diff --git a/src/input/pepxmlsaxhandler.cpp b/src/input/pepxmlsaxhandler.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..0879a049fcc08354a7891461b2c419269a2c0fcf
--- /dev/null
+++ b/src/input/pepxmlsaxhandler.cpp
@@ -0,0 +1,555 @@
+/**
+ * \file input/pepxmlsaxhandler.cpp
+ * \date 18/6/2018
+ * \author Olivier Langella
+ * \brief parse pepxml result file
+ */
+
+
+/*******************************************************************************
+ * Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ ******************************************************************************/
+
+#include "pepxmlsaxhandler.h"
+
+
+#include <pappsomspp/exception/exceptionnotfound.h>
+#include <cmath>
+#include "../core/peptideevidence.h"
+#include "../utils/peptidestore.h"
+#include "../utils/proteinstore.h"
+
+PepXmlSaxHandler::PepXmlSaxHandler(WorkMonitorInterface *p_monitor,
+ Project *p_project)
+ : _p_project(p_project)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _p_monitor = p_monitor;
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+}
+
+PepXmlSaxHandler::~PepXmlSaxHandler()
+{
+}
+
+
+bool
+PepXmlSaxHandler::startElement(const QString &namespaceURI,
+ const QString &localName, const QString &qName,
+ const QXmlAttributes &attributes)
+{
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ _tag_stack.push_back(qName);
+ bool is_ok = true;
+
+ try
+ {
+ // startElement_group
+ if(_tag_stack.size() == 1)
+ {
+ _is_xtpcpp_xpip = true;
+ if(qName != "xpip")
+ {
+ _is_xtpcpp_xpip = false;
+ throw pappso::ExceptionNotFound(
+ QObject::tr("ERROR this file is not a pep xml file %1")
+ .arg(qName));
+ }
+ }
+ else if(qName == "protein_match")
+ {
+ if(_count_total % 100 == 0)
+ {
+ _p_monitor->message(QString("reading protein matches %1 on %2")
+ .arg(_count_protein_matches)
+ .arg(_total_protein_matches),
+ _count_total);
+ }
+ is_ok = startElement_protein_match(attributes);
+ }
+ else if(qName == "peptide_match")
+ {
+ is_ok = startElement_peptide_match(attributes);
+ }
+ else if(qName == "protein")
+ {
+ if(_count_total % 100 == 0)
+ {
+ _p_monitor->message(QString("reading proteins %1 on %2")
+ .arg(_count_proteins)
+ .arg(_total_proteins),
+ _count_total);
+ }
+ is_ok = startElement_protein(attributes);
+ }
+ else if(qName == "identification_source")
+ {
+ is_ok = startElement_identification_source(attributes);
+ }
+ else if(qName == "param")
+ {
+ is_ok = startElement_param(attributes);
+ }
+ else if(qName == "stat")
+ {
+ is_ok = startElement_stat(attributes);
+ }
+ else if(qName == "identification_group")
+ {
+ is_ok = startElement_identification_group(attributes);
+ }
+ else if(qName == "peptide_evidence_list")
+ {
+ is_ok = startElement_peptide_evidence_list(attributes);
+ }
+ else if(qName == "counts")
+ {
+ is_ok = startElement_counts(attributes);
+ }
+ else if(qName == "label_method")
+ {
+ is_ok = startElement_label_method(attributes);
+ }
+ //<sample value="P6_08_10"/>
+ else if(qName == "msrun")
+ {
+ is_ok = startElement_msrun(attributes);
+ }
+ else if(qName == "peptide")
+ {
+ if(_count_total % 100 == 0)
+ {
+ _p_monitor->message(QObject::tr("reading peptide %1 on %2")
+ .arg(_count_peptides)
+ .arg(_total_peptides),
+ _count_total);
+ }
+ is_ok = startElement_peptide(attributes);
+ }
