abstract class for suffix array More...
#include <OpenMS/DATASTRUCTURES/SuffixArray.h>
 
  
 | Public Member Functions | |
| SuffixArray (const String &st, const String &filename) | |
| constructor taking the string and the filename for writing or reading  More... | |
| SuffixArray (const SuffixArray &sa) | |
| copy constructor  More... | |
| virtual | ~SuffixArray ()=0 | 
| destructor  More... | |
| virtual String | toString ()=0 | 
| transforms suffix array to a printable String  More... | |
| virtual void | findSpec (std::vector< std::vector< std::pair< std::pair< SignedSize, SignedSize >, DoubleReal > > > &candidates, const std::vector< DoubleReal > &spec)=0 | 
| the function that will find all peptide candidates for a given spectrum  More... | |
| virtual bool | save (const String &filename)=0 | 
| saves the suffix array to disc  More... | |
| virtual bool | open (const String &filename)=0 | 
| opens the suffix array  More... | |
| virtual void | setTolerance (DoubleReal t)=0 | 
| setter for tolerance  More... | |
| virtual DoubleReal | getTolerance () const =0 | 
| getter for tolerance  More... | |
| virtual bool | isDigestingEnd (const char aa1, const char aa2) const =0 | 
| returns if an enzyme will cut after first character  More... | |
| virtual void | setTags (const std::vector< String > &tags)=0 | 
| setter for tags  More... | |
| virtual const std::vector < String > & | getTags ()=0 | 
| getter for tags  More... | |
| virtual void | setUseTags (bool use_tags)=0 | 
| setter for use_tags  More... | |
| virtual bool | getUseTags ()=0 | 
| getter for use_tags  More... | |
| virtual void | setNumberOfModifications (Size number_of_mods)=0 | 
| setter for number of modifications  More... | |
| virtual Size | getNumberOfModifications ()=0 | 
| getter for number of modifications  More... | |
| virtual void | printStatistic ()=0 | 
| output for statistic  More... | |
| SuffixArray () | |
| constructor  More... | |
abstract class for suffix array
| SuffixArray | ( | const String & | st, | 
| const String & | filename | ||
| ) | 
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 | 
| filename | the filename for writing or reading the suffix array | 
| Exception::InvalidValue | if string does not start with empty string ($) | 
| Exception::FileNotFound | is thrown if the given filename is not found | 
| SuffixArray | ( | const SuffixArray & | sa | ) | 
copy constructor
| 
 | pure virtual | 
destructor
| SuffixArray | ( | ) | 
constructor
| 
 | pure virtual | 
the function that will find all peptide candidates for a given spectrum
| spec | const reference of DoubleReal vector describing the spectrum | 
| candidates | the candidates which are returned for the masses given in spec | 
| InvalidValue | if the spectrum is not sorted ascendingly | 
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
| 
 | pure virtual | 
getter for number of modifications
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
| 
 | pure virtual | 
getter for tags
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
| 
 | pure virtual | 
getter for tolerance
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
| 
 | pure virtual | 
getter for use_tags
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
| 
 | 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.
| 
 | pure virtual | 
opens the suffix array
| filename | const reference string describing the filename | 
| FileNotFound | 
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
| 
 | pure virtual | 
output for statistic
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
| 
 | pure virtual | 
saves the suffix array to disc
| filename | const reference string describing the filename | 
| UnableToCreateFile | if file could not be created (e.x. if you have no rigths) | 
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
| 
 | pure virtual | 
setter for number of modifications
| number_of_mods | 
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
| 
 | 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.
| 
 | pure virtual | 
setter for tolerance
| t | DoubleReal with tolerance | 
| InvalidValue | if tolerance is negative | 
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
| 
 | pure virtual | 
setter for use_tags
| use_tags | indicating whether tags should be used or not | 
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
| 
 | pure virtual | 
transforms suffix array to a printable String
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:29 using doxygen 1.8.5 |