Mass++ mzML IO Plugin v2.7.5
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Public Member Functions | Static Public Member Functions | Protected Member Functions | Static Protected Member Functions | Protected Attributes | List of all members
kome::io::mzml::MzmlManager Class Reference

mzML IO management class More...

#include <MzmlManager.h>

Public Member Functions

bool exportDataSet (const char *path, kome::objects::DataSet &dataSet, kome::core::Progress &progress, kome::objects::SettingParameterValues *saveSettings)
 

Static Public Member Functions

static MzmlManager & getInstance ()
 gets mzML IO management object More...
 

Protected Member Functions

 MzmlManager ()
 constructor
 
virtual ~MzmlManager ()
 destructor
 
void init ()
 initializes variables
 
void exportDataSet (FILE *fp, kome::objects::DataSet &dataSet, kome::core::Progress &progress, kome::objects::SettingParameterValues *saveSettings)
 
void writeHeader (FILE *fp)
 writes header More...
 
void writeFileDescription (FILE *fp, std::vector< kome::objects::Sample * > &samples)
 writes file description More...
 
void writeFileContent (FILE *fp, std::vector< kome::objects::Sample * > &samples)
 writes file content More...
 
void writeSourceFileList (FILE *fp, std::vector< kome::objects::Sample * > &samples)
 writes source file list More...
 
void writeReferenceableParamGroup (FILE *fp, const bool specFlg, const bool chromFlg)
 writes referenceable parameters group More...
 
void writeSoftwareList (FILE *fp, std::vector< kome::objects::Sample * > &samples)
 writes software list More...
 
void writeInstrumentList (FILE *fp, std::vector< kome::objects::Sample * > &samples)
 writes instrument list More...
 
void writeProcessingList (FILE *fp)
 writes processing list More...
 
void writeRun (FILE *fp, std::vector< kome::objects::Sample * > &samples, std::vector< kome::objects::Spectrum * > &spectra, std::vector< kome::objects::Chromatogram * > &chroms, kome::core::Progress *specPrgs, kome::core::Progress *chromPrgs, kome::objects::SettingParameterValues *saveSettings)
 writes run tag More...
 
void writeSpectrum (FILE *fp, kome::objects::Spectrum &spec, kome::objects::SettingParameterValues *saveSettings)
 writes spectrum More...
 
void writeChromatogram (FILE *fp, kome::objects::Chromatogram &chrom, kome::objects::SettingParameterValues *saveSettings)
 writes chromatogram More...
 
void writeIndexList (FILE *fp, std::vector< kome::objects::Spectrum * > &spectra, std::vector< kome::objects::Chromatogram * > &chroms)
 writes index list More...
 

Static Protected Member Functions

static bool lessSpec (kome::objects::Spectrum *spec0, kome::objects::Spectrum *spec1)
 compare spectra to sort More...
 
static double getSimilarityScore (const char *s0, const char *s1)
 gets similarity score between two character strings More...
 
static double getMatchScore (const char *s0, int idx0, const char *s1, int idx1)
 gets match score More...
 

Protected Attributes

std::map
< kome::objects::Spectrum
*, long long > 		m_specIdxMap
 
std::map
< kome::objects::Chromatogram
*, long long > 		m_chromIdxMap
 
const bool m_reverseFlg
 

Detailed Description

mzML IO management class

Definition at line 26 of file MzmlManager.h.

Member Function Documentation

static MzmlManager & kome::io::mzml::MzmlManager::getInstance ( )
static

gets mzML IO management object

Returns
mzML IO management object (This is the only object.)

Definition at line 1177 of file MzmlManager.cpp.

1177  {
1178  // create object (This is the only object.)
1179  static MzmlManager mgr;
1180 
1181  return mgr;
1182 }
kome::io::mzml::MzmlManager
mzML IO management class
Definition: MzmlManager.h:26
static double kome::io::mzml::MzmlManager::getMatchScore ( const char *  s0,
int  idx0,
const char *  s1,
int  idx1 
)
staticprotected

gets match score

Parameters
s0character string
idx0position
s1character string
idx1position
Returns
match score

Definition at line 1151 of file MzmlManager.cpp.

1151  {
1152  // character
1153  char c0 = s0[ idx0 ];
1154  char c1 = s1[ idx1 ];
1155 
1156  bool a0 = ( isalnum( c0 ) != 0 );
1157  bool a1 = ( isalnum( c1 ) != 0 );
1158 
1159  // score
1160  if( a0 && a1 ) {
1161  if( tolower( c0 ) == tolower( c1 ) ) {
1162  return 1.0;
1163  }
1164  else {
1165  return -1.0;
1166  }
1167  }
1168 
1169  if( !a0 && !a1 ) {
1170  return 1.0;
1171  }
1172 
1173  return - 0.1;
1174 }
static double kome::io::mzml::MzmlManager::getSimilarityScore ( const char *  s0,
const char *  s1 
)
staticprotected

gets similarity score between two character strings

Parameters
s0character string
s1character string
Returns
similarity score

Definition at line 1126 of file MzmlManager.cpp.

1126  {
1127  // check parameters
1128  if( s0 == NULL || s1 == NULL ) {
1129  return ( - FLT_MAX );
1130  }
1131 
1132  // size
1133  unsigned int l0 = strlen( s0 );
1134  unsigned int l1 = strlen( s1 );
1135 
1136  if( l0 == 0 && l1 == 0 ) {
1137  return 0;
1138  }
1139  else if( l0 == 0 || l1 == 0 ) {
1140  return ( - FLT_MAX );
1141  }
1142 
1143  // dynamic programing
1144  kome::numeric::DynamicPrograming dp( l0, l1 );
1145  dp.calculate( boost::bind( getMatchScore, s0, _1, s1, _2 ), 0.1 );
1146 
1147  return dp.getAccumulatedScore( (int)l0 - 1, (int)l1 - 1 );
1148 }
kome::io::mzml::MzmlManager::getMatchScore
static double getMatchScore(const char *s0, int idx0, const char *s1, int idx1)
gets match score
Definition: MzmlManager.cpp:1151

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static bool kome::io::mzml::MzmlManager::lessSpec ( kome::objects::Spectrum *  spec0,
kome::objects::Spectrum *  spec1 
)
staticprotected

compare spectra to sort

Parameters
spec0spectrum to be compared
spec1spectrum to compare
Returns
If true, spec0 sorts before spec1.