+ else if(qName == "peptide_evidence")
+ {
+ if(_count_total % 100 == 0)
+ {
+ _p_monitor->message(
+ QObject::tr("reading peptide evidence %1 on %2")
+ .arg(_count_peptide_evidences)
+ .arg(_total_peptide_evidences),
+ _count_total);
+ }
+ is_ok = startElement_peptide_evidence(attributes);
+ }
+ else if(qName == "modification")
+ {
+ is_ok = startElement_modification(attributes);
+ }
+ else if(qName == "mod")
+ {
+ is_ok = startElement_mod(attributes);
+ }
+ else if(qName == "filter_params")
+ {
+ is_ok = startElement_filter_params(attributes);
+ }
+ else if(qName == "description")
+ {
+ is_ok = startElement_description(attributes);
+ }
+ else if(qName == "fasta_file")
+ {
+ is_ok = startElement_fasta_file(attributes);
+ }
+ else if(qName == "contaminants")
+ {
+ is_ok = startElement_contaminants(attributes);
+ }
+ else if(qName == "decoys")
+ {
+ is_ok = startElement_decoys(attributes);
+ }
+
+ _current_text.clear();
+ }
+ catch(pappso::PappsoException exception_pappso)
+ {
+ _errorStr = QObject::tr("ERROR in PepXmlSaxHandler::startElement tag "
+ "%1, PAPPSO exception:\n%2")
+ .arg(qName)
+ .arg(exception_pappso.qwhat());
+ return false;
+ }
+ catch(std::exception exception_std)
+ {
+ _errorStr =
+ QObject::tr(
+ "ERROR in PepXmlSaxHandler::startElement tag %1, std exception:\n%2")
+ .arg(qName)
+ .arg(exception_std.what());
+ return false;
+ }
+ return is_ok;
+}
+
+bool
+PepXmlSaxHandler::endElement(const QString &namespaceURI,
+ const QString &localName, const QString &qName)
+{
+
+ qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
+ bool is_ok = true;
+ // endElement_peptide_list
+ try
+ {
+ if(qName == "protein")
+ {
+ is_ok = endElement_protein();
+ }
+ else if(qName == "peptide")
+ {
+ is_ok = endElement_peptide();
+ }
+ else if(qName == "msrun")
+ {
+ is_ok = endElement_msrun();
+ }
+ else if(qName == "sequence")
+ {
+ is_ok = endElement_sequence();
+ }
+ else if(qName == "protein_match")
+ {
+ is_ok = endElement_protein_match();
+ }
+ else if(qName == "peptide_evidence")
+ {
+ is_ok = endElement_peptide_evidence();
+ }
+ else if(qName == "peptide_evidence_list")
+ {
+ is_ok = endElement_peptide_evidence_list();
+ }
+ else if(qName == "identification_group")
+ {
+ is_ok = endElement_identification_group();
+ }
+ else if(qName == "identification_source")
+ {
+ is_ok = endElement_identification_source();
+ }
+
+ // end of detection_moulon
+ // else if ((_tag_stack.size() > 1) &&
+ // (_tag_stack[_tag_stack.size() - 2] == "detection_moulon"))
+ }
+ catch(pappso::PappsoException exception_pappso)
+ {
+ _errorStr = QObject::tr("ERROR in PepXmlSaxHandler::endElement tag %1, "
+ "PAPPSO exception:\n%2")
+ .arg(qName)
+ .arg(exception_pappso.qwhat());
+ return false;
+ }
+ catch(std::exception exception_std)
+ {
+ _errorStr =
+ QObject::tr(
+ "ERROR in PepXmlSaxHandler::endElement tag %1, std exception:\n%2")
+ .arg(qName)
+ .arg(exception_std.what());
+ return false;
+ }
+
+ _current_text.clear();
+ _tag_stack.pop_back();
+
+ return is_ok;
+}
+
+// <msms_pipeline_analysis date="2015-01-19T13:28:41"
+// xmlns="http://regis-web.systemsbiology.net/pepXML"
+// xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+// xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v117.xsd"
