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Class Summary |
| BlastCommand |
This implementation wraps around Blast. |
| BlastContext |
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| BlastGeneProduct |
Blast gene products, as predicted with genescan from a dna sequence. |
| BlastResult |
Encapsulates different versions of BlastOutput. |
| ExtractAC |
Extracts the accession numbers from the definition line of a BLAST output. |
| ExtractAcIdentity |
Extracts the accession numbers from the definition line of a BLAST output. |
| ExtractDefLine |
Extracts the definition line from the first hit of a BLAST output. |
| HitSummary |
Stores the query sequence definition (queryId), the length of the query sequence (queryLen),
the definition of the hit (subjId), the long definition of the hit (defLine),
the percentage similarity between the query sequence and the hit HSP (percentId, between 0 and 1, not 0 and 100),
the e-value of the hit HSP (eValue), and the length of the HSP (hitLength). |
| MegablastHSIterator |
Iterates through a megablast -D 3 output file, returns HitSummaries. |
| seqinfo |
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| XMLBlastHSIterator |
Iterates through an XML BLAST output file, returns HitSummaries. |