getProteinStore().getInstance(sp_xtp_protein));
+
+ _p_identification_group->addProteinMatch(_p_protein_match);
+ //qDebug() << "startElement_protein end" ;
+ return is_ok;
}
bool XtandemSaxHandler::startElement_file(QXmlAttributes attributes) {
+ bool is_ok = true;
//<file type="peptide" URL="/gorgone/pappso/formation/TD/Database/Genome_Z_mays_5a.fasta"/>
if (attributes.value("type") == "peptide") {
//prot_.setDatabase(identification_.getDatabaseSet().getInstance(
- // attrs.getValue("URL")));
+ // attrs.getValue("URL")));
}
+ return is_ok;
}
bool XtandemSaxHandler::startElement_domain(QXmlAttributes attributes) {
//<domain id="1976.1.1" start="620" end="629" expect="9.7e-04" mh="1120.5307" delta="-0.0012" hyperscore="29.9"
//nextscore="10.2" y_score="10.4" y_ions="7" b_score="11.2" b_ions="3" pre="QLYR" post="RYGV"
//seq="AQEEMAQVAK" missed_cleavages="0">
-
qDebug() << "startElement_domain ";
+ bool is_ok = true;
+ _current_text = _current_text.simplified().replace(" ", "");
+ if (!_current_text.isEmpty()) {
+ _p_protein_match->getProteinXtpSp().get()->setSequence(_current_text);
+ }
+
+ // <domain id="4017.1.1" start="21" end="31" expect="2.0e-06"
+ // mh="1263.575"
+ // delta="0.998" hyperscore="32.9" nextscore="12.2" y_score="10.7"
+ // y_ions="9" b_score="0.0" b_ions="0"
+ // pre="VLGR" post="VEFM" seq="TGSQGQCTQVR" missed_cleavages="10">
+
+ // valeur généric du scan
+ _current_peptide_sp = PeptideXtp(attributes.value("seq").simplified()).makePeptideXtpSp();
+ _p_peptide_match = new PeptideMatch(_sp_msrun.get(), attributes.value("id").simplified().section(".",0,0).toUInt());
+
+ _p_peptide_match->setRetentionTime(_retention_time);
+ _p_peptide_match->setEvalue(attributes.value("expect").simplified().toDouble());
+
+ pappso::pappso_double xtandem_mhtheo = attributes.value("mh").simplified().toDouble();
+ pappso::pappso_double xtandem_delta = attributes.value("delta").simplified().toDouble();
+
+ pappso::pappso_double exp_mass = xtandem_mhtheo - xtandem_delta;
- MsRunSp ms_run = _p_project->getMsRunStore().getInstance(attributes.value("value").simplified());
- ms_run.get()->setXmlId(attributes.value("value").simplified());
- ms_run.get()->setFilename(attributes.value("value").simplified());
- _p_identification_group->addMsRunSp(ms_run);
- qDebug() << "startElement_domain end" ;
- return true;
-}
-bool XtandemSaxHandler::startElement_peptide(QXmlAttributes attributes) {
-
-//<peptide sample="20120208_Blein_rep4_1_B03_DW21-4-26-328"
- //sample_file="/gorgone/pappso/moulon/users/Melisande/test-param-masschroq/20120208_Blein_rep4_1_B03_DW21-4-26-328.xml"
- //scan="2589" scan_in_xtandem="2589" RT="603" mhplus_obser="873.5401" mhplus_theo="873.5408" deltamass="-7.0E-4"
- //sequence="IATAIEKK" pre="NPAR" post="AADA" start="331" stop="338" charge="2" evalue="9.2E-4" hypercorr="35.2" validate="true">
-//<modifs></modifs></peptide>
-
- //<modifs><modif aa="M" modvalue="15.99491" posi="17" posi_in_prot="49"/>
-//</modifs>
- qDebug() << "startElement_peptide ";
- _current_peptide_sp = PeptideXtp(attributes.value("sequence").simplified()).makePeptideXtpSp();
- MsRunSp ms_run_id = _p_project->getMsRunStore().getInstance(attributes.value("sample").simplified());
- _p_peptide_match = new PeptideMatch(ms_run_id.get(), attributes.value("scan").simplified().toUInt());
- _p_peptide_match->setRetentionTime(attributes.value("RT").simplified().toDouble());
- _p_peptide_match->setEvalue(attributes.value("evalue").simplified().toDouble());
- pappso::pappso_double exp_mass = attributes.value("mhplus_obser").simplified().toDouble() - pappso::MHPLUS;
_p_peptide_match->setExperimentalMass(exp_mass);
_p_peptide_match->setStart(attributes.value("start").simplified().toUInt()-1);
- _p_peptide_match->setCharge(attributes.value("charge").simplified().toUInt());
-
- _p_peptide_match->setCharge(attributes.value("charge").simplified().toUInt());
+ _p_peptide_match->setCharge(_charge);
- IdentificationDataSource* p_identification_data_source = _p_project->getIdentificationDataSourceStore().getInstance(attributes.value("sample_file").simplified()).get();
- _p_peptide_match->setIdentificationDataSource( p_identification_data_source);
- if (p_identification_data_source->getMsRunSp().get() == nullptr) {
- p_identification_data_source->setMsRunSp(ms_run_id);
- }
- if (p_identification_data_source->getMsRunSp().get() != ms_run_id.get()) {
- throw pappso::PappsoException(QObject::tr("p_identification_data_source->getMsRunSp().get() != ms_run_id.get()"));
- }
+ _p_peptide_match->setIdentificationDataSource( _p_identification_data_source);
_p_peptide_match->setChecked(false);
if (attributes.value("validate").simplified().toLower() == "true") {
_p_peptide_match->setChecked(true);
}
_p_protein_match->addPeptideMatch(_p_peptide_match);
- qDebug() << "startElement_peptide end" ;
- return true;
+
+
+
+ // missing informations
+ //peptide.set_hypercorr(Float.valueOf(attrs.getValue("hyperscore")));
+ //peptide.set_pre(attrs.getValue("pre"));
+ //peptide.set_post(attrs.getValue("post"));
+ //qDebug() << "startElement_domain end" ;
+ return is_ok;
}
bool XtandemSaxHandler::startElement_aa(QXmlAttributes attributes) {
//<aa type="M" at="624" modified="15.99491" />
+ bool is_ok = true;
qDebug() << "startElement_aa ";
- pappso::AaModificationP modif = _map_massstr_aamod[attributes.value("modvalue").simplified()];
- unsigned int position = attributes.value("posi").simplified().toUInt();
- _current_peptide_sp.get()->addAaModification(modif, position-1);
+ pappso::AaModificationP modif = getAaModificationP(attributes.value("modified").simplified().toDouble());
+ unsigned int position_in_prot = attributes.value("at").simplified().toUInt()-1;
+ _current_peptide_sp.get()->addAaModification(modif, position_in_prot-_p_peptide_match->getStart());
qDebug() << "startElement_aa end" ;
- return true;
+ return is_ok;
}
bool XtandemSaxHandler::endElement_note() {
//<note label="description">GRMZM2G083841_P01 P04711 Phosphoenolpyruvate carboxylase 1 (PEPCase 1)(PEPC 1)(EC //4.1.1.31) seq=translation; coord=9:61296279..61301686:1; parent_transcript=GRMZM2G083841_T01;
////parent_gene=GRMZM2G083841</note>
+ bool is_ok = true;
if (_is_protein_description) {
_p_protein_match->getProteinXtpSp().get()->setDescription(_current_text.section(" ",1));
}
- return true;
+ return is_ok;
}
diff --git a/src/input/xtandemsaxhandler.h b/src/input/xtandemsaxhandler.h
index c1864f9d81f58ea89d7cad090c2b478079f34d62..f129e5c30d53b0777e1de5c6ef60b95e50a1604b 100644
--- a/src/input/xtandemsaxhandler.h
+++ b/src/input/xtandemsaxhandler.h
@@ -43,7 +43,8 @@
class XtandemSaxHandler: public QXmlDefaultHandler
{
public:
- XtandemSaxHandler(Project * p_project, IdentificationGroup * p_identification_group);
+ XtandemSaxHandler(Project * p_project, IdentificationGroup * p_identification_group,
+ IdentificationDataSource * p_identification_data_source);
~XtandemSaxHandler();
bool startElement(const QString & namespaceURI, const QString & localName,
@@ -65,15 +66,14 @@ public:
private:
- bool startElement_group(QXmlAttributes attrs);
- bool startElement_peptide(QXmlAttributes attributes);
+ bool startElement_group(QXmlAttributes attrs);
bool startElement_protein(QXmlAttributes attributes);
bool startElement_note(QXmlAttributes attributes);
bool startElement_file(QXmlAttributes attributes);
bool startElement_aa(QXmlAttributes attributes);
bool startElement_domain(QXmlAttributes attributes);
bool endElement_note();
-
+
pappso::AaModificationP getAaModificationP(pappso::mz mass) const;
private:
@@ -83,14 +83,16 @@ private:
Project * _p_project;
IdentificationGroup * _p_identification_group;
-
+ IdentificationDataSource * _p_identification_data_source;
+ MsRunSp _sp_msrun;
+
ProteinMatch * _p_protein_match;
PeptideMatch * _p_peptide_match;
ProteinXtp _current_protein;
PeptideXtpSp _current_peptide_sp;
-
+
QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
-
+
QString _current_group_label;
QString _current_group_type;
unsigned int _scan;