The class representing a peptide sequence candidate. More...

#include <cCandidate.h>

Public Member Functions
	cCandidate ()
	The default constructor.

	cCandidate (vector< string > &composition, vector< nodeEdge > &path, eFragmentIonType startiontype, int startmodifID, int endmodifID, int middlemodifID, int middlepos)
	The constructor. More...

	cCandidate (vector< string > &composition, vector< nodeEdge > &path, eFragmentIonType startiontype, int startmodifID, int endmodifID, int middlemodifID, int branchstart, int branchend)
	The constructor. More...

void	setCandidate (vector< string > &composition, vector< nodeEdge > &path, eFragmentIonType startiontype, int startmodifID, int endmodifID, int middlemodifID, int middlepos)
	Set a peptide sequence candidate. More...

void	setCandidate (vector< string > &composition, vector< nodeEdge > &path, eFragmentIonType startiontype, int startmodifID, int endmodifID, int middlemodifID, int branchstart, int branchend)
	Set a peptide sequence candidate. More...

void	clear ()
	Clear the candidate.

string &	getComposition ()
	Access to the composition of the peptide sequence candidate. More...

void	revertComposition ()
	Reverse the bricks composition of the candidate.

void	prepareBranchedCandidates (cCandidateSet &result, ePeptideType peptidetype, bool *terminatecomputation)
	Prepare candidates of a branched or a branch-cyclic peptide. More...

string	getTComposition ()
	Get a T-composition of a branched peptide. More...

string	getRevertedTComposition (bool usebrackets)
	Get a reverted T-composition of a branched peptide. More...

string	getAcronymsTComposition (cBricksDatabase &brickdatabase)
	Get a T-composition of a branched peptide composed from acronyms of bricks. More...

string	getRealNameTComposition (cBricksDatabase &brickdatabase)
	Get a T-composition of a branched peptide composed from real names of bricks. More...

int	getBranchSize ()
	Get a number of blocks forming a branch. More...

int	getBranchStart ()
	Get starting position of a branch. More...

int	getBranchEnd ()
	Get end position of a branch. More...

void	getPermutationsOfBranches (vector< TRotationInfo > &tpermutations)
	Get permutations of branches a branched peptide. More...

double	calculatePrecursorMassFromBricks (cBricksDatabase &brickdatabasewithcombinations, cParameters *parameters)
	Calculate the precursor mass of the peptide sequence candidate from bricks. More...

bool	isEqualTo (cCandidate &candidate)
	Compare two candidates. More...

void	getPermutations (cCandidateSet &permutations, bool *terminatecomputation)
	Get a set of candidates with permutations of bricks. More...

int	getStartModifID ()
	Get id of a terminal modification (at the beginning of a spectrum). More...

void	setStartModifID (int id)
	Set id of a terminal modification (at the beginning of a spectrum). More...

int	getEndModifID ()
	Get id of a terminal modification (at the end of a spectrum). More...

void	setEndModifID (int id)
	Set id of a terminal modification (at the end of a spectrum). More...

int	getMiddleModifID ()
	Get id of a terminal modification of a branched peptide (in the middle of a spectrum). More...

void	setMiddleModifID (int id)
	Set id of a terminal modification of a branched peptide (in the middle of a spectrum). More...

bool	compare (cCandidate &candidate)
	Compare two candidates. More...

vector< nodeEdge > &	getPath ()
	Get a path in the de novo graph corresponding to the peptide sequence candidate. More...

bool	hasEqualTPermutations (cCandidate &candidate)
	compare TPermutations of two candidates. More...

bool	hasOnlyArtificialBricks (cBricksDatabase &brickdatabasewithcombinations)
	Check whether the candidate is composed exclusively from artificial bricks. More...

bool	hasFirstBrickArtificial (cBricksDatabase &brickdatabasewithcombinations)
	Check if the first brick is artificial. More...

bool	hasLastBrickArtificial (cBricksDatabase &brickdatabasewithcombinations)
	Check if the last brick is artificial. More...

bool	hasLastBrickInvalid (cBricksDatabase &brickdatabasewithcombinations)
	Check if the last brick is invalid. More...

void	getRotations (vector< string > &rotations, bool includerevertedrotations)
	Get rotations of a cyclic peptide sequence. More...

void	getBranchCyclicRotations (vector< cCandidate > &branchcyclicrotations, bool includerevertedrotations)
	Get branch-cyclic rotations of a branch-cyclic peptide sequence. More...

