org.strbio.local
Class TBlastN

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

All Implemented Interfaces:

Blast

public class TBlastN
extends BlastP

Runs a local copy of tblastn. This requires that blastall be in your path (it should be in /pub/share/blast/bin), and that you have a ~/.ncbirc similar to the following:

  [NCBI]
  Data=/pub/share/blast/bin/data

  [BLAST]
  BLASTDB=/pub/share/blast/lib
  

  Version 1.0, 10/19/01 - original version
  

Version:

1.0, 10/19/01

Author:

JMC

Field Summary

java.lang.String

databases databases to search in.

Fields inherited from class org.strbio.local.BlastP

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

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

TBlastN(Protein p)
Initialize with a given protein.

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

Method Summary

java.lang.String

programName() What's the name of this program?

Methods inherited from class org.strbio.local.BlastP

arguments, 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

Field Detail

databases

public java.lang.String databases

databases to search in. (default = nrfilt) More than 1 should be separated by spaces... but this feature does not work for now due to a Java bug!!! (can't shell out commands including the '"' character)

Constructor Detail

TBlastN

public TBlastN()

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

TBlastN

public TBlastN(java.lang.String sequence)

Initialize with a given query sequence.

TBlastN

public TBlastN(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