org.strbio.net
Class PSIBlastWeb

java.lang.Object
  org.strbio.mol.lib.BlastAdapter
      org.strbio.net.BlastWeb
          org.strbio.net.PSIBlastWeb

All Implemented Interfaces:

Blast, PSIBlast

Direct Known Subclasses:

PSIBlastNCBI

public class PSIBlastWeb
extends BlastWeb
implements PSIBlast

Does a PSI-BLAST search in the NR database over the web. main web gateway.

  Version 1.1, 4/11/00 - fixed to conform to new cgi interface
  Version 1.0, 1/29/99 - adapted from PSIBlastNCBI 1.0, added
    PSIBlastMatrices interface.
  

Version:

1.1, 4/11/00

Author:

JMC

Field Summary

int	iterations How many iterations to do this for?

Fields inherited from class org.strbio.mol.lib.BlastAdapter

query

Constructor Summary

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

PSIBlastWeb(Protein p)
Initialize with a given protein.

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

Method Summary

java.lang.String	blastInitial(Printf outfile) Return a string containg initial results from the web server.
java.lang.String	blastRaw(Printf outfile) Return a string containing the raw HTML from the server.
java.lang.String	blastStepN(int step, Printf outfile) Return a string containing the html from step N.
PSIBlastMatrices	getPSIBlastMatrices() Get scoring matrix.

Methods inherited from class org.strbio.net.BlastWeb

blastAll, blastGetInitial, blastGetResult, getBaseURL, setBaseURL

Methods inherited from class org.strbio.mol.lib.BlastAdapter

blastProfile, blastProteinSet, setQuery, setQuery

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

blastAll, blastProfile, blastProteinSet, setQuery, setQuery

Field Detail

iterations

public int iterations

How many iterations to do this for?

Constructor Detail

PSIBlastWeb

public PSIBlastWeb()

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

PSIBlastWeb

public PSIBlastWeb(java.lang.String sequence)

Initialize with a given query sequence.

PSIBlastWeb

public PSIBlastWeb(Protein p)

Initialize with a given protein.

Method Detail

getPSIBlastMatrices

public PSIBlastMatrices getPSIBlastMatrices()

Get scoring matrix.

Specified by:

getPSIBlastMatrices in interface PSIBlast

blastInitial

public java.lang.String blastInitial(Printf outfile)

Return a string containg initial results from the web server.

blastStepN

public java.lang.String blastStepN(int step,
                                   Printf outfile)

Return a string containing the html from step N.

blastRaw

public java.lang.String blastRaw(Printf outfile)

Return a string containing the raw HTML from the server.

Overrides:

blastRaw in class BlastWeb