cSequence Class Reference

The class representing a sequence. More...

#include <cSequence.h>

Public Member Functions
	cSequence ()
	The constructor.
void	clear ()
	Clear the structure.
void	store (ofstream &os)
	Store the structure into an output stream. More...
void	load (ifstream &is, int fileversionpart1, int fileversionpart2, int fileversionpart3)
	Load the structure from an input stream. More...
ePeptideType	getPeptideType ()
	Get peptide type. More...
string &	getSequence ()
	Get sequence. More...
string &	getName ()
	Get name. More...
double	getMinimumRetentionTime ()
	Get minimum retention time. More...
double	getMaximumRetentionTime ()
	Get maximum retention time. More...
string &	getReference ()
	Get reference. More...
void	setPeptideType (ePeptideType peptidetype)
	Set peptide type. More...
void	setSequence (const string &sequence)
	Set sequence. More...
void	setName (const string &name)
	Set name. More...
void	setRetentionTime (double rtmin, double rtmax)
	Set retention time. More...
void	setReference (const string &reference)
	Set reference. More...
void	setNTterminalModification (const string &modification)
	Set N-terminal modification. More...
void	setCTterminalModification (const string &modification)
	Set C-terminal modification. More...
void	setBranchModification (const string &modification)
	Set branch modification. More...
string &	getNTterminalModification ()
	Get N-terminal modification. More...
string &	getCTterminalModification ()
	Get C-terminal modification. More...
string &	getBranchModification ()
	Get branch modification. More...
string	getNameWithReferenceAsHTMLString ()
	Get name of sequence as a HTML link to sequence reference. More...
void	setSummaryFormula (const string &formula)
	Set the summary formula. More...
string	getSummaryFormula ()
	Get the summary formula. More...
bool	isDecoy ()
	Check if sequence/compound is decoy. More...
void	setDecoy (bool decoy)
	Set decoy flag. More...

Detailed Description

The class representing a sequence.

Member Function Documentation

getBranchModification()

string & cSequence::getBranchModification

(

)

Get branch modification.

Return values

string

name of a branch modification

getCTterminalModification()

string & cSequence::getCTterminalModification

(

)

Get C-terminal modification.

Return values

string

name of C-terminal modification

getMaximumRetentionTime()

double cSequence::getMaximumRetentionTime

(

)

Get maximum retention time.

Return values

double

maximum retention time

getMinimumRetentionTime()

double cSequence::getMinimumRetentionTime

(

)

Get minimum retention time.

Return values

double

minimum retention time

getName()

string & cSequence::getName

(

)

Get name.

Return values

string

name

getNameWithReferenceAsHTMLString()

string cSequence::getNameWithReferenceAsHTMLString

(

)

Get name of sequence as a HTML link to sequence reference.

Return values

string

HTML link

getNTterminalModification()

string & cSequence::getNTterminalModification

(

)

Get N-terminal modification.

Return values

string

name of N-terminal modification

getPeptideType()

ePeptideType cSequence::getPeptideType

(

)

Get peptide type.

Return values

ePeptideType

peptide type

getReference()

string & cSequence::getReference

(

)

Get reference.

Return values

string

reference

getSequence()

string & cSequence::getSequence

(

)

Get sequence.

Return values

string

sequence

getSummaryFormula()

string cSequence::getSummaryFormula

(

)

Get the summary formula.

Return values

string

summary formula

isDecoy()

bool cSequence::isDecoy

(

)

Check if sequence/compound is decoy.

Return values

bool	true if sequence is decoy, false otherwise

load()

void cSequence::load	(	ifstream &	is,
		int	fileversionpart1,
		int	fileversionpart2,
		int	fileversionpart3
	)

Load the structure from an input stream.

Parameters

is	an input stream
fileversionpart1	first number of .res the file version
fileversionpart2	second number of .res the file version
fileversionpart3	third number of .res the file version

setBranchModification()

void cSequence::setBranchModification

(

const string &

modification

)

Set branch modification.

Parameters

modification

name of a branch modification

setCTterminalModification()

void cSequence::setCTterminalModification

(

const string &

modification

)

Set C-terminal modification.

Parameters

modification

name of a C-terminal modification

setDecoy()

void cSequence::setDecoy

(

bool

decoy

)

Set decoy flag.

Parameters

decoy

true if sequence is decoy, false otherwise

setName()

void cSequence::setName

(

const string &

name

)

Set name.

Parameters

name

name

setNTterminalModification()

void cSequence::setNTterminalModification

(

const string &

modification

)

Set N-terminal modification.

Parameters

modification

name of an N-terminal modification

setPeptideType()

void cSequence::setPeptideType

(

ePeptideType

peptidetype

)

Set peptide type.

Parameters

peptidetype

peptide type

setReference()

void cSequence::setReference

(

const string &

reference

)

Set reference.

Parameters

reference

reference

setRetentionTime()

void cSequence::setRetentionTime	(	double	rtmin,
		double	rtmax
	)

Set retention time.

Parameters

rtmin	minimum retention time
rtmax	maximum retention time

setSequence()

void cSequence::setSequence

(

const string &

sequence

)

Set sequence.

Parameters

sequence

sequence

setSummaryFormula()

void cSequence::setSummaryFormula

(

const string &

formula

)

Set the summary formula.

Parameters

formula

summary formula

store()

void cSequence::store

(

ofstream &

os

)

Store the structure into an output stream.

Parameters

os	an output stream

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

• core/cSequence.h
• core/cSequence.cpp