libpappsomspp
Library for mass spectrometry
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pappso::cbor::psm::SageTsvHandler Class Reference

#include <sagetsvhandler.h>

Inheritance diagram for pappso::cbor::psm::SageTsvHandler:

Classes

struct  Line
struct  Psm
struct  Scan
struct  Sample

Public Types

enum class  Columns : std::int8_t {
  psm_id , peptide , proteins , num_proteins ,
  filename , scannr , rank , label ,
  expmass , calcmass , charge , peptide_len ,
  missed_cleavages , semi_enzymatic , isotope_error , precursor_ppm ,
  fragment_ppm , hyperscore , delta_next , delta_best ,
  rt , aligned_rt , predicted_rt , delta_rt_model ,
  ion_mobility , predicted_mobility , delta_mobility , matched_peaks ,
  longest_b , longest_y , longest_y_pct , matched_intensity_pct ,
  scored_candidates , poisson , sage_discriminant_score , posterior_error ,
  spectrum_q , peptide_q , protein_q , ms2_intensity
}

Public Member Functions

 SageTsvHandler (pappso::UiMonitorInterface *p_monitor, const SageReader &sage_reader, PsmProteinMap &psm_protein_map)
virtual ~SageTsvHandler ()
virtual void startSheet (const QString &sheet_name) override
virtual void endSheet () override
virtual void startLine () override
virtual void endLine () override
virtual void setCell (const OdsCell &cell) override
virtual void endDocument () override
void writeSampleList ()

Private Member Functions

void parsePeptide (const QString &peptide_str)
void parseProteins (const QString &proteins_str)
bool parseSpectrumStringId (const QString &spectrum_string_id)
void parseMsRunFilename (const QString &msrun_filename)
void recordLine ()
void writeSample (const Sample &one_sample)
void writeScan (const Scan &one_scan)
void writePsm (const Psm &one_psm)

Private Attributes

const SageReader & m_sageReader
PsmProteinMap & m_psmProteinMap
pappso::UiMonitorInterface * mp_monitor = nullptr
std::size_t m_progressIndex = 0
std::size_t m_lineNumber = 0
std::size_t m_columnNumber = 0
std::vector< Columns > m_columnTypeList
pappso::PeptideSp msp_peptide
std::vector< SageReader::SageModification > m_staticModificationList
std::vector< SageReader::SageModification > m_variableModificationList
std::size_t m_spectrumIndex
Line m_line
QString m_decoyTag
QStringList m_proteinList
QString m_spectrumNativeId
std::map< QString, Sample > m_sampleMap
Sample * mp_currentSample

Detailed Description

Todo
write docs

Definition at line 49 of file sagetsvhandler.h.

Member Enumeration Documentation

◆ Columns

enum class pappso::cbor::psm::SageTsvHandler::Columns : std::int8_t
strong
Enumerator
psm_id 
peptide 
proteins 
num_proteins 
filename 
scannr 
rank 
label 
expmass 
calcmass 
charge 
peptide_len 
missed_cleavages 
semi_enzymatic 
isotope_error 
precursor_ppm 
fragment_ppm 
hyperscore 
delta_next 
delta_best 
rt 
aligned_rt 
predicted_rt 
delta_rt_model 
ion_mobility 
predicted_mobility 
delta_mobility 
matched_peaks 
longest_b 
longest_y 
longest_y_pct 
matched_intensity_pct 
scored_candidates 
poisson 
sage_discriminant_score 
posterior_error 
spectrum_q 
peptide_q 
protein_q 
ms2_intensity 

Definition at line 52 of file sagetsvhandler.h.

53 {
54 psm_id,
55 peptide,
56 proteins,
57 num_proteins,
58 filename,
59 scannr,
60 rank,
61 label,
62 expmass,
63 calcmass,
64 charge,
65 peptide_len,
66 missed_cleavages,
67 semi_enzymatic,
68 isotope_error,
69 precursor_ppm,
70 fragment_ppm,
71 hyperscore,
72 delta_next,
73 delta_best,
74 rt,
75 aligned_rt,
76 predicted_rt,
77 delta_rt_model,
78 ion_mobility,
79 predicted_mobility,
80 delta_mobility,
81 matched_peaks,
82 longest_b,
83 longest_y,
84 longest_y_pct,
85 matched_intensity_pct,
86 scored_candidates,
87 poisson,
88 sage_discriminant_score,
89 posterior_error,
90 spectrum_q,
91 peptide_q,
92 protein_q,
93 ms2_intensity,
94 };
pappso::Enums::DataKind::rt
@ rt
Retention time.
Definition types.h:251

Constructor & Destructor Documentation

◆ SageTsvHandler()

pappso::cbor::psm::SageTsvHandler::SageTsvHandler ( pappso::UiMonitorInterface * p_monitor,
const SageReader & sage_reader,
PsmProteinMap & psm_protein_map )

Default constructor

Definition at line 47 of file sagetsvhandler.cpp.

50 : m_sageReader(sage_reader), m_psmProteinMap(psm_protein_map)
51{
52 mp_monitor = p_monitor;
53 m_staticModificationList = sage_reader.getStaticModificationList();
54 m_variableModificationList = sage_reader.getVariableModificationList();
55 m_decoyTag = sage_reader.getDecoyTag();
56}
pappso::cbor::psm::SageTsvHandler::m_staticModificationList
std::vector< SageReader::SageModification > m_staticModificationList
Definition sagetsvhandler.h:222
pappso::cbor::psm::SageTsvHandler::mp_monitor
pappso::UiMonitorInterface * mp_monitor
Definition sagetsvhandler.h:215
pappso::cbor::psm::SageTsvHandler::m_variableModificationList
std::vector< SageReader::SageModification > m_variableModificationList
Definition sagetsvhandler.h:223

References pappso::cbor::psm::SageReader::getDecoyTag(), pappso::cbor::psm::SageReader::getStaticModificationList(), pappso::cbor::psm::SageReader::getVariableModificationList(), m_decoyTag, m_psmProteinMap, m_sageReader, m_staticModificationList, m_variableModificationList, and mp_monitor.