+// summary_xml="/gorgone/pappso/abrf_2015/mzXML/JD_06232014_sample1-A.pep.xml">
+
+bool
+PepXmlSaxHandler::startElement_msms_pipeline_analysis(QXmlAttributes attributes)
+{
+ QString original_filename = attributes.value("summary_xml");
+}
+
+// <msms_run_summary
+// base_name="/gorgone/pappso/abrf_2015/mzXML/JD_06232014_sample1-A"
+// msManufacturer="Thermo Scientific" msModel="Q Exactive"
+// raw_data_type="raw" raw_data=".mzXML">
+bool
+PepXmlSaxHandler::startElement_msms_run_summary(QXmlAttributes attributes)
+{
+ QString mz_datafile = QString("%1%2")
+ .arg(attributes.value("base_name"))
+ .arg(attributes.value("raw_data"));
+}
+
+// <search_database
+// local_path="/gorgone/pappso/abrf_2015/fasta/iPRG2015.fasta" type="AA"/>
+bool
+PepXmlSaxHandler::startElement_search_database(QXmlAttributes attributes)
+{
+ QString fastafile = attributes.value("local_path");
+}
+
+// <search_summary
+// base_name="/gorgone/pappso/moulon/users/Olivier/Delphine_Pecqueur/mzXML/330_01_01_C3G3_150122_01"
+// search_engine="X! Tandem (k-score)" precursor_mass_type="monoisotopic"
+// fragment_mass_type="monoisotopic" search_id="1">
+bool
+PepXmlSaxHandler::startElement_search_summary(QXmlAttributes attributes)
+{
+ _current_search_engine = attributes.value("search_engine");
+}
+
+// <spectrum_query spectrum="JD_06232014_sample1-A.00005.00005.2"
+// start_scan="5" end_scan="5" precursor_neutral_mass="819.347822"
+// assumed_charge="2" index="1" retention_time_sec="1.4">
+// <spectrum_query spectrum="JD_06232014_sample1-A.00006.00006.2"
+// start_scan="6" end_scan="6" precursor_neutral_mass="870.405029296875"
+// assumed_charge="2" index="1">
+bool
+PepXmlSaxHandler::startElement_spectrum_query(QXmlAttributes attributes)
+{
+ unsigned int start_scan = attributes.value("start_scan").toUInt();
+ unsigned int end_scan = attributes.value("end_scan").toUInt();
+ if(start_scan != end_scan)
+ {
+ String message = "ERROR reading pepxml file :\n" +
+ "unable to read search results from '" +
+ this.currentSearchEngine + "' as start " +
+ currentStartScan + " and end " + currentEndScan +
+ " scans are different";
+ logger.error(message);
+ throw new MSMSException(message);
+ }
+ currentZ = new Integer(attrs.getValue("assumed_charge"));
+ if(attrs.getValue("retention_time_sec") == null)
+ {
+ String message =
+ "ERROR reading pepxml file :\n" +
+ "unable to read search results from '" + this.currentSearchEngine +
+ "' as retention time is not given in spectrum_query elements";
+ logger.warn(message);
+ // throw new MSMSException(message);
+
+ currentRt = (double)0;
+ }
+ else
+ {
+ currentRt = new Double(attrs.getValue("retention_time_sec"));
+ }
+ currentPrecursorNeutralMass =
+ new Double(attrs.getValue("precursor_neutral_mass")) + Utils.mhplus;
+}
+
+// <search_hit hit_rank="5" peptide="MKDFSTK" peptide_prev_aa="K"
+// peptide_next_aa="R" protein="sp|P34218|SAS3_YEAST" num_tot_proteins="1"
+// num_matched_ions="2" tot_num_ions="12" calc_neutral_pep_mass="871.410939"
+// massdiff="-1.006264" num_tol_term="2" num_missed_cleavages="1"
+// num_matched_peptides="190">
+bool
+PepXmlSaxHandler::startElement_search_hit(QXmlAttributes attributes)
+{
+ QString proteinName = attributes.value("protein");
+
+ Protein protein = new Protein();
+ protein.set_description(proteinName);
