libpappsomspp
Library for mass spectrometry
Public Member Functions | Private Member Functions | Private Attributes | List of all members
pappso::TimsBinDec Class Reference

#include <timsbindec.h>

Public Member Functions

 TimsBinDec (const QFileInfo &timsBinFile, int timsCompressionType)
 
 TimsBinDec (const TimsBinDec &other)
 
 ~TimsBinDec ()
 
TimsFrameSPtr getTimsFrameSPtrByOffset (std::size_t timsId, std::size_t timsOffset)
 

Private Member Functions

void indexingFile ()
 

Private Attributes

int m_timsCompressionType
 
QString m_timsBinFile
 
char * mpa_memoryBuffer = nullptr
 
qint64 m_memoryBufferSize = 0
 
char * mpa_decompressMemoryBuffer = nullptr
 
std::size_t m_decompressMemoryBufferSize = 0
 

Detailed Description

Todo:
write docs

Definition at line 40 of file timsbindec.h.

Constructor & Destructor Documentation

◆ TimsBinDec() [1/2]

TimsBinDec::TimsBinDec ( const QFileInfo &  timsBinFile,
int  timsCompressionType 
)

Default constructor

Definition at line 37 of file timsbindec.cpp.

38  : m_timsBinFile(timsBinFile.absoluteFilePath())
39 {
40  m_timsCompressionType = timsCompressionType;
41  if((timsCompressionType != 1) && (timsCompressionType != 2))
42  {
43  throw pappso::ExceptionNotImplemented(
44  QObject::tr("compression type %1 not handled by this library")
45  .arg(timsCompressionType));
46  }
47  if(m_timsBinFile.isEmpty())
48  {
49  throw pappso::PappsoException(
50  QObject::tr("No TIMS binary file name specified"));
51  }
52  QFile file(m_timsBinFile);
53  if(!file.open(QIODevice::ReadOnly))
54  {
55  throw PappsoException(
56  QObject::tr("ERROR opening TIMS binary file %1 for read")
57  .arg(timsBinFile.absoluteFilePath()));
58  }
59 }
pappso::TimsBinDec::m_timsBinFile
QString m_timsBinFile
Definition: timsbindec.h:70

References m_timsBinFile, and m_timsCompressionType.

◆ TimsBinDec() [2/2]

TimsBinDec::TimsBinDec ( const TimsBinDec &  other)

Copy constructor

Parameters
otherTODO

Definition at line 62 of file timsbindec.cpp.

63  : m_timsBinFile(other.m_timsBinFile)
64 {
65 }

◆ ~TimsBinDec()

TimsBinDec::~TimsBinDec ( )

Destructor

Definition at line 67 of file timsbindec.cpp.

68 {
69  if(mpa_memoryBuffer != nullptr)
70  {
71  delete[] mpa_memoryBuffer;
72  mpa_memoryBuffer = nullptr;
73  }
74 
75 
76  if(mpa_decompressMemoryBuffer != nullptr)
77  {
78  delete[] mpa_decompressMemoryBuffer;
79  }
80 }
pappso::TimsBinDec::mpa_memoryBuffer
char * mpa_memoryBuffer
Definition: timsbindec.h:72
pappso::TimsBinDec::mpa_decompressMemoryBuffer
char * mpa_decompressMemoryBuffer
Definition: timsbindec.h:76

References mpa_decompressMemoryBuffer, and mpa_memoryBuffer.

Member Function Documentation

◆ getTimsFrameSPtrByOffset()

TimsFrameSPtr TimsBinDec::getTimsFrameSPtrByOffset ( std::size_t  timsId,
std::size_t  timsOffset 
)

Definition at line 155 of file timsbindec.cpp.

