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java.lang.Object charite.christo.AbstractProxy charite.christo.strap.AbstractAlignerProxy charite.christo.strap.extensions.PairAlignerJAlignerPROXY
public class PairAlignerJAlignerPROXY
HELP
JAligner: Java-implementation of the Smith Waterman algorithm for local sequence alignments.
Author: Ahmed Moustafa.
Home: http://jaligner.sourceforge.net/
Field Summary |
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Fields inherited from class charite.christo.AbstractProxy |
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ACTIVATION, ADAPTERS_JAR, BIOJAVA_3D, COMMONS_COLLECTIONS, GLUGEN, JCOMMON, JOGL, LOG4J, PFX_INSTALLED, TRY_BOOT_CLASSLOADER |
Fields inherited from interface charite.christo.protein.SequenceAligner |
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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 | |
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PairAlignerJAlignerPROXY()
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Method Summary | |
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long |
getPropertyFlags()
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java.lang.String |
getRequiredJars()
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Methods inherited from class charite.christo.strap.AbstractAlignerProxy |
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compute, getAlignedSequences, getOptions, getProteins, getResult, getSequences, setOptions, setProteins, setSequences |
Methods inherited from class charite.christo.AbstractProxy |
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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 |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface charite.christo.protein.SequenceAligner |
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compute, getAlignedSequences, getOptions, getSequences, setOptions, setSequences |
Methods inherited from interface charite.christo.HasSharedControlPanel |
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getSharedControlPanel |
Methods inherited from interface charite.christo.NeedsSharedInstance |
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getSharedInstance, setSharedInstance |
Methods inherited from interface charite.christo.HasScore |
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getScore |
Constructor Detail |
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public PairAlignerJAlignerPROXY()
Method Detail |
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public java.lang.String getRequiredJars()
getRequiredJars
in class AbstractProxy
public final long getPropertyFlags()
getPropertyFlags
in interface SequenceAligner
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