org.strbio.local
Class BlastP

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

All Implemented Interfaces:

Blast

Direct Known Subclasses:

BlastClient, PSIBlastP, TBlastN

public class BlastP
extends BlastPAdapter

Runs a local copy of blastp. 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 2.2, 3/27/03 - specify max number of hits returned as maxN
  Version 2.1, 10/29/02 - turns -I T on to not strip gi numbers
  Version 2.0, 2/21/02 - allows saving of intermediate files
  Version 1.12, 3/26/1 - changed default db to nrfilt
  Version 1.11, 5/1/00 - fixed cleanup so that if it crashes due to lack
    of memory, the tmp files are left
  Version 1.1, 10/4/99 - fixed kludge in readBLAST
  Version 1.0, 1/19/99 - original version
  

Version:

2.2, 3/27/03

Author:

JMC

Field Summary

java.lang.String	databases databases to search in.
double	e Expectation value (E) (default = 10.0)
boolean	filter Filter out promiscuous input.
double	maxN Number of sequences returned (default = 250)
protected java.lang.String	savedBlastOutfile output file name to save BLAST output

Fields inherited from class org.strbio.local.BlastPAdapter

query

Fields inherited from class org.strbio.local.Program

processError, processInput, processOutput, PROGRAM_NAME

Constructor Summary

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

BlastP(Protein p)
Initialize with a given protein.

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

Method Summary

protected java.lang.String	arguments() return arguments for the program.
Profile	blastAll(Printf outfile) Return a profile containing responses to the blast query.
protected Profile	blastPBlastAll(Printf outfile) kludge to allow super.super() reference to blastAll method.
java.lang.String	programName() What's the name of this program?
void	setOutputFile(java.lang.String outfileName) set output file name to save BLAST output, or null to use a temporary file

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)

filter

public boolean filter

Filter out promiscuous input. (default = true)

e

public double e

Expectation value (E) (default = 10.0)

maxN

public double maxN

Number of sequences returned (default = 250)

savedBlastOutfile

protected java.lang.String savedBlastOutfile

output file name to save BLAST output

Constructor Detail

BlastP

public BlastP()

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

BlastP

public BlastP(java.lang.String sequence)

Initialize with a given query sequence.

BlastP

public BlastP(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 Program

arguments

protected java.lang.String arguments()

return arguments for the program.

setOutputFile

public void setOutputFile(java.lang.String outfileName)

set output file name to save BLAST output, or null to use a temporary file

blastPBlastAll

protected Profile blastPBlastAll(Printf outfile)

kludge to allow super.super() reference to blastAll method.

blastAll

public 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.