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 33 of file peptidemodificatorpipeline.cpp.

34{
35}

◆ PeptideModificatorPipeline() [2/2]

PeptideModificatorPipeline::PeptideModificatorPipeline ( const PeptideModificatorPipeline other)

Definition at line 37 of file peptidemodificatorpipeline.cpp.

39{
40 throw PappsoException(
41 QObject::tr("unable to copy PeptideModificatorPipeline object"));
42 if(other.mp_peptideModificatorTee != nullptr)
43 {
44 // mp_peptideModificatorTee = new
45 // PeptideModificatorTee(other.mp_peptideModificatorTee);
46 }
47
49 mp_firstModificator = nullptr;
50 for(auto p_mod : other.m_pepModificatorPtrList)
51 {
52 delete(p_mod);
53 }
54
55
56 m_sink = other.m_sink;
57
59
61
63}
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 65 of file peptidemodificatorpipeline.cpp.

66{
67
68 for(auto p_mod : m_pepModificatorPtrList)
69 {
70 delete(p_mod);
71 }
72 if(mp_peptideModificatorTee == nullptr)
73 {
75 }
76}

References m_pepModificatorPtrList, and mp_peptideModificatorTee.

Member Function Documentation

◆ addFixedCterModificationString()

void PeptideModificatorPipeline::addFixedCterModificationString ( const QString &  mod_str)

Definition at line 106 of file peptidemodificatorpipeline.cpp.

108{
109 privAddFixedModificationString(mod_str, false, true, false);
110}
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 95 of file peptidemodificatorpipeline.cpp.

96{
97 privAddFixedModificationString(mod_str, true, true, true);
98}

References privAddFixedModificationString().

◆ addFixedNterModificationString()

void PeptideModificatorPipeline::addFixedNterModificationString ( const QString &  mod_str)

Definition at line 100 of file peptidemodificatorpipeline.cpp.

102{
103 privAddFixedModificationString(mod_str, true, false, false);
104}

References privAddFixedModificationString().

◆ addLabeledModificationString()

void PeptideModificatorPipeline::addLabeledModificationString ( const QString &  mod_str)

Definition at line 259 of file peptidemodificatorpipeline.cpp.

260{
261
262 if(m_sink == nullptr)
263 {
264 throw PappsoException(QObject::tr(
265 "Please use setSink before addLabeledModificationString function"));
266 }
267 if(mp_peptideModificatorTee == nullptr)
268 {
270 }
271 if(mp_firstModificator == nullptr)
272 {
274 }
275
276 // backup pointers
277 PeptideModificatorInterface *backup_sink = m_sink;
278
279 PeptideSpSinkInterface *backup_p_last_peptide_sink_interface =
281
282 PeptideModificatorInterface *backup_p_first_modificator = mp_firstModificator;
283
284
285 QStringList mod_list_str =
286 mod_str.simplified().replace(" ", "").split(",", Qt::SkipEmptyParts);
287 for(auto i = 0; i < mod_list_str.size(); ++i)
288 {
289 parseLabeledModification(mod_list_str[i], true, true, true);
290
291 if(i == 0)
292 {
294 }
295 }
296
297 m_sink = backup_sink;
298 mp_lastPeptideSinkInterface = backup_p_last_peptide_sink_interface;
299 mp_firstModificator = backup_p_first_modificator;
300
302}
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 179 of file peptidemodificatorpipeline.cpp.

181{
182 privAddPotentialModificationString(mod_str, false, true, false);
183}
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 165 of file peptidemodificatorpipeline.cpp.

167{
168 privAddPotentialModificationString(mod_str, true, true, true);
169}

References privAddPotentialModificationString().

◆ addPotentialNterModificationString()

void PeptideModificatorPipeline::addPotentialNterModificationString ( const QString &  mod_str)

Definition at line 172 of file peptidemodificatorpipeline.cpp.

174{
175 privAddPotentialModificationString(mod_str, true, false, false);
176}

References privAddPotentialModificationString().

◆ parseFixedModification()

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

Definition at line 133 of file peptidemodificatorpipeline.cpp.

137{
138
139 QStringList str_split = mod_str.split("@", Qt::SkipEmptyParts);
140
142
145 mod->setModificationPattern(str_split[1]);
146 mod->setSink(m_sink);
147 mod->setProtNter(Nter);
148 mod->setProtCter(Cter);
149 mod->setProtElse(else_prot);
150
151 m_pepModificatorPtrList.push_back(mod);
152
153 if(mp_firstModificator == nullptr)
154 {
156 }
157 else
158 {
160 }
162}
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 207 of file peptidemodificatorpipeline.cpp.

211{
212
213 QStringList str_split = mod_str.split("@", Qt::SkipEmptyParts);
214
215 QString mod_acc_str = str_split[0];
216 QStringList str_acc_split = mod_acc_str.split("(", Qt::SkipEmptyParts);
218 AaModification::getInstance(str_acc_split[0]);
219
222
223 // qDebug() << "PeptideModificatorPipeline::parsePotentialModification " << ;
224 if(str_acc_split.length() == 2)
225 {
226 QStringList max_num_str_list =
227 str_acc_split[1].replace(")", "").split("-", Qt::SkipEmptyParts);
228 if(max_num_str_list.length() == 1)
229 {
230 mod->setModificationCounter(max_num_str_list[0].toUInt());
231 }
232 else if(max_num_str_list.length() == 2)
233 {
234 mod->setMinNumberMod(max_num_str_list[0].toUInt());
235 mod->setMaxNumberMod(max_num_str_list[1].toUInt());
236 }
237 }
238 mod->setModificationPattern(str_split[1]);
239 mod->setSink(m_sink);
240 mod->setProtNter(Nter);
241 mod->setProtCter(Cter);
242 mod->setProtElse(else_prot);
243
244 m_pepModificatorPtrList.push_back(mod);
245
246 if(mp_firstModificator == nullptr)
247 {
249 }
250 else
251 {
253 }
255}
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 113 of file peptidemodificatorpipeline.cpp.

115{
116 //"MOD:00397@C, MOD:00398@R"
117 if(mp_peptideModificatorTee != nullptr)
118 {
119 throw PappsoException(
120 QObject::tr("Unable to add fixed modification string after "
121 "addLabeledModificationString function"));
122 }
123 QStringList mod_list_str =
124 mod_str.simplified().replace(" ", "").split(",", Qt::SkipEmptyParts);
125 for(auto i = 0; i < mod_list_str.size(); ++i)
126 {
127 parseFixedModification(mod_list_str[i], Nter, Cter, else_prot);
128 }
129}
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 186 of file peptidemodificatorpipeline.cpp.

188{
189 //"MOD:00397@C, MOD:00398@R"
190 if(mp_peptideModificatorTee != nullptr)
191 {
192 throw PappsoException(
193 QObject::tr("Unable to add potential modification string after "
194 "addLabeledModificationString function"));
195 }
196
197 QStringList mod_list_str =
198 mod_str.simplified().replace(" ", "").split(",", Qt::SkipEmptyParts);
199 for(auto i = 0; i < mod_list_str.size(); ++i)
200 {
201 parsePotentialModification(mod_list_str[i], Nter, Cter, else_prot);
202 }
203}
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 367 of file peptidemodificatorpipeline.cpp.

375{
376
377 qDebug() << "PeptideModificatorPipeline::setPeptide begin";
378
379 Peptide peptide(peptide_str);
380
381 PeptideSp peptide_sp = peptide.makePeptideSp();
382
383 qDebug() << "PeptideModificatorPipeline::setPeptide m_sink->setPeptideSp";
384 setPeptideSp(sequence_database_id,
385 protein_sp,
386 is_decoy,
387 peptide_sp,
388 start,
389 is_nter,
390 missed_cleavage_number,
391 semi_enzyme);
392 qDebug() << "PeptideModificatorPipeline::setPeptide end";
393}
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 332 of file peptidemodificatorpipeline.cpp.

340{
341 if(mp_firstModificator == nullptr)
342 {
343 m_sink->setPeptideSp(sequence_database_id,
344 protein_sp,
345 is_decoy,
346 peptide_sp_original,
347 start,
348 is_nter,
349 missed_cleavage_number,
350 semi_enzyme);
351 }
352 else
353 {
354 mp_firstModificator->setPeptideSp(sequence_database_id,
355 protein_sp,
356 is_decoy,
357 peptide_sp_original,
358 start,
359 is_nter,
360 missed_cleavage_number,
361 semi_enzyme);
362 }
363}
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 79 of file peptidemodificatorpipeline.cpp.

80{
81 if(mp_peptideModificatorTee != nullptr)
82 {
83 throw PappsoException(QObject::tr(
84 "Please use setSink before addLabeledModificationString function"));
85 }
86
87 m_sink = sink;
88 if(mp_firstModificator != nullptr)
89 {
91 }
92};

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: