Matrix Science Mascot Parser toolkit
 
Loading...
Searching...
No Matches
ms_mascotresfile_dat.hpp
1/*
2##############################################################################
3# file: ms_mascotresfile_dat.hpp #
4# 'msparser' toolkit #
5# Encapsulates a mascot results file #
6##############################################################################
7# COPYRIGHT NOTICE #
8# Copyright 1998-2023 Matrix Science Limited All Rights Reserved. #
9# #
10##############################################################################
11# $Archive:: /MowseBranches/ms_mascotresfile_dat_1.2/include/ms_mascotresfi $ #
12# $Author: villek@matrixscience.com $ #
13# $Date: 2024-09-23 15:56:03 +0100 $ #
14# $Revision: 09156baa48968c2f3ca3f6899bf06cc9caec40b7 | MSPARSER_REL_3_0_0-2024-09-24-0-g93ebaeb4f4 $ #
15# $NoKeywords:: $ #
16##############################################################################
17*/
18
19#ifndef MS_MASCOTRESFILE_DAT_HPP
20#define MS_MASCOTRESFILE_DAT_HPP
21
22
23
24// Includes from the standard template library
25#include <stdarg.h>
26#include <time.h>
27#include <string>
28#include <list>
29#include <vector>
30#include <set>
31
32namespace msparser_internal {
33 class ms_cdb;
34 class ms_peptidesumcdb;
35 class ms_mutex;
36 class ms_peptidesummarybase;
37 class ms_proteinsummarybase;
38
39}
40
41namespace matrix_science {
42 class ms_umod_configfile;
43 class ms_masses;
44 class ms_enzymefile;
45 class ms_taxonomyfile;
46 class ms_mascotresults_params;
47
53#ifndef SWIG
54 class multiBuf {
55 public:
56 multiBuf() {pMem_ = 0; len_ = 0; pEnd_ = 0;}
57 public :
58 char *pMem_; // pointer to first block of memory
59 int len_; // excluding any null terminator
60 char *pEnd_; // Pointer to last byte (not the null terminator)
61 private:
62 };
63 typedef std::vector<multiBuf> multiBuf_v;
64
65 class multiBufMemPtr {
66 public:
67 enum MBMP { MBMP_INVALID = -1, MBMP_USING_CDB = -2 };
68 multiBufMemPtr(int bufNum, char *pMem)
69 : bufNum_(bufNum), pMem_(pMem) {};
70 multiBufMemPtr() : bufNum_(MBMP_INVALID), pMem_(0) {};
71 void decrement(const multiBuf_v & buffers);
72 void decrementUntil(const multiBuf_v & buffers, const char * chars);
73 void increment(const multiBuf_v & buffers);
74 bool isValid() const {return bufNum_ != MBMP_INVALID;}
75 bool operator<(const multiBufMemPtr & rhs);
76 bool operator<=(const multiBufMemPtr & rhs);
77
78 public:
79 int bufNum_;
80 char * pMem_;
81 };
82
83 // ms_sortByKeyCriterion class is used internally in the library
84 // to give fast access to the keys. Don't use it from outside the DLL
85 class ms_sortByKeyCriterion
86 {
87 public:
88 enum CMP_MODE {CASE_INSENSITIVE=0x01, CASE_SENSITIVE=0x02, QUOTED=0x04};
89 ms_sortByKeyCriterion(int m=(int)CASE_INSENSITIVE) : mode_(m) {}
90 bool operator() (const char * p1, const char * p2) const;
91
92 private:
93 int mode_;
94 // Unfortunately, when called from Perl in Windows,
95 // the toupper function ends up calling extra functions
96 // to convert to wide char and back again. We don't
97 // want language independent conversion here - the
98 // key names are all single byte.
99 inline char my_toupper(char ch) const
100 {
101 if ((mode_ & CASE_INSENSITIVE) && ch >= 'a' && ch <= 'z')
102 return static_cast<char>('A' + (ch-'a'));
103 else
104 return ch;
105 }
106
107 };
108#endif
109
111
120 class MS_MASCOTRESFILE_API ms_mascotresfile_dat : public ms_mascotresfilebase
121 {
122 friend class msparser_internal::ms_peptidesumcdb;
123 public:
124
126
129 // Developer note: Add new sections to this enum just before
130 // SEC_INDEX, so that existing values are not changed.
131 enum section
132 {
133 SEC_PARAMETERS,
134 SEC_HEADER,
135 SEC_MASSES,
136 SEC_SUMMARY,
137 SEC_MIXTURE,
138 SEC_PEPTIDES,
139 SEC_PROTEINS,
140 SEC_QUERY1,
141 SEC_QUANTITATION,
142 SEC_UNIMOD,
143 SEC_ENZYME,
144 SEC_TAXONOMY,
145 SEC_DECOYSUMMARY,
146 SEC_DECOYMIXTURE,
147 SEC_DECOYPEPTIDES,
148 SEC_DECOYPROTEINS,
149 SEC_ERRTOLSUMMARY,
150 SEC_ERRTOLPEPTIDES,
151 SEC_SPECTRAL_LIBRARY,
152 SEC_LIBRARYPEPTIDES,
153 SEC_LIBRARYSUMMARY,
154 SEC_CROSSLINK_SUMMARY,
155 SEC_CROSSLINK_PEPTIDES,
156 SEC_CROSSLINKING,
157 SEC_UNIMOD_XL,
158 SEC_ERRTOLDECOYSUMMARY,
159 SEC_ERRTOLDECOYPEPTIDES,
160 SEC_INDEX,
161 SEC_NUMSECTIONS
162 };
163
164
166 static const char *getSectionName(const section sec);
167
169 static section getSummarySection(const ms_peptide::PSM_TYPE pepType);
170
172 static section getPeptideSection(const ms_peptide::PSM_TYPE pepType);
173
174
176
183 enum err
184 {
185 ERR_NO_ERROR = 0x0000,
186 ERR_NOMEM = 0x0001,
187 ERR_NOSUCHFILE = 0x0002,
188 ERR_READINGFILE = 0x0003,
189 ERR_QUERYOUTOFRANGE = 0x0004,
190 ERR_MISSINGENTRY = 0x0005,
191 ERR_PEPSUMMPEPGET = 0x0006,
192 ERR_PEPTIDESTR = 0x0007,
193 ERR_ACCINPEPTIDESTR = 0x0008,
194 ERR_PROTSUMM = 0x0009,
195 ERR_PROTSUMMPEP = 0x000A,
196 ERR_ADDPEPTIDES = 0x000B,
197 ERR_MISSINGHIT = 0x000C,
198 ERR_MISSINGSECTION = 0x000D,
199 ERR_MISSINGSECTIONEND = 0x000E,
200 ERR_MALFORMED_ERR_TOL = 0x000F,
201 ERR_NO_ERR_TOL_PARENT = 0x0010,
202 ERR_NULL_ACC_PEP_SUM = 0x0011,
203 ERR_NULL_ACC_PROT_SUM = 0x0012,
204 ERR_DUPE_ACCESSION = 0x0013,
205 ERR_UNASSIGNED_PROG = 0x0014,
206 ERR_UNASSIGNED_RANGE = 0x0015,
207 ERR_UNASSIGNED_UNK = 0x0016,
208 ERR_NO_UNIGENE_FILE = 0x0017,
209 ERR_DUPLICATE_KEY = 0x0018,
210 ERR_OLDRESULTSFILE = 0x0019,
211 ERR_MALFORMED_TAG = 0x001A,
212 ERR_MALFORMED_DRANGE = 0x001B,
213 ERR_INVALID_NUMQUERIES = 0x001C,
214 ERR_MALFORMED_TERMS = 0x001D,
215 ERR_INVALID_RESFILE = 0x001E,
216 ERR_INVALID_PROTDB = 0x001F,
217 ERR_UNIGENE_MULTIDB = 0x0020,
218 ERR_INVALID_CACHE_DIR = 0x0021,
219 ERR_FAIL_OPEN_DAT_FILE = 0x0022,
220 ERR_MISSING_CDB_FILE = 0x0023,
221 ERR_FAIL_MK_CACHE_DIR = 0x0024,
222 ERR_FAIL_MK_CDB_FILE = 0x0025,
223 ERR_FAIL_CLOSE_FILE = 0x0026,
