charite.christo.strap.extensions
Class PairAlignerJAlignerPROXY

java.lang.Object
  charite.christo.AbstractProxy
      charite.christo.strap.AbstractAlignerProxy
          charite.christo.strap.extensions.PairAlignerJAlignerPROXY

All Implemented Interfaces:

HasPropertyMap, HasScore, HasSharedControlPanel, NeedsSharedInstance, SequenceAligner

public class PairAlignerJAlignerPROXY
extends AbstractAlignerProxy
implements SequenceAligner, HasSharedControlPanel, HasScore

HELP JAligner: Java-implementation of the Smith Waterman algorithm for local sequence alignments.
Author: Ahmed Moustafa.
Home: http://jaligner.sourceforge.net/

Field Summary

Fields inherited from class charite.christo.AbstractProxy

ACTIVATION, ADAPTERS_JAR, BIOJAVA_3D, COMMONS_COLLECTIONS, GLUGEN, JCOMMON, JOGL, LOG4J, PFX_INSTALLED, TRY_BOOT_CLASSLOADER

Fields inherited from interface charite.christo.protein.SequenceAligner

OPTION_CHECK_PERFECT_MATCH, OPTION_NOT_TO_SECURITY_LIST, OPTION_USE_SECONDARY_STRUCTURE, PROPERTY_LOCAL_ALIGNMENT, PROPERTY_ONLY_TWO_SEQUENCES, SCORE_FOR_PERFECT_MATCH

Constructor Summary

PairAlignerJAlignerPROXY()

Method Summary

long	getPropertyFlags()
java.lang.String	getRequiredJars()

Methods inherited from class charite.christo.strap.AbstractAlignerProxy

compute, getAlignedSequences, getOptions, getProteins, getResult, getSequences, setOptions, setProteins, setSequences

Methods inherited from class charite.christo.AbstractProxy

dispose, disposeProxy, getControlPanel, getPrgParas, getPropertyMap, getProxy, getScore, getSharedControlPanel, getSharedInstance, interpret, jarFile, jarsContainingNativeLibraries, proxyObject, proxyObjectRun, remoteURLs, setOptions, setSharedInstance, usrShareJava

Methods inherited from class java.lang.Object

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

Methods inherited from interface charite.christo.protein.SequenceAligner

compute, getAlignedSequences, getOptions, getSequences, setOptions, setSequences

Methods inherited from interface charite.christo.HasSharedControlPanel

getSharedControlPanel

Methods inherited from interface charite.christo.NeedsSharedInstance

getSharedInstance, setSharedInstance

Methods inherited from interface charite.christo.HasScore

getScore

Constructor Detail

PairAlignerJAlignerPROXY

public PairAlignerJAlignerPROXY()

Method Detail

getRequiredJars

public java.lang.String getRequiredJars()

Specified by:

getRequiredJars in class AbstractProxy

getPropertyFlags

public final long getPropertyFlags()

Specified by:

getPropertyFlags in interface SequenceAligner