libpappsomspp
Library for mass spectrometry
msrunxicextractordiskbuffer.cpp
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1 /**
2  * \file pappsomspp/xicextractor/private/msrunxicextractordiskbuffer.cpp
3  * \date 18/05/2018
4  * \author Olivier Langella
5  * \brief proteowizard based XIC extractor featuring disk cache + write buffer
6  */
7 
8 /*******************************************************************************
9  * Copyright (c) 2018 Olivier Langella <Olivier.Langella@u-psud.fr>.
10  *
11  * This file is part of the PAPPSOms++ library.
12  *
13  * PAPPSOms++ 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++ 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++. If not, see <http://www.gnu.org/licenses/>.
25  *
26  * Contributors:
27  * Olivier Langella <Olivier.Langella@u-psud.fr> - initial API and
28  *implementation
29  ******************************************************************************/
30 
31 
33 #include <QDebug>
34 #include "../../pappsoexception.h"
35 #include "../../massspectrum/massspectrum.h"
36 
37 namespace pappso
38 {
39 
41  MsRunReaderSPtr &msrun_reader, const QDir &temporary_dir)
42  : MsRunXicExtractorDisk(msrun_reader, temporary_dir)
43 {
44 
45  m_sliceBufferMap.clear();
46 }
47 
49  const MsRunXicExtractorDiskBuffer &other)
50  : MsRunXicExtractorDisk(other)
51 {
52 
53  m_sliceBufferMap.clear();
54 }
55 
57 {
58 }
59 
60 void
62  std::map<unsigned int, MassSpectrum> &slice_vector, std::size_t ipos)
63 {
64 
65  m_bufferSize++;
66  for(auto &&msrun_slice : slice_vector)
67  {
68  appendSliceInBuffer(msrun_slice.first, msrun_slice.second, ipos);
69  }
70 
72  {
74  }
75 }
76 
77 void
79  MassSpectrum &spectrum,
80  std::size_t ipos)
81 {
82  qDebug();
83 
84  std::size_t spectrum_size = spectrum.size();
85 
86  if(spectrum_size == 0)
87  return;
88  try
89  {
90  std::pair<std::map<unsigned int, QByteArray>::iterator, bool> ret =
91  m_sliceBufferMap.insert(
92  std::pair<unsigned int, QByteArray>(slice_number, QByteArray()));
93 
94 
95  if(ret.second)
96  { // new buffer
97  ret.first->second.resize(0);
98  QDataStream outstream(&ret.first->second, QIODevice::WriteOnly);
99  outstream << (quint32)ipos;
100  outstream << spectrum;
101  }
102  else
103  {
104  QDataStream outstream(&ret.first->second,
105  QIODevice::WriteOnly | QIODevice::Append);
106  outstream << (quint32)ipos;
107  outstream << spectrum;
108  }
109  }
110  catch(PappsoException &error_pappso)
111  {
113  QObject::tr("appendSliceInBuffer : error ipos=%1 :\n%2")
114  .arg(ipos)
115  .arg(error_pappso.qwhat()));
116  }
117  catch(std::exception &error)
118  {
120  QObject::tr("appendSliceInBuffer slice_number=%1 ipos=%2 error :\n%3")
121  .arg(slice_number)
122  .arg(ipos)
123  .arg(error.what()));
124  }
125  qDebug();
126 }
127 
128 
129 void
131 {
132  qDebug();
133 
134  try
135  {
136  for(auto &buffer_pair : m_sliceBufferMap)
137  {
138 
139  if(buffer_pair.second.size() > 0)
140  {
141  QFile slice_file(QString("%1/%2")
142  .arg(mpa_temporaryDirectory->path())
143  .arg(buffer_pair.first));
144  bool new_file = false;
145  if(!slice_file.exists())
146  {
147  new_file = true;
148 
149  if(!slice_file.open(QIODevice::WriteOnly))
150  {
152  QObject::tr("unable to open file %1")
153  .arg(slice_file.fileName()));
154  }
155  }
156  else
157  {
158  if(!slice_file.open(QIODevice::WriteOnly | QIODevice::Append))
159  {
161  QObject::tr("unable to open file %1")
162  .arg(slice_file.fileName()));
163  }
164  }
165 
166  QDataStream stream(&slice_file);
167 
168  if(new_file)
169  {
170  stream << (quint32)buffer_pair.first;
171  stream << (quint32)m_rtSize;
172  stream.writeRawData(buffer_pair.second.constData(),
173  buffer_pair.second.size());
174  }
175  else
176  {
177  stream.writeRawData(buffer_pair.second.constData(),
178  buffer_pair.second.size());
179  }
180 
181 
182  slice_file.flush();
183  slice_file.close();
184  }
185  // buffer_pair.second = std::vector<MassSpectrum>();
186  }
187 
188  m_bufferSize = 0;
189  m_sliceBufferMap.clear();
190  }
191  catch(PappsoException &error_pappso)
192  {
194  QObject::tr("flushBufferOnDisk error :\n%1").arg(error_pappso.qwhat()));
195  }
196  catch(std::exception &error)
197  {
199  QObject::tr("flushBufferOnDisk error :\n%1").arg(error.what()));
200  }
201  qDebug();
202 }
203 
204 
205 void
207 {
209 
210  m_sliceBufferMap.clear();
211 
212  msp_msrun_reader.get()->releaseDevice();
213 }
214 } // namespace pappso
Class to represent a mass spectrum.
Definition: massspectrum.h:71
void appendSliceInBuffer(unsigned int slice_number, MassSpectrum &spectrum, std::size_t ipos)
std::map< unsigned int, QByteArray > m_sliceBufferMap
MsRunXicExtractorDiskBuffer(const MsRunXicExtractorDiskBuffer &other)
virtual void storeSlices(std::map< unsigned int, MassSpectrum > &slice_vector, std::size_t ipos) override
store MassSpectrum slices (by daltons) for a given retention time
virtual const QString & qwhat() const
proteowizard based XIC extractor featuring disk cache + write buffer
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::shared_ptr< MsRunReader > MsRunReaderSPtr
Definition: msrunreader.h:185