charite.christo.blast
Class Blaster_local_Wu
java.lang.Object
charite.christo.blast.AbstractBlaster
charite.christo.blast.Blaster_local_Wu
- All Implemented Interfaces:
- SequenceBlaster, Disposable, HasControlPanel, java.awt.event.ActionListener, java.util.EventListener
- Direct Known Subclasses:
- Blaster_local_NCBI
public class Blaster_local_Wu
- extends AbstractBlaster
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
Methods inherited from class charite.christo.blast.AbstractBlaster |
actionPerformed, button, cachedResultsNotOlderThanSec, cacheSK, compute, defineParameters, dispose, enableDisable, getAvailableDatabases, getBlastProgram, getControlPanel, getDatabase, getMatrix, getNumberOfAlignments, getPrgParas, getQuery, getQuerySequence, getResultXml, getSensitivity, getSharedInstance, isAAQuery, isDisposed, log, setAAQuerySequence, setDatabase, setMatrix, setNTQuerySequence, setNumberOfAlignments, setSensitivity, setSharedInstance, setUrlResultHtml, skipDatabases |
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Blaster_local_Wu
public Blaster_local_Wu()
getCommandLine
public java.lang.String getCommandLine()
computeIt
public BA computeIt()
- Specified by:
computeIt
in class AbstractBlaster
getAvailableMatrices
public java.lang.String[] getAvailableMatrices()
- Description copied from class:
AbstractBlaster
- FIXME
- Specified by:
getAvailableMatrices
in interface SequenceBlaster
- Overrides:
getAvailableMatrices
in class AbstractBlaster
getAvailableDBs
public java.lang.String[] getAvailableDBs(int opt)
- Specified by:
getAvailableDBs
in class AbstractBlaster
setShellVariableBLASTDB
public void setShellVariableBLASTDB(java.lang.String db,
java.lang.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(java.lang.String prg)
setAdditionalOptions
public void setAdditionalOptions(java.lang.String options)
'The most important classes are StrapAlign, Protein and StrapEvent.'