org.strbio.local
Class BlastPAdapter

java.lang.Object
  org.strbio.local.Program
      org.strbio.local.BlastPAdapter

All Implemented Interfaces:

Blast

Direct Known Subclasses:

BlastP

public abstract class BlastPAdapter
extends Program
implements Blast

This is an adapter class for Blast which should extend both Program and BlastAdapter. Instead, the routines from BlastAdapter are copied here... be sure to change both!

  Version 1.1, 11/02/01 - don't remove redundant seqs
  Version 1.0, 1/19/99 - original version
  

Version:

1.0, 1/19/99

Author:

JMC

Field Summary

protected Protein

query

Fields inherited from class org.strbio.local.Program

processError, processInput, processOutput, PROGRAM_NAME

Constructor Summary

BlastPAdapter()

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 org.strbio.local.Program

clean, exists, programName, run, runBackground, runSilent, setError, setInput, setOutput, setProgramName

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

BlastPAdapter

public BlastPAdapter()

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