◆ ~SageTsvHandler()

pappso::cbor::psm::SageTsvHandler::~SageTsvHandler ( )
virtual

Destructor

Definition at line 58 of file sagetsvhandler.cpp.

59{
60}

Member Function Documentation

◆ endDocument()

void pappso::cbor::psm::SageTsvHandler::endDocument ( )
overridevirtual

Definition at line 423 of file sagetsvhandler.cpp.

424{
425}

◆ endLine()

void pappso::cbor::psm::SageTsvHandler::endLine ( )
overridevirtual

callback that indicates a line ending. Override it if needed.

Definition at line 72 of file sagetsvhandler.cpp.

73{
74 if(m_line.charge != 0)
75 recordLine();
76 m_lineNumber++;
77}

References m_line, m_lineNumber, and recordLine().

◆ endSheet()

void pappso::cbor::psm::SageTsvHandler::endSheet ( )
overridevirtual

callback that indicates the end of the current data sheet. Override it if needed

Definition at line 80 of file sagetsvhandler.cpp.

81{
82}

◆ parseMsRunFilename()

void pappso::cbor::psm::SageTsvHandler::parseMsRunFilename ( const QString & msrun_filename)
private

Definition at line 536 of file sagetsvhandler.cpp.

537{
538
539
540 // find the sample :
541 auto it_insert = m_sampleMap.insert({msrun_filename, {}});
542 mp_currentSample = &(it_insert.first->second);
543 if(it_insert.second)
544 {
545 // new sample
546 it_insert.first->second.name = msrun_filename;
547 QCborMap ms_file;
548 QCborMap identification_file;
549
550 it_insert.first->second.cbor_core_sample.insert(QString("name"),
551 QFileInfo(msrun_filename).baseName());
552
553 // identification_file_list
554 QCborArray identification_file_list;
555 identification_file.insert(QString("name"), m_sageReader.getmJsonAbsoluteFilePath());
556 identification_file_list.push_back(identification_file);
557 it_insert.first->second.cbor_core_sample.insert(QString("identification_file_list"),
558 identification_file_list);
559
560
561 ms_file.insert(QString("name"), m_sageReader.getMzmlPath(msrun_filename));
562 it_insert.first->second.cbor_core_sample.insert(QString("peaklist_file"), ms_file);
563 }
564
565 /*
566 msp_msrun = m_sageReader.getSageFileReader().getMsRunSpWithFileName(msrun_filename);
567 qDebug() << msp_msrun.get()->getFileName();
568
569 msp_identificationSageJsonFileSp =
570 m_sageReader.getSageFileReader().getIdentificationSageJsonFileSpWithFileName(msrun_filename);
571
572 mp_identificationGroup =
573 m_sageReader.getSageFileReader().getIdentificationGroupPtrWithFileName(msrun_filename);
574 qDebug() << msp_msrun.get()->getFileName();
575 */
576}
pappso::cbor::psm::SageTsvHandler::m_sampleMap
std::map< QString, Sample > m_sampleMap
Definition sagetsvhandler.h:229

References m_sageReader, m_sampleMap, and mp_currentSample.

Referenced by setCell().

◆ parsePeptide()

void pappso::cbor::psm::SageTsvHandler::parsePeptide ( const QString & peptide_str)
private

Definition at line 440 of file sagetsvhandler.cpp.

441{
442 qDebug();
443 QString peptide_str_verif = peptide_str;
444 // fixed modifications :
445 for(SageReader::SageModification modif : m_staticModificationList)
446 {
447 qDebug() << modif.strModification;
448 qDebug() << modif.modification->getAccession();
449 peptide_str_verif = peptide_str_verif.replace(
450 modif.strModification, QString("[%1]").arg(modif.modification->getAccession()));
451 }
452 // variable modifications :
453 for(SageReader::SageModification modif : m_variableModificationList)
454 {
455 qDebug() << modif.strModification;
456 qDebug() << modif.modification->getAccession();
457 peptide_str_verif = peptide_str_verif.replace(
458 modif.strModification, QString("[%1]").arg(modif.modification->getAccession()));
459 }
460
461 qDebug() << peptide_str_verif;
462 // LPMFGC[+57.0216]NDATQVYK
463 msp_peptide = pappso::PeptideProFormaParser::parseString(peptide_str_verif);
464 qDebug();
465 // variable modifications :
466 /*
467 setVariableModifications(peptide_sp,
468 peptide_line.peptide_string_list.at(6));
469*/
470 qDebug() << msp_peptide.get()->toProForma();
471}
pappso::PeptideProFormaParser::parseString
static PeptideSp parseString(const QString &pepstr)
Definition peptideproformaparser.cpp:228

References m_staticModificationList, m_variableModificationList, msp_peptide, and pappso::PeptideProFormaParser::parseString().

Referenced by setCell().

◆ parseProteins()

void pappso::cbor::psm::SageTsvHandler::parseProteins ( const QString & proteins_str)
private

Definition at line 475 of file sagetsvhandler.cpp.

476{
477 m_proteinList.clear();
478 m_proteinList = proteins_str.split(";");
479 for(QString accession : m_proteinList)
480 {
481
482 PsmProtein psm_protein;
483 psm_protein.protein_sp = std::make_shared<pappso::Protein>(accession, "");
484 psm_protein.isTarget = true;
485 if(accession.startsWith(m_decoyTag))
486 {
487 psm_protein.isTarget = false;
488 }
489
490 m_psmProteinMap.insert(psm_protein);
491 }
492}

References pappso::cbor::psm::PsmProtein::isTarget, m_decoyTag, m_proteinList, m_psmProteinMap, and pappso::cbor::psm::PsmProtein::protein_sp.

Referenced by setCell().

◆ parseSpectrumStringId()

bool pappso::cbor::psm::SageTsvHandler::parseSpectrumStringId ( const QString & spectrum_string_id)
private

Definition at line 495 of file sagetsvhandler.cpp.

496{
497 m_spectrumNativeId = spectrum_string_id;
498 qDebug() << spectrum_string_id;
499 // controllerType=0 controllerNumber=1 scan=176056
500
501 bool is_ok = false;
502 QStringList scan_list = spectrum_string_id.split("scan=");
503 if(scan_list.size() == 2)
504 {
505 // we bet that there is a scan number, easy to parse
506 m_spectrumIndex = scan_list.at(1).toULongLong(&is_ok);
507 if(m_spectrumIndex > 0)
508 m_spectrumIndex--;
509 }
510 if(is_ok == false)
511 { /*
512 if(msp_previousMsrun != msp_msrun)
513 {
514 mp_monitor->setStatus(
515 QObject::tr("Reading mz data file %1").arg(msp_msrun.get()->getFileName()));
516 msp_previousMsrun = msp_msrun;
517 }
518
519 pappso::MsRunReader *msrunreader_p = msp_msrun.get()->getMsRunReaderSPtr().get();
520 if(msrunreader_p->getMsRunId()->getMsDataFormat() == pappso::MsDataFormat::brukerTims)
521 {
522 m_spectrumIndex = spectrum_string_id.toInt() * 2 - 1;
523 }
524 else
525 {
526 m_spectrumIndex =
527 msrunreader_p->spectrumStringIdentifier2SpectrumIndex(spectrum_string_id);
528 }*/
529 }
530
531 qDebug() << spectrum_string_id;
532 return is_ok;
533}

References m_spectrumIndex, and m_spectrumNativeId.

Referenced by setCell().

◆ recordLine()

void pappso::cbor::psm::SageTsvHandler::recordLine ( )
private

Definition at line 579 of file sagetsvhandler.cpp.