224 ERR_FAIL_CDB_INIT = 0x0027,
225 ERR_INVALID_CDB_FILE = 0x0028,
226 ERR_WRITE_CDB_FILE = 0x0029,
227 ERR_CDB_TOO_LARGE = 0x002A,
228 ERR_NEED_64_BIT = 0x002B,
229 ERR_CDB_64_BIT_REMAKE = 0x002C,
230 ERR_CDB_OLD_VER_RETRY = 0x002D,
231 ERR_CDB_OLD_VER_NO_RETRY = 0x002E,
232 ERR_CDB_INCOMPLETE_RETRY = 0x002F,
233 ERR_CDB_INCOMPLETE_NO_RETRY = 0x0030,
234 ERR_CDB_BEING_CREATED = 0x0031,
235 ERR_CDB_FAIL_REMOVE = 0x0032,
236 ERR_CDB_FAIL_LOCK = 0x0033,
237 ERR_CDB_FAIL_UNLOCK = 0x0034,
238 ERR_CDB_SOURCE_CHANGE_RETRY = 0x0035,
239 ERR_CDB_SOURCE_CHANGE_NO_RETRY = 0x0036,
240 ERR_MISSING_PERCOLATOR_FILE = 0x0037,
241 ERR_CANNOT_APPEND_RESFILE = 0x0038,
242 ERR_CANNOT_APPEND_RESFILE_NO_FNAMES = 0x0039,
243 ERR_RESULTS_NOT_CREATED = 0x003A,
244 ERR_LASTONE = 0x003B
245 };
246 // this list has to be included into ms_errors.hpp file too !!!
247
248
250 ms_mascotresfile_dat(const char * szFileName,
251 const int keepAliveInterval = 0,
252 const char * keepAliveText = "<!-- %d seconds -->\n",
253 const unsigned int flags = RESFILE_NOFLAG,
254 const char * cacheDirectory = "../data/cache/%Y/%m",
255 const char * XMLschemaDirectory = 0,
256 ms_progress_info * progressMonitor = 0);
257
258 virtual ~ms_mascotresfile_dat();
259
260 // ------------------- Basic generic functions -------------------
261
262
264 int appendResfile(const char * filename,
265 int flags=RESFILE_USE_PARENT_PARAMS,
266 const char * cacheDirectory = 0) override; // returns 'id' of added file
267
269 const ms_mascotresfile_dat* getResfile(int id) const override;
270
272 int getNumberOfResfiles() const override;
273
275 bool doesSectionExist(const section sec) const;
276
278 bool anyPeptideSummaryMatches(const section sec=SEC_PEPTIDES) const;
279
280 bool anyFastaMatches(const bool isDecoy=false) const override;
281
282 bool anySpectralLibraryMatches(const bool isDecoy=false) const override;
283
284 bool anyErrorTolerantMatches(const bool isDecoy=false) const override;
285
286 bool anyCrosslinkedMatches(const bool isDecoy=false) const override;
287
288 // When calling 'getSectionValue' from outside the dll, be careful
289 // that enough space is 'reserved' in the string.
