charite.christo.strap.extensions
Class Aligner3D_Smolign

java.lang.Object
  charite.christo.strap.AbstractAligner
      charite.christo.strap.extensions.Aligner3D_Smolign

All Implemented Interfaces:

CanBeStopped, Disposable, HasControlPanel, HasNativeExec, HasPropertyMap, IsEnabled, NeedsProteins, SequenceAligner, SequenceAligner3D

public class Aligner3D_Smolign
extends AbstractAligner
implements SequenceAligner3D

Author: Ivaylo Ilinkin and Ravi Janardan Publication: PUBMED:20122279

Field Summary

Fields inherited from class charite.christo.strap.AbstractAligner

MFA_FILE, PFX_DPKG, RPLC_WIN_DOT_EXE

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

Fields inherited from interface charite.christo.Disposable

NONE

Fields inherited from interface charite.christo.CanBeStopped

vALIGNMENTS

Constructor Summary

Aligner3D_Smolign()

Method Summary

Superimpose3D.Result	computeResult(byte[][] sequ, Protein[] pp)
static void	main(java.lang.String[] argv)

Methods inherited from class charite.christo.strap.AbstractAligner

addProfile, cbCommutative, compute, defineParameters, dirTemp, dispose, getAlignedSequences, getControlPanel, getIndicesOfSequences, getMaxNumberOfProfiles, getNativeExec, getOptions, getPrgParas, getProfiles, getPropertyFlags, getPropertyMap, getProteins, getResult, getRmsd, getScore, getSequences, getSharedInstance, initX, insertWhereNoCoordinates, isEnabled, mfaInFile, parse, pdbFile, setOptions, setPropertyFlags, setProteins, setSequences, setSharedInstance, stop

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, getPropertyFlags, getSequences, setOptions, setSequences

Methods inherited from interface charite.christo.protein.NeedsProteins

setProteins

Constructor Detail

Aligner3D_Smolign

public Aligner3D_Smolign()

Method Detail

computeResult

public Superimpose3D.Result computeResult(byte[][] sequ,
                                          Protein[] pp)

Specified by:

computeResult in class AbstractAligner

main

public static void main(java.lang.String[] argv)
                 throws java.lang.Exception

Throws:

java.lang.Exception