#include <OpenMS/DATASTRUCTURES/SuffixArray.h>
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 |
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
st | the string as const reference with which the suffix array will be build | |
saFileName | the filename for writing or reading the suffix array |
Exception::InvalidValue | if string does not start with empty string ($) |
SuffixArray | ( | const SuffixArray & | sa | ) |
copy constructor
virtual ~SuffixArray | ( | ) | [pure virtual] |
destructor
SuffixArray | ( | ) |
constructor
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
spec | const reference of double vector describing the spectrum |
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
filename | const reference string describing the filename |
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
filename | const reference string describing the filename |
Exception::FileNotFound |
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
virtual void setTolerance | ( | double | t | ) | throw (Exception::InvalidValue) [pure virtual] |
setter for tolerance
t | double with tolerance |
Exception::InvalidValue | if tolerance is negative |
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
virtual double getTolerance | ( | ) | const [pure virtual] |
getter for 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
aa1 | const char as first aminoacid | |
aa2 | const char as second aminoacid |
Implemented in SuffixArraySeqan, SuffixArrayTrypticCompressed, and SuffixArrayTrypticSeqan.
virtual void setTags | ( | const std::vector< String > & | tags | ) | throw (Exception::InvalidValue) [pure virtual] |
setter for tags
tags | const vector of strings with tags with length 3 each |
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
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
virtual void setUseTags | ( | bool | use_tags | ) | [pure virtual] |
setter for use_tags
use_tags | indicating whether tags should be used or not |
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
virtual bool getUseTags | ( | ) | [pure virtual] |
getter for use_tags
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
virtual void setNumberOfModifications | ( | unsigned int | number_of_mods | ) | [pure virtual] |
setter for number of modifications
number_of_mods |
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
virtual unsigned int getNumberOfModifications | ( | ) | [pure virtual] |
getter for number of modifications
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
virtual void printStatistic | ( | ) | [pure virtual] |
Generated Tue Apr 1 15:36:44 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |