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SuffixArray Class Reference

#include <OpenMS/DATASTRUCTURES/SuffixArray.h>

Inheritance diagram for SuffixArray:

SuffixArraySeqan SuffixArrayTrypticCompressed SuffixArrayTrypticSeqan

List of all members.


Detailed Description

abstract class for suffix array

Public Member Functions

 SuffixArray (const String &st, const String &sa_file_name) throw (Exception::InvalidValue, Exception::FileNotFound)
 constructor taking the string and the filename for writing or reading
 SuffixArray (const SuffixArray &sa)
 copy constructor
virtual ~SuffixArray ()=0
 destructor
virtual String toString ()=0
 transforms suffix array to a printable String
virtual void findSpec (std::vector< std::vector< std::pair< std::pair< int, int >, float > > > &candidates, const std::vector< double > &spec)=0 throw (Exception::InvalidValue)
 the function that will find all peptide candidates for a given spectrum
virtual bool save (const String &file_name)=0 throw (Exception::UnableToCreateFile)
 saves the suffix array to disc
virtual bool open (const String &file_name)=0 throw (Exception::FileNotFound)
 opens the suffix array
virtual void setTolerance (double t)=0 throw (Exception::InvalidValue)
 setter for tolerance
virtual double getTolerance () const =0
 getter for tolerance
virtual bool isDigestingEnd (const char aa1, const char aa2) const =0
 returns if an enzyme will cut after first character
virtual void setTags (const std::vector< String > &tags)=0 throw (Exception::InvalidValue)
 setter for tags
virtual const std::vector
< String > & 
getTags ()=0
 getter for tags
virtual void setUseTags (bool use_tags)=0
 setter for use_tags
virtual bool getUseTags ()=0
 getter for use_tags
virtual void setNumberOfModifications (unsigned int number_of_mods)=0
 setter for number of modifications
virtual unsigned int getNumberOfModifications ()=0
 getter for number of modifications
virtual void printStatistic ()=0
 output for statistic
 SuffixArray ()
 constructor

Constructor & Destructor Documentation

SuffixArray ( const String st,
const String sa_file_name 
) throw (Exception::InvalidValue, Exception::FileNotFound)

constructor taking the string and the filename for writing or reading

Parameters:
st the string as const reference with which the suffix array will be build
saFileName the filename for writing or reading the suffix array
Exceptions:
Exception::InvalidValue if string does not start with empty string ($)

SuffixArray ( const SuffixArray sa  ) 

copy constructor

virtual ~SuffixArray (  )  [pure virtual]

destructor

SuffixArray (  ) 

constructor


Member Function Documentation

virtual String toString (  )  [pure virtual]

transforms suffix array to a printable String

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.

virtual void findSpec ( std::vector< std::vector< std::pair< std::pair< int, int >, float > > > &  candidates,
const std::vector< double > &  spec 
) throw (Exception::InvalidValue) [pure virtual]

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

Parameters:
spec const reference of double vector describing the spectrum
Returns:
a vector of int pairs.
Exceptions:
Exception::InvalidValue if the spectrum is not sorted ascendingly

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.

virtual bool save ( const String file_name  )  throw (Exception::UnableToCreateFile) [pure virtual]

saves the suffix array to disc

Parameters:
filename const reference string describing the filename
Returns:
bool if operation was succesful
Exceptions:
Exception::UnableToCreateFile if file could not be created (e.x. if you have no rigths)

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.

virtual bool open ( const String file_name  )  throw (Exception::FileNotFound) [pure virtual]

opens the suffix array

Parameters:
filename const reference string describing the filename
Returns:
bool if operation was succesful
Exceptions:
Exception::FileNotFound 

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.

virtual void setTolerance ( double  t  )  throw (Exception::InvalidValue) [pure virtual]

setter for tolerance

Parameters:
t double with tolerance
Exceptions:
Exception::InvalidValue if tolerance is negative

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.

virtual double getTolerance (  )  const [pure virtual]

getter for tolerance

Returns:
double with tolerance

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.

virtual bool isDigestingEnd ( const char  aa1,
const char  aa2 
) const [pure virtual]

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

Implemented in SuffixArraySeqan, SuffixArrayTrypticCompressed, and SuffixArrayTrypticSeqan.

virtual void setTags ( const std::vector< String > &  tags  )  throw (Exception::InvalidValue) [pure virtual]

setter for tags

Parameters:
tags const vector of strings with tags with length 3 each
Exceptions:
Exception::InvalidValue if at least one tag does not have size of 3

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.

virtual const std::vector<String>& getTags (  )  [pure virtual]

getter for tags

Returns:
const vector of string with tags

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.

virtual void setUseTags ( bool  use_tags  )  [pure virtual]

setter for use_tags

Parameters:
use_tags indicating whether tags should be used or not

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.

virtual bool getUseTags (  )  [pure virtual]

getter for use_tags

Returns:
bool indicating whether tags are used or not

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.

virtual void setNumberOfModifications ( unsigned int  number_of_mods  )  [pure virtual]

setter for number of modifications

Parameters:
number_of_mods 

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.

virtual unsigned int getNumberOfModifications (  )  [pure virtual]

getter for number of modifications

Returns:
unsigned int describing number of modifications

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.

virtual void printStatistic (  )  [pure virtual]

output for statistic

Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1