charite.christo.strap.extensions
Class Blaster_local_Wu

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

All Implemented Interfaces:

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

Direct Known Subclasses:

Blaster_local_NCBI

public class Blaster_local_Wu
extends AbstractBlaster
implements NeedsInternet

HELP WU-BLAST can be downloaded from http://blast.wustl.edu/licensing/. The WU-BLAST directory must be added to the PATH environment variable. Further the environment variables WUBLASTMAT and WUBLASTDB must be set.

export WUBLASTMAT=/local/bioinf/wu-blast/matrix

WUBLASTDB points to the directory where the blast databases are installed. After formating a blast-database it contains files with the endings ".xpd", ".xps" and ".xpt".

export WUBLASTDB=/local/bioinf/db/wu-blast

The WUBLASTDB is also evaluated by STRAP to determine the available databases. The databases are created from multiple fasta files using the command

xdformat -p  -C x multipleFastaFile

Strap calls the Blast-program with the method Runtime#exec(String[]). A valid Blast command is for example:

wu-blastall -p blastp -d uniref50.fasta -i ~/testBlast/t.fa -b 300 -m 7

SEE_CLASS:Blaster_local_NCBI

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_Wu()

Method Summary

AbstractBlaster.Result	computeIt()
String[]	getAvailableDatabases() Names of available databases depend on the type of query (AA or NT)
String[]	getAvailableMatrices() FIXME
String	getCommandLine()
Container	getControlPanel()
void	setAdditionalOptions(String options)
void	setProgramName(String prg)
void	setShellVariableBLASTDB(String db, String extensionOfDatabaseFiles) The variable ..BLASTDB points to the directory where databases are installed.

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_Wu

public Blaster_local_Wu()

Method Detail

getCommandLine

public String getCommandLine()

computeIt

public AbstractBlaster.Result computeIt()

Specified by:

computeIt in class AbstractBlaster

getControlPanel

public Container getControlPanel()

Specified by:

getControlPanel in interface HasControlPanel

Specified by:

getControlPanel in class AbstractBlaster

getAvailableMatrices

public String[] getAvailableMatrices()

Description copied from class: AbstractBlaster

FIXME

Specified by:

getAvailableMatrices in interface SequenceBlaster

Overrides:

getAvailableMatrices in class AbstractBlaster

getAvailableDatabases

public String[] getAvailableDatabases()

Description copied from interface: SequenceBlaster

Names of available databases depend on the type of query (AA or NT)

Specified by:

getAvailableDatabases in interface SequenceBlaster

setShellVariableBLASTDB

public void setShellVariableBLASTDB(String db,
                                    String extensionOfDatabaseFiles)

The variable ..BLASTDB points to the directory where databases are installed. STRAP reads this directory to provide a List of available databases.

setProgramName

public void setProgramName(String prg)

setAdditionalOptions

public void setAdditionalOptions(String options)