abstract class for suffix array More...
#include <OpenMS/DATASTRUCTURES/SuffixArray.h>
Inheritance diagram for SuffixArray:
Public Member Functions | |
| SuffixArray (const String &st, const String &filename) | |
| 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< SignedSize, SignedSize >, DoubleReal > > > &candidates, const std::vector< DoubleReal > &spec)=0 |
| the function that will find all peptide candidates for a given spectrum | |
| virtual bool | save (const String &filename)=0 |
| saves the suffix array to disc | |
| virtual bool | open (const String &filename)=0 |
| opens the suffix array | |
| virtual void | setTolerance (DoubleReal t)=0 |
| setter for tolerance | |
| virtual DoubleReal | 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 |
| 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 (Size number_of_mods)=0 |
| setter for number of modifications | |
| virtual Size | getNumberOfModifications ()=0 |
| getter for number of modifications | |
| virtual void | printStatistic ()=0 |
| output for statistic | |
| SuffixArray () | |
| constructor | |
Detailed Description
abstract class for suffix array
Constructor & Destructor Documentation
| SuffixArray | ( | const String & | st, | |
| const String & | filename | |||
| ) |
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 filename the filename for writing or reading the suffix array
- Exceptions:
-
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
| virtual ~SuffixArray | ( | ) | [pure virtual] |
destructor
| SuffixArray | ( | ) |
constructor
Member Function Documentation
| virtual void findSpec | ( | std::vector< std::vector< std::pair< std::pair< SignedSize, SignedSize >, DoubleReal > > > & | candidates, | |
| const std::vector< DoubleReal > & | spec | |||
| ) | [pure virtual] |
the function that will find all peptide candidates for a given spectrum
- Parameters:
-
spec const reference of DoubleReal vector describing the spectrum candidates the candidates which are returned for the masses given in spec
- Returns:
- a vector of SignedSize pairs.
- Exceptions:
-
InvalidValue if the spectrum is not sorted ascendingly
| virtual Size getNumberOfModifications | ( | ) | [pure virtual] |
getter for number of modifications
- Returns:
- Size describing number of modifications
| virtual const std::vector<String>& getTags | ( | ) | [pure virtual] |
getter for tags
- Returns:
- const vector of string with tags
| virtual DoubleReal getTolerance | ( | ) | const [pure virtual] |
getter for tolerance
- Returns:
- DoubleReal with tolerance
| virtual bool getUseTags | ( | ) | [pure virtual] |
getter for use_tags
- Returns:
- bool indicating whether tags are used or not
| 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 describing if it is a digesting site
| virtual bool open | ( | const String & | filename | ) | [pure virtual] |
opens the suffix array
- Parameters:
-
filename const reference string describing the filename
- Returns:
- bool if operation was succesful
- Exceptions:
-
FileNotFound
| virtual void printStatistic | ( | ) | [pure virtual] |
output for statistic
| virtual bool save | ( | const String & | filename | ) | [pure virtual] |
saves the suffix array to disc
- Parameters:
-
filename const reference string describing the filename
- Returns:
- bool if operation was succesful
- Exceptions:
-
UnableToCreateFile if file could not be created (e.x. if you have no rigths)
| virtual void setNumberOfModifications | ( | Size | number_of_mods | ) | [pure virtual] |
setter for number of modifications
- Parameters:
-
number_of_mods
| virtual void setTags | ( | const std::vector< String > & | tags | ) | [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
| virtual void setTolerance | ( | DoubleReal | t | ) | [pure virtual] |
setter for tolerance
- Parameters:
-
t DoubleReal with tolerance
- Exceptions:
-
InvalidValue if tolerance is negative
| virtual void setUseTags | ( | bool | use_tags | ) | [pure virtual] |
setter for use_tags
- Parameters:
-
use_tags indicating whether tags should be used or not
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:53 using doxygen 1.7.1 |