cSummaryFormula	calculateSummaryFormulaFromBricks (cParameters &parameters, ePeptideType peptidetype, double precursormass=0)
	Calculate the summary formula of the peptide sequence candidate. More...

cSummaryFormula &	getSummaryFormula ()
	Get the summary formula of the peptide sequence candidate. More...

void	setSummaryFormula (cSummaryFormula &summary)
	Set the summary formula of the peptide sequence candidate. More...

void	store (ofstream &os)
	Store the structure into an output stream. More...

void	load (ifstream &is)
	Load the structure from an input stream. More...

void	setName (string &name)
	Set the name of peptide. More...

string &	getName ()
	Get the name of peptide. More...

void	setAcronyms (cBricksDatabase &bricksdatabase)
	Set a vector of acronyms corresponding to a peptide sequence candidate. More...

void	setBackboneAcronyms (cBricksDatabase &bricksdatabase)
	Set a vector of acronyms corresponding to a backbone of a peptide sequence candidate. More...

void	setBranchAcronyms (cBricksDatabase &bricksdatabase)
	Set a vector of acronyms corresponding to a branch of a peptide sequence candidate. More...

vector< string > &	getAcronyms ()
	Get a vector of acronyms corresponding to a peptide sequence candidate. More...

vector< string > &	getBackboneAcronyms ()
	Get a vector of acronyms corresponding to a backbone of a peptide sequence candidate. More...

vector< string > &	getBranchAcronyms ()
	Get a vector of acronyms corresponding to a branch of a peptide sequence candidate. More...

void	setPath (cDeNovoGraph &graph, cParameters *parameters)
	Set a path in the de novo graph corresponding to the candidate. More...

string &	getPathAsString ()
	Get a path in the de novo graph corresponding to the candidate as a string. More...

void	setRealPeptideName (cBricksDatabase &bricksdatabase, ePeptideType peptidetype)
	Set a real peptide name. More...

void	setAcronymPeptideNameWithHTMLReferences (cBricksDatabase &bricksdatabase, ePeptideType peptidetype)
	Set an acronym peptide name. More...

string &	getRealPeptideName ()
	Get a real peptide name. More...

string &	getAcronymPeptideNameWithHTMLReferences ()
	Get an acronym peptide name. More...

void	setStartIonType (eFragmentIonType iontype)
	Set start ion type used in the de novo graph. More...

eFragmentIonType	getStartIonType ()
	Get start ion type used in the de novo graph. More...

bool	checkKetideSequence (cBricksDatabase &bricksdatabase, ePeptideType peptidetype, bool regularblocksorder)
	Check if the order of blocks is correct. More...

eResidueLossType	getLeftResidueType (cBricksDatabase &bricksdatabase)
	Get the residue type of the left-most building block. More...

eResidueLossType	getRightResidueType (cBricksDatabase &bricksdatabase)
	Get the residue type of the right-most building block. More...

bool	checkKetideBlocks (cBricksDatabase &bricksdatabase, ePeptideType peptidetype, bool regularblocksorder)
	Check if the numbers of H2 loss and H2O loss blocks are correct. More...

Detailed Description

The class representing a peptide sequence candidate.

Constructor & Destructor Documentation

◆ cCandidate() [1/2]

cCandidate::cCandidate	(	vector< string > &	composition,
		vector< nodeEdge > &	path,
		eFragmentIonType	startiontype,
		int	startmodifID,
		int	endmodifID,
		int	middlemodifID,
		int	middlepos
	)

The constructor.

Parameters

composition	reference to a vector of strings where each string is a sequence of ids of bricks separated by '-' (each string corresponds to an edge in the de novo graph)
path	reference to a path in the de novo graph which corresponds to a peptide sequence candidate
startiontype	start ion type in the de novo graph
startmodifID	id of a terminal modification (at the beginning of a spectrum)
endmodifID	id of a terminal modification (at the end of a spectrum)
middlemodifID	id of a terminal modification of a branched peptide (in the middle of a spectrum)
middlepos	position in composition corresponding to a branch of a branched peptide

◆ cCandidate() [2/2]

cCandidate::cCandidate	(	vector< string > &	composition,
		vector< nodeEdge > &	path,
		eFragmentIonType	startiontype,
		int	startmodifID,
		int	endmodifID,
		int	middlemodifID,
		int	branchstart,
		int	branchend
	)

The constructor.

