diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index ee6256af1b489084e5e97e5aa98be71980f8e029..acfe1d7f3cfb83d55c4c0af33597371fc450f1d9 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -66,6 +66,7 @@ SET(CPP_FILES
core/automaticfilterparameters.cpp
core/identificationgroup.cpp
core/identification_sources/identificationdatasource.cpp
+ core/identification_sources/identificationmascotdatfile.cpp
core/identification_sources/identificationpwizfile.cpp
core/identification_sources/identificationxtandemfile.cpp
core/labeling/label.cpp
@@ -92,6 +93,8 @@ SET(CPP_FILES
grouping/ptm/ptmislandgroup.cpp
grouping/ptm/ptmislandsubgroup.cpp
grouping/ptm/ptmsamplescan.cpp
+ input/mascot/mascotdatparser.cpp
+ input/mascot/mimeparser.cpp
input/condorqxmlsaxhandler.cpp
input/identificationpwizreader.cpp
input/xpipsaxhandler.cpp
diff --git a/src/core/identification_sources/identificationmascotdatfile.cpp b/src/core/identification_sources/identificationmascotdatfile.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..4df4124220e15490717abfdaaa503ed9d38903f6
--- /dev/null
+++ b/src/core/identification_sources/identificationmascotdatfile.cpp
@@ -0,0 +1,100 @@
+/**
+ * \file /core/identification_sources/identificationmascotdatfile.cpp
+ * \date 17/2/2018
+ * \author Olivier Langella
+ * \brief mascot dat identification file handler
+ */
+
+/*******************************************************************************
+* 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/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include "identificationmascotdatfile.h"
+
+#include <pappsomspp/pappsoexception.h>
+#include "../project.h"
+#include "../../input/mascot/mascotdatparser.h"
+
+IdentificationMascotDatFile::IdentificationMascotDatFile(const QFileInfo & mascot_dat_file) : IdentificationDataSource(mascot_dat_file.absoluteFilePath()), _mascot_dat_file(mascot_dat_file)
+{
+ _engine = IdentificationEngine::mascot;
+}
+
+IdentificationMascotDatFile::IdentificationMascotDatFile(const IdentificationMascotDatFile& other) : IdentificationDataSource(other),_mascot_dat_file (other._mascot_dat_file)
+{
+ _engine = IdentificationEngine::mascot;
+}
+
+IdentificationMascotDatFile::~IdentificationMascotDatFile()
+{
+
+}
+
+bool IdentificationMascotDatFile::operator==(const IdentificationMascotDatFile& other) const
+{
+
+}
+
+pappso::SpectrumSp IdentificationMascotDatFile::getSpectrumSp(unsigned int scan_number) const {
+ pappso::SpectrumSp spectrum_sp = IdentificationDataSource::getSpectrumSp(scan_number);
+ return spectrum_sp;
+}
+
+
+void IdentificationMascotDatFile::parseTo(Project* p_project) {
+ qDebug() << "IdentificationMascotDatFile::parseTo begin";
+
+ qDebug() << "Read Mascot dat result file '" << _mascot_dat_file.absoluteFilePath() << "'";
+
+ MsRunSp msrun_sp = p_project->getMsRunStore().getInstance(QFileInfo(_mascot_dat_file).baseName());
+ setMsRunSp(msrun_sp);
+ std::vector<IdentificationGroup *> identification_list = p_project->getIdentificationGroupList();
+ IdentificationGroup * identification_group_p = nullptr;
+ if (p_project->getProjectMode() == ProjectMode::combined) {
+ if (identification_list.size() == 0) {
+ identification_group_p = p_project->newIdentificationGroup();
+ }
+ else {
+ identification_group_p = identification_list[0];
+ }
+ }
+ else {
+ for (IdentificationGroup * identification_p_flist : identification_list) {
+ if (identification_p_flist->containSample(msrun_sp.get()->getSampleName())) {
+ identification_group_p = identification_p_flist;
+ break;
+ }
+ }
+ if (identification_group_p == nullptr) {
+ identification_group_p = p_project->newIdentificationGroup();
+ }
+ }
+
+ identification_group_p->addIdentificationDataSourceP(this);
+ MascotDatParser mascot_parser(p_project, identification_group_p, this);
+
+ QFile qfile(_mascot_dat_file.absoluteFilePath());
+ mascot_parser.parse(&qfile);
+
+ qfile.close();
+
+ qDebug() << "IdentificationMascotDatFile::parseTo end";
+}
diff --git a/src/core/identification_sources/identificationmascotdatfile.h b/src/core/identification_sources/identificationmascotdatfile.h
new file mode 100644
index 0000000000000000000000000000000000000000..94ed456ad128cf8ab6fa9680a1dd66c4436d7f3e
--- /dev/null
+++ b/src/core/identification_sources/identificationmascotdatfile.h
@@ -0,0 +1,51 @@
+/**
+ * \file /core/identification_sources/identificationmascotdatfile.h
+ * \date 17/2/2018
+ * \author Olivier Langella
+ * \brief mascot dat identification file handler
+ */
+
+/*******************************************************************************
+* 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/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#ifndef IDENTIFICATIONMASCOTDATFILE_H
+#define IDENTIFICATIONMASCOTDATFILE_H
+
+#include "identificationdatasource.h"
+#include <QFileInfo>
+
+class IdentificationMascotDatFile: public IdentificationDataSource
+{
+public:
+ IdentificationMascotDatFile(const QFileInfo & mascot_dat_file);
+ IdentificationMascotDatFile(const IdentificationMascotDatFile& other);
+ ~IdentificationMascotDatFile();
+ bool operator==(const IdentificationMascotDatFile& other) const;
+
+ virtual pappso::SpectrumSp getSpectrumSp(unsigned int scan_number) const override;
+ virtual void parseTo(Project* p_project) override;
+
+private:
+ const QFileInfo _mascot_dat_file;
+};
+
+#endif // IDENTIFICATIONMASCOTDATFILE_H
diff --git a/src/input/mascot/mascotdatparser.cpp b/src/input/mascot/mascotdatparser.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..724d913403a8ee86d03729c662a5dcef68c7531c
--- /dev/null
+++ b/src/input/mascot/mascotdatparser.cpp
@@ -0,0 +1,76 @@
+/**
+ * \file /input/mascot/mascotdatparser.h
+ * \date 17/2/2018
+ * \author Olivier Langella
+ * \brief MASCOT dat file parser
+ */
+
+/*******************************************************************************
+* 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/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#include "mascotdatparser.h"
+#include "mimeparser.h"
+#include <QDebug>
+
+MascotDatParser::MascotDatParser(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;
+
+}
+MascotDatParser::~MascotDatParser() {
+}
+void MascotDatParser::parse(QIODevice * in_stream) {
+ qDebug() << "MascotDatParser::parse begin";
+ MimeParser mime_parser(in_stream);
+ mime_parser.open();
+
+ for(bool more=mime_parser.goToFirstFile(); more; more=mime_parser.goToNextFile()) {
+ qDebug() << "MascotDatParser::parse mimetype=" << mime_parser.getCurrentMimeType() << " filename=" << mime_parser.getCurrentFileName();
+
+ if (mime_parser.getCurrentFileName() == "proteins") {
+ while(!mime_parser.getCurrentTextStream().atEnd()) {
+ parseProteinLine( mime_parser.getCurrentTextStream().readLine());
+ }
+ }
+ }
+
+ mime_parser.close();
+ qDebug() << "MascotDatParser::parse end";
+}
+void MascotDatParser::parseProteinLine(const QString & protein_line) {
+ //02::"tr|A0A0D9SF80|A0A0D9SF80_HUMAN"=55120.88,"General transcription factor II-I repeat domain-containing protein 2A OS=Homo sapiens GN=GTF2IRD2B PE=4 SV=1"
+ QRegExp regexp_protein("^(.*)::\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
+ if (regexp_protein.exactMatch(protein_line)) {
+ QStringList protein_list = regexp_protein.capturedTexts();
+ }
+ else {
+ QRegExp regexp_proteinb("^\"(.*)\"=([0-9]+\\.[0-9]+),\"(.*)\"$");
+ if (regexp_proteinb.exactMatch(protein_line)) {
+ QStringList protein_list = regexp_proteinb.capturedTexts();
+ }
+ else {
+ qDebug() << "MascotDatParser::parseProteinLine error " << protein_line;
+ }
+ }
+}
diff --git a/src/input/mascot/mascotdatparser.h b/src/input/mascot/mascotdatparser.h
new file mode 100644
index 0000000000000000000000000000000000000000..880ba7ba0b92b2f2f7a8a706a27c48d4e62fee0d
--- /dev/null
+++ b/src/input/mascot/mascotdatparser.h
@@ -0,0 +1,50 @@
+/**
+ * \file /input/mascot/mascotdatparser.h
+ * \date 17/2/2018
+ * \author Olivier Langella
+ * \brief MASCOT dat file parser
+ */
+
+/*******************************************************************************
+* 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/>.
+*
+* Contributors:
+* Olivier Langella <olivier.langella@u-psud.fr> - initial API and implementation
+******************************************************************************/
+
+#ifndef MASCOTDATPARSER_H
+#define MASCOTDATPARSER_H
+
+#include "../../core/project.h"
+
+class MascotDatParser
+{
+public:
+ MascotDatParser(Project * p_project, IdentificationGroup * p_identification_group,
+ IdentificationDataSource * p_identification_data_source);
+ virtual ~MascotDatParser();
+ void parse(QIODevice * in_stream);
+private:
+ void parseProteinLine(const QString & protein_line);
+private:
+ Project * _p_project;
+ IdentificationGroup * _p_identification_group;
+ IdentificationDataSource * _p_identification_data_source;
+};
+
+#endif // MASCOTDATPARSER_H
diff --git a/src/input/mascot/mimeparser.cpp b/src/input/mascot/mimeparser.cpp
index 634959866e41d4115c4c0348fa806f07684f5e46..d922f347112dba565830a58d04fc8524d5ce964e 100644
--- a/src/input/mascot/mimeparser.cpp
+++ b/src/input/mascot/mimeparser.cpp
@@ -29,16 +29,34 @@
#include "mimeparser.h"
#include <QRegExp>
+#include <QDebug>
+#include <pappsomspp/pappsoexception.h>
MimeParser::MimeParser(QIODevice * p_inputstream) {
_p_inputstream = p_inputstream;
}
+
+MimeParser::~MimeParser() {
+ close();
+}
bool MimeParser::open() {
- _p_inputstream->open(QIODevice::ReadOnly);
- _real_in = new QTextStream(_p_inputstream);
+ qDebug() << "MimeParser::open begin";
+ if (_p_inputstream->open(QIODevice::ReadOnly)) {
+ _real_in = new QTextStream(_p_inputstream);
+ }
+ else {
+ throw pappso::PappsoException(QObject::tr("Error opening mime QIODevice"));
+ }
+ qDebug() << "MimeParser::open end";
}
bool MimeParser::close() {
+ qDebug() << "MimeParser::close begin";
+
+ _priv_file_string = "";
+ if (_p_current_file_content != nullptr) {
+ delete _p_current_file_content;
+ }
if (_real_in !=nullptr) {
delete _real_in;
_real_in =nullptr;
@@ -49,8 +67,10 @@ bool MimeParser::close() {
delete _p_inputstream;
_p_inputstream =nullptr;
}
+ qDebug() << "MimeParser::close end";
}
bool MimeParser::goToFirstFile() {
+ qDebug() << "MimeParser::goToFirstFile begin";
/*
MIME-Version: 1.0 (Generated by Mascot version 1.0)
@@ -63,18 +83,71 @@ bool MimeParser::goToFirstFile() {
while(!_real_in->atEnd()) {
QString line = _real_in->readLine();
+ qDebug() << "MimeParser::goToFirstFile line=" << line;
if (regexp_boundary.exactMatch(line)) {
QStringList boundary_list = regexp_boundary.capturedTexts();
- _boundary = boundary_list[1];
+ _boundary = QString("--%1").arg(boundary_list[1]);
break;
}
}
+ if (_boundary.isEmpty()) {
+ qDebug() << "MimeParser::goToFirstFile _boundary.isEmpty";
+ return false;
+ }
+
+ while(!_real_in->atEnd()) {
+ QString line = _real_in->readLine();
+ if (line == _boundary) break;
+ }
+ qDebug() << "MimeParser::goToFirstFile end";
+ return readFile();
+}
+bool MimeParser::readFile() {
+ qDebug() << "MimeParser::readFile begin";
+ _current_mime_type = "";
+ _current_file_name = "";
+ _priv_file_string = "";
+
+ if (_p_current_file_content != nullptr) {
+ delete _p_current_file_content;
+ }
+ _p_current_file_content = new QTextStream(&_priv_file_string);
+