+ if(identification.contain_protein(protein))
+ {
+ // new protein, new match
+ currentMatch = new Match();
+ currentMatch.set_protein_match(protein);
+ identification.add_protein(protein, currentMatch);
+ }
+
+ else
+ {
+ // get existing match for this protein
+ currentMatch = (Match)identification.get_match(protein);
+ }
+ protein = currentMatch.get_protein_match();
+ protein.setDatabase(
+ identification.getDatabaseSet().getInstance(this.fastaFile.getName()));
+
+ this.currentPeptide = new PeptideProphet();
+ currentPeptide.set_sample_id(
+ identification.getMsRunSet().getInstance(identificationDataSource),
+ identificationDataSource);
+
+ _current_peptide_sp =
+ PeptideXtp(attributes.value("peptide").simplified()).makePeptideXtpSp();
+
+ currentPeptide.set_pre(attrs.getValue("peptide_prev_aa"));
+ currentPeptide.set_post(attrs.getValue("peptide_next_aa"));
+
+ currentPeptide.set_scan(this.currentEndScan.intValue());
+ Double calc_neutral_pep_mass =
+ new Double(attrs.getValue("calc_neutral_pep_mass")) + Utils.mhplus;
+ Double massdiff = new Double(attrs.getValue("massdiff"));
+
+ currentPeptide.set_mhplus_theo(calc_neutral_pep_mass);
+ currentPeptide.set_deltamass(massdiff);
+ currentPeptide.set_mhplus_obser(currentPrecursorNeutralMass);
+ currentPeptide.set_charge(this.currentZ);
+ currentPeptide.setRt(this.currentRt.floatValue());
+
+ /*
+ * if (Math.abs(massdiff) > 1) { String message =
+ * "massdiff is too high"; logger.error(message); throw new
+ * MSMSException(message); }
+ */
+ // valeur specifique de la séquence matche
+ // peptide.set_start(Integer.parseInt(attrs.getValue("start")));
+ // peptide.set_stop(Integer.parseInt(attrs.getValue("end")));
+ // peptide.set_evalue(Float.valueOf(attrs.getValue("expect")));
+ // peptide.set_hypercorr(Float.valueOf(attrs.getValue("hyperscore")));
+}
+
+bool
+XtpXpipSaxHandler::endElement_search_hit()
+{
+ if(currentPeptideProphetProbability != null)
+ {
+ currentPeptide.setProphetProbability(currentPeptideProphetProbability);
+ }
+ if(currentPeptideInterProphetProbability != null)
+ {
+ currentPeptide.setInterProphetProbability(
+ currentPeptideInterProphetProbability);
+ }
+ currentPeptide.setSearchEngine(this.currentSearchEngine);
+
+ identification.add_peptide(this.currentPeptide);
+ currentMatch.add_peptide_match(currentPeptide);
+
+ currentPeptideProphetProbability = null;
+ currentPeptideInterProphetProbability = null;
+ currentExpectedValue = null;
+}
+
+// <peptideprophet_result probability="0.0245"
+// all_ntt_prob="(0.0000,0.0093,0.0245)">
+bool
+PepXmlSaxHandler::startElement_peptideprophet_result(QXmlAttributes attributes)
+{
+ this.currentPeptideProphetProbability =
+ Double.parseDouble(attrs.getValue("probability"));
+}
+
+// <interprophet_result probability="0.00886064"
+// all_ntt_prob="(0,0.0033303,0.00886064)">
+bool
+PepXmlSaxHandler::startElement_interprophet_result(QXmlAttributes attributes)
+{
+ this.currentPeptideInterProphetProbability =
+ Double.parseDouble(attrs.getValue("probability"));
+}
+
+/*
+ * <search_score name="xcorr" value="0.528"/> <search_score name="deltacn"
+ * value="0.059"/> <search_score name="deltacnstar" value="0.000"/>
+ * <search_score name="spscore" value="29.4"/> <search_score name="sprank"
