org.strbio.mol.lib
Class BlastAdapter

java.lang.Object
  org.strbio.mol.lib.BlastAdapter

All Implemented Interfaces:

Blast

Direct Known Subclasses:

BlastWeb

public abstract class BlastAdapter
extends java.lang.Object
implements Blast

Adapter class to implement the routines in Blast.

  Version 1.1, 11/02/01 - don't remove redundant sequences!
  Version 1.01, 1/21/99 - added outfile option
  Version 1.0, 1/19/99 - original version
  

Version:

1.1, 11/02/01

Author:

JMC

Field Summary

protected Protein

query

Constructor Summary

BlastAdapter()

Method Summary

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) Sets a query sequence (just protein for now).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.strbio.mol.lib.Blast

blastAll

Field Detail

query

protected Protein query

Constructor Detail

BlastAdapter

public BlastAdapter()

Method Detail

setQuery

public void setQuery(Protein p)

Sets a query protein.

Specified by:

setQuery in interface Blast

setQuery

public void setQuery(java.lang.String sequence)

Sets a query sequence (just protein for now).

Specified by:

setQuery in interface Blast

blastProfile

public Profile blastProfile(Printf outfile)

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

Specified by:

blastProfile in interface Blast

blastProteinSet

public 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.

Specified by:

blastProteinSet in interface Blast