290 // Return value is length of the actual string that it wanted to
291 // to return, so if this is larger than maxLen, then you are
292 // missing some of the string. Best to call getSectionValueStr
294 int getSectionValue(const section sec, const char * key, char * str, int maxLen) const;
295
297 int getSectionValueInt(const section sec, const char * key) const;
298
300 double getSectionValueDouble(const section sec, const char * key) const;
301
303 std::string getSectionValueStr(const section sec, const char * key) const;
304
306 int getQuerySectionValue(const int query, const char * key, char * str, int maxLen) const;
307
309 int getQuerySectionValueInt(const int query, const char * key) const;
310
312 double getQuerySectionValueDouble(const int query, const char * key) const;
313
315 std::string getQuerySectionValueStr(const int query, const char * key) const;
316
318 int getJobNumber(const int resfileID = 1) const override;
319
321 std::string enumerateSectionKeys(const section sec,
322 const int num,
323 int * pPreviousNum = 0,
324 OFFSET64_T * pPreviousOffset = 0) const;
325
327 std::string enumerateQuerySectionKeys(const int query,
328 const int num,
329 int * pPreviousNum = 0,
330 OFFSET64_T * pPreviousOffset = 0) const;
331
332 // ----------------- Specific results functions ------------------
334 int getNumQueries(const int resfileID = 0) const override;
335
337 int getNumHits(const section sec=SEC_SUMMARY) const;
338
340 int getNumSeqs(const int idx = 0) const override;
341
343 int getNumSeqsAfterTax(const int idx = 0) const override;
344
346 int getNumEtSeqsSearched(const int idx = 0) const override;
347
349 int getNumLibraryEntries(const int idx = 0) const override;
350
352 double getNumResidues(const int idx = 0) const override;
353
355 bool isDatabaseTypeAvailable() const override;
357 DATABASE_TYPE getDatabaseType(const int idx) const override;
359 int getReferenceDatabaseNumberOfSL(const int idx) const override;
360
362 std::vector<int> getSLDatabaseNumbersOfReference(const int idx) const override;
363
365
367 int getExecTime() const override { return execTime_; }
368
370
372 int getDate() const override { return searchDate_; }
373
375
377 std::string getMascotVer() const override { return version_; }
378
380 std::string getFastaVer(int idx = 1) const override;
381
383 std::string getFastaPath(int idx = 1) const override;
384
386 std::string getUniqueTaskID() const override;
387
389 ms_mascotoptions::DECOY_ALGORITHM getDecoyTypeForDB(const int idx = 1) const override;
390
392 double getSLFragmentTolerance(int idx = 1) const override;
393
395 std::string getSLFragmentToleranceUnit(int idx = 1) const override;
396
398 virtual std::string getSLExecCommand(int idx = 1) const override;
399
401 bool isPMF() const override;
402
404 bool isMSMS() const override;
405
407 bool isSQ() const override;
408
410 bool isErrorTolerant() const override;
411
413 bool anyPMF() const override;
414
416 bool anyMSMS() const override;
417
419 bool anySQ() const override;
420
422 bool anyTag() const override;
423
425 double getObservedMass(const int query) const override;
426
428 int getObservedCharge(const int query, const bool decoy=false) const override;
429
431 double getObservedMrValue(const int query, const bool decoy=false) const override;
432
434 double getObservedIntensity(const int query) const override;
435
437 std::string getRepeatSearchString(const int query, const bool fullQuery = false) const override;
438
440 std::string getFileName(const int id = 1) const override;
441
443 bool getQuantitation(ms_quant_configfile *qfile) const override;
444
446 bool getUnimod(ms_umod_configfile *ufile, bool useSchemaFromResfile = false) const override;
447
449 bool getUnimodXL(ms_umod_configfile *ufile, bool useSchemaFromResfile = false) const override;
450
452 bool getEnzyme(ms_enzymefile *efile, const char * enzymeFileName = 0) const override;
453
455 bool getTaxonomy(ms_taxonomyfile *tfile) const override;
456
458 std::string getCacheDirectory(bool processed = true) const override;
459
461 std::string getCacheFileName() const override;
462
463#ifndef SWIG
465 bool getSrcQueryAndFileIdForMultiFile(const int q, int & gsqNewQuery, int & gsqFileId) const override;
466#else // SWIG Multiple return values
467 bool getSrcQueryAndFileIdForMultiFile(const int q, int & OUTPUT, int & OUTPUT) const override;
468#endif
470 int getMultiFileQueryNumber(const int localQuery, const int fileId) const override;
471
473 bool hasEnzyme() const override;
474
476 bool hasRT() const override;
477
479 bool hasQuantitation() const override;
480
482 ms_inputquery getInputQuery(const int queryNum) const override;
483
484#ifndef SWIG
486 void getHeaderKeyValues(std::vector<std::string> & keys, std::vector<std::string> & values) const override;
487
489 void getSearchParametersKeyValues(std::vector<std::string> & keys, std::vector<std::string> & values) const override;
490
492 void getMassesKeyValues(std::vector<std::string> & keys, std::vector<double> & values) const override;
493#else
494 void getHeaderKeyValues(std::vector<std::string> & OUTPUT, std::vector<std::string> & OUTPUT) const override;
495
496 void getSearchParametersKeyValues(std::vector<std::string> & OUTPUT, std::vector<std::string> & OUTPUT) const override;
497
498 void getMassesKeyValues(std::vector<std::string> & OUTPUT, std::vector<double> & OUTPUT) const override;
499#endif
500
502 virtual std::string getHeaderValue(const std::string& key) const override;
503
505 virtual std::string getSearchParameter(const std::string& key) const override;
506
508 virtual double getMassValue(const std::string& key) const override;
509
511 int getLibraryMods(std::vector<std::string> & modNames, std::vector<double> & modDeltas) const override;
512
514 int64_t getQmatch(const int query, const ms_peptide::PSM_TYPE pepType) const override;
515
517 double getQplughole(const int query, const ms_peptide::PSM_TYPE pepType) const override;
518
520 double getFirstPassThreshold() const override;
521
522
523 protected:
524#ifndef SWIG
525 // Not safe to copy or assign this object.