Definition at line 1186 of file MzmlManager.cpp.

1186  {
1187  return ( spec0->getRt() < spec1->getRt() );
1188 }
void kome::io::mzml::MzmlManager::writeChromatogram ( FILE *  fp,
kome::objects::Chromatogram &  chrom,
kome::objects::SettingParameterValues *  saveSettings 
)
protected

writes chromatogram

Parameters
fpfile descriptor
chromchromatogram

Definition at line 946 of file MzmlManager.cpp.

950  {
951  // get data status
952  bool op = saveSettings->getBoolValue( DATA_STATUS,false ); // @date 2012/08/21 <Add> FUJITA
953 
954  // data points
955  kome::core::DataPoints dps( kome::core::DataPoints::FLOAT );
956 // chrom.getXYData( &dps, false ); // @date 2012/08/21 <Del> FUJITA
957  chrom.getXYData( &dps, op ); // @date 2012/08/21 <Add> FUJITA
958 
959  // reverse
960  const unsigned int len = dps.getLength();
961  if( m_reverseFlg ) {
962  float* xArr = (float*)dps.getXData();
963  float* yArr = (float*)dps.getYData();
964 
965  for( unsigned int i = 0; i < len; i++ ) {
966  memreverse( xArr + i, sizeof( float ) );
967  memreverse( yArr + i, sizeof( float ) );
968  }
969  }
970 
971  // index
972  const int idx = m_chromIdxMap.size();
973 
974  // start tag
975  fprintf( fp, " " );
976 
977  m_chromIdxMap[ &chrom ] = filetell( fp );
978 
979  fprintf(
980  fp,
981  "<chromatogram id=\"%s\" index=\"%d\" defaultArrayLength=\"%d\">\n",
982  chrom.getName(),
983  idx,
984  len
985  );
986 
987  // data points
988  if( len > 0 ) {
989  // prepare
990  unsigned long buffLength = len * sizeof( float ) * 2;
991  char* base64Buff = new char[ buffLength ];
992 
993  fprintf( fp, " <binaryDataArrayList count=\"2\">\n" );
994 
995  // RT
996  unsigned long size = kome::core::Base64::encode( dps.getXData(), sizeof( float ) * len, base64Buff, buffLength );
997 
998  fprintf( fp, " <binaryDataArray encodedLength=\"%d\">\n", size );
999 
1000 #ifdef MZML_USE_REFERENCEABLE_PARAM_GROUP
1001  fprintf( fp, " <referenceableParamGroupRef ref=\"rt_params\"/>\n" );
1002 #else
1003  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000595\" name=\"time array\" value=\"\"\n" );
1004  fprintf( fp, " unitCvRef=\"UO\" unitAccession=\"UO:0000031\" unitName=\"minute\"/>\n" );
1005  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000521\" name=\"32-bit float\" value=\"\"/>\n" );
1006  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000576\" name=\"no compression\" value=\"\"/>\n" );
1007 #endif // MZML_USE_REFERENCEABLE_PARAM_GROUP
1008 
1009  fprintf( fp, " <binary>" );
1010 
1011  char* pos = base64Buff;
1012  while( size > 0 ) {
1013  int writeSize = MIN( size, 1024 );
1014  writeSize = fwrite( pos, 1, writeSize, fp );
1015  size -= writeSize;
1016  pos += writeSize;
1017  }
1018 
1019  fprintf( fp, "</binary>\n" );
1020  fprintf( fp, " </binaryDataArray>\n" );
1021 
1022  // intensity
1023  size = kome::core::Base64::encode( dps.getYData(), sizeof( float ) * len, base64Buff, buffLength );
1024 
1025  fprintf( fp, " <binaryDataArray encodedLength=\"%d\">\n", size );
1026 
1027 #ifdef MZML_USE_REFERENCEABLE_PARAM_GROUP
1028  fprintf( fp, " <referenceableParamGroupRef ref=\"int_params\"/>\n" );
1029 #else
1030  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000515\" name=\"intensity array\" value=\"\"/>\n" );
1031  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000521\" name=\"32-bit float\" value=\"\"/>\n" );
1032  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000576\" name=\"no compression\" value=\"\"/>\n" );
1033 #endif // MZML_USE_REFERENCEABLE_PARAM_GROUP
1034 
1035  fprintf( fp, " <binary>" );
1036 
1037  pos = base64Buff;
1038  while( size > 0 ) {
1039  int writeSize = MIN( size, 1024 );
1040  writeSize = fwrite( pos, 1, writeSize, fp );
1041  size -= writeSize;
1042  pos += writeSize;
1043  }
1044 
1045  fprintf( fp, "</binary>\n" );
1046  fprintf( fp, " </binaryDataArray>\n" );
1047 
1048  fprintf( fp, " </binaryDataArrayList>\n" );
1049 
1050  delete[] base64Buff;
1051  }
1052 
1053  // end tag
1054  fprintf( fp, " </chromatogram>\n" );
1055 }
kome::io::mzml::MzmlManager::m_chromIdxMap
std::map< kome::objects::Chromatogram *, long long > m_chromIdxMap
Definition: MzmlManager.h:45
void kome::io::mzml::MzmlManager::writeFileContent ( FILE *  fp,
std::vector< kome::objects::Sample * > &  samples 
)
protected

writes file content

Parameters
fpfile descriptor
samplesthe array of samples

Definition at line 245 of file MzmlManager.cpp.