+ * value="2"/> <search_score name="expect" value="1.00E+00"/>
+ */
+bool
+PepXmlSaxHandler::startElement_search_score(QXmlAttributes attributes)
+{
+ String name = attrs.getValue("name");
+ String valueStr = attrs.getValue("value");
+ if(!valueStr.isEmpty())
+ {
+ if(name.equals("expect"))
+ {
+ currentExpectedValue = new Double(valueStr);
+ currentPeptide.set_evalue(currentExpectedValue.floatValue());
+ }
+ // <search_score name="hyperscore" value="232"/>
+ if(name.equals("hyperscore"))
+ {
+ currentPeptide.set_hypercorr(Float.parseFloat(valueStr));
+ }
+ }
+}
+
+// <modification_info modified_peptide="SQRDCR"> <mod_aminoacid_mass
+// position="5" mass="160.030649"/> </modification_info>
+bool
+PepXmlSaxHandler::startElement_mod_aminoacid_mass(QXmlAttributes attributes)
+{
+ double massFloat = attributes.value("mass").toDouble();
+ int position = attributes.value("position").toUInt();
+ String aa = _current_peptide_sp.get()->getSequence().substring(position - 1, position);
+ Float massDiff = massFloat - Utils.getAaMass(aa.charAt(0));
+
+ this.currentPeptide.set_Modifs(aa, position - 1, massDiff);
+ // modifs liste for isotopic analysis
+ identification.add_modifs_to_liste(new Modifs(massFloat));
+
+ pappso::AaModificationP modif = Utils::guessAaModificationPbyMonoisotopicMassDelta(attributes.value("modified").simplified().toDouble());
+
+pappso::AaModificationP modif = pappso::AaModification::getInstance(attributes.value("mass").simplified());
+ unsigned int position = attributes.value("position").simplified().toUInt();
+ _current_peptide_sp.get()->addAaModification(modif, position-1);
+}
+
+
+bool
+PepXmlSaxHandler::endElement_modification_info()
+{
+}
+
+
+bool PepXmlSaxHandler::error(const QXmlParseException &exception) {
+ _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+ "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
+ exception.message());
+
+ return false;
+}
+
+
+bool PepXmlSaxHandler::fatalError(const QXmlParseException &exception) {
+ _errorStr = QObject::tr("Parse error at line %1, column %2 :\n"
+ "%3").arg(exception.lineNumber()).arg(exception.columnNumber()).arg(
+ exception.message());
+ return false;
+}
+
+QString PepXmlSaxHandler::errorString() const {
+ return _errorStr;
+}
+
+
+bool PepXmlSaxHandler::endDocument() {
+ return true;
+}
+
+bool PepXmlSaxHandler::startDocument() {
+ return true;
+}
+
+bool PepXmlSaxHandler::characters(const QString &str) {
+ _current_text += str;
+ return true;
+}
diff --git a/src/input/pepxmlsaxhandler.h b/src/input/pepxmlsaxhandler.h
new file mode 100644
index 0000000000000000000000000000000000000000..2892c9859612fd5b473bfbdfa88d0d6552cd27f3
--- /dev/null
+++ b/src/input/pepxmlsaxhandler.h
@@ -0,0 +1,106 @@
+/**
+ * \file input/pepxmlsaxhandler.h
+ * \date 18/6/2018
+ * \author Olivier Langella
+ * \brief parse pepxml result file
+ */
+
+
+/*******************************************************************************
+* Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.fr>.
+*
+* This file is part of XTPcpp.
+*
+* XTPcpp is free software: you can redistribute it and/or modify
+* it under the terms of the GNU General Public License as published by
+* the Free Software Foundation, either version 3 of the License, or
+* (at your option) any later version.
+*
+* XTPcpp is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+*
+******************************************************************************/
+
+
+#ifndef PEPXMLSAXHANDLER_H
+#define PEPXMLSAXHANDLER_H
+
+#include <QXmlDefaultHandler>
+#include <pappsomspp/pappsoexception.h>
+#include "../core/proteinxtp.h"
+#include "../core/peptidextp.h"
+#include <pappsomspp/amino_acid/aamodification.h>
+#include "../core/project.h"
+#include "../core/proteinmatch.h"
+
+class PepXmlSaxHandler : public QXmlDefaultHandler
+{
+ public:
+ PepXmlSaxHandler(Project *p_project,
+ IdentificationGroup *p_identification_group,
+ IdentificationDataSource *p_identification_data_source);
+ ~PepXmlSaxHandler();
+
+ bool startElement(const QString &namespaceURI, const QString &localName,
+ const QString &qName, const QXmlAttributes &attributes);
+
+ bool endElement(const QString &namespaceURI, const QString &localName,
+ const QString &qName);
+
+ bool startDocument();
+
+ bool endDocument();
+
+ bool characters(const QString &str);
+
+ bool fatalError(const QXmlParseException &exception);
+ bool error(const QXmlParseException &exception);
+
+ QString errorString() const;
+
+
+ private:
+ bool startElement_msms_pipeline_analysis(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_domain();
+ bool endElement_note();
+
+ private:
+ std::vector<QString> _tag_stack;
+ QString _errorStr;
+ QString _current_text;
+
+ Project *_p_project;
+ IdentificationGroup *_p_identification_group;
+ IdentificationDataSource *_p_identification_data_source;
+ MsRunSp _sp_msrun;
+
+ ProteinMatch *_p_protein_match;
+ PeptideEvidence *_p_peptide_evidence;
+ PeptideMatch _current_peptide_match;
+ ProteinXtp _current_protein;
+ PeptideXtpSp _current_peptide_sp;
+
+ QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
+
+ QString _current_group_label;
+ QString _current_group_type;
+ QString _current_note_label;
+ QString _current_note_type;
+ unsigned int _scan;
+ pappso::pappso_double _mhplus_obser;
+ unsigned int _charge;
+ pappso::pappso_double _retention_time;
+ bool _is_protein_description = false;
+};
+
+#endif // PEPXMLSAXHANDLER_H
diff --git a/src/input/xtandemsaxhandler.h b/src/input/xtandemsaxhandler.h
index a344676a7de3bec3f9f8e58e34e4dd4d901e664e..aa5bef914393fff6233b1a8225757724b35d384b 100644
--- a/src/input/xtandemsaxhandler.h
+++ b/src/input/xtandemsaxhandler.h
@@ -7,26 +7,27 @@
/*******************************************************************************
-* Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
-*
-* This file is part of XTPcpp.
-*
-* XTPcpp is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* XTPcpp is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2017 Olivier Langella <Olivier.Langella@u-psud.fr>.
+ *
+ * This file is part of XTPcpp.