580{
581 qDebug();
582
583 for(const QString &accession : m_proteinList)
584 {
585 PsmProtein psm_protein;
586 psm_protein.protein_sp = std::make_shared<pappso::Protein>(accession, "");
587
588 auto it = m_psmProteinMap.insert(psm_protein);
589 it.first->second.cborEval.insert(QString("protein_q"), m_line.protein_q);
590 }
591 /*
592 PeptideEvidence pe(msp_msrun.get(), m_spectrumIndex, true);
593 pe.setCharge(m_line.charge);
594 pe.setChecked(true);
595 pe.setExperimentalMass(m_line.expmass);
596 pe.setPeptideXtpSp(msp_peptide);
597 pe.setIdentificationDataSource(msp_identificationSageJsonFileSp.get());
598 pe.setIdentificationEngine(m_identificationEngine);
599 pe.setRetentionTime(m_line.rt);
600 pe.setParam(PeptideEvidenceParam::tandem_hyperscore, m_line.hyperscore);
601 pe.setParam(PeptideEvidenceParam::sage_sage_discriminant_score,
602 m_line.sage_discriminant_score);
603 pe.setParam(PeptideEvidenceParam::sage_peptide_q, m_line.peptide_q);
604 pe.setParam(PeptideEvidenceParam::sage_posterior_error, m_line.posterior_error);
605 pe.setParam(PeptideEvidenceParam::sage_spectrum_q, m_line.spectrum_q);
606 pe.setParam(PeptideEvidenceParam::sage_predicted_rt, m_line.predicted_rt);
607 pe.setParam(PeptideEvidenceParam::sage_isotope_error, m_line.isotope_error);
608
609
610 PeptideMatch peptide_match;
611 // peptide_match.setStart(mz_peptide_evidence.start);
612 peptide_match.setPeptideEvidenceSp(
613 msp_identificationSageJsonFileSp.get()->getPeptideEvidenceStore().getInstance(&pe));
614 */
615
616 // find the scan in sample
617 auto it_insert = mp_currentSample->scan_map.insert({m_spectrumNativeId, Scan()});
618 Scan *current_cbor_scan_p = &(it_insert.first->second);
619 if(it_insert.second)
620 {
621 // new scan
622 QCborMap &scan_id = it_insert.first->second.cbor_id;
623 scan_id.insert(QString("index"), (qint64)m_spectrumIndex);
624 scan_id.insert(QString("native_id"), m_spectrumNativeId);
625
626 QCborMap &scan_ms2 = it_insert.first->second.cbor_ms2;
627 scan_ms2.insert(QString("rt"), m_line.rt);
628
629 QCborMap &scan_precursor = it_insert.first->second.cbor_precursor;
630 scan_precursor.insert(QString("z"), m_line.charge);
631 scan_precursor.insert(QString("mz"), m_line.expmass);
632 }
633
634 Psm one_psm;
635 one_psm.peptide_sequence_li = msp_peptide.get()->getSequenceLi();
636 one_psm.proforma = msp_peptide.get()->toProForma();
637 one_psm.protein_list = m_proteinList;
638
639
640 one_psm.cbor_eval.insert(QString("aligned_rt"), m_line.aligned_rt);
641 one_psm.cbor_eval.insert(QString("calcmass"), m_line.calcmass);
642 one_psm.cbor_eval.insert(QString("delta_best"), m_line.delta_best);
643 one_psm.cbor_eval.insert(QString("delta_mobility"), m_line.delta_mobility);
644 one_psm.cbor_eval.insert(QString("delta_next"), m_line.delta_next);
645 one_psm.cbor_eval.insert(QString("delta_rt_model"), m_line.delta_rt_model);
646 one_psm.cbor_eval.insert(QString("fragment_ppm"), m_line.fragment_ppm);
647 one_psm.cbor_eval.insert(QString("hyperscore"), m_line.hyperscore);
648 one_psm.cbor_eval.insert(QString("ion_mobility"), m_line.ion_mobility);
649 one_psm.cbor_eval.insert(QString("isotope_error"), m_line.isotope_error);
650 one_psm.cbor_eval.insert(QString("label"), m_line.label);
651 one_psm.cbor_eval.insert(QString("longest_b"), (qint64)m_line.longest_b);
652 one_psm.cbor_eval.insert(QString("longest_y"), (qint64)m_line.longest_y);
653 one_psm.cbor_eval.insert(QString("longest_y_pct"), m_line.longest_y_pct);
654 one_psm.cbor_eval.insert(QString("matched_intensity_pct"), m_line.matched_intensity_pct);
655 one_psm.cbor_eval.insert(QString("matched_peaks"), (qint64)m_line.matched_peaks);
656 one_psm.cbor_eval.insert(QString("missed_cleavages"), m_line.missed_cleavages);
657 one_psm.cbor_eval.insert(QString("ms2_intensity"), m_line.ms2_intensity);
658 one_psm.cbor_eval.insert(QString("peptide_len"), (qint64)m_line.peptide_len);
659 one_psm.cbor_eval.insert(QString("peptide_q"), m_line.peptide_q);
660 one_psm.cbor_eval.insert(QString("poisson"), m_line.poisson);
661 one_psm.cbor_eval.insert(QString("posterior_error"), m_line.posterior_error);
662 one_psm.cbor_eval.insert(QString("precursor_ppm"), m_line.precursor_ppm);
663 one_psm.cbor_eval.insert(QString("predicted_mobility"), m_line.predicted_mobility);
664 one_psm.cbor_eval.insert(QString("predicted_rt"), m_line.predicted_rt);
665 one_psm.cbor_eval.insert(QString("protein_q"), m_line.protein_q);
666 one_psm.cbor_eval.insert(QString("rank"), m_line.rank);
667 one_psm.cbor_eval.insert(QString("sage_discriminant_score"), m_line.sage_discriminant_score);
668 one_psm.cbor_eval.insert(QString("scored_candidates"), (qint64)m_line.scored_candidates);
669 one_psm.cbor_eval.insert(QString("semi_enzymatic"), m_line.semi_enzymatic);
670 one_psm.cbor_eval.insert(QString("spectrum_q"), m_line.spectrum_q);
671
672 current_cbor_scan_p->psm_list.emplace_back(one_psm);
673
674
675 std::size_t progress = m_lineNumber / 10000;
676 if(progress > m_progressIndex)
677 {
678 if(mp_monitor->shouldIstop())
679 {
680 throw pappso::ExceptionInterrupted(
681 QObject::tr("Sage TSV data reading process interrupted"));
682 }
683 m_progressIndex = progress;
684 mp_monitor->setStatus(QString("%1K ").arg(m_progressIndex * 10));
685 }
686}

References pappso::cbor::psm::SageTsvHandler::Psm::cbor_eval, m_line, m_lineNumber, m_progressIndex, m_proteinList, m_psmProteinMap, m_spectrumIndex, m_spectrumNativeId, mp_currentSample, mp_monitor, msp_peptide, pappso::cbor::psm::SageTsvHandler::Psm::peptide_sequence_li, pappso::cbor::psm::SageTsvHandler::Psm::proforma, pappso::cbor::psm::SageTsvHandler::Psm::protein_list, pappso::cbor::psm::PsmProtein::protein_sp, and pappso::cbor::psm::SageTsvHandler::Scan::psm_list.

Referenced by endLine().

◆ setCell()

void pappso::cbor::psm::SageTsvHandler::setCell ( const OdsCell & cell)
overridevirtual

callback that report the content of the current cell in a dedicated Cell object. Override it if you need to retrieve cell content.

Definition at line 85 of file sagetsvhandler.cpp.

86{
87 if(m_lineNumber == 0)
88 {
89 // header
90 QString tag = cell.getStringValue();
91 if(tag == "psm_id")
92 {
93 m_columnTypeList.push_back(Columns::psm_id);
94 }
95 else if(tag == "peptide")
96 {
97 m_columnTypeList.push_back(Columns::peptide);
98 }
99 else if(tag == "proteins")
100 {
101 m_columnTypeList.push_back(Columns::proteins);
102 }
103 else if(tag == "num_proteins")
104 {
105 m_columnTypeList.push_back(Columns::num_proteins);
106 }
107 else if(tag == "filename")
108 {
109 m_columnTypeList.push_back(Columns::filename);
110 }
111 else if(tag == "scannr")
112 {
113 m_columnTypeList.push_back(Columns::scannr);
114 }
115 else if(tag == "rank")
116 {
117 m_columnTypeList.push_back(Columns::rank);
118 }
119 else if(tag == "label")
120 {
121 m_columnTypeList.push_back(Columns::label);
122 }
123 else if(tag == "expmass")
124 {
125 m_columnTypeList.push_back(Columns::expmass);
126 }
127
128 else if(tag == "calcmass")
129 {
130 m_columnTypeList.push_back(Columns::calcmass);
131 }
132 else if(tag == "charge")
133 {
134 m_columnTypeList.push_back(Columns::charge);
135 }
136 else if(tag == "peptide_len")
137 {
138 m_columnTypeList.push_back(Columns::peptide_len);
139 }
140 else if(tag == "missed_cleavages")
141 {
142 m_columnTypeList.push_back(Columns::missed_cleavages);
143 }
144 else if(tag == "semi_enzymatic")
145 {
146 m_columnTypeList.push_back(Columns::semi_enzymatic);
147 }
148 else if(tag == "isotope_error")
149 {
150 m_columnTypeList.push_back(Columns::isotope_error);
151 }
152 else if(tag == "precursor_ppm")
153 {
154 m_columnTypeList.push_back(Columns::precursor_ppm);
155 }
156 else if(tag == "fragment_ppm")
157 {
158 m_columnTypeList.push_back(Columns::fragment_ppm);
159 }
160 else if(tag == "hyperscore")
161 {
162 m_columnTypeList.push_back(Columns::hyperscore);
163 }
164 else if(tag == "delta_next")
165 {
166 m_columnTypeList.push_back(Columns::delta_next);
167 }
168 else if(tag == "delta_best")
169 {
170 m_columnTypeList.push_back(Columns::delta_best);
171 }
172 else if(tag == "rt")
173 {
174 m_columnTypeList.push_back(Columns::rt);
175 }
176 else if(tag == "aligned_rt")
177 {
178 m_columnTypeList.push_back(Columns::aligned_rt);
179 }
180 else if(tag == "predicted_rt")
181 {
182 m_columnTypeList.push_back(Columns::predicted_rt);
183 }
184 else if(tag == "delta_rt_model")
185 {
186 m_columnTypeList.push_back(Columns::delta_rt_model);
187 }
188 else if(tag == "ion_mobility")
189 {
190 m_columnTypeList.push_back(Columns::ion_mobility);
191 }
192 else if(tag == "predicted_mobility")
193 {
194 m_columnTypeList.push_back(Columns::predicted_mobility);
195 }
196 else if(tag == "delta_mobility")
197 {
198 m_columnTypeList.push_back(Columns::delta_mobility);
199 }
200 else if(tag == "matched_peaks")
201 {
202 m_columnTypeList.push_back(Columns::matched_peaks);
203 }
204 else if(tag == "longest_b")
205 {
206 m_columnTypeList.push_back(Columns::longest_b);
207 }
208 else if(tag == "longest_y")
209 {
210 m_columnTypeList.push_back(Columns::longest_y);
211 }
212 else if(tag == "longest_y_pct")
213 {
214 m_columnTypeList.push_back(Columns::longest_y_pct);
215 }
216 else if(tag == "matched_intensity_pct")
217 {
218 m_columnTypeList.push_back(Columns::matched_intensity_pct);
219 }
220 else if(tag == "scored_candidates")
221 {
222 m_columnTypeList.push_back(Columns::scored_candidates);
223 }
224 else if(tag == "poisson")
225 {
226 m_columnTypeList.push_back(Columns::poisson);
227 }
228 else if(tag == "sage_discriminant_score")
229 {
230 m_columnTypeList.push_back(Columns::sage_discriminant_score);
231 }
232 else if(tag == "posterior_error")
233 {
234 m_columnTypeList.push_back(Columns::posterior_error);
235 }
236 else if(tag == "spectrum_q")
237 {
238 m_columnTypeList.push_back(Columns::spectrum_q);
239 }
240 else if(tag == "peptide_q")
241 {
242 m_columnTypeList.push_back(Columns::peptide_q);
243 }
244 else if(tag == "protein_q")
245 {
246 m_columnTypeList.push_back(Columns::protein_q);
247 }
248 else if(tag == "ms2_intensity")
249 {
250 m_columnTypeList.push_back(Columns::ms2_intensity);
251 }
252 else
253 {
254 throw pappso::ExceptionNotPossible(QObject::tr("column \"%1\" not defined").arg(tag));
255 }
256 }
257 else
258 {
259 if(m_columnNumber >= m_columnTypeList.size())
260 {
261 throw pappso::ExceptionOutOfRange(
262 QObject::tr("the value %1 is out of range").arg(cell.getStringValue()));
263 }
264 Columns column_type = m_columnTypeList[m_columnNumber];
265 switch(column_type)
266 {
267 case Columns::psm_id:
268 break;
269 case Columns::peptide:
270 parsePeptide(cell.toString());
271 break;
272 case Columns::proteins:
273 parseProteins(cell.toString());
274 break;
275 case Columns::num_proteins:
276 if((std::size_t)cell.getDoubleValue() != (std::size_t)m_proteinList.size())
277 {
278 throw pappso::PappsoException(
