Function
addSeed
Adds a seed to an existing SeedSet using different algorithms for local chaining.
Include Headers
seqan/seeds.h
Parameters
The set to add the seed to. Types: SeedSet | |
The seed to be added. Types: Seed | |
Database sequence (horizontal). Types: SequenceConcept Remarks: Only required for Chaos Chaining. | |
Query sequence (vertical). Types: SequenceConcept Remarks: Only required for Chaos Chaining. | |
The scoring scheme. Types: Simple Score Remarks: Note, only Chaos and SimpleChain require the score. | |
The maximal distance between the end point of the upper left and the begin point of the lower right Seed allowed for local chaining. Types: IntegerConcept Remarks: Note, only Chaos, SimpleChain and Merge require the distance information. | |
The window size to search for a chainable Seed. Types: IntegerConcept Remarks: Note, only Chaos requires the bandwidth information. | |
The algorithm that is used to add the new seed. Types: Local Chaining Remarks: Note that not every algorithm can be used with each type of Seed. See special signatures above. The seed is copied and then added. |
Return Values
Boolean if successfully added.
Remarks: Always true for Tag Single.
Member of
Examples
File "seeds_add_seed.cpp"
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The output is as follows:
Seed: Seed<Simple, TConfig>(4, 5, 8, 9, lower diag = -1, upper diag = -1)
Seed: Seed<Simple, TConfig>(10, 10, 15, 15, lower diag = 0, upper diag = 0)
Seed: Seed<Simple, TConfig>(14, 14, 18, 18, lower diag = 0, upper diag = 0)
Seed: Seed<Simple, TConfig>(21, 21, 24, 24, lower diag = 0, upper diag = 0)
Merge Method:
Seed: Seed<Simple, TConfig>(4, 5, 8, 9, lower diag = -1, upper diag = -1)
Seed: Seed<Simple, TConfig>(10, 10, 18, 18, lower diag = 0, upper diag = 0)
Seed: Seed<Simple, TConfig>(21, 21, 24, 24, lower diag = 0, upper diag = 0)
Chaos Method:
Seed: Seed<Simple, TConfig>(4, 5, 15, 15, lower diag = -1, upper diag = 0)
Seed: Seed<Simple, TConfig>(14, 14, 18, 18, lower diag = 0, upper diag = 0)
Seed: Seed<Simple, TConfig>(21, 21, 24, 24, lower diag = 0, upper diag = 0)
See Also
SeqAn - Sequence Analysis Library - www.seqan.de