charite.christo.strap.extensions
Class Blaster_ebi_ac_uk

java.lang.Object
  charite.christo.strap.extensions.AbstractBlaster
      charite.christo.strap.extensions.AbstractBlasterHTTP
          charite.christo.strap.extensions.Blaster_ebi_ac_uk

All Implemented Interfaces:

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

public class Blaster_ebi_ac_uk
extends AbstractBlasterHTTP
implements NeedsInternet

HELP Permission to use the WIKI:BLAST service at http://www.ebi.ac.uk/blast2/ was kindly granted by the EBI. The terms of use of this service can be read here http://www.ebi.ac.uk/Information/termsofuse.html.

The results are cached on HD. To override cached results deactivate the cache-check-box or delete the respective cache files in STRING:CacheResult#dir()

This class uses the EBI service. Advantage over local installation: Nothing needs to be installed by the user. Disadvantages: Slower than a local Blast installation, High network traffic.
If a large number of sequences should be processed, or if a customized database should be used, then consider to install Blast locally instead, instead.

Nested Class Summary

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

AbstractBlaster.Result

Field Summary

static String[]	DATABASES
static String[]	DATABASES_AA
static String[]	DATABASES_NT
static String[]	MATRICES_AA
static String[]	MATRICES_NT

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_ebi_ac_uk()

Method Summary

AbstractBlaster.Result	computeIt()
String[]	getAvailableDatabases() Names of available databases depend on the type of query (AA or NT)
String[]	getAvailableMatrices() FIXME
static String[]	uniprotIdForSequence(String seq, int minScore)

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

getControlPanel, toString

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, wait, wait, wait

Field Detail

DATABASES_AA

public static final String[] DATABASES_AA

DATABASES_NT

public static final String[] DATABASES_NT

DATABASES

public static final String[] DATABASES

MATRICES_AA

public static final String[] MATRICES_AA

MATRICES_NT

public static final String[] MATRICES_NT

Constructor Detail

Blaster_ebi_ac_uk

public Blaster_ebi_ac_uk()

Method Detail

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

getAvailableMatrices

public String[] getAvailableMatrices()

Description copied from class: AbstractBlaster

FIXME

Specified by:

getAvailableMatrices in interface SequenceBlaster

Overrides:

getAvailableMatrices in class AbstractBlaster

computeIt

public AbstractBlaster.Result computeIt()

Specified by:

computeIt in class AbstractBlaster

uniprotIdForSequence

public static String[] uniprotIdForSequence(String seq,
                                            int minScore)