Parameters

composition	reference to a vector of strings where each string is a sequence of ids of bricks separated by '-' (each string corresponds to an edge in the de novo graph)
path	reference to a path in the de novo graph which corresponds to a peptide sequence candidate
startiontype	start ion type in the de novo graph
startmodifID	id of a terminal modification (at the beginning of a spectrum)
endmodifID	id of a terminal modification (at the end of a spectrum)
middlemodifID	id of a terminal modification of a branched peptide (in the middle of a spectrum)
branchstart	position of a brick where a branch of a branched peptide starts (it is assumed that all strings in composition are concatenated)
branchend	position of a brick where a branch of a branched peptide ends (it is assumed that all strings in composition are concatenated)

Member Function Documentation

◆ calculatePrecursorMassFromBricks()

double cCandidate::calculatePrecursorMassFromBricks	(	cBricksDatabase &	brickdatabasewithcombinations,
		cParameters *	parameters
	)

Calculate the precursor mass of the peptide sequence candidate from bricks.

Parameters

brickdatabasewithcombinations	reference to an input database of bricks with combinations of bricks
parameters	a pointer to the parameters of the application

Return values

double precursor mass of the candidate

◆ calculateSummaryFormulaFromBricks()

cSummaryFormula cCandidate::calculateSummaryFormulaFromBricks	(	cParameters &	parameters,
		ePeptideType	peptidetype,
		double	precursormass = `0`
	)

Calculate the summary formula of the peptide sequence candidate.

Parameters

parameters	a reference to the parameters of the application
peptidetype	the type of peptide
precursormass	experimantal precursor mass

Return values

string summary formula

◆ checkKetideBlocks()

bool cCandidate::checkKetideBlocks	(	cBricksDatabase &	bricksdatabase,
		ePeptideType	peptidetype,
		bool	regularblocksorder
	)

Check if the numbers of H2 loss and H2O loss blocks are correct.

Parameters

bricksdatabase	a database of building blocks
peptidetype	the type of peptide
regularblocksorder	check regular order of ketide blocks

Return values

bool	true when the numbers of blocks are correct

◆ checkKetideSequence()

bool cCandidate::checkKetideSequence	(	cBricksDatabase &	bricksdatabase,
		ePeptideType	peptidetype,
		bool	regularblocksorder
	)

Check if the order of blocks is correct.

Parameters

bricksdatabase	a database of building blocks
peptidetype	the type of peptide
regularblocksorder	check regular order of ketide blocks

Return values

bool	true when the order of blocks is correct; false otherwise

◆ compare()

bool cCandidate::compare ( cCandidate & candidate )

Compare two candidates.

Parameters

candidate reference to the other candidate

Return values

bool	true when the other candidate is greater

◆ getAcronymPeptideNameWithHTMLReferences()

string & cCandidate::getAcronymPeptideNameWithHTMLReferences ( )

Get an acronym peptide name.

Return values

string reference to the acronym peptide name

◆ getAcronyms()

vector< string > & cCandidate::getAcronyms ( )

Get a vector of acronyms corresponding to a peptide sequence candidate.

Return values

vector<string> a vector of acronyms

◆ getAcronymsTComposition()

string cCandidate::getAcronymsTComposition ( cBricksDatabase & brickdatabase )

Get a T-composition of a branched peptide composed from acronyms of bricks.

Parameters

brickdatabase reference to the database of bricks

Return values

string containing acronyms of bricks separated by '-', the branch is specified by '(' and ')'

◆ getBackboneAcronyms()

vector< string > & cCandidate::getBackboneAcronyms ( )

Get a vector of acronyms corresponding to a backbone of a peptide sequence candidate.

Return values

vector<string> a vector of acronyms

◆ getBranchAcronyms()

vector< string > & cCandidate::getBranchAcronyms ( )

Get a vector of acronyms corresponding to a branch of a peptide sequence candidate.

Return values

vector<string> a vector of acronyms

◆ getBranchCyclicRotations()

void cCandidate::getBranchCyclicRotations	(	vector< cCandidate > &	branchcyclicrotations,
		bool	includerevertedrotations
	)

Get branch-cyclic rotations of a branch-cyclic peptide sequence.

Parameters

branchcyclicrotations	reference to an output vector containing branch-cyclic rotations of a sequence
includerevertedrotations	if true then reverted branch-cyclic rotations are also included

◆ getBranchEnd()

int cCandidate::getBranchEnd ( )

Get end position of a branch.

Return values

int	end position of a branch

◆ getBranchSize()

int cCandidate::getBranchSize ( )

Get a number of blocks forming a branch.

Return values

int	number of blocks

◆ getBranchStart()

int cCandidate::getBranchStart ( )

Get starting position of a branch.

Return values

int	starting position of a branch

◆ getComposition()

string & cCandidate::getComposition ( )

Access to the composition of the peptide sequence candidate.

Return values

reference to a string of ids of bricks separated by '-'

◆ getEndModifID()

int cCandidate::getEndModifID ( )

Get id of a terminal modification (at the end of a spectrum).

Return values

int	id of a terminal modification

◆ getLeftResidueType()

eResidueLossType cCandidate::getLeftResidueType ( cBricksDatabase & bricksdatabase )

Get the residue type of the left-most building block.

Parameters

bricksdatabase a database of building blocks

Return values

eResidueLossType residue loss type of the left-most building block

◆ getMiddleModifID()

int cCandidate::getMiddleModifID ( )

Get id of a terminal modification of a branched peptide (in the middle of a spectrum).

Return values

int	id of a terminal modification

◆ getName()

string & cCandidate::getName ( )

Get the name of peptide.

Return values

string name

◆ getPath()

vector< nodeEdge > & cCandidate::getPath ( )

Get a path in the de novo graph corresponding to the peptide sequence candidate.

Return values

vector<nodeEdge> vector of pairs node and edge

◆ getPathAsString()

string & cCandidate::getPathAsString ( )

Get a path in the de novo graph corresponding to the candidate as a string.

Return values

string reference to a path corresponding to the spectrum

◆ getPermutations()

void cCandidate::getPermutations	(	cCandidateSet &	permutations,
		bool *	terminatecomputation
	)

Get a set of candidates with permutations of bricks.

Parameters

permutations	reference to an output set of candidates
terminatecomputation	pointer to a variable determining that the computation must be stopped

◆ getPermutationsOfBranches()

void cCandidate::getPermutationsOfBranches ( vector< TRotationInfo > & tpermutations )

Get permutations of branches a branched peptide.

Parameters

tpermutations reference to an output vector of auxiliary structures where permutations will be stored

◆ getRealNameTComposition()

string cCandidate::getRealNameTComposition ( cBricksDatabase & brickdatabase )

Get a T-composition of a branched peptide composed from real names of bricks.

Parameters

brickdatabase reference to the database of bricks

Return values

string containing real names of bricks separated by '-', the branch is specified by '(' and ')'

◆ getRealPeptideName()

string & cCandidate::getRealPeptideName ( )

Get a real peptide name.

Return values

string reference to the real peptide name

◆ getRevertedTComposition()

string cCandidate::getRevertedTComposition ( bool usebrackets )

Get a reverted T-composition of a branched peptide.

Parameters

usebrackets if true then the branch is separated by '(' and ')' else '-' is used instead of brackets

Return values

string containing ids of bricks separated by '-', the branch may be specified by '(' and ')'; example: 1-2-3(4-5)6-7

◆ getRightResidueType()

eResidueLossType cCandidate::getRightResidueType ( cBricksDatabase & bricksdatabase )

Get the residue type of the right-most building block.

Parameters

bricksdatabase a database of building blocks

Return values

eResidueLossType residue loss type of the right-most building block

◆ getRotations()

void cCandidate::getRotations	(	vector< string > &	rotations,
		bool	includerevertedrotations
	)

Get rotations of a cyclic peptide sequence.

Parameters

rotations	reference to an output vector containing rotations of a sequence
includerevertedrotations	if true then reverted rotations are also included

◆ getStartIonType()

eFragmentIonType cCandidate::getStartIonType ( )

Get start ion type used in the de novo graph.

Return values

eFragmentIonType fragment ion type

◆ getStartModifID()

int cCandidate::getStartModifID ( )

Get id of a terminal modification (at the beginning of a spectrum).

Return values

int	id of a terminal modification

◆ getSummaryFormula()

cSummaryFormula & cCandidate::getSummaryFormula ( )

Get the summary formula of the peptide sequence candidate.

Return values

cSummaryFormula summary formula

◆ getTComposition()

string cCandidate::getTComposition ( )

Get a T-composition of a branched peptide.

Return values

string containing ids of bricks separated by '-', the branch is specified by '(' and ')'; example: 1-2-3(4-5)6-7

◆ hasEqualTPermutations()

bool cCandidate::hasEqualTPermutations ( cCandidate & candidate )

compare TPermutations of two candidates.