526 ms_mascotresfile_dat(const ms_mascotresfile_dat & rhs);
527 ms_mascotresfile_dat & operator=(const ms_mascotresfile_dat & rhs);
528#endif
529 bool getCrosslinking(ms_crosslinking_configfile *crosslinkingFile) const override;
530
531 private:
532
533 void validateResfileVersion() override;
534
535 std::string getPepSumCacheFilename(
536 const unsigned int flags,
537 double minProbability,
538 int maxHitsToReport,
539 const char * unigeneIndexFile,
540 double ignoreIonsScoreBelow,
541 int minPepLenInPepSummary,
542 const char * singleHit,
543 const unsigned int flags2) const override;
544
545 std::string getPepSumCacheFilename(const ms_mascotresults_params & parameters) const override;
546
547 int getNumHitsInProteinSummary(const ms_peptide::PSM_TYPE psmType) const override;
548
549 bool willCreatePepSumCache(
550 const unsigned int flags,
551 double minProbability,
552 int maxHitsToReport,
553 const char * unigeneIndexFile,
554 double ignoreIonsScoreBelow,
555 int minPepLenInPepSummary,
556 const char * singleHit,
557 const unsigned int flags2) const override;
558
559 bool willCreatePepSumCache(const ms_mascotresults_params &parameters) const override;
560
561 bool willCreatePepSumCache(const ms_mascotresults_params & parameters,
562 const ms_mascotoptions & opts,
563 std::string & peptideSummaryCacheFileName,
564 unsigned int & cacheStatus) const override;
565
566 void buildPeptideSummaryImpl(ms_peptidesummary & pepSum,
567 const ms_mascotresults_params & parameters,
568 std::shared_ptr<msparser_internal::ms_mascotresultsbase> & results,
569 std::shared_ptr<msparser_internal::ms_peptidesummarybase> & iPepSum) const override;
570
571 void buildProteinSummaryImpl(ms_proteinsummary & protSum,
572 const ms_mascotresults_params & parameters,
573 std::shared_ptr<msparser_internal::ms_mascotresultsbase> & results,
574 std::shared_ptr<msparser_internal::ms_proteinsummarybase> & iProtSum) const override;
575
576 std::shared_ptr<msparser_internal::ms_inputquerybase> buildInputQueryImpl(const int q) const override;
577
578 std::shared_ptr<msparser_internal::ms_searchparamsbase> buildSearchParamsImpl() const override;
579
580 std::vector<int> multifileNumQueries_; // 0 based vector, with 0 being the primary file
581 typedef std::vector<ms_mascotresfile_dat *> resfileV_t; // 0 based vector, with 0 being the primary file
582 resfileV_t multifileResfiles_;
583 int protSummaryHits_;
584 int numSequences_;
585 int numSequencesAfterTax_;
586 double numResidues_;
587 int numLibraryEntries_;
588 int execTime_;
589 int searchDate_;
590
591
592 std::vector<DATABASE_TYPE> dbType_;
593 std::vector<int> slReferenceMap_;
594
595 bool anyMSMS_;
596 bool cachedAnyMSMS_;
597 bool anyPMF_;
598 bool cachedAnyPMF_;
599 bool anySQ_;
600 bool cachedAnySQ_;
601 bool anyTag_;
602 bool cachedAnyTag_;
603 mutable bool isErrorTolerant_;
604 mutable bool cachedIsErrorTolerant_;
605
606 msparser_internal::ms_cdb * pIndexFile_;
607 bool useIndexFile_;
608 int hFile_;
609 mutable char * readlnBuf_;
610 mutable unsigned int readlnBufSize_;
611 msparser_internal::ms_mutex * pMutex_;
612
613
614 const char * sectionTitles_[SEC_NUMSECTIONS];
615
616 multiBufMemPtr sectionStart_[SEC_NUMSECTIONS];
617 multiBufMemPtr sectionEnd_ [SEC_NUMSECTIONS];
618
619 multiBuf_v buffers_;
620
621 std::string endSectionKey_;
622 std::string lineBasedEndSectionKey_;
