libpappsomspp
Library for mass spectrometry
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wraptandemresults.cpp
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1/**
2 * \file pappsomspp/processing/tandemwrapper/wraptandemresults.cpp
3 * \date 13/11/2021
4 * \author Olivier Langella
5 * \brief rewrites tandem xml output file with temporary files
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2021 Olivier Langella <Olivier.Langella@u-psud.fr>.
10 *
11 * This file is part of PAPPSOms-tools.
12 *
13 * PAPPSOms-tools is free software: you can redistribute it and/or modify
14 * it under the terms of the GNU General Public License as published by
15 * the Free Software Foundation, either version 3 of the License, or
16 * (at your option) any later version.
17 *
18 * PAPPSOms-tools is distributed in the hope that it will be useful,
19 * but WITHOUT ANY WARRANTY; without even the implied warranty of
20 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 * GNU General Public License for more details.
22 *
23 * You should have received a copy of the GNU General Public License
24 * along with PAPPSOms-tools. If not, see <http://www.gnu.org/licenses/>.
25 *
26 ******************************************************************************/
27
28#include "wraptandemresults.h"
29#include <QFileInfo>
30#include "../../pappsoexception.h"
31
32
33namespace pappso
34{
35
36WrapTandemResults::WrapTandemResults(const QString &final_tandem_output,
37 const QString &original_msdata_file_name)
38 : m_destinationTandemOutputFile(final_tandem_output)
39{
40 qDebug() << final_tandem_output;
42 QFileInfo(original_msdata_file_name).absoluteFilePath();
43 if(!m_destinationTandemOutputFile.open(QIODevice::WriteOnly))
44 {
46 QObject::tr("ERROR: unable to open %1 to write XML output")
47 .arg(final_tandem_output));
48 }
50 m_writerXmlTandemOutput.writeStartDocument("1.0");
51 m_writerXmlTandemOutput.setAutoFormatting(true);
52}
53
57
58void
59WrapTandemResults::setInputParameters(const QString &label_name_attribute,
60 const QString &input_value)
61{
63 std::pair<QString, QString>(label_name_attribute, input_value));
64}
65
66void
68{
70 while(m_qxmlStreamReader.readNext() && !m_qxmlStreamReader.isEndElement())
71 {
72 if(m_qxmlStreamReader.isStartElement())
73 {
74 QString type =
75 m_qxmlStreamReader.attributes().value("type").toString();
76 QString label =
77 m_qxmlStreamReader.attributes().value("label").toString();
78 qDebug() << "type=" << type << " label=" << label;
79 // qDebug() << "XtandemParamSaxHandler::endElement_note begin " <<
80 // <note type="input" label="spectrum,
81 // path">/tmp/tandemwrapper-IehrEL/msdata.mzxml</note>
82
83 if(label == "spectrum, path")
84 {
85 //<note type="input"
86 // label="spectrum,path">/gorgone/pappso/jouy/raw/2019_Lumos/20191222_107_Juste/20191222_18_EF1.mzXML</note>
87 // m_originMzDataFileName = m_currentText;
88 // p_writeXmlTandemOutput->writeCharacters(m_destinationMzXmlFileName);
89
90 m_writerXmlTandemOutput.writeStartElement("note");
91 m_writerXmlTandemOutput.writeAttributes(
92 m_qxmlStreamReader.attributes());
94 m_writerXmlTandemOutput.writeEndElement();
95
96
97 for(auto pair_input : m_mapTandemInputParameters)
98 {
99 m_writerXmlTandemOutput.writeStartElement("note");
100 m_writerXmlTandemOutput.writeAttribute("type", "input");
101 m_writerXmlTandemOutput.writeAttribute("label",
102 pair_input.first);
103 m_writerXmlTandemOutput.writeCharacters(pair_input.second);
104
105 m_writerXmlTandemOutput.writeEndElement();
106 }
107 m_qxmlStreamReader.skipCurrentElement();
108 }
109 else if(label == "output, path")
110 {
111
112 //<note type="input" label="output,
113 // path">/tmp/tandemwrapper-sSGxtE/output_tandem.xml</note>
114
115 m_writerXmlTandemOutput.writeStartElement("note");
116 m_writerXmlTandemOutput.writeAttributes(
117 m_qxmlStreamReader.attributes());
118 m_writerXmlTandemOutput.writeCharacters(
119 QFileInfo(m_destinationTandemOutputFile).absoluteFilePath());
120 m_writerXmlTandemOutput.writeEndElement();
121 m_qxmlStreamReader.skipCurrentElement();
122 }
123 else
124 {
126 }
127 }
128 }
129 m_writerXmlTandemOutput.writeEndElement();
130}
131
132void
134{
135 qDebug();
136 if(m_qxmlStreamReader.readNextStartElement())
137 {
138 if(m_qxmlStreamReader.name().toString() == "bioml")
139 {
141 qDebug();
142 while(m_qxmlStreamReader.readNextStartElement())
143 {
144 if(m_qxmlStreamReader.name().toString() == "group")
145 {
146 QString type =
147 m_qxmlStreamReader.attributes().value("type").toString();
148 if(type == "model")
149 {
151 }
152 else if(type == "parameters")
153 {
154 QString label = m_qxmlStreamReader.attributes()
155 .value("label")
156 .toString();
157 if(label == "performance parameters")
158 {
160 }
161 else if(label == "input parameters")
162 {
164 // cloneElement(m_writerXmlTandemOutput);
165 }
166 else if(label == "unused input parameters")
167 {
169 }
170 else
171 {
172 m_qxmlStreamReader.skipCurrentElement();
173 }
174 }
175 }
176 else
177 {
178 qDebug() << m_qxmlStreamReader.name();
179 // read_note();
181
182
183 m_writerXmlTandemOutput.writeCharacters(
184 m_qxmlStreamReader.readElementText());
185
186 m_writerXmlTandemOutput.writeEndElement();
187 }
188 }
189 }
190 else
191 {
192 m_qxmlStreamReader.raiseError(
193 QObject::tr("Not an X!Tandem result file"));
194 m_qxmlStreamReader.skipCurrentElement();
195 }
196 }
197 m_writerXmlTandemOutput.writeEndDocument();
199 qDebug();
200}
201
202} // namespace pappso
QXmlStreamWriter m_writerXmlTandemOutput
WrapTandemResults(const QString &final_tandem_output, const QString &original_msdata_file_name)
virtual void readStream() override
std::map< QString, QString > m_mapTandemInputParameters
void setInputParameters(const QString &label_name_attribute, const QString &input_value)
void cloneStartElement(QXmlStreamWriter &output) const
void cloneElement(QXmlStreamWriter &output)
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
rewrites tandem xml output file with temporary files