org.strbio.net
Class BlastWeb

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

All Implemented Interfaces:

Blast

Direct Known Subclasses:

BlastNCBI, PSIBlastWeb

public class BlastWeb
extends BlastAdapter

Does a BlastP search in the NR database at over the web.

  Version 1.3, 3/13/1 - uses IO.getURLData
  Version 1.2, 4/11/00 - fixed to conform to new cgi interface
  Version 1.1, 10/4/99 - fixed to adapt to new readBLAST interface
  Version 1.0, 1/29/99 - adapted from BlastNCBI 1.11
  

Version:

1.3, 3/13/1

Author:

JMC

Field Summary

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

query

Constructor Summary

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

BlastWeb(Protein p)
Initialize with a given protein.

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

Method Summary

Profile	blastAll(Printf outfile) Returns a profile with all responses to the query.
java.lang.String	blastGetInitial(Printf outfile) Query the blast server for the queue data.
java.lang.String	blastGetResult(Printf outfile) Query the blast server for the queue data.
java.lang.String	blastRaw(Printf outfile) Return a string containing the raw HTML from the server.
java.lang.String	getBaseURL() Returns the current base url.
void	setBaseURL(java.lang.String url) Sets the base url; i.e. to "http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST/"

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

Constructor Detail

BlastWeb

public BlastWeb()

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

BlastWeb

public BlastWeb(java.lang.String sequence)

Initialize with a given query sequence.

BlastWeb

public BlastWeb(Protein p)

Initialize with a given protein.

Method Detail

getBaseURL

public java.lang.String getBaseURL()

Returns the current base url.

setBaseURL

public void setBaseURL(java.lang.String url)

Sets the base url; i.e. to "http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST/"

blastGetInitial

public java.lang.String blastGetInitial(Printf outfile)

Query the blast server for the queue data.

blastGetResult

public java.lang.String blastGetResult(Printf outfile)

Query the blast server for the queue data.

blastRaw

public java.lang.String blastRaw(Printf outfile)

Return a string containing the raw HTML from the server.

blastAll

public Profile blastAll(Printf outfile)

Returns a profile with all responses to the query. The first sequence (and the consensus) will be the query protein. Redundant sequences are not removed