Package edu.mssm.crover.tools.blast

Provides an API to access BLAST from Java.

See:
          Description

Interface Summary
HitSummaryIterator  
 

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.
TabularBlastOutput Storage class representing the tabular form of a BLAST hit.
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



Copyright © 2004 Weill Cornell Medical College. All Rights Reserved.