org.strbio.local
Class BlastClient

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

All Implemented Interfaces:

Blast

public class BlastClient
extends BlastP

Runs a local copy of blastclient. This requires that blastcl3 be in your path (it should be in /pub/share/blast/bin on cohen machines), and a network connection to www.ncbi.nlm.nih.gov.

  Version 1.1, 4/18/00 - uses blastcl3 instead of blastcl2
  Version 1.0, 1/20/99 - original version
  

Version:

1.1, 4/18/00

Author:

JMC

Field Summary

Fields inherited from class org.strbio.local.BlastP

databases, e, filter, maxN, savedBlastOutfile

Fields inherited from class org.strbio.local.BlastPAdapter

query

Fields inherited from class org.strbio.local.Program

processError, processInput, processOutput, PROGRAM_NAME

Constructor Summary

BlastClient()
Initialize with no information; you still have to call setQuery before starting Blast.

BlastClient(Protein p)
Initialize with a given protein.

BlastClient(java.lang.String sequence)
Initialize with a given query sequence.

Method Summary

protected java.lang.String	arguments() return arguments for the program.
java.lang.String	programName() What's the name of this program?

Methods inherited from class org.strbio.local.BlastP

blastAll, blastPBlastAll, setOutputFile

Methods inherited from class org.strbio.local.BlastPAdapter

blastProfile, blastProteinSet, setQuery, setQuery

Methods inherited from class org.strbio.local.Program

clean, exists, 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

Constructor Detail

BlastClient

public BlastClient()

Initialize with no information; you still have to call setQuery before starting Blast.

BlastClient

public BlastClient(java.lang.String sequence)

Initialize with a given query sequence.

BlastClient

public BlastClient(Protein p)

Initialize with a given protein.

Method Detail

programName

public java.lang.String programName()

Description copied from class: Program

What's the name of this program?

Overrides:

programName in class BlastP

arguments

protected java.lang.String arguments()

return arguments for the program.

Overrides:

arguments in class BlastP