156 {
157  qDebug() << "timsId:" << timsId << "timsOffset:" << timsOffset;
158 
159  // QMutexLocker locker(&m_mutex);
160  QFile file(m_timsBinFile);
161  if(!file.open(QIODevice::ReadOnly))
162  {
163  throw PappsoException(
164  QObject::tr("ERROR opening TIMS binary file %1 for read")
165  .arg(m_timsBinFile));
166  }
167  qDebug();
168  bool seekpos_ok = file.seek(timsOffset);
169  if(!seekpos_ok)
170  {
171  throw PappsoException(
172  QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: "
173  "m_timsBinFile.seek(%3) failed")
174  .arg(timsId)
175  .arg(m_timsBinFile)
176  .arg(timsOffset));
177  }
178 
179  qDebug();
180  quint32 frame_length;
181  file.read((char *)&frame_length, 4);
182  // frame_length = qToBigEndian(frame_length);
183 
184  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
185  // << " frame_length=" << frame_length;
186 
187  qDebug();
188  quint32 scan_number;
189  file.read((char *)&scan_number, 4);
190  // scan_number = qToBigEndian(scan_number);
191  frame_length -= 8;
192 
193  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
194  // << " pos=" << m_timsBinFile.pos();
195 
196  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
197  // << " scan_number=" << scan_number;
198  // m_timsBinFile.seek(m_indexArray.at(timsId) + 8);
199 
200 
201  qDebug();
202 
203  // if (m_memoryBufferSize
204  if(mpa_memoryBuffer == nullptr)
205  {
206  qDebug() << "mpa_memoryBuffer == nullptr";
207  m_memoryBufferSize = (qint64)frame_length + 10;
208  mpa_memoryBuffer = new char[m_memoryBufferSize];
209  }
210  if((m_memoryBufferSize - 10) < frame_length)
211  {
212  if(mpa_memoryBuffer != nullptr)
213  {
214  delete[] mpa_memoryBuffer;
215  }
216  m_memoryBufferSize = (qint64)frame_length + 10;
217  mpa_memoryBuffer = new char[m_memoryBufferSize];
218  }
219 
220 
221  // QByteArray frame_byte_array(mpa_memoryBuffer, m_memoryBufferSize);
222 
223  qDebug();
224  qint64 read_length = file.read(mpa_memoryBuffer, (qint64)frame_length + 2);
225  qDebug();
226  file.close();
227 
228  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
229  // << " +frame_length-1="
230  // << (quint8) * (frame_byte_array.constData() + frame_length - 1);
231  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
232  // << " +frame_length="
233  // << (quint8) * (frame_byte_array.constData() + frame_length);
234  // m_timsBinFile.seek(m_indexArray.at(timsId) + 8);
235 
236  if(read_length - 2 != (qint64)frame_length)
237  {
238  throw PappsoException(
239  QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: "
240  "read_length=%3 != %4frame_length")
241  .arg(timsId)
242  .arg(m_timsBinFile)
243  .arg(read_length)
244  .arg(frame_length));
245  }
246  qDebug();
247  TimsFrameSPtr frame_sptr;
248  if(frame_length > 0)
249  {
250  qDebug();
251  if(m_timsCompressionType == 2)
252  {
253  auto decompressed_size2 =
254  ZSTD_getFrameContentSize(mpa_memoryBuffer, frame_length);
255  qDebug();
256  if(decompressed_size2 == ZSTD_CONTENTSIZE_UNKNOWN)
257  {
258  throw PappsoException(
259  QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: "
260  " decompressed_size2 == ZSTD_CONTENTSIZE_UNKNOWN, "
261  "frame_length=%3")
262  .arg(timsId)
263  .arg(m_timsBinFile)
264  .arg(frame_length));
265  }
266  qDebug();
267  if(decompressed_size2 == ZSTD_CONTENTSIZE_ERROR)
268  {
269  qDebug();
270  throw PappsoException(
271  QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: "
272  " decompressed_size2 == ZSTD_CONTENTSIZE_ERROR, "
273  "frame_length=%3")
274  .arg(timsId)
275  .arg(m_timsBinFile)
276  .arg(frame_length));
277  }
278  qDebug() << " decompressed_size2=" << decompressed_size2;
279 
280  if(m_decompressMemoryBufferSize < (decompressed_size2 + 10))
281  {
282  if(mpa_decompressMemoryBuffer != nullptr)
283  {
284  delete[] mpa_decompressMemoryBuffer;
285  }
286  m_decompressMemoryBufferSize = decompressed_size2 + 10;
287  mpa_decompressMemoryBuffer =
288  new char[m_decompressMemoryBufferSize];
289  }
290  std::size_t decompressed_size =
291  ZSTD_decompress(mpa_decompressMemoryBuffer,
292  m_decompressMemoryBufferSize,
293  mpa_memoryBuffer,
294  frame_length);
295  qDebug();
296 
297  if(decompressed_size != decompressed_size2)
298  {
299  throw PappsoException(
300  QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: "
301  "decompressed_size != decompressed_size2")
302  .arg(timsId)
303  .arg(m_timsBinFile)
304  .arg(decompressed_size)
305  .arg(decompressed_size2));
306  }
307 
308  qDebug();
309 
310  frame_sptr = std::make_shared<TimsFrame>(
311  timsId, scan_number, mpa_decompressMemoryBuffer, decompressed_size);
312  }
313  else
314  {
315 
316  if(m_timsCompressionType == 1)
317  {
318  frame_sptr = std::make_shared<TimsFrameType1>(
319  timsId, scan_number, mpa_memoryBuffer, frame_length);
320  }
321  }
322  // delete[] mpa_decompressMemoryBuffer;
323  }
324  else
325  {
326  frame_sptr = std::make_shared<TimsFrame>(timsId, scan_number, nullptr, 0);
327  }
328  return frame_sptr;
329 }
pappso::TimsBinDec::m_decompressMemoryBufferSize
std::size_t m_decompressMemoryBufferSize
Definition: timsbindec.h:77
pappso::TimsBinDec::m_memoryBufferSize
qint64 m_memoryBufferSize
Definition: timsbindec.h:73
pappso::TimsFrameSPtr
std::shared_ptr< TimsFrame > TimsFrameSPtr
Definition: timsframe.h:41

References m_decompressMemoryBufferSize, m_memoryBufferSize, m_timsBinFile, m_timsCompressionType, mpa_decompressMemoryBuffer, and mpa_memoryBuffer.

Referenced by pappso::TimsData::getTimsFrameCstSPtr().

◆ indexingFile()

void TimsBinDec::indexingFile ( )
private

Definition at line 84 of file timsbindec.cpp.

85 {
86 
87  qDebug();
88  QFile file(m_timsBinFile);
89  QDataStream bin_in(&file);
90  bin_in.setByteOrder(QDataStream::ByteOrder::LittleEndian);
91  // m_indexArray.push_back(0);
92 
93  // QChar first_char;
94  // txt_in >> first_char;
95  quint32 number_in;
96  qint64 position(0);
97  qint8 trash;
98  while(!bin_in.atEnd())
99  {
100  while((!bin_in.atEnd()) && (position % 4 != 0))
101  {
102  bin_in >> trash;
103  position += 1;
104  if(trash != 0)
105  { /*
106  throw PappsoException(
107  QObject::tr("ERROR reading TIMS frame %1 TIMS binary file %2: "
108  "trash%3 != 0")
109  .arg(m_indexArray.size())
110  .arg(m_timsBinFile.fileName())
111  .arg(trash));*/
112  }
113  }
114  quint32 frame_len(0);
115  while((!bin_in.atEnd()) && (frame_len == 0))
116  {
117  bin_in >> frame_len;
118  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
119  // << " i=" << i;
120  position += 4;
121  }
122 
123  // m_indexArray.push_back(position - 4);
124  /*
125  qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__
126  << " frame_len=" << frame_len
127  << " frameid=" << m_indexArray.size() - 1
128  << " back=" << m_indexArray.back() << " position=" <<
129  position;
130 
131 
132  quint64 next_frame = m_indexArray.back() + frame_len;
133  */
134 
135  bin_in >> number_in;
136  position += 4;
137  qDebug() << " number_in(nb scans)=" << number_in
138  << " position=" << position;
139  ;
140  /*
141 
142  while((!bin_in.atEnd()) && (position < next_frame))
143  {
144  bin_in >> trash;
145  // qDebug() << __FILE__ << " " << __FUNCTION__ << " " <<
146  __LINE__
147  // << " i=" << i;
148  position += 1;
149  }*/
150  }
151  qDebug();
152 }

References m_timsBinFile.

Member Data Documentation

◆ m_decompressMemoryBufferSize

std::size_t pappso::TimsBinDec::m_decompressMemoryBufferSize = 0
private

Definition at line 77 of file timsbindec.h.

Referenced by getTimsFrameSPtrByOffset().

◆ m_memoryBufferSize

qint64 pappso::TimsBinDec::m_memoryBufferSize = 0
private

Definition at line 73 of file timsbindec.h.

Referenced by getTimsFrameSPtrByOffset().

◆ m_timsBinFile

QString pappso::TimsBinDec::m_timsBinFile
private

Definition at line 70 of file timsbindec.h.

Referenced by TimsBinDec(), getTimsFrameSPtrByOffset(), and indexingFile().

◆ m_timsCompressionType

int pappso::TimsBinDec::m_timsCompressionType
private

Definition at line 69 of file timsbindec.h.

Referenced by TimsBinDec(), and getTimsFrameSPtrByOffset().

◆ mpa_decompressMemoryBuffer

char* pappso::TimsBinDec::mpa_decompressMemoryBuffer = nullptr
private

Definition at line 76 of file timsbindec.h.

Referenced by ~TimsBinDec(), and getTimsFrameSPtrByOffset().

◆ mpa_memoryBuffer

char* pappso::TimsBinDec::mpa_memoryBuffer = nullptr
private

Definition at line 72 of file timsbindec.h.

Referenced by ~TimsBinDec(), and getTimsFrameSPtrByOffset().

The documentation for this class was generated from the following files: