libpappsomspp
Library for mass spectrometry
pappso::PeptideModificatorPipeline Class Reference

#include <peptidemodificatorpipeline.h>

Inheritance diagram for pappso::PeptideModificatorPipeline:
pappso::PeptideModificatorInterface pappso::PeptideSpSinkInterface pappso::EnzymeProductInterface

Public Member Functions

 PeptideModificatorPipeline ()
 
 PeptideModificatorPipeline (const PeptideModificatorPipeline &other)
 
virtual ~PeptideModificatorPipeline ()
 
void addFixedModificationString (const QString &mod_str)
 
void addFixedNterModificationString (const QString &mod_str)
 
void addFixedCterModificationString (const QString &mod_str)
 
void addPotentialModificationString (const QString &mod_str)
 
void addPotentialNterModificationString (const QString &mod_str)
 
void addPotentialCterModificationString (const QString &mod_str)
 
void setSink (PeptideModificatorInterface *sink) override
 
void setPeptideSp (std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp_original, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme) override
 function to give the products of modifications for a digested peptide More...
 
void setPeptide (std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const QString &peptide_str, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme) override
 function to give the products of a protein digestion by an enzyme More...
 
void addLabeledModificationString (const QString &mod_str)
 
- Public Member Functions inherited from pappso::PeptideModificatorInterface
virtual ~PeptideModificatorInterface ()
 
virtual void setPeptideSp (std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme)=0
 function to give the products of modifications for a digested peptide More...
 
virtual void setSink (PeptideModificatorInterface *sink)=0
 
virtual void setPeptide (std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideStr &peptide, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme)=0
 function to give the products of a protein digestion by an enzyme More...
 

Private Member Functions

void parseFixedModification (const QString &mod_str, bool Nter, bool Cter, bool else_prot)
 
void privAddFixedModificationString (const QString &mod_str, bool Nter, bool Cter, bool else_prot)
 
void parsePotentialModification (const QString &mod_str, bool Nter, bool Cter, bool else_prot)
 
void privAddPotentialModificationString (const QString &mod_str, bool Nter, bool Cter, bool else_prot)
 
void parseLabeledModification (const QString &mod_str, bool Nter, bool Cter, bool else_prot)
 

Private Attributes

PeptideModificatorTeemp_peptideModificatorTee = nullptr
 
PeptideModificatorInterfacem_sink = nullptr
 
PeptideSpSinkInterfacemp_lastPeptideSinkInterface
 
PeptideModificatorInterfacemp_firstModificator = nullptr
 
std::vector< PeptideModificatorInterface * > m_pepModificatorPtrList
 

Detailed Description

Definition at line 33 of file peptidemodificatorpipeline.h.

Constructor & Destructor Documentation

◆ PeptideModificatorPipeline() [1/2]

PeptideModificatorPipeline::PeptideModificatorPipeline ( )

Definition at line 35 of file peptidemodificatorpipeline.cpp.

36{
37}

◆ PeptideModificatorPipeline() [2/2]

PeptideModificatorPipeline::PeptideModificatorPipeline ( const PeptideModificatorPipeline other)

Definition at line 39 of file peptidemodificatorpipeline.cpp.

41{
42 throw PappsoException(
43 QObject::tr("unable to copy PeptideModificatorPipeline object"));
44 if(other.mp_peptideModificatorTee != nullptr)
45 {
46 // mp_peptideModificatorTee = new
47 // PeptideModificatorTee(other.mp_peptideModificatorTee);
48 }
49
51 mp_firstModificator = nullptr;
52 for(auto p_mod : other.m_pepModificatorPtrList)
53 {
54 delete(p_mod);
55 }
56
57
58 m_sink = other.m_sink;
59
61
63
65}
std::vector< PeptideModificatorInterface * > m_pepModificatorPtrList
PeptideModificatorInterface * mp_firstModificator
PeptideSpSinkInterface * mp_lastPeptideSinkInterface

References m_pepModificatorPtrList, m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, and mp_peptideModificatorTee.

◆ ~PeptideModificatorPipeline()

PeptideModificatorPipeline::~PeptideModificatorPipeline ( )
virtual

Definition at line 67 of file peptidemodificatorpipeline.cpp.

68{
69
70 for(auto p_mod : m_pepModificatorPtrList)
71 {
72 delete(p_mod);
73 }
74 if(mp_peptideModificatorTee == nullptr)
75 {
77 }
78}

References m_pepModificatorPtrList, and mp_peptideModificatorTee.

Member Function Documentation

◆ addFixedCterModificationString()

void PeptideModificatorPipeline::addFixedCterModificationString ( const QString &  mod_str)

Definition at line 108 of file peptidemodificatorpipeline.cpp.

110{
111 privAddFixedModificationString(mod_str, false, true, false);
112}
void privAddFixedModificationString(const QString &mod_str, bool Nter, bool Cter, bool else_prot)

References privAddFixedModificationString().

◆ addFixedModificationString()

void PeptideModificatorPipeline::addFixedModificationString ( const QString &  mod_str)

Definition at line 97 of file peptidemodificatorpipeline.cpp.

98{
99 privAddFixedModificationString(mod_str, true, true, true);
100}

References privAddFixedModificationString().

◆ addFixedNterModificationString()

void PeptideModificatorPipeline::addFixedNterModificationString ( const QString &  mod_str)

Definition at line 102 of file peptidemodificatorpipeline.cpp.

104{
105 privAddFixedModificationString(mod_str, true, false, false);
106}

References privAddFixedModificationString().

◆ addLabeledModificationString()

void PeptideModificatorPipeline::addLabeledModificationString ( const QString &  mod_str)

Definition at line 261 of file peptidemodificatorpipeline.cpp.

262{
263
264 if(m_sink == nullptr)
265 {
266 throw PappsoException(QObject::tr(
267 "Please use setSink before addLabeledModificationString function"));
268 }
269 if(mp_peptideModificatorTee == nullptr)
270 {
272 }
273 if(mp_firstModificator == nullptr)
274 {
276 }
277
278 // backup pointers
279 PeptideModificatorInterface *backup_sink = m_sink;
280
281 PeptideSpSinkInterface *backup_p_last_peptide_sink_interface =
283
284 PeptideModificatorInterface *backup_p_first_modificator = mp_firstModificator;
285
286
287 QStringList mod_list_str =
288 mod_str.simplified().replace(" ", "").split(",", Qt::SkipEmptyParts);
289 for(auto i = 0; i < mod_list_str.size(); ++i)
290 {
291 parseLabeledModification(mod_list_str[i], true, true, true);
292
293 if(i == 0)
294 {
296 }
297 }
298
299 m_sink = backup_sink;
300 mp_lastPeptideSinkInterface = backup_p_last_peptide_sink_interface;
301 mp_firstModificator = backup_p_first_modificator;
302
304}
void parseLabeledModification(const QString &mod_str, bool Nter, bool Cter, bool else_prot)
void addModificator(PeptideModificatorInterface *p_peptide_mod)
virtual void setSink(PeptideModificatorInterface *sink)=0

References pappso::PeptideModificatorTee::addModificator(), m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, mp_peptideModificatorTee, parseLabeledModification(), and pappso::PeptideSpSinkInterface::setSink().

◆ addPotentialCterModificationString()

void PeptideModificatorPipeline::addPotentialCterModificationString ( const QString &  mod_str)

Definition at line 181 of file peptidemodificatorpipeline.cpp.

183{
184 privAddPotentialModificationString(mod_str, false, true, false);
185}
void privAddPotentialModificationString(const QString &mod_str, bool Nter, bool Cter, bool else_prot)

References privAddPotentialModificationString().

◆ addPotentialModificationString()

void PeptideModificatorPipeline::addPotentialModificationString ( const QString &  mod_str)

Definition at line 167 of file peptidemodificatorpipeline.cpp.

169{
170 privAddPotentialModificationString(mod_str, true, true, true);
171}

References privAddPotentialModificationString().

◆ addPotentialNterModificationString()

void PeptideModificatorPipeline::addPotentialNterModificationString ( const QString &  mod_str)

Definition at line 174 of file peptidemodificatorpipeline.cpp.

