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 >, double > > > &candidates, const std::vector< double > &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 (double t)=0 |
setter for tolerance More... | |
virtual double | 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
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pure virtual |
the function that will find all peptide candidates for a given spectrum
spec | const reference of double 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.
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pure virtual |
getter for number of modifications
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
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pure virtual |
getter for tags
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
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pure virtual |
getter for tolerance
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
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pure virtual |
getter for use_tags
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
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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.
opens the suffix array
filename | const reference string describing the filename |
FileNotFound |
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
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pure virtual |
output for statistic
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
saves the suffix array to disc
filename | const reference string describing the filename |
UnableToCreateFile | if file could not be created (e.g. if you have no rights) |
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
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pure virtual |
setter for number of modifications
number_of_mods |
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
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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.
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pure virtual |
setter for tolerance
t | double with tolerance |
InvalidValue | if tolerance is negative |
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
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pure virtual |
setter for use_tags
use_tags | indicating whether tags should be used or not |
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
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pure virtual |
transforms suffix array to a printable String
Implemented in SuffixArraySeqan, and SuffixArrayTrypticCompressed.
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Aug 25 2015 05:54:08 using doxygen 1.8.9.1 |