Parameters

candidate reference to the second candidate

Return values

true	when candidates have equal TPermutations

◆ hasFirstBrickArtificial()

bool cCandidate::hasFirstBrickArtificial ( cBricksDatabase & brickdatabasewithcombinations )

Check if the first brick is artificial.

Parameters

brickdatabasewithcombinations reference to an input database of bricks with combinations of bricks

Return values

bool	true if the first brick is artificial, false otherwise

◆ hasLastBrickArtificial()

bool cCandidate::hasLastBrickArtificial ( cBricksDatabase & brickdatabasewithcombinations )

Check if the last brick is artificial.

Parameters

brickdatabasewithcombinations reference to an input database of bricks with combinations of bricks

Return values

bool	true if the last brick is artificial, false otherwise

◆ hasLastBrickInvalid()

bool cCandidate::hasLastBrickInvalid ( cBricksDatabase & brickdatabasewithcombinations )

Check if the last brick is invalid.

Parameters

brickdatabasewithcombinations reference to an input database of bricks with combinations of bricks

Return values

bool	true if the last brick is invalid, false otherwise

◆ hasOnlyArtificialBricks()

bool cCandidate::hasOnlyArtificialBricks ( cBricksDatabase & brickdatabasewithcombinations )

Check whether the candidate is composed exclusively from artificial bricks.

Parameters

brickdatabasewithcombinations reference to an input database of bricks with combinations of bricks

Return values

bool	true when the candidate is composed exclusively from artificial bricks; false when the candidate constains a regular brick

◆ isEqualTo()

bool cCandidate::isEqualTo ( cCandidate & candidate )

Compare two candidates.

Parameters

candidate reference to the other candidate

Return values

bool	true when the candidates are equal

◆ load()

void cCandidate::load ( ifstream & is )

Load the structure from an input stream.

Parameters

is	an input stream

◆ prepareBranchedCandidates()

void cCandidate::prepareBranchedCandidates	(	cCandidateSet &	result,
		ePeptideType	peptidetype,
		bool *	terminatecomputation
	)

Prepare candidates of a branched or a branch-cyclic peptide.

Parameters

result	reference to an output set of possible peptide sequence candidates
peptidetype	a type of an analyzed peptide
terminatecomputation	pointer to a variable determining that the computation must be stopped

◆ setAcronymPeptideNameWithHTMLReferences()

void cCandidate::setAcronymPeptideNameWithHTMLReferences	(	cBricksDatabase &	bricksdatabase,
		ePeptideType	peptidetype
	)

Set an acronym peptide name.

Parameters

bricksdatabase	the database of building blocks
peptidetype	the type of peptide

◆ setAcronyms()

void cCandidate::setAcronyms ( cBricksDatabase & bricksdatabase )

Set a vector of acronyms corresponding to a peptide sequence candidate.

Parameters

bricksdatabase a database of building blocks

◆ setBackboneAcronyms()

void cCandidate::setBackboneAcronyms ( cBricksDatabase & bricksdatabase )

Set a vector of acronyms corresponding to a backbone of a peptide sequence candidate.

Parameters

bricksdatabase a database of building blocks

◆ setBranchAcronyms()

void cCandidate::setBranchAcronyms ( cBricksDatabase & bricksdatabase )

Set a vector of acronyms corresponding to a branch of a peptide sequence candidate.

Parameters

bricksdatabase a database of building blocks

◆ setCandidate() [1/2]

void cCandidate::setCandidate	(	vector< string > &	composition,
		vector< nodeEdge > &	path,
		eFragmentIonType	startiontype,
		int	startmodifID,
		int	endmodifID,
		int	middlemodifID,
		int	branchstart,
		int	branchend
	)

Set a peptide sequence candidate.

Parameters

composition	reference to a vector of strings where each string is a sequence of ids of bricks separated by '-' (each string corresponds to an edge in the de novo graph)
path	reference to a path in the de novo graph which corresponds to a peptide sequence candidate
startiontype	start ion type in the de novo graph
startmodifID	id of a terminal modification (at the beginning of a spectrum)
endmodifID	id of a terminal modification (at the end of a spectrum)
middlemodifID	id of a terminal modification of a branched peptide (in the middle of a spectrum)
branchstart	position of a brick where a branch of a branched peptide starts (it is assumed that all strings in composition are concatenated)
branchend	position of a brick where a branch of a branched peptide ends (it is assumed that all strings in composition are concatenated)

◆ setCandidate() [2/2]

void cCandidate::setCandidate	(	vector< string > &	composition,
		vector< nodeEdge > &	path,
		eFragmentIonType	startiontype,
		int	startmodifID,
		int	endmodifID,
		int	middlemodifID,
		int	middlepos
	)

Set a peptide sequence candidate.

Parameters

composition	reference to a vector of strings where each string is a sequence of ids of bricks separated by '-' (each string corresponds to an edge in the de novo graph)
path	reference to a path in the de novo graph which corresponds to a peptide sequence candidate
startiontype	start ion type in the de novo graph
startmodifID	id of a terminal modification (at the beginning of a spectrum)
endmodifID	id of a terminal modification (at the end of a spectrum)
middlemodifID	id of a terminal modification of a branched peptide (in the middle of a spectrum)
middlepos	position in composition corresponding to a branch of a branched peptide

◆ setEndModifID()

void cCandidate::setEndModifID ( int id )

Set id of a terminal modification (at the end of a spectrum).

Parameters

id	of a terminal modification

◆ setMiddleModifID()

void cCandidate::setMiddleModifID ( int id )

Set id of a terminal modification of a branched peptide (in the middle of a spectrum).

Parameters

id	of a terminal modification

◆ setName()

void cCandidate::setName ( string & name )

Set the name of peptide.

Parameters

name name

◆ setPath()

void cCandidate::setPath	(	cDeNovoGraph &	graph,
		cParameters *	parameters
	)

Set a path in the de novo graph corresponding to the candidate.

Parameters

graph	reference to the de novo graph
parameters	parameters of the application

◆ setRealPeptideName()

void cCandidate::setRealPeptideName	(	cBricksDatabase &	bricksdatabase,
		ePeptideType	peptidetype
	)

Set a real peptide name.

Parameters

bricksdatabase	the database of building blocks
peptidetype	the type of peptide

◆ setStartIonType()

void cCandidate::setStartIonType ( eFragmentIonType iontype )

Set start ion type used in the de novo graph.

Parameters

iontype fragment ion type

◆ setStartModifID()

void cCandidate::setStartModifID ( int id )

Set id of a terminal modification (at the beginning of a spectrum).

Parameters

id	of a terminal modification

◆ setSummaryFormula()

void cCandidate::setSummaryFormula ( cSummaryFormula & summary )

Set the summary formula of the peptide sequence candidate.

Parameters

summary summary formula

◆ store()

void cCandidate::store ( ofstream & os )

Store the structure into an output stream.

Parameters

os	an output stream

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

core/cCandidate.h
core/cCandidate.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ cCandidate() [1/2]

◆ cCandidate() [2/2]

Member Function Documentation

◆ calculatePrecursorMassFromBricks()

◆ calculateSummaryFormulaFromBricks()

◆ checkKetideBlocks()

◆ checkKetideSequence()

◆ compare()

◆ getAcronymPeptideNameWithHTMLReferences()

◆ getAcronyms()

◆ getAcronymsTComposition()

◆ getBackboneAcronyms()

◆ getBranchAcronyms()

◆ getBranchCyclicRotations()

◆ getBranchEnd()

◆ getBranchSize()

◆ getBranchStart()

◆ getComposition()

◆ getEndModifID()

◆ getLeftResidueType()

◆ getMiddleModifID()

◆ getName()

◆ getPath()

◆ getPathAsString()

◆ getPermutations()

◆ getPermutationsOfBranches()

◆ getRealNameTComposition()

◆ getRealPeptideName()

◆ getRevertedTComposition()

◆ getRightResidueType()

◆ getRotations()

◆ getStartIonType()

◆ getStartModifID()

◆ getSummaryFormula()

◆ getTComposition()

◆ hasEqualTPermutations()

◆ hasFirstBrickArtificial()

◆ hasLastBrickArtificial()

◆ hasLastBrickInvalid()

◆ hasOnlyArtificialBricks()

◆ isEqualTo()

◆ load()

◆ prepareBranchedCandidates()

◆ setAcronymPeptideNameWithHTMLReferences()

◆ setAcronyms()

◆ setBackboneAcronyms()

◆ setBranchAcronyms()

◆ setCandidate() [1/2]

◆ setCandidate() [2/2]

◆ setEndModifID()

◆ setMiddleModifID()

◆ setName()

◆ setPath()

◆ setRealPeptideName()

◆ setStartIonType()

◆ setStartModifID()

◆ setSummaryFormula()

◆ store()