Package edu.mssm.crover.tools.blast

Provides an API to access BLAST from Java.

See:
Description

Class Summary

BlastCommand	This implementation wraps around Blast.
BlastContext
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.
XMLBlastHSIterator	Iterates through an XML BLAST output file, returns HitSummaries.

Exception Summary

DatabaseNotFound
WrongFileFormatException	Gives details of which file format the program was expecting to read

Package edu.mssm.crover.tools.blast Description

Provides an API to access BLAST from Java.

Package Specification

See the sub-packages for a list of available tools.

Related Documentation