Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum. More...

#include <OpenMS/DATASTRUCTURES/SuffixArraySeqan.h>

Inheritance diagram for SuffixArraySeqan:

Public Member Functions
	SuffixArraySeqan (const String &st, const String &filename, const WeightWrapper::WEIGHTMODE weight_mode=WeightWrapper::MONO)
	constructor
	SuffixArraySeqan (const SuffixArraySeqan &source)
	copy constructor
virtual	~SuffixArraySeqan ()
	destructor
String	toString ()
	converts suffix array to a printable string
void	findSpec (std::vector< std::vector< std::pair< std::pair< SignedSize, SignedSize >, DoubleReal > > > &candidates, const std::vector< DoubleReal > &spec)
	the function that will find all peptide candidates for a given spectrum
bool	save (const String &filename)
	saves the suffix array to disc
bool	open (const String &filename)
	opens the suffix array
void	setTolerance (DoubleReal t)
	setter for tolerance
DoubleReal	getTolerance () const
	getter for tolerance
bool	isDigestingEnd (const char aa1, const char aa2) const
	returns if an enzyme will cut after first character
void	setTags (const std::vector< OpenMS::String > &tags)
	setter for tags
const std::vector < OpenMS::String > &	getTags ()
	getter for tags
void	setUseTags (bool use_tags)
	setter for use_tags
bool	getUseTags ()
	getter for use_tags
void	setNumberOfModifications (Size number_of_mods)
	setter for number of modifications
Size	getNumberOfModifications ()
	getter for number of modifications
void	printStatistic ()
Protected Member Functions
void	goNextSubTree_ (TIter &it, DoubleReal &m, std::stack< DoubleReal > &allm, std::stack< std::map< DoubleReal, SignedSize > > &mod_map)
	overwriting goNextSubTree_ from seqan index_esa_stree.h for mass update during suffix array traversal
void	goNextSubTree_ (TIter &it)
	goes to the next sub tree
void	goNext_ (TIter &it, DoubleReal &m, std::stack< DoubleReal > &allm, std::stack< std::map< DoubleReal, SignedSize > > &mod_map)
	overwriting goNext from seqan index_esa_stree.h for mass update during suffix array traversal
void	parseTree_ (TIter &it, std::vector< std::pair< SignedSize, SignedSize > > &out_number, std::vector< std::pair< SignedSize, SignedSize > > &edge_length, std::vector< SignedSize > &leafe_depth)
SignedSize	findFirst_ (const std::vector< DoubleReal > &spec, DoubleReal &m)
	binary search for finding the index of the first element of the spectrum that matches the desired mass within the tolerance.
SignedSize	findFirst_ (const std::vector< DoubleReal > &spec, DoubleReal &m, SignedSize start, SignedSize end)
	binary search for finding the index of the first element of the spectrum that matches the desired mass within the tolerance. it searches recursivly.
Protected Attributes
TIndex	index_
	seqan suffix array
TIter *	it_
	seqan suffix array iterator
const String &	s_
	reference to strings for which the suffix array is build
DoubleReal	masse_ [255]
	amino acid masses
SignedSize	number_of_modifications_
	number of allowed modifications
std::vector< String >	tags_
	all tags
bool	use_tags_
	if tags are used
DoubleReal	tol_
	tolerance
Private Types
typedef seqan::TopDown < seqan::ParentLinks<> >	TIterSpec
typedef seqan::Index < seqan::String< char > , seqan::IndexEsa< TIterSpec > >	TIndex
typedef seqan::Iter< TIndex, seqan::VSTree< TIterSpec > >	TIter

Detailed Description

Class that uses SEQAN library for a suffix array. It can be used to find peptide Candidates for a MS spectrum.

This class uses SEQAN suffix array. It can just be used for finding peptide Candidates for a given MS Spectrum within a certain mass tolerance. The suffix array can be saved to disc for reused so it has to be build just once.

Member Typedef Documentation

typedef seqan::Index<seqan::String<char>, seqan::IndexEsa<TIterSpec> > TIndex [private]

typedef seqan::Iter<TIndex, seqan::VSTree<TIterSpec> > TIter [private]

typedef seqan::TopDown<seqan::ParentLinks<> > TIterSpec [private]

Constructor & Destructor Documentation

SuffixArraySeqan	(	const String &	st,
		const String &	filename,
		const WeightWrapper::WEIGHTMODE	weight_mode = `WeightWrapper::MONO`
	)

constructor

Parameters:

	st	const string reference with the string for which the suffix array should be build
	filename	const string reference with filename for opening or saving the suffix array
	weight_mode	if not monoistopic weight should be used, this parameters can be set to AVERAGE

Exceptions:

	FileNotFound	is thrown if the given file is not found
	InvalidValue	if the given suffix array string is invalid

SuffixArraySeqan ( const SuffixArraySeqan & source )

copy constructor

virtual ~SuffixArraySeqan ( ) [virtual]

destructor

Member Function Documentation

SignedSize findFirst_	(	const std::vector< DoubleReal > &	spec,
		DoubleReal &	m
	)			`[protected]`

binary search for finding the index of the first element of the spectrum that matches the desired mass within the tolerance.

Parameters:

	spec	const reference to spectrum
	m	mass

Returns:: SignedSize with the index of the first occurence

Note:: requires that there is at least one occurence

SignedSize findFirst_	(	const std::vector< DoubleReal > &	spec,
		DoubleReal &	m,
		SignedSize	start,
		SignedSize	end
	)			`[protected]`

binary search for finding the index of the first element of the spectrum that matches the desired mass within the tolerance. it searches recursivly.

