org.strbio.local
Class PSIBlastP2

java.lang.Object
  org.strbio.local.Program
      org.strbio.local.BlastPAdapter
          org.strbio.local.BlastP
              org.strbio.local.PSIBlastP
                  org.strbio.local.PSIBlastP2

All Implemented Interfaces:

Blast, PSIBlast

public class PSIBlastP2
extends PSIBlastP
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 text checkpoint or non-cp file
  Version 1.1, 8/6/1 - fixed number of rounds to 1 on 2nd search.
  Version 1.0, 4/21/00 - original version
  

Version:

2.2, 3/27/03

Author:

JMC

Field Summary

java.lang.String	databases2 databases to search in.
boolean	keepAllResults Keep the results from the first search as well as the second?
protected java.lang.String	savedBlastOutfile2 output file name to save BLAST output from 2nd search

Fields inherited from class org.strbio.local.PSIBlastP

checkpointName, includeThreshold, loadCheckpoint, loadCheckpointName, pbm, rounds, savedBlastCheckpoint, smithWaterman, 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

PSIBlastP2()
Initialize with no information; you still have to call setQuery before starting Blast.

PSIBlastP2(Protein p)
Initialize with a given protein.

PSIBlastP2(java.lang.String sequence)
Initialize with a given query sequence.

Method Summary

protected java.lang.String	arguments() return the correct arguments, depending on whether this is the 1st or 2nd run.
protected java.lang.String	arguments2() return arguments for the program, the second time it's run.
Profile	blastAll(Printf outfile) Blast, and get the checkpoint info.
void	setOutputFile2(java.lang.String outfileName) set output file name to save BLAST output from 2nd search, or null to use a temporary file

Methods inherited from class org.strbio.local.PSIBlastP

getPSIBlastMatrices, programName, setCheckpointFile, setMatrixFile, setPSIBlastMatrices

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.PSIBlast

getPSIBlastMatrices

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

blastProfile, blastProteinSet, setQuery, setQuery

Field Detail

databases2

public java.lang.String databases2

databases to search in. (default = pdbaa) 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). The original "databases" variable is used to construct the matrix.

keepAllResults

public boolean keepAllResults

Keep the results from the first search as well as the second?

savedBlastOutfile2

protected java.lang.String savedBlastOutfile2

output file name to save BLAST output from 2nd search

Constructor Detail

PSIBlastP2

public PSIBlastP2()

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

PSIBlastP2

public PSIBlastP2(java.lang.String sequence)

Initialize with a given query sequence.

PSIBlastP2

public PSIBlastP2(Protein p)

Initialize with a given protein.

Method Detail

arguments2

protected java.lang.String arguments2()

return arguments for the program, the second time it's run.

arguments

protected java.lang.String arguments()

return the correct arguments, depending on whether this is the 1st or 2nd run.

Overrides:

arguments in class PSIBlastP

setOutputFile2

public void setOutputFile2(java.lang.String outfileName)

set output file name to save BLAST output from 2nd search, or null to use a temporary file

blastAll

public Profile blastAll(Printf outfile)

Blast, and get the checkpoint info.

Specified by:

blastAll in interface Blast

Overrides:

blastAll in class PSIBlastP