176{
177 privAddPotentialModificationString(mod_str, true, false, false);
178}

References privAddPotentialModificationString().

◆ parseFixedModification()

void PeptideModificatorPipeline::parseFixedModification ( const QString &  mod_str,
bool  Nter,
bool  Cter,
bool  else_prot 
)
private

Definition at line 135 of file peptidemodificatorpipeline.cpp.

139{
140
141 QStringList str_split = mod_str.split("@", Qt::SkipEmptyParts);
142
144
147 mod->setModificationPattern(str_split[1]);
148 mod->setSink(m_sink);
149 mod->setProtNter(Nter);
150 mod->setProtCter(Cter);
151 mod->setProtElse(else_prot);
152
153 m_pepModificatorPtrList.push_back(mod);
154
155 if(mp_firstModificator == nullptr)
156 {
158 }
159 else
160 {
162 }
164}
static AaModificationP getInstance(const QString &accession)
void setProtElse(bool arg1)
this modification concerns all peptides between Nter and Cter
void setProtCter(bool arg1)
this modification concerns the Cter peptide
void setSink(PeptideModificatorInterface *sink) override
void setProtNter(bool arg1)
this modification concerns the Nter peptide
virtual void setModificationPattern(QString &pattern) final
set the pattern on which the modification will be applied (usually the list of concerned AA)

References pappso::Cter, pappso::AaModification::getInstance(), m_pepModificatorPtrList, m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, pappso::Nter, pappso::PeptideModificatorBase::setModificationPattern(), pappso::PeptideFixedModificationBuilder::setProtCter(), pappso::PeptideFixedModificationBuilder::setProtElse(), pappso::PeptideFixedModificationBuilder::setProtNter(), pappso::PeptideFixedModificationBuilder::setSink(), and pappso::PeptideSpSinkInterface::setSink().

Referenced by privAddFixedModificationString().

◆ parseLabeledModification()

void PeptideModificatorPipeline::parseLabeledModification ( const QString &  mod_str,
bool  Nter,
bool  Cter,
bool  else_prot 
)
private

◆ parsePotentialModification()

void PeptideModificatorPipeline::parsePotentialModification ( const QString &  mod_str,
bool  Nter,
bool  Cter,
bool  else_prot 
)
private

Definition at line 209 of file peptidemodificatorpipeline.cpp.

213{
214
215 QStringList str_split = mod_str.split("@", Qt::SkipEmptyParts);
216
217 QString mod_acc_str = str_split[0];
218 QStringList str_acc_split = mod_acc_str.split("(", Qt::SkipEmptyParts);
220 AaModification::getInstance(str_acc_split[0]);
221
224
225 // qDebug() << "PeptideModificatorPipeline::parsePotentialModification " << ;
226 if(str_acc_split.length() == 2)
227 {
228 QStringList max_num_str_list =
229 str_acc_split[1].replace(")", "").split("-", Qt::SkipEmptyParts);
230 if(max_num_str_list.length() == 1)
231 {
232 mod->setModificationCounter(max_num_str_list[0].toUInt());
233 }
234 else if(max_num_str_list.length() == 2)
235 {
236 mod->setMinNumberMod(max_num_str_list[0].toUInt());
237 mod->setMaxNumberMod(max_num_str_list[1].toUInt());
238 }
239 }
240 mod->setModificationPattern(str_split[1]);
241 mod->setSink(m_sink);
242 mod->setProtNter(Nter);
243 mod->setProtCter(Cter);
244 mod->setProtElse(else_prot);
245
246 m_pepModificatorPtrList.push_back(mod);
247
248 if(mp_firstModificator == nullptr)
249 {
251 }
252 else
253 {
255 }
257}
Modify a peptide shared pointer with a variable modification on one AA.
void setSink(PeptideModificatorInterface *sink) override
void setProtNter(bool arg1)
this modification concerns the Nter peptide
void setProtElse(bool arg1)
this modification concerns all peptides between Nter and Cter
void setProtCter(bool arg1)
this modification concerns the Cter peptide

References pappso::Cter, pappso::AaModification::getInstance(), m_pepModificatorPtrList, m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, pappso::Nter, pappso::PeptideVariableModificationBuilder::setMaxNumberMod(), pappso::PeptideVariableModificationBuilder::setMinNumberMod(), pappso::PeptideVariableModificationBuilder::setModificationCounter(), pappso::PeptideModificatorBase::setModificationPattern(), pappso::PeptideVariableModificationBuilder::setProtCter(), pappso::PeptideVariableModificationBuilder::setProtElse(), pappso::PeptideVariableModificationBuilder::setProtNter(), pappso::PeptideVariableModificationBuilder::setSink(), and pappso::PeptideSpSinkInterface::setSink().

Referenced by privAddPotentialModificationString().

◆ privAddFixedModificationString()

void PeptideModificatorPipeline::privAddFixedModificationString ( const QString &  mod_str,
bool  Nter,
bool  Cter,
bool  else_prot 
)
private

Definition at line 115 of file peptidemodificatorpipeline.cpp.

117{
118 //"MOD:00397@C, MOD:00398@R"
119 if(mp_peptideModificatorTee != nullptr)
120 {
121 throw PappsoException(
122 QObject::tr("Unable to add fixed modification string after "
123 "addLabeledModificationString function"));
124 }
125 QStringList mod_list_str =
126 mod_str.simplified().replace(" ", "").split(",", Qt::SkipEmptyParts);
127 for(auto i = 0; i < mod_list_str.size(); ++i)
128 {
129 parseFixedModification(mod_list_str[i], Nter, Cter, else_prot);
130 }
131}
void parseFixedModification(const QString &mod_str, bool Nter, bool Cter, bool else_prot)

References pappso::Cter, mp_peptideModificatorTee, pappso::Nter, and parseFixedModification().

Referenced by addFixedCterModificationString(), addFixedModificationString(), and addFixedNterModificationString().

◆ privAddPotentialModificationString()

void PeptideModificatorPipeline::privAddPotentialModificationString ( const QString &  mod_str,
bool  Nter,
bool  Cter,
bool  else_prot 
)
private

Definition at line 188 of file peptidemodificatorpipeline.cpp.

190{
191 //"MOD:00397@C, MOD:00398@R"
192 if(mp_peptideModificatorTee != nullptr)
193 {
194 throw PappsoException(
195 QObject::tr("Unable to add potential modification string after "
196 "addLabeledModificationString function"));
197 }
198
199 QStringList mod_list_str =
200 mod_str.simplified().replace(" ", "").split(",", Qt::SkipEmptyParts);
201 for(auto i = 0; i < mod_list_str.size(); ++i)
202 {
203 parsePotentialModification(mod_list_str[i], Nter, Cter, else_prot);
204 }
205}
void parsePotentialModification(const QString &mod_str, bool Nter, bool Cter, bool else_prot)

References pappso::Cter, mp_peptideModificatorTee, pappso::Nter, and parsePotentialModification().

Referenced by addPotentialCterModificationString(), addPotentialModificationString(), and addPotentialNterModificationString().

◆ setPeptide()

void PeptideModificatorPipeline::setPeptide ( std::int8_t  sequence_database_id,
const ProteinSp protein_sp,
bool  is_decoy,
const QString &  peptide,
unsigned int  start,
bool  is_nter,
unsigned int  missed_cleavage_number,
bool  semi_enzyme 
)
overridevirtual

function to give the products of a protein digestion by an enzyme

Parameters
sequence_database_idinteger that references the sequence fatabase (file, stream, url...)
protein_spshared pointer on the protein that was digested
is_decoytell if the current protein is a decoy (true) or normal (false) protein
peptideamino acid sequence of the peptide (string) produced by the digestion
startthe position of the first amino acid of the peptide in the original protein sequence. the first amino acid of the protein is at position 1.
is_nterboolean to tell if the peptide is an Nter peptide (to allow Methionin Nter removal)
missed_cleavage_numbernumber of missed cleavage sites (that the enzyme has not cut) fot the product
semi_enzymeboolean that tells if this peptide is the produce of a semi enzymatic lysis

Implements pappso::EnzymeProductInterface.

Definition at line 369 of file peptidemodificatorpipeline.cpp.

377{
378
379 qDebug() << "PeptideModificatorPipeline::setPeptide begin";
380
381 Peptide peptide(peptide_str);
382
383 PeptideSp peptide_sp = peptide.makePeptideSp();
384
385 qDebug() << "PeptideModificatorPipeline::setPeptide m_sink->setPeptideSp";
386 setPeptideSp(sequence_database_id,
387 protein_sp,
388 is_decoy,
389 peptide_sp,
390 start,
391 is_nter,
392 missed_cleavage_number,
393 semi_enzyme);
394 qDebug() << "PeptideModificatorPipeline::setPeptide end";
395}
void setPeptideSp(std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp_original, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme) override
function to give the products of modifications for a digested peptide
std::shared_ptr< const Peptide > PeptideSp

References pappso::Peptide::makePeptideSp(), and setPeptideSp().

◆ setPeptideSp()

void PeptideModificatorPipeline::setPeptideSp ( std::int8_t  sequence_database_id,
const ProteinSp protein_sp,
bool  is_decoy,
const PeptideSp peptide_sp,
unsigned int  start,
bool  is_nter,
unsigned int  missed_cleavage_number,
bool  semi_enzyme 
)
overridevirtual

function to give the products of modifications for a digested peptide

Parameters
sequence_database_idinteger that references the sequence fatabase (file, stream, url...)
protein_spshared pointer on the protein that was initialy digested
is_decoytell if the current protein is a decoy (true) or normal (false) protein
peptidePeptide object containing sequence and possible modifications
startthe position of the first amino acid of the peptide in the original protein sequence. the first amino acid of the protein is at position 1.
is_nterboolean to tell if the peptide is an Nter peptide (to allow Methionin Nter removal)
missed_cleavage_numbernumber of missed cleavage sites (that the enzyme has not cut) fot the product
semi_enzymeboolean that tells if this peptide is the produce of a semi enzymatic lysis

Implements pappso::PeptideModificatorInterface.

Definition at line 334 of file peptidemodificatorpipeline.cpp.

342{
343 if(mp_firstModificator == nullptr)
344 {
345 m_sink->setPeptideSp(sequence_database_id,
346 protein_sp,
347 is_decoy,
348 peptide_sp_original,
349 start,
350 is_nter,
351 missed_cleavage_number,
352 semi_enzyme);
353 }
354 else
355 {
356 mp_firstModificator->setPeptideSp(sequence_database_id,
357 protein_sp,
358 is_decoy,
359 peptide_sp_original,
360 start,
361 is_nter,
362 missed_cleavage_number,
363 semi_enzyme);
364 }
365}
virtual void setPeptideSp(std::int8_t sequence_database_id, const ProteinSp &protein_sp, bool is_decoy, const PeptideSp &peptide_sp, unsigned int start, bool is_nter, unsigned int missed_cleavage_number, bool semi_enzyme)=0
function to give the products of modifications for a digested peptide

References m_sink, mp_firstModificator, and pappso::PeptideModificatorInterface::setPeptideSp().

Referenced by setPeptide().

◆ setSink()

void PeptideModificatorPipeline::setSink ( PeptideModificatorInterface sink)
overridevirtual

Implements pappso::PeptideSpSinkInterface.

Definition at line 81 of file peptidemodificatorpipeline.cpp.

82{
83 if(mp_peptideModificatorTee != nullptr)
84 {
85 throw PappsoException(QObject::tr(
86 "Please use setSink before addLabeledModificationString function"));
87 }
88
89 m_sink = sink;
90 if(mp_firstModificator != nullptr)
91 {
93 }
94};

References m_sink, mp_firstModificator, mp_lastPeptideSinkInterface, mp_peptideModificatorTee, and pappso::PeptideSpSinkInterface::setSink().

Member Data Documentation

◆ m_pepModificatorPtrList

std::vector<PeptideModificatorInterface *> pappso::PeptideModificatorPipeline::m_pepModificatorPtrList
private

◆ m_sink

◆ mp_firstModificator

◆ mp_lastPeptideSinkInterface

PeptideSpSinkInterface* pappso::PeptideModificatorPipeline::mp_lastPeptideSinkInterface
private

◆ mp_peptideModificatorTee


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