+ QString line = _real_in->readLine();
+ if (line.isEmpty()) return false;
+ //Content-Type: application/x-Mascot; name="masses"
+ QRegExp regexp_mimetype("^Content-Type:\\s(.*);\\sname=\"(.*)\"$");
+ if (regexp_mimetype.exactMatch(line)) {
+ QStringList mimetype_list = regexp_mimetype.capturedTexts();
+ _current_mime_type = mimetype_list[1];
+ _current_file_name = mimetype_list[2];
+ }
+ else {
+ return false;
+ }
+ _real_in->readLine();
+ while(!_real_in->atEnd()) {
+ QString line = _real_in->readLine();
+ if (line == _boundary) break;
+ *_p_current_file_content << line << endl;
+ }
+ qDebug() << "MimeParser::readFile end";
+ return true;
}
bool MimeParser::goToNextFile() {
+ return readFile();
}
-const QString & MimeParser::getCurrentFileName() {
+const QString & MimeParser::getCurrentMimeType() const {
+ return _current_mime_type;
+}
+const QString & MimeParser::getCurrentFileName() const {
return _current_file_name;
}
QTextStream & MimeParser::getCurrentTextStream() {
+ if (_p_current_file_content == nullptr) {
+ throw pappso::PappsoException(QObject::tr("Error current file content empty"));
+ }
+ _p_current_file_content->reset();
+ return *_p_current_file_content;
}
diff --git a/src/input/mascot/mimeparser.h b/src/input/mascot/mimeparser.h
index 641d418bd04f92c4fbb757645264a6312672dc76..2c792abf47f40178a3f4548c40bcebc7483c0d15 100644
--- a/src/input/mascot/mimeparser.h
+++ b/src/input/mascot/mimeparser.h
@@ -37,18 +37,26 @@ class MimeParser
{
public:
MimeParser(QIODevice * p_inputstream);
+ virtual ~MimeParser();
bool open();
bool close();
bool goToFirstFile();
bool goToNextFile();
- const QString & getCurrentFileName();
+ const QString & getCurrentMimeType() const;
+ const QString & getCurrentFileName() const;
QTextStream & getCurrentTextStream();
+private:
+ bool readFile();
+
private:
QString _current_file_name;
+ QString _current_mime_type;
QIODevice * _p_inputstream = nullptr;
QTextStream * _real_in = nullptr;
QString _boundary;
+ QTextStream * _p_current_file_content = nullptr;
+ QString _priv_file_string;
};
#endif // MIMEPARSER_H
diff --git a/src/utils/identificationdatasourcestore.cpp b/src/utils/identificationdatasourcestore.cpp
index c0e100dd0cc71d1702fc39c1d7618925430548bd..e4e16ba50294ae4afea4265bdef3b080692dccb9 100644
--- a/src/utils/identificationdatasourcestore.cpp
+++ b/src/utils/identificationdatasourcestore.cpp
@@ -30,6 +30,7 @@
#include "identificationdatasourcestore.h"
#include "../core/identification_sources/identificationxtandemfile.h"
+#include "../core/identification_sources/identificationmascotdatfile.h"
#include "../core/identification_sources/identificationpwizfile.h"
#include <pappsomspp/pappsoexception.h>
#include <pappsomspp/utils.h>
@@ -98,6 +99,9 @@ IdentificationDataSourceSp IdentificationDataSourceStore::getInstance(const QStr
} else if (ext.toLower() == "pep") {
//pep xml file
p_identfile = std::make_shared<IdentificationPwizFile>(location_file);
+ } else if (ext.toLower() == "dat") {
+ //MASCOT dat file
+ p_identfile = std::make_shared<IdentificationMascotDatFile>(location_file);
} else {
p_identfile = std::make_shared<IdentificationPwizFile>(location_file);
}