245  {
246  // start tag
247  fprintf( fp, " <fileContent>\n" );
248 
249  // file content
250  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000580\" name=\"MSn spectrum\" value=\"\"/>\n" );
251 
252  // end tag
253  fprintf( fp, " </fileContent>\n" );
254 }
void kome::io::mzml::MzmlManager::writeFileDescription ( FILE *  fp,
std::vector< kome::objects::Sample * > &  samples 
)
protected

writes file description

Parameters
fpfile descriptor
samplesthe array of samples

Definition at line 232 of file MzmlManager.cpp.

232  {
233  // start tag
234  fprintf( fp, " <fileDescription>\n" );
235 
236  writeFileContent( fp, samples );
237  writeSourceFileList( fp, samples );
238 
239  // end tag
240  fprintf( fp, " </fileDescription>\n" );
241 
242 }
kome::io::mzml::MzmlManager::writeSourceFileList
void writeSourceFileList(FILE *fp, std::vector< kome::objects::Sample * > &samples)
writes source file list
Definition: MzmlManager.cpp:257
kome::io::mzml::MzmlManager::writeFileContent
void writeFileContent(FILE *fp, std::vector< kome::objects::Sample * > &samples)
writes file content
Definition: MzmlManager.cpp:245

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void kome::io::mzml::MzmlManager::writeHeader ( FILE *  fp)
protected

writes header

Parameters
fpfile descriptor

Definition at line 210 of file MzmlManager.cpp.

210  {
211  fprintf( fp, "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n" );
212  fprintf( fp, "<indexedmzML xmlns=\"http://psi.hupo.org/ms/mzml\"\n" );
213  fprintf( fp, " xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n" );
214  fprintf( fp, " xsi:schemaLocation=\"http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0_idx.xsd\">\n" );
215  fprintf( fp, " <mzML xmlns=\"http://psi.hupo.org/ms/mzml\"\n" );
216  fprintf( fp, " xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\"\n" );
217  fprintf( fp, " xsi:schemaLocation=\"http://psi.hupo.org/ms/mzml http://psidev.info/files/ms/mzML/xsd/mzML1.1.0.xsd\"\n" );
218  fprintf( fp, " version=\"1.1.0\">\n" );
219  fprintf( fp, " <cvList count=\"2\">\n" );
220  fprintf( fp, " <cv id=\"MS\"\n" );
221  fprintf( fp, " fullName=\"Proteomics Standards Initiative Mass Spectrometry Ontology\"\n" );
222  fprintf( fp, " version=\"1.3.1\"\n" );
223  fprintf( fp, " URI=\"http://psidev.info/ms/mzML/psi-ms.obo\" />\n" );
224  fprintf( fp, " <cv id=\"UO\"\n" );
225  fprintf( fp, " fullName=\"Unit Ontology\"\n" );
226  fprintf( fp, " version=\"1.15\"\n" );
227  fprintf( fp, " URI=\"http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo\" />\n" );
228  fprintf( fp, " </cvList>\n" );
229 }
void kome::io::mzml::MzmlManager::writeIndexList ( FILE *  fp,
std::vector< kome::objects::Spectrum * > &  spectra,
std::vector< kome::objects::Chromatogram * > &  chroms 
)
protected

writes index list

Parameters
fpfile descriptor
spectrathe array of spectra
chromsthe array of chromatograms

Definition at line 1058 of file MzmlManager.cpp.

1062  {
1063  // end mzML tag
1064  fprintf( fp, " </mzML>\n" );
1065 
1066  // list count
1067  int listCnt = 0;
1068  if( spectra.size() > 0 ) {
1069  listCnt++;
1070  }
1071  if( chroms.size() > 0 ) {
1072  listCnt++;
1073  }
1074 
1075  // write index list
1076  const long long idxOffset = filetell( fp ) + 2;
1077  if( listCnt > 0 ) {
1078  // start tag
1079  fprintf( fp, " <indexList count=\"%d\">\n", listCnt );
1080 
1081  // spectra
1082  if( spectra.size() > 0 ) {
1083  fprintf( fp, " <index name=\"spectrum\">\n" );
1084 
1085  for( unsigned int i = 0; i < spectra.size(); i++ ) {
1086  kome::objects::Spectrum* spec = spectra[ i ];
1087  if( m_specIdxMap.find( spec ) != m_specIdxMap.end() ) {
1088  const long long offset = m_specIdxMap[ spec ];
1089 
1090  fprintf( fp, " <offset idRef=\"%s\">%lld</offset>\n", spec->getName(), offset );
1091  }
1092  }
1093 
1094  fprintf( fp, " </index>\n" );
1095  }
1096 
1097  // chromatograms
1098  if( chroms.size() > 0 ) {
1099  fprintf( fp, " <index name=\"chromatogram\">\n" );
1100 
1101  for( unsigned int i = 0; i < chroms.size(); i++ ) {
1102  kome::objects::Chromatogram* chrom = chroms[ i ];
1103  if( m_chromIdxMap.find( chrom ) != m_chromIdxMap.end() ) {
1104  const long long offset = m_chromIdxMap[ chrom ];
1105 
1106  fprintf( fp, " <offset idRef=\"%s\">%lld</offset>\n", chrom->getName(), offset );
1107  }
1108  }
1109 
1110  fprintf( fp, " </index>\n" );
1111  }
1112 
1113  // end tag
1114  fprintf( fp, " </indexList>\n" );
1115 
1116  // index offset
1117  fprintf( fp, " " );
1118  fprintf( fp, "<indexListOffset>%lld</indexListOffset>\n", idxOffset );
1119  }
1120 
1121  // end root tag
1122  fprintf( fp, "</indexedmzML>\n" );
1123 }
kome::io::mzml::MzmlManager::m_chromIdxMap
std::map< kome::objects::Chromatogram *, long long > m_chromIdxMap
Definition: MzmlManager.h:45
kome::io::mzml::MzmlManager::m_specIdxMap
std::map< kome::objects::Spectrum *, long long > m_specIdxMap
Definition: MzmlManager.h:42
void kome::io::mzml::MzmlManager::writeInstrumentList ( FILE *  fp,
std::vector< kome::objects::Sample * > &  samples 
)
protected

writes instrument list

Parameters
fpfile descriptor
samplesthe array of samples

Definition at line 423 of file MzmlManager.cpp.

423  {
424  // manager
425  AccessionManager& accMgr = AccessionManager::getInstance();
426 
427  // instruments
428  std::vector< std::string > instruments;
429  std::set< std::string > instrumentSet;
430 
431  for( unsigned int i = 0; i < samples.size(); i++ ) {
432  std::string instrument = samples[ i ]->getInstrument();
433  if( instrument.empty() ) {
434  instrument = "undefined";
435  }
436 
437  if( instrumentSet.find( instrument ) == instrumentSet.end() ) {
438  instrumentSet.insert( instrument );
439  instruments.push_back( instrument );
440  }
441  }
442 
443  // start tag
444  fprintf( fp, " <instrumentConfigurationList count=\"%d\">\n", instruments.size() );
445 
446  // each instruments
447  Accession* parentAcc = accMgr.getAccession( MACHINE_ACC );
448  const double minScore = 3.0;
449 
450  for( unsigned int i = 0; i < instruments.size(); i++ ) {
451  // accession
452  std::string instrument = instruments[ i ];
453  Accession* machineAcc = NULL;
454  double score = minScore - 0.01;
455 
456  for( unsigned int j = 0; j < accMgr.getNumberOfAccessions(); j++ ) {
457  Accession* tmp = accMgr.getAccession( j );
458  if( tmp->getOrigin() == parentAcc ) {
459  double tmpScore = getSimilarityScore( tmp->getName(), instrument.c_str() );
460  if( tmpScore > score ) {
461  machineAcc = tmp;
462  score = tmpScore;
463  }
464  }
465  }
466 
467  // tag
468  fprintf( fp, " <instrumentConfiguration id=\"%s\"", instrument.c_str() );
469  if( machineAcc == NULL ) {
470  fprintf( fp, "/>\n" );
471  }
472  else {
473  fprintf(
474  fp,
475  ">\n <cvParam cvRef=\"MS\" accession=\"%s\" name=\"%s\" value=\"\"/>\n",
476  machineAcc->getId(),
477  machineAcc->getName()
478  );
479  fprintf( fp, " </instrumentConfiguration>\n" );
480  }
481  }
482 
483  // end tag
484  fprintf( fp, " </instrumentConfigurationList>\n" );
485 }
kome::io::mzml::AccessionManager::getInstance
static AccessionManager & getInstance()
gets accession manager object (This is the only object.)
Definition: AccessionManager.cpp:154
kome::io::mzml::Accession::getId
const char * getId()
gets accession ID
Definition: Accession.cpp:47
kome::io::mzml::Accession::getName
const char * getName()
gets accession name
Definition: Accession.cpp:57
kome::io::mzml::Accession::getOrigin
Accession * getOrigin()
gets origin accesion
Definition: Accession.cpp:72
kome::io::mzml::AccessionManager::getAccession
Accession * getAccession(const unsigned int idx)
gets accession
Definition: AccessionManager.cpp:58
kome::io::mzml::AccessionManager
accession object management class
Definition: AccessionManager.h:26
kome::io::mzml::Accession
accession information class
Definition: Accession.h:24
kome::io::mzml::MzmlManager::getSimilarityScore
static double getSimilarityScore(const char *s0, const char *s1)
gets similarity score between two character strings
Definition: MzmlManager.cpp:1126
kome::io::mzml::AccessionManager::getNumberOfAccessions
unsigned int getNumberOfAccessions()
gets the number of accessions
Definition: AccessionManager.cpp:53

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void kome::io::mzml::MzmlManager::writeProcessingList ( FILE *  fp)
protected

writes processing list

Parameters
fpfile descriptor

Definition at line 488 of file MzmlManager.cpp.

488  {
489  // start tag
490  fprintf( fp, " <dataProcessingList count=\"1\">\n" );
491 
492  fprintf( fp, " <dataProcessing id=\"Mspp_proc\">\n" );
493  fprintf( fp, " <processingMethod softwareRef=\"Mass_plus_plus\" order=\"1\">\n" );
494  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000544\" name=\"Conversion to mzML\" value=\"\"/>\n" );
495  fprintf( fp, " </processingMethod>\n" );
496  fprintf( fp, " </dataProcessing>\n" );
497 
498  // end tag
499  fprintf( fp, " </dataProcessingList>\n" );
500 }
void kome::io::mzml::MzmlManager::writeReferenceableParamGroup ( FILE *  fp,
const bool  specFlg,
const bool  chromFlg 
)
protected

writes referenceable parameters group

Parameters
fpfile descriptor
specFlgspectrum flag
chromFlgchromatogram flag

Definition at line 294 of file MzmlManager.cpp.

294  {
295 
296 #ifdef MZML_USE_REFERENCEABLE_PARAM_GROUP
297 
298  // count
299  int cnt = 0;
300  if( specFlg && chromFlg ) {
301  cnt = 3;
302  }
303  else if( specFlg || chromFlg ) {
304  cnt = 2;
305  }
306  if( cnt == 0 ) {
307  return;
308  }
309 
310  // start tag
311  fprintf( fp, " <referenceableParamGroupList count=\"%d\">\n", cnt );
312 
313  // m/z
314  if( specFlg ) {
315  fprintf( fp, " <referenceableParamGroup id=\"mz_params\">\n" );
316  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000514\" name=\"m/z array\" value=\"\"\n" );
317  fprintf( fp, " unitCvRef=\"MS\" unitAccession=\"MS:1000040\" unitName=\"m/z\"/>\n" );
318  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000521\" name=\"32-bit float\" value=\"\"/>\n" );
319  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000576\" name=\"no compression\" value=\"\"/>\n" );
320  fprintf( fp, " </referenceableParamGroup>\n" );
321  }
322 
323  // RT
324  if( chromFlg ) {
325  fprintf( fp, " <referenceableParamGroup id=\"rt_params\">\n" );
326  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000595\" name=\"time array\" value=\"\"\n" );
327  fprintf( fp, " unitCvRef=\"UO\" unitAccession=\"UO:0000031\" unitName=\"minute\"/>\n" );
328  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000521\" name=\"32-bit float\" value=\"\"/>\n" );
329  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000576\" name=\"no compression\" value=\"\"/>\n" );
330  fprintf( fp, " </referenceableParamGroup>\n" );
331  }
332 
333  // intensity
334  fprintf( fp, " <referenceableParamGroup id=\"int_params\">\n" );
335  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000515\" name=\"intensity array\" value=\"\"/>\n" );
336  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000521\" name=\"32-bit float\" value=\"\"/>\n" );
337  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000576\" name=\"no compression\ value=\"\"/>\n" );
338  fprintf( fp, " </referenceableParamGroup>\n" );
339 
340  // end tag
341  fprintf( fp, " </referenceableParamGroupList>\n" );
342 
343 #endif // MZML_USE_REFERENCEABLE_PARAM_GROUP
344 }
void kome::io::mzml::MzmlManager::writeRun ( FILE *  fp,
std::vector< kome::objects::Sample * > &  samples,
std::vector< kome::objects::Spectrum * > &  spectra,
std::vector< kome::objects::Chromatogram * > &  chroms,
kome::core::Progress *  specPrgs,
kome::core::Progress *  chromPrgs,
kome::objects::SettingParameterValues *  saveSettings 
)
protected

writes run tag

Parameters
fpfile descriptor
samplesthe array of samples
spectrathe array of spectra
chromsthe array of chromatograms
specPrgsthe object to show the progress of writing spectra
chromPrgsthe object tos show the progress of writing chromatograms

Definition at line 503 of file MzmlManager.cpp.

511  {
512  // instrument
513  std::string instrument;
514  if( samples.size() > 0 ) {
515  instrument = samples.front()->getInstrument();
516  }
517  if( instrument.empty() ) {
518  instrument = "undefined";
519  }
520 
521  // start tag
522  fprintf( fp, " <run id=\"R1\" defaultInstrumentConfigurationRef=\"%s\">\n", instrument.c_str() );
523 
524  // write spectra
525  fprintf(
526  fp,
527  " <spectrumList defaultDataProcessingRef=\"Mspp_proc\" count=\"%d\"",
528  spectra.size()
529  );
530 
531  if( spectra.size() == 0 ) {
532  fprintf( fp, "/>\n" );
533  }
534  else {
535  fprintf( fp, ">\n" );
536 
537  specPrgs->setRange( 0, spectra.size() );
538  specPrgs->setPosition( 0 );
539 
540  // each spectra
541  for( unsigned int i = 0; i < spectra.size() && !specPrgs->isStopped(); i++ ) {
542  // spectrum
543  kome::objects::Spectrum* spec = spectra[ i ];
544 
545  std::string msg = FMT(
546  "Writing Spectrum [%d/%d] ..... %s",
547  ( i + 1 ),
548  spectra.size(),
549  spec->getName()
550  );
551  specPrgs->setStatus( msg.c_str() );
552 
553  // write spectrum
554  writeSpectrum( fp, *spec, saveSettings );
555  specPrgs->setPosition( i + 1 );
556  }
557 
558  if( specPrgs->isStopped() ) {
559  return;
560  }
561  specPrgs->fill();
562 
563  fprintf( fp, " </spectrumList>\n" );
564  }
565 
566  // write chromatograms
567  if( chroms.size() > 0 ) {
568  fprintf(
569  fp,
570  " <chromatogramList defaultDataProcessingRef=\"Mspp_proc\" count=\"%d\">\n",
571  chroms.size()
572  );
573 
574  chromPrgs->setRange( 0, chroms.size() );
575  chromPrgs->setPosition( 0 );
576 
577  // each chromatograms
578  for( unsigned int i = 0; i < chroms.size() && !chromPrgs->isStopped(); i++ ) {
579  // chromatogram
580  kome::objects::Chromatogram* chrom = chroms[ i ];
581 
582  std::string msg = FMT(
583  "Writing Chromatogram [%d/%d] ..... %s",
584  ( i + 1 ),
585  chroms.size(),
586  chrom->getName()
587  );
588  chromPrgs->setStatus( msg.c_str() );
589 
590  // write chromatogram
591  writeChromatogram( fp, *chrom, saveSettings );
592  chromPrgs->setPosition( i + 1 );
593  }
594 
595  if( chromPrgs->isStopped() ) {
596  return;
597  }
598  chromPrgs->fill();
599 
600  fprintf( fp, " </chromatogramList>\n" );
601  }
602 
603  // end tag
604  fprintf( fp, " </run>\n" );
605 }
kome::io::mzml::MzmlManager::writeChromatogram
void writeChromatogram(FILE *fp, kome::objects::Chromatogram &chrom, kome::objects::SettingParameterValues *saveSettings)
writes chromatogram
Definition: MzmlManager.cpp:946
kome::io::mzml::MzmlManager::writeSpectrum
void writeSpectrum(FILE *fp, kome::objects::Spectrum &spec, kome::objects::SettingParameterValues *saveSettings)
writes spectrum
Definition: MzmlManager.cpp:608

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void kome::io::mzml::MzmlManager::writeSoftwareList ( FILE *  fp,
std::vector< kome::objects::Sample * > &  samples 
)
protected

writes software list

Parameters
fpfile descriptor
samplesthe array of samples

Definition at line 347 of file MzmlManager.cpp.