279 QObject::tr("column \"num_proteins\"!=%1").arg(m_proteinList.size()));
280 }
281 break;
282 case Columns::filename:
283 parseMsRunFilename(cell.toString());
284 break;
285 case Columns::scannr:
286 parseSpectrumStringId(cell.toString());
287 break;
288 case Columns::rank:
289 m_line.rank = cell.getDoubleValue();
290 break;
291 case Columns::label:
292 m_line.label = cell.getDoubleValue();
293 break;
294 case Columns::expmass:
295 m_line.expmass = cell.getDoubleValue();
296 break;
297 case Columns::calcmass:
298 m_line.calcmass = cell.getDoubleValue();
299 break;
300 case Columns::charge:
301 m_line.charge = cell.getDoubleValue();
302 break;
303 case Columns::peptide_len:
304 m_line.peptide_len = cell.getDoubleValue();
305 break;
306 case Columns::missed_cleavages:
307 m_line.missed_cleavages = cell.getDoubleValue();
308 break;
309 case Columns::semi_enzymatic:
310 m_line.semi_enzymatic = cell.getDoubleValue();
311 break;
312 case Columns::isotope_error:
313 m_line.isotope_error = cell.getDoubleValue();
314 break;
315
316 case Columns::precursor_ppm:
317 m_line.precursor_ppm = cell.getDoubleValue();
318 break;
319 case Columns::fragment_ppm:
320 m_line.fragment_ppm = cell.getDoubleValue();
321 break;
322 case Columns::hyperscore:
323 m_line.hyperscore = cell.getDoubleValue();
324 break;
325 case Columns::delta_next:
326 m_line.delta_next = cell.getDoubleValue();
327 break;
328 case Columns::delta_best:
329 m_line.delta_best = cell.getDoubleValue();
330 break;
331 case Columns::rt:
332 m_line.rt = cell.getDoubleValue() * 60; // to convert retention time in seconds
333 break;
334 case Columns::aligned_rt:
335 m_line.aligned_rt = cell.getDoubleValue();
336 break;
337 case Columns::predicted_rt:
338 m_line.predicted_rt = cell.getDoubleValue();
339 break;
340 case Columns::delta_rt_model:
341 m_line.delta_rt_model = cell.getDoubleValue();
342 break;
343 case Columns::ion_mobility:
344 m_line.ion_mobility = cell.getDoubleValue();
345 break;
346 case Columns::predicted_mobility:
347 m_line.predicted_mobility = cell.getDoubleValue();
348 break;
349 case Columns::delta_mobility:
350 m_line.delta_mobility = cell.getDoubleValue();
351 break;
352 case Columns::matched_peaks:
353 m_line.matched_peaks = cell.getDoubleValue();
354 break;
355 case Columns::longest_b:
356 m_line.longest_b = cell.getDoubleValue();
357 break;
358 case Columns::longest_y:
359 m_line.longest_y = cell.getDoubleValue();
360 break;
361 case Columns::longest_y_pct:
362 m_line.longest_y_pct = cell.getDoubleValue();
363 break;
364 case Columns::matched_intensity_pct:
365 m_line.matched_intensity_pct = cell.getDoubleValue();
366 break;
367 case Columns::scored_candidates:
368 m_line.scored_candidates = cell.getDoubleValue();
369 break;
370 case Columns::poisson:
371 m_line.poisson = cell.getDoubleValue();
372 break;
373 case Columns::sage_discriminant_score:
374 m_line.sage_discriminant_score = cell.getDoubleValue();
375 break;
376 case Columns::posterior_error:
377 m_line.posterior_error = cell.getDoubleValue();
378 break;
379 case Columns::spectrum_q:
380 m_line.spectrum_q = cell.getDoubleValue();
381 break;
382 case Columns::peptide_q:
383 m_line.peptide_q = cell.getDoubleValue();
384 break;
385 case Columns::protein_q:
386 m_line.protein_q = cell.getDoubleValue();
387 break;
388 case Columns::ms2_intensity:
389 m_line.ms2_intensity = cell.getDoubleValue();
390 break;
391 default:
392 qDebug() << "m_line.calcmass=" << m_line.calcmass;
393 throw pappso::ExceptionNotImplemented(
394 QObject::tr("column type %1 not implemented").arg((std::uint8_t)column_type));
395 break;
396 }
397
398 /*
399
400 2333 TMISDSDYTEFENFTK
401 GRMZM2G018197_P01;GRMZM2G068952_P01;GRMZM5G822976_P01 3
402 20120906_balliau_extract_1_A01_urnb-1.mzML controllerType=0
403 controllerNumber=1 scan=12542 1 1 1926.8225 1926.8193 2 16 0 0
404 0.0 1.6471838 1.9796097 54.06803492297634 28.049970383419556 0.0 38.192993
405 0.76385987 0.7671368 0.0032769442 0.0 0.0 0.0 16 2 14 0.875 32.54396 380
406 -13.375352220427656 1.1570586 -34.13482 0.00016041065 0.00022231363
407 0.00040124074 1271951.1
408 */
409 }
410 m_columnNumber++;
411}
pappso::cbor::psm::SageTsvHandler::parseProteins
void parseProteins(const QString &proteins_str)
Definition sagetsvhandler.cpp:475
pappso::cbor::psm::SageTsvHandler::parsePeptide
void parsePeptide(const QString &peptide_str)
Definition sagetsvhandler.cpp:440
pappso::cbor::psm::SageTsvHandler::parseSpectrumStringId
bool parseSpectrumStringId(const QString &spectrum_string_id)
Definition sagetsvhandler.cpp:495
pappso::cbor::psm::SageTsvHandler::parseMsRunFilename
void parseMsRunFilename(const QString &msrun_filename)
Definition sagetsvhandler.cpp:536
pappso::cbor::psm::SageTsvHandler::m_columnTypeList
std::vector< Columns > m_columnTypeList
Definition sagetsvhandler.h:219

