Class SentinelRankDictionary
A rank dictionary, additional storing sentinel character which are not accounted for in a rank query.

Defined in <seqan/index.h>
Signature template <typename TRankDictionary, typename TSpec> class SentinelRankDictionary;

Template Parameters

TSpec Specialisation
TRankDictionary The rank dictionary of a text.

Interface Function Overview

Interface Functions Detail

clear(dictionary)

Clears the dictionary.

Parameters

dictionary The rank dictionary to be cleared.

Data Races

Thread safety unknown!

TSize countOccurrences(dictionary, character, pos);

Returns the number of occurrences of a specified character from the start to a specified position.

Parameters

dictionary The dictionary.
character The character.
pos The position (which is included in the counting).

Returns

TSize The number of occurrences (Metafunction: Size).

Data Races

Thread safety unknown!

void createSentinelRankDictionary(dictionary, text)

This functions creates the dictionary structure.

Parameters

text A text to be transfered into a dictionary. Types: String
dictionary The dictionary.

Data Races

Thread safety unknown!

empty(dictionary)

Returns whether or not the dictionary is empty.

Parameters

dictionary The rank dictionary to be checked.

Data Races

Thread safety unknown!

getFibre(dictionary, fibreTag)

Returns a specific fibre of a dictionary.

Parameters

fibreTag A tag that identifies the Fibre. Types: SentinelRankDictionary Fibres.
dictionary The dictionary holding the fibre.

Returns

TReturn A reference to the Fibre object.

Data Races

Thread safety unknown!

getSentinelSubstitute(dictionary)

Returns the character used to substitute the sentinel sign.

Parameters

dictionary The dictionary.

Data Races

Thread safety unknown!

getCharacter(dictionary, pos)

Returns the character of a specified position.

Parameters

pos The position
dictionary The rank dictionary.

Data Races

Thread safety unknown!

open(dictionary, fileName [, openMode])

This functions loads a dictionary from disk.

Parameters

openMode The combination of flags defining how the file should be opened.To open a file read-only, write-only or to read and write use OPEN_RDONLY, OPEN_WRONLY, or OPEN_RDWR.To create or overwrite a file add OPEN_CREATE.To append a file if existing add OPEN_APPEND.To circumvent problems, files are always opened in binary mode. Default: OPEN_RDWR | OPEN_CREATE | OPEN_APPEND
dictionary The dictionary. Types: SentinelRankDictionary
fileName C-style character string containing the file name.

Returns

TReturn A bool which is true on success.

Data Races

Thread safety unknown!

save(dictionary, fileName [, openMode])

This functions saves a dictionary to disk.

Parameters

openMode The combination of flags defining how the file should be opened.To open a file read-only, write-only or to read and write use OPEN_RDONLY, OPEN_WRONLY, or OPEN_RDWR.To create or overwrite a file add OPEN_CREATE.To append a file if existing add OPEN_APPEND.To circumvent problems, files are always opened in binary mode. Default: OPEN_RDWR | OPEN_CREATE | OPEN_APPEND
dictionary The dictionary. Types: SentinelRankDictionary
fileName C-style character string containing the file name.

Returns

TReturn A bool which is true on success.

Data Races

Thread safety unknown!

sentinelPosition(dictionary, pos)

Returns whether a specified position is a sentinel position.

Parameters

pos The position. Types: UnsignedIntegerConcept
dictionary The dictionary.

Data Races

Thread safety unknown!

setSentinelPosition(dictionary, pos)

Sets the sentinel position..

Parameters

pos The sentinel position. Types: UnsignedIntegerConcept
dictionary The dictionary.

Data Races

Thread safety unknown!

setSentinelSubstitute(dictionary, character)

Sets the character used to substitute the sentinel sign.

Parameters

character The sentinel substitute.
dictionary The dictionary.

Data Races

Thread safety unknown!