Chained Seed

Class Specialization

Chained Seed

Describes a seed with start and end position2 and diagonal upper and lower bounds.

Additionaly diagonal segments between start and end position2 are stored.

Chained Seed

Seed<TPosition, ChainedSeed>

Parameters

TPosition

The type of number that should be used. Must have negative numbers (e.g. int/long).

Specialization of

Metafunctions

Diagonal	Returns type of the value for the diagonal of a seed. (Seed)
Iterator	The seed diagonal iterator type.
Position	The position type of a SeedDiagonal. (Seed)
Reference	The seed diagonal reference type.
SeedScore	Returns type of the value for the score of a seed. (Seed)
Size	The position type of a SeedDiagonal. (Seed)
Value	The seed diagonal type.

Member Functions

Seed	Constructor

Functions

addSeed	Adds a seed to an existing set. (Seed)
appendDiagonal	Adds diagonal to the Chained Seed.
assign	Assigns one object to another object. (Seed)
beginDiagonal	Returns the diagonal of the start point. (Seed)
beginPositionH	Returns the begin position of the seed in the database. (Seed)
beginPositionV	Returns the begin position of the seed in the query. (Seed)
endDiagonal	Returns the diagonal of the end point. (Seed)
endPositionH	Returns the end position of the seed in the database. (Seed)
endPositionV	Returns the end position of the seed in the query. (Seed)
extendSeed	Extends a seed. (Seed)
length	Returns the number of diagonals in the chained seed.
lowerDiagonal	Returns the leftmost diagonal of the seed (minimum diagonal value). (Seed)
move	Hands over content from one container to another container. (Seed)
score	Returns the score of the seed. (Seed)
setBeginPositionH	Sets the begin position of the seed in the database. (Seed)
setBeginPositionV	Sets the begin position of the seed in the query. (Seed)
setEndPositionH	Sets the end position of the seed in the database. (Seed)
setEndPositionV	Returns the end position of the seed in the query. (Seed)
setLowerDiagonal	Sets a new value for the leftmost diagonal. (Seed)
setScore	Set the score value of a seed. (Seed)
setUpperDiagonal	Sets a new value for the rightmost diagonal. (Seed)
truncateDiagonals	Removes diagonals from the given first one to the end of the seed's diagonals.
upperDiagonal	Returns the rightmost diagonal of the seed (maximum diagonal value). (Seed)

SeqAn - Sequence Analysis Library - www.seqan.de