charite.christo.strap.extensions
Class PairAlignerJAligner

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

All Implemented Interfaces:

CanBeStopped, Disposable, HasControlPanel, HasNativeExec, HasPropertyMap, HasScore, IsEnabled, SequenceAligner

public class PairAlignerJAligner
extends AbstractAligner
implements SequenceAligner, HasScore

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

PairAlignerJAligner()

Method Summary

Superimpose3D.Result

computeResult(byte[][] ss, Protein[] ppNotNeeded)

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.HasScore

getScore

Constructor Detail

PairAlignerJAligner

public PairAlignerJAligner()

Method Detail

computeResult

public Superimpose3D.Result computeResult(byte[][] ss,
                                          Protein[] ppNotNeeded)

Specified by:

computeResult in class AbstractAligner