charite.christo.strap.extensions
Class Superimpose_GangstaPlus

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

All Implemented Interfaces:

CanBeStopped, Disposable, HasControlPanel, HasNativeExec, HasPropertyMap, HasScore, IsEnabled, NeedsProteins, Superimpose3D

public class Superimpose_GangstaPlus
extends AbstractAligner
implements HasScore, Superimpose3D

HELP GangstaPlus*
Authors: Aysam Guerler, Bjoern Kolbeck, Connie Wang, Patrick May, Thomas Steinke, Tobais Schmidt-Goenner, Group Leader: Ernst-Walter Knapp
Publication: PUBMED:18583523 PUBMED:17118190

Nested Class Summary

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

Superimpose3D.Result

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.Superimpose3D

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

Fields inherited from interface charite.christo.Disposable

NONE

Fields inherited from interface charite.christo.CanBeStopped

vALIGNMENTS

Constructor Summary

Superimpose_GangstaPlus()

Method Summary

Superimpose3D.Result

computeResult(byte[][] ssNotNeeded, Protein[] proteins)

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.HasScore

getScore

Methods inherited from interface charite.christo.protein.Superimpose3D

compute, getOptions, getProteins, getResult, setOptions

Methods inherited from interface charite.christo.protein.NeedsProteins

setProteins

Constructor Detail

Superimpose_GangstaPlus

public Superimpose_GangstaPlus()

Method Detail

computeResult

public Superimpose3D.Result computeResult(byte[][] ssNotNeeded,
                                          Protein[] proteins)

Specified by:

computeResult in class AbstractAligner