References aligned_rt, calcmass, charge, delta_best, delta_mobility, delta_next, delta_rt_model, expmass, filename, fragment_ppm, hyperscore, ion_mobility, isotope_error, label, longest_b, longest_y, longest_y_pct, m_columnNumber, m_columnTypeList, m_line, m_lineNumber, m_proteinList, matched_intensity_pct, matched_peaks, missed_cleavages, ms2_intensity, num_proteins, parseMsRunFilename(), parsePeptide(), parseProteins(), parseSpectrumStringId(), peptide, peptide_len, peptide_q, poisson, posterior_error, precursor_ppm, predicted_mobility, predicted_rt, protein_q, proteins, psm_id, rank, rt, sage_discriminant_score, scannr, scored_candidates, semi_enzymatic, and spectrum_q.

◆ startLine()

void pappso::cbor::psm::SageTsvHandler::startLine ( )
overridevirtual

callback that indicates a new line start. Override it if needed.

Definition at line 414 of file sagetsvhandler.cpp.

415{
416 m_columnNumber = 0;
417 msp_peptide = nullptr;
418 m_proteinList.clear();
419 m_line = Line();
420}

References m_columnNumber, m_line, m_proteinList, and msp_peptide.

◆ startSheet()

void pappso::cbor::psm::SageTsvHandler::startSheet ( const QString & sheet_name)
overridevirtual

callback that indicates the begining of a data sheet. Override it in order to retrieve information about the current data sheet.

Definition at line 427 of file sagetsvhandler.cpp.

428{
429 m_columnNumber = 0;
430 m_lineNumber = 0;
431 mp_monitor->setStatus(QObject::tr("reading Sage TSV file"));
432
433 if(mp_monitor->shouldIstop())
434 {
435 throw pappso::ExceptionInterrupted(QObject::tr("Sage TSV data reading process interrupted"));
436 }
437}

References m_columnNumber, m_lineNumber, and mp_monitor.

◆ writePsm()

void pappso::cbor::psm::SageTsvHandler::writePsm ( const Psm & one_psm)
private

Definition at line 739 of file sagetsvhandler.cpp.

740{
741 m_sageReader.getCborStreamWriter().startMap();
742 m_sageReader.getCborStreamWriter().append("proforma");
743 m_sageReader.getCborStreamWriter().append(one_psm.proforma);
744 m_sageReader.getCborStreamWriter().append("protein_list");
745
746 QCborArray cbor_protein_list;
747 for(const QString &accession : one_psm.protein_list)
748 {
749 // qWarning() << "accession=" << accession;
750 QCborMap cbor_protein;
751 cbor_protein.insert(QString("accession"), accession);
752
753
754 // start/end positions
755 QString protein_sequence =
756 QString(m_psmProteinMap.getByAccession(accession).protein_sp.get()->getSequence())
757 .replace("L", "I");
758 int position = protein_sequence.indexOf(one_psm.peptide_sequence_li);
759
760 QCborArray positions;
761 while(position >= 0)
762 {
763 positions.push_back(position);
764 position = protein_sequence.indexOf(one_psm.peptide_sequence_li, position + 1);
765 }
766
767 cbor_protein.insert(QString("positions"), positions);
768
769 cbor_protein_list.append(cbor_protein);
770 }
771
772
773 QCborValue(cbor_protein_list).toCbor(m_sageReader.getCborStreamWriter());
774
775 m_sageReader.getCborStreamWriter().append("eval");
776 m_sageReader.getCborStreamWriter().startMap();
777 m_sageReader.getCborStreamWriter().append("sage");
778 QCborValue(one_psm.cbor_eval).toCbor(m_sageReader.getCborStreamWriter());
779 m_sageReader.getCborStreamWriter().endMap();
780
781 m_sageReader.getCborStreamWriter().endMap();
782}

References pappso::cbor::psm::SageTsvHandler::Psm::cbor_eval, m_psmProteinMap, m_sageReader, pappso::cbor::psm::SageTsvHandler::Psm::peptide_sequence_li, pappso::cbor::psm::SageTsvHandler::Psm::proforma, and pappso::cbor::psm::SageTsvHandler::Psm::protein_list.

Referenced by writeScan().

◆ writeSample()

void pappso::cbor::psm::SageTsvHandler::writeSample ( const Sample & one_sample)
private

Definition at line 689 of file sagetsvhandler.cpp.

690{
691 m_sageReader.getCborStreamWriter().startMap();
692 m_sageReader.getCborStreamWriter().append("name");
693 one_sample.cbor_core_sample.value("name").toCbor(m_sageReader.getCborStreamWriter());
694
695 m_sageReader.getCborStreamWriter().append("identification_file_list");
696 one_sample.cbor_core_sample.value("identification_file_list")
697 .toCbor(m_sageReader.getCborStreamWriter());
698
699
700 m_sageReader.getCborStreamWriter().append("peaklist_file");
701 one_sample.cbor_core_sample.value("peaklist_file").toCbor(m_sageReader.getCborStreamWriter());
702 //"scan_list": [
703
704 m_sageReader.getCborStreamWriter().append("scan_list");
705 m_sageReader.getCborStreamWriter().startArray(one_sample.scan_map.size());
706 for(auto &it_scan : one_sample.scan_map)
707 {
708 writeScan(it_scan.second);
709 }
710 m_sageReader.getCborStreamWriter().endArray();
711
712
713 m_sageReader.getCborStreamWriter().endMap();
714}
pappso::cbor::psm::SageTsvHandler::writeScan
void writeScan(const Scan &one_scan)
Definition sagetsvhandler.cpp:717

References pappso::cbor::psm::SageTsvHandler::Sample::cbor_core_sample, m_sageReader, pappso::cbor::psm::SageTsvHandler::Sample::scan_map, and writeScan().

Referenced by writeSampleList().

◆ writeSampleList()

void pappso::cbor::psm::SageTsvHandler::writeSampleList ( )

Definition at line 63 of file sagetsvhandler.cpp.

64{
65 for(auto it_sample_map : m_sampleMap)
66 {
67 writeSample(it_sample_map.second);
68 }
69}
pappso::cbor::psm::SageTsvHandler::writeSample
void writeSample(const Sample &one_sample)
Definition sagetsvhandler.cpp:689

References m_sampleMap, and writeSample().

Referenced by pappso::cbor::psm::SageReader::readTsvFile().

◆ writeScan()

void pappso::cbor::psm::SageTsvHandler::writeScan ( const Scan & one_scan)
private

Definition at line 717 of file sagetsvhandler.cpp.

718{
719 m_sageReader.getCborStreamWriter().startMap();
720 m_sageReader.getCborStreamWriter().append("id");
721 QCborValue(one_scan.cbor_id).toCbor(m_sageReader.getCborStreamWriter());
722 m_sageReader.getCborStreamWriter().append("precursor");
723 QCborValue(one_scan.cbor_precursor).toCbor(m_sageReader.getCborStreamWriter());
724 m_sageReader.getCborStreamWriter().append("ms2");
725 QCborValue(one_scan.cbor_ms2).toCbor(m_sageReader.getCborStreamWriter());
726
727 m_sageReader.getCborStreamWriter().append("psm_list");
728 m_sageReader.getCborStreamWriter().startArray(one_scan.psm_list.size());
729 for(auto &it_psm : one_scan.psm_list)
730 {
731 writePsm(it_psm);
732 }
733 m_sageReader.getCborStreamWriter().endArray();
734
735 m_sageReader.getCborStreamWriter().endMap();
736}
pappso::cbor::psm::SageTsvHandler::writePsm
void writePsm(const Psm &one_psm)
Definition sagetsvhandler.cpp:739

References pappso::cbor::psm::SageTsvHandler::Scan::cbor_id, pappso::cbor::psm::SageTsvHandler::Scan::cbor_ms2, pappso::cbor::psm::SageTsvHandler::Scan::cbor_precursor, m_sageReader, pappso::cbor::psm::SageTsvHandler::Scan::psm_list, and writePsm().

Referenced by writeSample().

Member Data Documentation

◆ m_columnNumber

std::size_t pappso::cbor::psm::SageTsvHandler::m_columnNumber = 0
private

Definition at line 218 of file sagetsvhandler.h.

Referenced by setCell(), startLine(), and startSheet().

◆ m_columnTypeList

std::vector<Columns> pappso::cbor::psm::SageTsvHandler::m_columnTypeList
private

Definition at line 219 of file sagetsvhandler.h.

Referenced by setCell().

◆ m_decoyTag

QString pappso::cbor::psm::SageTsvHandler::m_decoyTag
private

Definition at line 226 of file sagetsvhandler.h.

Referenced by SageTsvHandler(), and parseProteins().

◆ m_line

Line pappso::cbor::psm::SageTsvHandler::m_line
private

Definition at line 225 of file sagetsvhandler.h.

Referenced by endLine(), recordLine(), setCell(), and startLine().

◆ m_lineNumber

std::size_t pappso::cbor::psm::SageTsvHandler::m_lineNumber = 0
private

Definition at line 217 of file sagetsvhandler.h.

Referenced by endLine(), recordLine(), setCell(), and startSheet().

◆ m_progressIndex

std::size_t pappso::cbor::psm::SageTsvHandler::m_progressIndex = 0
private

Definition at line 216 of file sagetsvhandler.h.

Referenced by recordLine().

◆ m_proteinList

QStringList pappso::cbor::psm::SageTsvHandler::m_proteinList
private

Definition at line 227 of file sagetsvhandler.h.

Referenced by parseProteins(), recordLine(), setCell(), and startLine().

◆ m_psmProteinMap

PsmProteinMap& pappso::cbor::psm::SageTsvHandler::m_psmProteinMap
private

Definition at line 214 of file sagetsvhandler.h.

Referenced by SageTsvHandler(), parseProteins(), recordLine(), and writePsm().

◆ m_sageReader

const SageReader& pappso::cbor::psm::SageTsvHandler::m_sageReader
private

Definition at line 213 of file sagetsvhandler.h.

Referenced by SageTsvHandler(), parseMsRunFilename(), writePsm(), writeSample(), and writeScan().

◆ m_sampleMap

std::map<QString, Sample> pappso::cbor::psm::SageTsvHandler::m_sampleMap
private

Definition at line 229 of file sagetsvhandler.h.

Referenced by parseMsRunFilename(), and writeSampleList().

◆ m_spectrumIndex

std::size_t pappso::cbor::psm::SageTsvHandler::m_spectrumIndex
private

Definition at line 224 of file sagetsvhandler.h.

Referenced by parseSpectrumStringId(), and recordLine().

◆ m_spectrumNativeId

QString pappso::cbor::psm::SageTsvHandler::m_spectrumNativeId
private

Definition at line 228 of file sagetsvhandler.h.

Referenced by parseSpectrumStringId(), and recordLine().

◆ m_staticModificationList

std::vector<SageReader::SageModification> pappso::cbor::psm::SageTsvHandler::m_staticModificationList
private

Definition at line 222 of file sagetsvhandler.h.

Referenced by SageTsvHandler(), and parsePeptide().

◆ m_variableModificationList

std::vector<SageReader::SageModification> pappso::cbor::psm::SageTsvHandler::m_variableModificationList
private

Definition at line 223 of file sagetsvhandler.h.

Referenced by SageTsvHandler(), and parsePeptide().

◆ mp_currentSample

Sample* pappso::cbor::psm::SageTsvHandler::mp_currentSample
private

Definition at line 230 of file sagetsvhandler.h.

Referenced by parseMsRunFilename(), and recordLine().

◆ mp_monitor

pappso::UiMonitorInterface* pappso::cbor::psm::SageTsvHandler::mp_monitor = nullptr
private

Definition at line 215 of file sagetsvhandler.h.

Referenced by SageTsvHandler(), recordLine(), and startSheet().

◆ msp_peptide

pappso::PeptideSp pappso::cbor::psm::SageTsvHandler::msp_peptide
private

Definition at line 221 of file sagetsvhandler.h.

Referenced by parsePeptide(), recordLine(), and startLine().

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