org.strbio.net
Class PSIBlastNCBI

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

All Implemented Interfaces:

Blast, PSIBlast

public class PSIBlastNCBI
extends PSIBlastWeb

Does a PSI-BLAST search in the NR database at NCBI, using the main web gateway.

  Version 1.1, 1/29/99 - moved most stuff to PSIBlastWeb
  Version 1.0, 1/20/99 - original version
  

Version:

1.1, 1/29/99

Author:

JMC

Field Summary

Fields inherited from class org.strbio.net.PSIBlastWeb

iterations

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

query

Constructor Summary

PSIBlastNCBI()

PSIBlastNCBI(Protein p)
Initialize with a given protein.

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

Method Summary

Methods inherited from class org.strbio.net.PSIBlastWeb

blastInitial, blastRaw, blastStepN, getPSIBlastMatrices

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

Constructor Detail

PSIBlastNCBI

public PSIBlastNCBI()

PSIBlastNCBI

public PSIBlastNCBI(java.lang.String sequence)

Initialize with a given query sequence.

PSIBlastNCBI

public PSIBlastNCBI(Protein p)

Initialize with a given protein.