347  {
348  // managers
349  kome::core::MsppManager& msppMgr = kome::core::MsppManager::getInstance();
350  AccessionManager& accMgr = AccessionManager::getInstance();
351 
352  // softwares
353  std::vector< std::pair< std::string, std::string > > softwares;
354  std::set< std::string > softwareSet;
355 
356  std::string software = "Mass_plus_plus";
357  std::string version = msppMgr.getVersion();
358 
359  softwareSet.insert( software );
360  softwares.push_back( std::make_pair( software, version ) );
361 
362  for( unsigned int i = 0; i < samples.size(); i++ ) {
363  kome::objects::Sample* smpl = samples[ i ];
364 
365  software = smpl->getSoftwareName();
366  version = smpl->getSoftwareVersion();
367 
368  if( !software.empty() && softwareSet.find( software ) == softwareSet.end() ) {
369  softwareSet.insert( software );
370  softwares.push_back( std::make_pair( software, version ) );
371  }
372  }
373 
374  // start tag
375  fprintf( fp, " <softwareList count=\"%d\">\n", softwares.size() );
376 
377  // software accession
378  Accession* parentAcc = accMgr.getAccession( SOFTWARE_ACC );
379  const double minScore = 3.0;
380 
381  // each softwares
382  for( unsigned int i = 0; i < softwares.size(); i++ ) {
383  // name, version
384  software = softwares[ i ].first;
385  version = softwares[ i ].second;
386 
387  // accession
388  Accession* softAcc = NULL;
389  double score = minScore - 0.01;
390 
391  for( unsigned int j = 0; j < accMgr.getNumberOfAccessions(); j++ ) {
392  Accession* tmp = accMgr.getAccession( j );
393  if( tmp->getOrigin() == parentAcc ) {
394  double tmpScore = getSimilarityScore( tmp->getName(), software.c_str() );
395  if( tmpScore > score ) {
396  softAcc = tmp;
397  score = tmpScore;
398  }
399  }
400  }
401 
402  // tag
403  fprintf( fp, " <software id=\"%s\" version=\"%s\"", software.c_str(), version.c_str() );
404  if( softAcc == NULL ) {
405  fprintf( fp, "/>\n" );
406  }
407  else {
408  fprintf(
409  fp,
410  ">\n <cvParam cvRef=\"MS\" accession=\"%s\" name=\"%s\" value=\"\"/>\n",
411  softAcc->getId(),
412  softAcc->getName()
413  );
414  fprintf( fp, " </software>\n" );
415  }
416  }
417 
418  // end tag
419  fprintf( fp, " </softwareList>\n" );
420 }
kome::io::mzml::AccessionManager::getInstance
static AccessionManager & getInstance()
gets accession manager object (This is the only object.)
Definition: AccessionManager.cpp:154
kome::io::mzml::Accession::getId
const char * getId()
gets accession ID
Definition: Accession.cpp:47
kome::io::mzml::Accession::getName
const char * getName()
gets accession name
Definition: Accession.cpp:57
kome::io::mzml::Accession::getOrigin
Accession * getOrigin()
gets origin accesion
Definition: Accession.cpp:72
kome::io::mzml::AccessionManager::getAccession
Accession * getAccession(const unsigned int idx)
gets accession
Definition: AccessionManager.cpp:58
kome::io::mzml::AccessionManager
accession object management class
Definition: AccessionManager.h:26
kome::io::mzml::Accession
accession information class
Definition: Accession.h:24
kome::io::mzml::MzmlManager::getSimilarityScore
static double getSimilarityScore(const char *s0, const char *s1)
gets similarity score between two character strings
Definition: MzmlManager.cpp:1126
kome::io::mzml::AccessionManager::getNumberOfAccessions
unsigned int getNumberOfAccessions()
gets the number of accessions
Definition: AccessionManager.cpp:53

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void kome::io::mzml::MzmlManager::writeSourceFileList ( FILE *  fp,
std::vector< kome::objects::Sample * > &  samples 
)
protected

writes source file list

Parameters
fpfile descriptor
samplesthe array of samples

Definition at line 257 of file MzmlManager.cpp.

257  {
258  // manager
259  AccessionManager& accMgr = AccessionManager::getInstance();
260 
261  // start tag
262  fprintf( fp, " <sourceFileList>\n" );
263 
264  // each samples
265  std::set< kome::objects::SampleSet* > sampleSets;
266 
267  for( unsigned int i = 0; i < samples.size(); i++ ) {
268  kome::objects::Sample* s = samples[ i ];
269  kome::objects::SampleSet* ss = s->getSampleSet();
270 
271  if( sampleSets.find( ss ) == sampleSets.end() ) {
272  sampleSets.insert( ss );
273 
274  // file name & directory
275  std::string fileName = ss->getFileName();
276  std::string fileDir = getdir( ss->getFilePath() );
277  fileDir = replacestring( fileDir.c_str(), "\\", "/" );
278 
279  fprintf(
280  fp,
281  " <sourceFile id=\"SF%d\" name=\"%s\" location=\"file://%s\" />\n",
282  ( i + 1 ),
283  fileName.c_str(),
284  fileDir.c_str()
285  );
286  }
287  }
288 
289  // end tag
290  fprintf( fp, " </sourceFileList>\n" );
291 }
kome::io::mzml::AccessionManager::getInstance
static AccessionManager & getInstance()
gets accession manager object (This is the only object.)
Definition: AccessionManager.cpp:154
kome::io::mzml::AccessionManager
accession object management class
Definition: AccessionManager.h:26

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void kome::io::mzml::MzmlManager::writeSpectrum ( FILE *  fp,
kome::objects::Spectrum &  spec,
kome::objects::SettingParameterValues *  saveSettings 
)
protected

writes spectrum

Parameters
fpfile descriptor
specspectrum

Definition at line 608 of file MzmlManager.cpp.

