charite.christo.strap.extensions
Class Superimpose_LajollaProtein

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

All Implemented Interfaces:

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

public final class Superimpose_LajollaProtein
extends AbstractAligner
implements HasScore, Superimpose3D

HELP
Depending on the settings it produces local or global sequence alignments.
Written in Java

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_LajollaProtein()

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_LajollaProtein

public Superimpose_LajollaProtein()

Method Detail

computeResult

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

Specified by:

computeResult in class AbstractAligner