org.strbio.mol.lib
Interface Blast

All Known Subinterfaces:

PSIBlast

All Known Implementing Classes:

BlastAdapter, BlastClient, BlastNCBI, BlastNCBI2, BlastP, BlastPAdapter, BlastWeb, PSIBlastNCBI, PSIBlastP, PSIBlastP2, PSIBlastWeb, TBlastN

public interface Blast

Interface for common Blast-related routines.

  Version 1.01, 1/21/99 - added outfile requirement
  Version 1.0, 1/19/99 - original version
  

Version:

1.01, 1/21/99

Author:

JMC

Method Summary

Profile	blastAll(Printf outfile) Return a profile containing responses to the blast query.
Profile	blastProfile(Printf outfile) Return a profile containing responses to the blast query.
ProteinSet	blastProteinSet(Printf outfile) Returns a set of proteins in response to a blast query.
void	setQuery(Protein p) Sets a query protein.
void	setQuery(java.lang.String sequence)

Method Detail

setQuery

void setQuery(Protein p)

Sets a query protein.

setQuery

void setQuery(java.lang.String sequence)

blastAll

Profile blastAll(Printf outfile)

Return a profile containing responses to the blast query. The first sequence (and the consensus) will be the query protein. Redundant sequences are not removed.

blastProfile

Profile blastProfile(Printf outfile)

Return a profile containing responses to the blast query. The first sequence (and the consensus) will be the query protein. Redundant sequences are removed.

blastProteinSet

ProteinSet blastProteinSet(Printf outfile)

Returns a set of proteins in response to a blast query. The first protein in the set will be the query protein. Redundant sequences are removed.