org.strbio.local
Class PSIBlastP

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

All Implemented Interfaces:

Blast, PSIBlast

Direct Known Subclasses:

PSIBlastP2

public class PSIBlastP
extends BlastP
implements PSIBlast

Runs a local copy of psiblast. This requires that blastpgp 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 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 - can save checkpoint and text matrix files
  Version 1.2, 8/1/01 - reflects new defaults for blastpgp 2.2.1.
    Does S-W alignments.
  Version 1.1, 7/13/00 - can load and save checkpoints
  Version 1.01, 1/29/99 - had to change the name because it
    conflicts with the interface name PSIBlast
  Version 1.0, 1/20/99 - original version
  

Version:

2.2, 3/27/03

Author:

JMC

Field Summary

protected java.lang.String	checkpointName
double	includeThreshold Expectation value (E) threshold for including values in the score matrix model.
protected boolean	loadCheckpoint load checkpoint?
protected java.lang.String	loadCheckpointName
protected PSIBlastMatrices	pbm
int	rounds How many rounds to do?
protected java.lang.String	savedBlastCheckpoint output file name to save BLAST checkpoint
boolean	smithWaterman Do Smith-Waterman alignments?
protected java.lang.String	textCheckpointName

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

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

PSIBlastP(Protein p)
Initialize with a given protein.

PSIBlastP(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) Blast, and get the checkpoint info.
PSIBlastMatrices	getPSIBlastMatrices() Get scoring matrix.
java.lang.String	programName() What's the name of this program?
void	setCheckpointFile(java.lang.String cpName) set output file name to save BLAST checkpoint, or null to use a temporary file
void	setMatrixFile(java.lang.String matName) set output file name to save BLAST matrix (text), or null to not save it
void	setPSIBlastMatrices(PSIBlastMatrices p) Get scoring matrix.

Methods inherited from class org.strbio.local.BlastP

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

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

blastProfile, blastProteinSet, setQuery, setQuery

Field Detail

includeThreshold

public double includeThreshold

Expectation value (E) threshold for including values in the score matrix model. Default is 0.005.

rounds

public int rounds

How many rounds to do? Default is 10. Quits if it converges earlier, though.

smithWaterman

public boolean smithWaterman

Do Smith-Waterman alignments?

loadCheckpoint

protected boolean loadCheckpoint

load checkpoint?

pbm

protected PSIBlastMatrices pbm

checkpointName

protected java.lang.String checkpointName

loadCheckpointName

protected java.lang.String loadCheckpointName

textCheckpointName

protected java.lang.String textCheckpointName

savedBlastCheckpoint

protected java.lang.String savedBlastCheckpoint

output file name to save BLAST checkpoint

Constructor Detail

PSIBlastP

public PSIBlastP()

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

PSIBlastP

public PSIBlastP(java.lang.String sequence)

Initialize with a given query sequence.

PSIBlastP

public PSIBlastP(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

getPSIBlastMatrices

public PSIBlastMatrices getPSIBlastMatrices()

Get scoring matrix.

Specified by:

getPSIBlastMatrices in interface PSIBlast

setPSIBlastMatrices

public void setPSIBlastMatrices(PSIBlastMatrices p)

Get scoring matrix.

arguments

protected java.lang.String arguments()

return arguments for the program.

Overrides:

arguments in class BlastP

setCheckpointFile

public void setCheckpointFile(java.lang.String cpName)

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

setMatrixFile

public void setMatrixFile(java.lang.String matName)

set output file name to save BLAST matrix (text), or null to not save it

blastAll

public Profile blastAll(Printf outfile)

Blast, and get the checkpoint info.

Specified by:

blastAll in interface Blast

Overrides:

blastAll in class BlastP