623 std::string genericQuerySectionKey_;
624 bool isWinIniFormat_;
625 std::vector<double> cachedMrValues_;
626 std::vector<double> cachedExpValues_;
627 std::vector<short> cachedCharges_;
628
629 multiBufMemPtr findSectionStart(const char * szSectionName,
630 const multiBufMemPtr * startLookingAt = 0) const;
631 multiBufMemPtr findSectionEnd(const multiBufMemPtr sectionStart) const;
632
633 // Array of maps for each section
634 typedef std::set<const char *,ms_sortByKeyCriterion> sortedKeys;
635 sortedKeys sorted_[SEC_NUMSECTIONS];
636 bool fillUpSortedList(const int section,
637 const multiBufMemPtr sectionStart,
638 const multiBufMemPtr sectionEnd,
639 sortedKeys & sorted_keys) const;
640
641 // There are an 'unknown' number of query sections
642 bool hasQuerySectionBeenIndexed;
643 std::vector<multiBufMemPtr> querySectionStart_;
644 std::vector<multiBufMemPtr> querySectionEnd_;
645 std::vector<sortedKeys> sortedQueries_;
646
647 // Private function to get string
648 bool inDLLgetSectVal(const section sec,
649 const int queryNumber,
650 const multiBufMemPtr sectionStart,
651 const multiBufMemPtr sectionEnd,
652 sortedKeys & sorted_keys,
653 const char * key,
654 std::string & result) const;
655
656 // Private function to get string
657 bool inDLLgetSectionAsString(const section sec,
658 std::string & result) const;
659
660 bool readFile(const char * szFileName);
661 bool readLine(char * & buf, unsigned int & bufSize) const;
662 void getSectionTitles();
663 void debugCheckReadFileOK();
664 bool createCDBFile();
665
666 int extractObservedCharge(char *szKey, std::string str) const;
667 std::string enumerateQuerySection(const int query,
668 const int num,
669 int * pPreviousNum,
670 OFFSET64_T * pPreviousOffset,
671 OFFSET64_T * pSectionEnd,
672 std::string & value) const;
673
674 void getSLFragmentToleranceAndUnit_Value(int idx, double & tolerance, std::string & toleranceUnit) const;
675
676 void getSectionKeyValues(std::vector<std::string> & keys, std::vector<std::string> & values, section sec, const std::string &startswith="") const;
677
678 void propagateKeepAlive(const int keepAliveInterval,
679 const char * keepAliveText,
680 const bool propagateToAppended,
681 const bool resetStartTime) override;
682
683 std::map<section, bool> mapSectionAnyMatch_;
684
685 }; // end of resfile_group
687} // matrix_science namespace
688#endif // MS_MASCOTRESFILE_DAT_HPP
689
690/*------------------------------- End of File -------------------------------*/
matrix_science::ms_crosslinking_configfile
This class represents the file crosslinking.xml.
Definition: ms_crosslinking_configfile.hpp:49
matrix_science::ms_enzymefile
Reads and parses the enzymes file that contains multiple enzyme definitions.
Definition: ms_enzyme.hpp:194
matrix_science::ms_inputquery
This class encapsulates the input queries (peak lists) in the Mascot results file.
Definition: ms_inputquery.hpp:43
matrix_science::ms_mascotoptions
An instance of this class represents all the parameters specified in the Options section of mascot....
Definition: ms_mascotoptions.hpp:91
matrix_science::ms_mascotoptions::DECOY_ALGORITHM
DECOY_ALGORITHM
Definitions for how the decoy sequences are generated.
Definition: ms_mascotoptions.hpp:156
matrix_science::ms_mascotresfile_dat
Class for parsing and reading files in dat28 format.
Definition: ms_mascotresfile_dat.hpp:121
matrix_science::ms_mascotresfile_dat::section
section
Section names in the standard mascot results files.
Definition: ms_mascotresfile_dat.hpp:132
matrix_science::ms_mascotresfile_dat::SEC_TAXONOMY
@ SEC_TAXONOMY
taxonomy section
Definition: ms_mascotresfile_dat.hpp:144
matrix_science::ms_mascotresfile_dat::SEC_SPECTRAL_LIBRARY
@ SEC_SPECTRAL_LIBRARY
spectral library section. See also Spectral libraries.
Definition: ms_mascotresfile_dat.hpp:151
matrix_science::ms_mascotresfile_dat::SEC_ERRTOLDECOYPEPTIDES
@ SEC_ERRTOLDECOYPEPTIDES
error tolerant decoy peptides section. See also Error tolerant searches.
Definition: ms_mascotresfile_dat.hpp:159
matrix_science::ms_mascotresfile_dat::SEC_ERRTOLDECOYSUMMARY
@ SEC_ERRTOLDECOYSUMMARY
error tolerant decoy summary section. See also Error tolerant searches.
Definition: ms_mascotresfile_dat.hpp:158
matrix_science::ms_mascotresfile_dat::SEC_MASSES
@ SEC_MASSES
masses section
Definition: ms_mascotresfile_dat.hpp:135
matrix_science::ms_mascotresfile_dat::SEC_DECOYPEPTIDES
@ SEC_DECOYPEPTIDES
decoy_peptides section. See also Target-decoy searches and false discovery rate.
Definition: ms_mascotresfile_dat.hpp:147
matrix_science::ms_mascotresfile_dat::SEC_DECOYSUMMARY
@ SEC_DECOYSUMMARY
decoy_summary section. See also Target-decoy searches and false discovery rate.
Definition: ms_mascotresfile_dat.hpp:145
matrix_science::ms_mascotresfile_dat::SEC_ENZYME
@ SEC_ENZYME
enzyme section
Definition: ms_mascotresfile_dat.hpp:143
matrix_science::ms_mascotresfile_dat::SEC_DECOYPROTEINS
@ SEC_DECOYPROTEINS
decoy_proteins section. See also Target-decoy searches and false discovery rate.
Definition: ms_mascotresfile_dat.hpp:148
matrix_science::ms_mascotresfile_dat::SEC_QUERY1
@ SEC_QUERY1
query1 section. Don't use, see getQuerySectionValueStr() etc.
Definition: ms_mascotresfile_dat.hpp:140
matrix_science::ms_mascotresfile_dat::SEC_INDEX
@ SEC_INDEX
index section
Definition: ms_mascotresfile_dat.hpp:160
matrix_science::ms_mascotresfile_dat::SEC_PARAMETERS
@ SEC_PARAMETERS
parameters section
Definition: ms_mascotresfile_dat.hpp:133
matrix_science::ms_mascotresfile_dat::SEC_LIBRARYPEPTIDES
@ SEC_LIBRARYPEPTIDES
spectral library peptides section. See also Spectral libraries.
Definition: ms_mascotresfile_dat.hpp:152
matrix_science::ms_mascotresfile_dat::SEC_HEADER
@ SEC_HEADER
header section
Definition: ms_mascotresfile_dat.hpp:134
matrix_science::ms_mascotresfile_dat::SEC_SUMMARY
@ SEC_SUMMARY
summary section
Definition: ms_mascotresfile_dat.hpp:136
matrix_science::ms_mascotresfile_dat::SEC_PEPTIDES
@ SEC_PEPTIDES
peptides section
Definition: ms_mascotresfile_dat.hpp:138
matrix_science::ms_mascotresfile_dat::SEC_UNIMOD
@ SEC_UNIMOD
unimod section
Definition: ms_mascotresfile_dat.hpp:142
matrix_science::ms_mascotresfile_dat::SEC_CROSSLINK_PEPTIDES
@ SEC_CROSSLINK_PEPTIDES
crosslink_peptides section. See also Crosslinked search results.
Definition: ms_mascotresfile_dat.hpp:155
matrix_science::ms_mascotresfile_dat::SEC_MIXTURE
@ SEC_MIXTURE
mixture section (pmf mixture)
Definition: ms_mascotresfile_dat.hpp:137
matrix_science::ms_mascotresfile_dat::SEC_PROTEINS
@ SEC_PROTEINS
proteins section
Definition: ms_mascotresfile_dat.hpp:139
matrix_science::ms_mascotresfile_dat::SEC_LIBRARYSUMMARY
@ SEC_LIBRARYSUMMARY
spectral library summary section. See also Spectral libraries.
Definition: ms_mascotresfile_dat.hpp:153
matrix_science::ms_mascotresfile_dat::SEC_QUANTITATION
@ SEC_QUANTITATION
quantitation section
Definition: ms_mascotresfile_dat.hpp:141
matrix_science::ms_mascotresfile_dat::SEC_CROSSLINKING
@ SEC_CROSSLINKING
crosslinking section
Definition: ms_mascotresfile_dat.hpp:156
matrix_science::ms_mascotresfile_dat::SEC_ERRTOLSUMMARY
@ SEC_ERRTOLSUMMARY
error tolerant summary section. See also Error tolerant searches.
Definition: ms_mascotresfile_dat.hpp:149
matrix_science::ms_mascotresfile_dat::SEC_CROSSLINK_SUMMARY
@ SEC_CROSSLINK_SUMMARY
crosslink_summary section. See also Crosslinked search results.
Definition: ms_mascotresfile_dat.hpp:154
matrix_science::ms_mascotresfile_dat::SEC_UNIMOD_XL
@ SEC_UNIMOD_XL
unimod_xl section
Definition: ms_mascotresfile_dat.hpp:157
matrix_science::ms_mascotresfile_dat::SEC_ERRTOLPEPTIDES
@ SEC_ERRTOLPEPTIDES
error tolerant peptides section. See also Error tolerant searches.
Definition: ms_mascotresfile_dat.hpp:150
matrix_science::ms_mascotresfile_dat::SEC_DECOYMIXTURE
@ SEC_DECOYMIXTURE
decoy_mixture section. See also Target-decoy searches and false discovery rate.
Definition: ms_mascotresfile_dat.hpp:146
matrix_science::ms_mascotresfile_dat::err
err
Definitions for error numbers.
Definition: ms_mascotresfile_dat.hpp:184
matrix_science::ms_mascotresfile_dat::getDate
int getDate() const override
Returns the date and time of the search in seconds since midnight January 1st 1970.
Definition: ms_mascotresfile_dat.hpp:372
matrix_science::ms_mascotresfile_dat::getExecTime
int getExecTime() const override
Returns the time taken for the search.
Definition: ms_mascotresfile_dat.hpp:367
matrix_science::ms_mascotresfile_dat::getMascotVer
std::string getMascotVer() const override
Returns the version of Mascot used to perform the search.
Definition: ms_mascotresfile_dat.hpp:377
matrix_science::ms_mascotresfilebase
Abstract base class of ms_mascotresfile_dat and ms_mascotresfile_msr.
Definition: ms_mascotresfilebase.hpp:72
matrix_science::ms_mascotresults_params
Class which provides constructor parameters for either ms_peptidesummary or ms_proteinsummary.
Definition: ms_mascotresults_params.hpp:32
matrix_science::ms_peptide::PSM_TYPE
PSM_TYPE
Specifies the search pass and origin of the peptide match.
Definition: ms_peptide.hpp:107
matrix_science::ms_peptidesummary
Use this class to get peptide summary results.
Definition: ms_peptidesummary.hpp:51
matrix_science::ms_progress_info
Contains information of the current progress of a task being performed.
Definition: ms_progress_info.hpp:40
matrix_science::ms_proteinsummary
Definition: ms_proteinsummary.hpp:45
matrix_science::ms_quant_configfile
Use this class in order to read/write quantitation.xml.
Definition: ms_quant_configfile.hpp:52
matrix_science::ms_taxonomyfile
Use this class in order to read in a taxonomy file.
Definition: ms_taxonomyfile.hpp:145
matrix_science::ms_umod_configfile
This class represents the file unimod.xml.
Definition: ms_umod_configfile.hpp:54
matrix_science::DATABASE_TYPE
DATABASE_TYPE
Definition: ms_databaseoptions.hpp:39