charite.christo.strap.extensions
Class Blaster_local_NCBI

java.lang.Object
  charite.christo.strap.extensions.AbstractBlaster
      charite.christo.strap.extensions.Blaster_local_Wu
          charite.christo.strap.extensions.Blaster_local_NCBI

All Implemented Interfaces:

CacheResult.Cacheable, ChRunnable, Disposable, HasControlPanel, NeedsInternet, SequenceBlaster, ActionListener, EventListener

Direct Known Subclasses:

Blaster_local_NCBI_gapped_PSI

public class Blaster_local_NCBI
extends Blaster_local_Wu

HELP NCBI-BLAST can be downloaded from ftp://ftp.ncbi.nih.gov/ or search GOOGLE{ ftp ncbi blast }. Download and extract ncbi.tar.gz for example in /local/bioinf. Install WIKI:csh or WIKI:tcsh if not already installed. Follow the installation instractions of ncbi/make/readme.unx.

Environment variables: The /ncbi/build/ directory which contains the blastall command must be added to the PATH environment variable. Example:

export  PATH=$PATH:/local/bioinf/ncbi/build

Further the environment variables BLASTDB must the directory where the Blast databases are installed on the HD. It is declared with a command like

export BLASTDB=/local/bioinf/blastdb/

The variable BLASTDB is evaluated by STRAP to obtain the list of available databases.
The databases are created from multiple fasta files using the command

formatdb -i  multipleFastaFile

Strap invokse Blast with a command like:

blastall -p blastp -d pdb.fasta -i ~/testBlast/t.fa -b 300 -m 7

Nested Class Summary

Nested classes/interfaces inherited from class charite.christo.strap.extensions.AbstractBlaster

AbstractBlaster.Result

Field Summary

Fields inherited from class charite.christo.strap.extensions.AbstractBlaster

isAAQuery, matrix, urlResultHtml

Fields inherited from interface charite.christo.interfaces.ChRunnable

APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, LOG, SET_ICON_IMAGE

Constructor Summary

Blaster_local_NCBI()

Method Summary

String[]

getAvailableMatrices() FIXME

Methods inherited from class charite.christo.strap.extensions.Blaster_local_Wu

computeIt, getAvailableDatabases, getCommandLine, getControlPanel, setAdditionalOptions, setProgramName, setShellVariableBLASTDB

Methods inherited from class charite.christo.strap.extensions.AbstractBlaster

actionPerformed, butViewTxt, butViewXml, compute, dispose, getBlastProgram, getCacheClass, getCacheKey, getCacheSection, getDatabase, getMatrix, getNumberOfAlignments, getQuery, getQuerySequence, getResultXml, isAAQuery, isDisposed, log, run, setAAQuerySequence, setDatabase, setMatrix, setNTQuerySequence, setNumberOfAlignments, urlResultHtml

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Blaster_local_NCBI

public Blaster_local_NCBI()

Method Detail

getAvailableMatrices

public String[] getAvailableMatrices()

Description copied from class: AbstractBlaster

FIXME

Specified by:

getAvailableMatrices in interface SequenceBlaster

Overrides:

getAvailableMatrices in class Blaster_local_Wu