org.strbio.net
Class BlastNCBI2

java.lang.Object
  org.strbio.mol.lib.BlastAdapter
      org.strbio.net.BlastWeb
          org.strbio.net.BlastNCBI
              org.strbio.net.BlastNCBI2

All Implemented Interfaces:

Blast

public class BlastNCBI2
extends BlastNCBI

Does a BlastP search in the NR database at NCBI, using the "stable" web gateway. Note: the old BlastNCBI2 class is now BlastNCBI21, and still works.

  Version 1.0, 1/19/99 - original version
  

Version:

1.0, 1/19/99

Author:

JMC

Field Summary

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

query

Constructor Summary

BlastNCBI2()
Initialize with no information; you still have to call setQuery before starting Blast.

BlastNCBI2(Protein p)
Initialize with a given protein.

BlastNCBI2(java.lang.String sequence)
Initialize with a given query sequence.

Method Summary

java.lang.String	blastRaw(Printf outfile) Return a stream containing the raw HTML from the NCBI server.
protected int	contentLength() Content length depends on the number of characters in the sequence, and what database you're searching.

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

Constructor Detail

BlastNCBI2

public BlastNCBI2()

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

BlastNCBI2

public BlastNCBI2(java.lang.String sequence)

Initialize with a given query sequence.

BlastNCBI2

public BlastNCBI2(Protein p)

Initialize with a given protein.

Method Detail

contentLength

protected int contentLength()

Content length depends on the number of characters in the sequence, and what database you're searching.

blastRaw

public java.lang.String blastRaw(Printf outfile)

Return a stream containing the raw HTML from the NCBI server.

Overrides:

blastRaw in class BlastWeb