charite.christo.strap.extensions
Class Superimpose_CEPROXY

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

All Implemented Interfaces:

HasPropertyMap, HasScore, NeedsProteins, SequenceAligner, SequenceAligner3D, Superimpose3D

public class Superimpose_CEPROXY
extends AbstractAlignerProxy
implements HasScore, Superimpose3D, SequenceAligner3D

HELP CE/CL ported to Java by Andreas Prlic

Nested Class Summary

Nested classes/interfaces inherited from interface charite.christo.protein.Superimpose3D

Superimpose3D.Result

Field Summary

static int

MIN_CALPHA

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.Superimpose3D

COLUMN_SEQUENCE, NO_BYTE, PARSE_ALIGNMENT, PARSE_MATRIX, PARSE_MSA_START_S, PARSE_SCORE, PRINT_HUMAN_READABLE

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

Superimpose_CEPROXY()

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.HasScore

getScore

Methods inherited from interface charite.christo.protein.Superimpose3D

compute, getOptions, getProteins, getResult, setOptions

Methods inherited from interface charite.christo.protein.SequenceAligner

compute, getAlignedSequences, getOptions, getSequences, setOptions, setSequences

Methods inherited from interface charite.christo.protein.NeedsProteins

setProteins

Field Detail

MIN_CALPHA

public static final int MIN_CALPHA

See Also:

Constant Field Values

Constructor Detail

Superimpose_CEPROXY

public Superimpose_CEPROXY()

Method Detail

getPropertyFlags

public long getPropertyFlags()

Specified by:

getPropertyFlags in interface SequenceAligner

getRequiredJars

public java.lang.String getRequiredJars()

Specified by:

getRequiredJars in class AbstractProxy