612  {
613  // get data status
614  bool op = saveSettings->getBoolValue( DATA_STATUS,false );
615 
616  // data points
617  kome::core::DataPoints tmpDps;
618  kome::core::DataPoints dps( kome::core::DataPoints::FLOAT );
619 
620  spec.getXYData( &tmpDps, op );
621  for( unsigned int i = 0; i < tmpDps.getLength(); i++ ) {
622  const double x = tmpDps.getX( i );
623  const double y = tmpDps.getY( i );
624 
625  if( y > 0.0 ) {
626  dps.addPoint( x, y );
627  }
628  }
629 
630  // reverse
631  const unsigned int len = dps.getLength();
632  if( m_reverseFlg ) {
633  float* xArr = (float*)dps.getXData();
634  float* yArr = (float*)dps.getYData();
635 
636  for( unsigned int i = 0; i < len; i++ ) {
637  memreverse( xArr + i, sizeof( float ) );
638  memreverse( yArr + i, sizeof( float ) );
639  }
640  }
641 
642  // index
643  const int idx = (int)m_specIdxMap.size();
644 
645  // start tag
646  fprintf( fp, " " );
647 
648  m_specIdxMap[ &spec ] = filetell( fp );
649 
650  // >>>>>> @Date:2013/08/19 <Modify> A.Ozaki
651  //
652  std::string strSpotId;
653  strSpotId.clear( );
654  if ( (char *)NULL != spec.getSpotId( ) )
655  {
656  strSpotId = FMT( "%s", spec.getSpotId( ) );
657  }
658 
659  if ( 0 == strSpotId.length( ) )
660  {
661  fprintf(
662  fp,
663  "<spectrum id=\"%s\" index=\"%d\" defaultArrayLength=\"%d\">\n",
664  spec.getName(),
665  idx,
666  len
667  );
668  }
669  else
670  {
671  fprintf(
672  fp,
673  "<spectrum id=\"%s\" index=\"%d\" defaultArrayLength=\"%d\" spotID=\"%s\">\n",
674  spec.getName(),
675  idx,
676  len,
677  strSpotId.c_str( )
678  );
679  }
680  //
681  // <<<<<< @Date:2013/08/19 <Modify> A.Ozaki
682 
683  // properties
684  kome::core::Properties& props = spec.getProperties();
685 
686  if( spec.getMsStage() >= 1 ) {
687  fprintf(
688  fp,
689  " <cvParam cvRef=\"MS\" accession=\"MS:1000511\" name=\"ms level\" value=\"%d\"/>\n",
690  spec.getMsStage()
691  );
692  }
693 
694  if( spec.isCentroidMode() ) {
695  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000127\" name=\"centroid spectrum\" value=\"\"/>\n" );
696  }
697  else {
698  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000128\" name=\"profile spectrum\" value=\"\"/>\n" );
699  }
700 
701  if( spec.getPolarity() == kome::objects::Spectrum::POLARITY_NEGATIVE ) {
702  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000129\" name=\"negative scan\" value=\"\"/>\n" );
703  }
704  else if( spec.getPolarity() == kome::objects::Spectrum::POLARITY_POSITIVE ) {
705  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000130\" name=\"positive scan\" value=\"\"/>\n" );
706  }
707 
708  if( spec.getTotalIntensity() >= 0.0 ) {
709  fprintf(
710  fp,
711  " <cvParam cvRef=\"MS\" accession=\"MS:1000285\" name=\"total ion current\" value=\"%f\"/>\n",
712  spec.getTotalIntensity()
713  );
714  }
715 
716  if( spec.getBasePeakMass() >= 0.0 ) {
717  fprintf(
718  fp,
719  " <cvParam cvRef=\"MS\" accession=\"MS:1000504\" name=\"base peak m/z\" value=\"%f\"/>\n",
720  spec.getBasePeakMass()
721  );
722  }
723 
724  if( spec.getMaxIntensity() >= 0.0 ) {
725  fprintf(
726  fp,
727  " <cvParam cvRef=\"MS\" accession=\"MS:1000505\" name=\"base peak intensity\" value=\"%f\"/>\n",
728  spec.getMaxIntensity()
729  );
730  }
731 
732  // scan list
733  fprintf(
734  fp,
735  " <scanList count=\"1\">\n"
736  );
737 
738  std::string instrument = spec.getSample()->getInstrument();
739  if( instrument.empty() ) {
740  instrument = "undefined";
741  }
742 
743  fprintf(
744  fp,
745  " <scan>\n"
746  );
747 
748  std::string filter = props.getStringValue( "Filter", "" );
749  if( !filter.empty() ) {
750  fprintf(
751  fp,
752  " <cvParam cvRef=\"MS\" accession=\"MS:1000512\" name=\"filter string\" value=\"%s\"/>\n",
753  filter.c_str()
754  );
755  }
756 
757  if( spec.getRt() >= 0.0 ) {
758  fprintf(
759  fp,
760  " <cvParam cvRef=\"MS\" accession=\"MS:1000016\" name=\"scan start time\" value=\"%f\"\n",
761  spec.getRt()
762  );
763 
764  fprintf(
765  fp,
766  " unitCvRef=\"UO\" unitAccession=\"UO:0000031\" unitName=\"minute\"/>\n"
767  );
768  }
769 
770  fprintf(
771  fp,
772  " <scanWindowList count=\"1\">\n"
773  );
774 
775  fprintf(
776  fp,
777  " <scanWindow>\n"
778  );
779 
780  if( spec.getMinX() >= 0.0 ) {
781  fprintf(
782  fp,
783  " <cvParam cvRef=\"MS\" accession=\"MS:1000501\" name=\"scan window lower limit\" value=\"%f\"/>\n",
784  spec.getMinX()
785  );
786  }
787  if( spec.getMaxX() >= 0.0 ) {
788  fprintf(
789  fp,
790  " <cvParam cvRef=\"MS\" accession=\"MS:1000500\" name=\"scan window upper limit\" value=\"%f\"/>\n",
791  spec.getMaxX()
792  );
793  }
794 
795  fprintf(
796  fp,
797  " </scanWindow>\n"
798  );
799 
800  fprintf(
801  fp,
802  " </scanWindowList>\n"
803  );
804 
805  fprintf(
806  fp,
807  " </scan>\n"
808  );
809 
810  fprintf(
811  fp,
812  " </scanList>\n"
813  );
814 
815  // p recursor
816  const double precursor = spec.getPrecursor();
817  if( precursor >= 0.0 ) {
818  kome::objects::Spectrum* parent = spec.getParentSpectrum();
819  std::string parentId = ( parent == NULL ? "" : parent->getName() );
820 
821  fprintf(
822  fp,
823  " <precursorList count=\"1\">\n"
824  );
825 
826  fprintf(
827  fp,
828  " <precursor spectrumRef=\"%s\">\n",
829  parentId.c_str()
830  );
831 
832  fprintf(
833  fp,
834  " <selectedIonList count=\"1\">\n"
835  );
836 
837  fprintf(
838  fp,
839  " <selectedIon>\n"
840  );
841 
842  fprintf(
843  fp,
844  " <cvParam cvRef=\"MS\" accession=\"MS:1000744\" name=\"selected ion m/z\"\n"
845  );
846 
847  fprintf(
848  fp,
849  " value=\"%f\" unitCvRef=\"MS\" unitAccession=\"MS:1000040\" unitName=\"m/z\"/>\n",
850  precursor
851  );
852 
853  fprintf(
854  fp,
855  " </selectedIon>\n"
856  );
857 
858  fprintf(
859  fp,
860  " </selectedIonList>\n"
861  );
862 
863  fprintf(
864  fp,
865  " </precursor>\n"
866  );
867 
868  fprintf(
869  fp,
870  " </precursorList>\n"
871  );
872  }
873 
874  // data points
875  if( len > 0 ) {
876  // prepare
877  unsigned long buffLength = len * sizeof( float ) * 2;
878  char* base64Buff = new char[ buffLength ];
879 
880  fprintf( fp, " <binaryDataArrayList count=\"2\">\n" );
881 
882  // m/z
883  unsigned long size = kome::core::Base64::encode( dps.getXData(), sizeof( float ) * len, base64Buff, buffLength );
884 
885  fprintf( fp, " <binaryDataArray encodedLength=\"%d\">\n", size );
886 
887 #ifdef MZML_USE_REFERENCEABLE_PARAM_GROUP
888  fprintf( fp, " <referenceableParamGroupRef ref=\"mz_params\"/>\n" );
889 #else
890  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000514\" name=\"m/z array\" value=\"\"\n" );
891  fprintf( fp, " unitCvRef=\"MS\" unitAccession=\"MS:1000040\" unitName=\"m/z\"/>\n" );
892  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000521\" name=\"32-bit float\" value=\"\"/>\n" );
893  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000576\" name=\"no compression\" value=\"\"/>\n" );
894 #endif // MZML_USE_REFERENCEABLE_PARAM_GROUP
895 
896  fprintf( fp, " <binary>" );
897 
898 
899  char* pos = base64Buff;
900  while( size > 0 ) {
901  int writeSize = MIN( size, 1024 );
902  writeSize = fwrite( pos, 1, writeSize, fp );
903  size -= writeSize;
904  pos += writeSize;
905  }
906 
907  fprintf( fp, "</binary>\n" );
908  fprintf( fp, " </binaryDataArray>\n" );
909 
910  // intensity
911  size = kome::core::Base64::encode( dps.getYData(), sizeof( float ) * len, base64Buff, buffLength );
912 
913  fprintf( fp, " <binaryDataArray encodedLength=\"%d\">\n", size );
914 
915 #ifdef MZML_USE_REFERENCEABLE_PARAM_GROUP
916  fprintf( fp, " <referenceableParamGroupRef ref=\"int_params\"/>\n" );
917 #else
918  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000515\" name=\"intensity array\" value=\"\"/>\n" );
919  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000521\" name=\"32-bit float\" value=\"\"/>\n" );
920  fprintf( fp, " <cvParam cvRef=\"MS\" accession=\"MS:1000576\" name=\"no compression\" value=\"\"/>\n" );
921 #endif // MZML_USE_REFERENCEABLE_PARAM_GROUP
922 
923  fprintf( fp, " <binary>" );
924 
925  pos = base64Buff;
926  while( size > 0 ) {
927  int writeSize = MIN( size, 1024 );
928  writeSize = fwrite( pos, 1, writeSize, fp );
929  size -= writeSize;
930  pos += writeSize;
931  }
932 
933  fprintf( fp, "</binary>\n" );
934  fprintf( fp, " </binaryDataArray>\n" );
935 
936  fprintf( fp, " </binaryDataArrayList>\n" );
937 
938  delete[] base64Buff;
939  }
940 
941  // end tag
942  fprintf( fp, " </spectrum>\n" );
943 }
kome::io::mzml::MzmlManager::m_specIdxMap
std::map< kome::objects::Spectrum *, long long > m_specIdxMap
Definition: MzmlManager.h:42

Member Data Documentation

std::map< kome::objects::Chromatogram*, long long > kome::io::mzml::MzmlManager::m_chromIdxMap
protected

chromatogram index map

Definition at line 45 of file MzmlManager.h.

const bool kome::io::mzml::MzmlManager::m_reverseFlg
protected

reverse flag

Definition at line 48 of file MzmlManager.h.

std::map< kome::objects::Spectrum*, long long > kome::io::mzml::MzmlManager::m_specIdxMap
protected

spectrum index map

Definition at line 42 of file MzmlManager.h.

The documentation for this class was generated from the following files:
Generated on Sun Mar 18 2018 12:31:28 for Mass++ mzML IO Plugin v2.7.5 by   doxygen 1.8.6