Class
Seed
A seed in a dotplot.
Stores the start and end positions in the horizonal and vertical dimension.
Include Headers
seqan/seeds.h
Parameters
The seed specialization type. | |
The configuration object to use for this seed. |
Specializations
Describes a seed with start and end position2 and diagonal upper and lower bounds. | |
Describes a seed with start and end position and diagonal upper and lower bounds. |
Metafunctions
Returns type of the value for the diagonal of a seed. | |
The position type of a SeedDiagonal. | |
Returns type of the value for the score of a seed. | |
The position type of a SeedDiagonal. |
Functions
Adds a seed to an existing SeedSet using different algorithms for local chaining. | |
Assigns one object to another object. | |
Returns the diagonal of the start point. | |
Returns the begin position of the seed in the database. | |
Returns the begin position of the seed in the query. | |
Returns the diagonal of the end point. | |
Returns the end position of the seed in the database. | |
Returns the end position of the seed in the query. | |
Extends a seed. | |
Returns the leftmost diagonal of the seed (minimum diagonal value). | |
Hands over content from one container to another container. | |
Returns the score of the seed. | |
Sets the begin position of the seed in the database. | |
Sets the begin position of the seed in the query. | |
Sets the end position of the seed in the database. | |
Returns the end position of the seed in the query. | |
Sets a new value for the leftmost diagonal. | |
Set the score value of a seed. | |
Sets a new value for the rightmost diagonal. | |
Returns the rightmost diagonal of the seed (maximum diagonal value). |
Examples
The following example shows the usage of three seed extension algorithms the tags MatchExtend, UngappedXDrop, and GappedXDrop:
File "seeds_extension.cpp"
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The output is as follows:
endPositionV(seed1) = 6
endPositionH(seed2) = 9
endPositionV(seed2) = 9
endPositionH(seed3) = 14
endPositionV(seed3) = 13
This is an example for global seed chaining:
File "seeds_chaining.cpp"
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SeqAn - Sequence Analysis Library - www.seqan.de