Parameters:

	spec	const reference to spectrum
	m	mass
	start	start index
	end	end index

Returns:: SignedSize with the index of the first occurence

Note:: requires that there is at least one occurence

void findSpec	(	std::vector< std::vector< std::pair< std::pair< SignedSize, SignedSize >, DoubleReal > > > &	candidates,
		const std::vector< DoubleReal > &	spec
	)

the function that will find all peptide candidates for a given spectrum

Parameters:

	spec	const reference of DoubleReal vector describing the spectrum
	candidates	output parameters which holds the candidates of the masses given in spec after call

Returns:: a vector of SignedSize pairs.

for every mass within the spectrum all candidates described by as pairs of ints are returned. All masses are searched for the same time in just one suffix array traversal. In order to accelerate the traversal the skip and lcp table are used. The mass wont be calculated for each entry but it will be updated during traversal using a stack datastructure

Size getNumberOfModifications ( )

getter for number of modifications

Returns:: number of modifications

const std::vector<OpenMS::String>& getTags ( )

getter for tags

Returns:: const reference to vector of strings

DoubleReal getTolerance ( ) const

getter for tolerance

Returns:: DoubleReal with tolerance

bool getUseTags ( )

getter for use_tags

Returns:: bool indicating whether tags are used or not

void goNext_	(	TIter &	it,
		DoubleReal &	m,
		std::stack< DoubleReal > &	allm,
		std::stack< std::map< DoubleReal, SignedSize > > &	mod_map
	)			`[inline, protected]`

overwriting goNext from seqan index_esa_stree.h for mass update during suffix array traversal

the suffix array is treated as a suffix tree. this function goes to the next node that has not been visited yet. During this traversal the mass will be updated using the stack with edge masses.

Parameters:

	it	reference to the suffix array iterator
	m	reference to actual mass
	allm	reference to the stack with history of traversal
	mod_map	input parameters which specifies the modification masses allowed in the candidates

See also:: goNextSubTree_

void goNextSubTree_ ( TIter & it ) [inline, protected]

goes to the next sub tree

Parameters:

it

reference to the suffix array iterator

See also:: goNext

void goNextSubTree_	(	TIter &	it,
		DoubleReal &	m,
		std::stack< DoubleReal > &	allm,
		std::stack< std::map< DoubleReal, SignedSize > > &	mod_map
	)			`[inline, protected]`

overwriting goNextSubTree_ from seqan index_esa_stree.h for mass update during suffix array traversal

the suffix array is treated as a suffix tree. this function skips the subtree under the actual node and goes directly to the next subtree that has not been visited yet. During this traversal the mass will be updated using the stack with edge masses.

Parameters:

	it	reference to the suffix array iterator
	m	reference to actual mass
	allm	reference to the stack with history of traversal
	mod_map	input parameters which specifies the modification massen allowed in the candidates

See also:: goNext

bool isDigestingEnd	(	const char	aa1,
		const char	aa2
	)			const

returns if an enzyme will cut after first character

Parameters:

	aa1	const char as first aminoacid
	aa2	const char as second aminoacid

Returns:: bool descibing if it is a digesting site

Reimplemented in SuffixArrayTrypticSeqan.

bool open ( const String & filename )

opens the suffix array

Parameters:

filename

const reference string describing the filename

Returns:: bool if operation was succesful

Exceptions:

FileNotFound

is thrown if the given file could not be found

void parseTree_	(	TIter &	it,
		std::vector< std::pair< SignedSize, SignedSize > > &	out_number,
		std::vector< std::pair< SignedSize, SignedSize > > &	edge_length,
		std::vector< SignedSize > &	leafe_depth
	)			`[inline, protected]`

void printStatistic ( )

bool save ( const String & filename )

saves the suffix array to disc

Parameters:

filename

const reference string describing the filename

Returns:: bool if operation was succesful

Exceptions:

UnableToCreateFile

is thrown if the output files could not be created

void setNumberOfModifications ( Size number_of_mods )

setter for number of modifications

Parameters:

number_of_mods

void setTags ( const std::vector< OpenMS::String > & tags )

setter for tags

Parameters:

tags

reference to vector of strings with tags

Note:: sets use_tags = true

void setTolerance ( DoubleReal t )

setter for tolerance

Parameters:

t

DoubleReal with tolerance, only 0 or greater is allowed

Exceptions:

InvalidValue

is thrown if given tolerance is negative

void setUseTags ( bool use_tags )

setter for use_tags

Parameters:

use_tags

indicating whether tags should be used or not

String toString ( )

converts suffix array to a printable string

Member Data Documentation

TIndex index_ [protected]

seqan suffix array

TIter* it_ [protected]

seqan suffix array iterator

DoubleReal masse_[255] [protected]

amino acid masses

SignedSize number_of_modifications_ [protected]

number of allowed modifications

const String& s_ [protected]

reference to strings for which the suffix array is build

std::vector<String> tags_ [protected]

all tags

DoubleReal tol_ [protected]

tolerance

bool use_tags_ [protected]

if tags are used

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:53 using doxygen 1.7.1

SuffixArraySeqan Class Reference

Public Member Functions

Protected Member Functions

Protected Attributes

Private Types

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation