charite.christo.strap.extensions
Class PairAlignerNeoBioPROXY

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

All Implemented Interfaces:

HasPropertyMap, HasScore, SequenceAligner

public class PairAlignerNeoBioPROXY
extends AbstractAlignerProxy
implements SequenceAligner, HasScore

HELP Home: http://neobio.sourceforge.net/
Depending on the settings it produces local or global sequence alignments.
Written in Java

Field Summary

static java.lang.String	GLOBAL_CROCHEMORELANDAUZIVUKELSON
static java.lang.String	GLOBAL_NEEDLEMANWUNSCH
static java.lang.String	LOCAL_CROCHEMORELANDAUZIVUKELSON
static java.lang.String	LOCAL_SMITHWATERMAN
static java.lang.String	PARA_ALGORITHM
static java.lang.String	PARA_GAP
static java.lang.String	PARA_MATCH
static java.lang.String	PARA_MISMATCH

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

PairAlignerNeoBioPROXY()

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.HasScore

getScore

Field Detail

PARA_ALGORITHM

public static final java.lang.String PARA_ALGORITHM

See Also:

Constant Field Values

PARA_MATCH

public static final java.lang.String PARA_MATCH

See Also:

Constant Field Values

PARA_MISMATCH

public static final java.lang.String PARA_MISMATCH

See Also:

Constant Field Values

PARA_GAP

public static final java.lang.String PARA_GAP

See Also:

Constant Field Values

GLOBAL_NEEDLEMANWUNSCH

public static final java.lang.String GLOBAL_NEEDLEMANWUNSCH

See Also:

Constant Field Values

LOCAL_SMITHWATERMAN

public static final java.lang.String LOCAL_SMITHWATERMAN

See Also:

Constant Field Values

GLOBAL_CROCHEMORELANDAUZIVUKELSON

public static final java.lang.String GLOBAL_CROCHEMORELANDAUZIVUKELSON

See Also:

Constant Field Values

LOCAL_CROCHEMORELANDAUZIVUKELSON

public static final java.lang.String LOCAL_CROCHEMORELANDAUZIVUKELSON

See Also:

Constant Field Values

Constructor Detail

PairAlignerNeoBioPROXY

public PairAlignerNeoBioPROXY()

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