+ *
+ * XTPcpp is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * XTPcpp is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with XTPcpp. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
+ *implementation
+ ******************************************************************************/
#ifndef XTANDEMSAXHANDLER_H
#define XTANDEMSAXHANDLER_H
@@ -40,68 +41,69 @@
#include "../core/project.h"
#include "../core/proteinmatch.h"
-class XtandemSaxHandler: public QXmlDefaultHandler
+class XtandemSaxHandler : public QXmlDefaultHandler
{
-public:
- XtandemSaxHandler(Project * p_project, IdentificationGroup * p_identification_group,
- IdentificationDataSource * p_identification_data_source);
- ~XtandemSaxHandler();
-
- bool startElement(const QString & namespaceURI, const QString & localName,
- const QString & qName, const QXmlAttributes & attributes);
-
- bool endElement(const QString & namespaceURI, const QString & localName,
- const QString & qName);
-
- bool startDocument();
-
- bool endDocument();
-
- bool characters(const QString &str);
-
- bool fatalError(const QXmlParseException &exception);
- bool error(const QXmlParseException &exception);
-
- QString errorString() const;
-
-
-private:
- 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_domain();
- bool endElement_note();
-
-private:
- std::vector<QString> _tag_stack;
- QString _errorStr;
- QString _current_text;
-
- Project * _p_project;
- IdentificationGroup * _p_identification_group;
- IdentificationDataSource * _p_identification_data_source;
- MsRunSp _sp_msrun;
-
- ProteinMatch * _p_protein_match;
- PeptideEvidence * _p_peptide_evidence;
- PeptideMatch _current_peptide_match;
- ProteinXtp _current_protein;
- PeptideXtpSp _current_peptide_sp;
-
- QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
-
- QString _current_group_label;
- QString _current_group_type;
- QString _current_note_label;
- QString _current_note_type;
- unsigned int _scan;
- pappso::pappso_double _mhplus_obser;
- unsigned int _charge;
- pappso::pappso_double _retention_time;
- bool _is_protein_description = false;
+ public:
+ XtandemSaxHandler(Project *p_project,
+ IdentificationGroup *p_identification_group,
+ IdentificationDataSource *p_identification_data_source);
+ ~XtandemSaxHandler();
+
+ bool startElement(const QString &namespaceURI, const QString &localName,
+ const QString &qName, const QXmlAttributes &attributes);
+
+ bool endElement(const QString &namespaceURI, const QString &localName,
+ const QString &qName);
+
+ bool startDocument();
+
+ bool endDocument();
+
+ bool characters(const QString &str);
+
+ bool fatalError(const QXmlParseException &exception);
+ bool error(const QXmlParseException &exception);
+
+ QString errorString() const;
+
+
+ private:
+ 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_domain();
+ bool endElement_note();
+
+ private:
+ std::vector<QString> _tag_stack;
+ QString _errorStr;
+ QString _current_text;
+
+ Project *_p_project;
+ IdentificationGroup *_p_identification_group;
+ IdentificationDataSource *_p_identification_data_source;
+ MsRunSp _sp_msrun;
+
+ ProteinMatch *_p_protein_match;
+ PeptideEvidence *_p_peptide_evidence;
+ PeptideMatch _current_peptide_match;
+ ProteinXtp _current_protein;
+ PeptideXtpSp _current_peptide_sp;
+
+ QMap<QString, pappso::AaModificationP> _map_massstr_aamod;
+
+ QString _current_group_label;
+ QString _current_group_type;
+ QString _current_note_label;
+ QString _current_note_type;
+ unsigned int _scan;
+ pappso::pappso_double _mhplus_obser;
+ unsigned int _charge;
+ pappso::pappso_double _retention_time;
+ bool _is_protein_description = false;
};
#endif // XTANDEMSAXHANDLER_H
diff --git a/src/main.cpp b/src/main.cpp
index cf3dac47b669a293b98f8491ddbd8e07577a8921..c42ce2257ee01f84d985c526d5c2ff38a0c6dbd2 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -1,76 +1,79 @@
/*******************************************************************************
-* Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
-*
-* This file is part of PAPPSOms-tools.
-*
-* PAPPSOms-tools is free software: you can redistribute it and/or modify
-* it under the terms of the GNU General Public License as published by
-* the Free Software Foundation, either version 3 of the License, or
-* (at your option) any later version.
-*
-* PAPPSOms-tools is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
-*
-* Contributors:
-* Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and implementation
-******************************************************************************/
+ * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
+ *
+ * This file is part of PAPPSOms-tools.
+ *
+ * PAPPSOms-tools is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * PAPPSOms-tools is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
+ *
+ * Contributors:
+ * Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
+ *implementation
+ ******************************************************************************/
+#include "config.h"
+#include "gui/mainwindow.h"
+#include "utils/types.h"
#include <QApplication>
#include <QTimer>
#include <iostream>
#include <pappsomspp/pappsoexception.h>
-#include "config.h"
-#include "gui/mainwindow.h"
-#include "utils/types.h"
using namespace std;
-int main(int argc, char *argv[])
+int
+main(int argc, char *argv[])
{
- QTextStream errorStream(stderr, QIODevice::WriteOnly);
- QApplication app(argc, argv);
+ QTextStream errorStream(stderr, QIODevice::WriteOnly);
+ QApplication app(argc, argv);
- qRegisterMetaType<TandemRunBatch>("TandemRunBatch");
- qRegisterMetaType<std::vector<pappso::mz>>("std::vector<pappso::mz>");
- qRegisterMetaType<pappso::PrecisionP>("pappso::PrecisionP");
- qRegisterMetaType<std::vector<pappso::XicSp>>("std::vector<pappso::XicSp>");
- qRegisterMetaType<pappso::PeptideSp>("pappso::PeptideSp");
- qRegisterMetaType<pappso::XicExtractMethod>("pappso::XicExtractMethod");
- qRegisterMetaType<pappso::SpectrumSp>("pappso::SpectrumSp");
- qRegisterMetaType<MsRunSp>("MsRunSp");
- qRegisterMetaType<std::vector<pappso::PeptideNaturalIsotopeAverageSp>>("std::vector<pappso::PeptideNaturalIsotopeAverageSp>");
-
+ qRegisterMetaType<TandemRunBatch>("TandemRunBatch");
+ qRegisterMetaType<std::vector<pappso::mz>>("std::vector<pappso::mz>");
+ qRegisterMetaType<pappso::PrecisionP>("pappso::PrecisionP");
+ qRegisterMetaType<std::vector<pappso::XicSp>>("std::vector<pappso::XicSp>");
+ qRegisterMetaType<pappso::PeptideSp>("pappso::PeptideSp");
+ qRegisterMetaType<pappso::XicExtractMethod>("pappso::XicExtractMethod");
+ qRegisterMetaType<pappso::SpectrumSp>("pappso::SpectrumSp");
+ qRegisterMetaType<MsRunSp>("MsRunSp");
+ qRegisterMetaType<std::vector<pappso::PeptideNaturalIsotopeAverageSp>>(
+ "std::vector<pappso::PeptideNaturalIsotopeAverageSp>");
- try {
- QCoreApplication::setOrganizationName("PAPPSO");
- QCoreApplication::setOrganizationDomain("pappso.inra.fr");
- QCoreApplication::setApplicationName("xtpcpp");
- MainWindow window;
- window.show();
+ try
+ {
+ QCoreApplication::setOrganizationName("PAPPSO");
+ QCoreApplication::setOrganizationDomain("pappso.inra.fr");
+ QCoreApplication::setApplicationName("xtpcpp");
+ MainWindow window;
+ window.show();
- // This code will start the messaging engine in QT and in
- // 10ms it will start the execution in the MainClass.run routine;
- QTimer::singleShot(10, &window, SLOT(run()));
+ // This code will start the messaging engine in QT and in
+ // 10ms it will start the execution in the MainClass.run routine;
+ QTimer::singleShot(10, &window, SLOT(run()));
- return app.exec();
+ return app.exec();
}
- catch (pappso::PappsoException& error)
+ catch(pappso::PappsoException &error)
{
- errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
- errorStream << error.qwhat() << endl;
- app.exit(1);
+ errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
+ errorStream << error.qwhat() << endl;
+ app.exit(1);
}
- catch (std::exception& error)
+ catch(std::exception &error)
{
- errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
- errorStream << error.what() << endl;
- app.exit(1);
+ errorStream << "Oops! an error occurred in XTPcpp. Dont Panic :" << endl;
+ errorStream << error.what() << endl;
+ app.exit(1);
}
}