charite.christo.strap.extensions
Class MultipleAlignerAmap

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

All Implemented Interfaces:

CanBeStopped, Disposable, HasControlPanel, HasNativeExec, HasPrgParas, HasPropertyMap, IsEnabled, NeedsSharedInstance, SequenceAligner, SequenceAlignerSorting

public final class MultipleAlignerAmap
extends AbstractAligner
implements SequenceAlignerSorting, HasPrgParas

HELP Author: A.S. Schwartz, E.W. Myers and L. Pachter
WIKI:AMAP

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.HasPrgParas

FURTHER_PARAMETERS

Fields inherited from interface charite.christo.Disposable

NONE

Fields inherited from interface charite.christo.CanBeStopped

vALIGNMENTS

Constructor Summary

MultipleAlignerAmap()

Method Summary

Superimpose3D.Result

computeResult(byte[][] seqs, Protein[] proteinsNotNeeded)

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.SequenceAlignerSorting

getIndicesOfSequences

Methods inherited from interface charite.christo.protein.SequenceAligner

compute, getAlignedSequences, getOptions, getPropertyFlags, getSequences, setOptions, setSequences

Methods inherited from interface charite.christo.HasPrgParas

defineParameters, getPrgParas

Methods inherited from interface charite.christo.NeedsSharedInstance

getSharedInstance, setSharedInstance

Constructor Detail

MultipleAlignerAmap

public MultipleAlignerAmap()

Method Detail

computeResult

public Superimpose3D.Result computeResult(byte[][] seqs,
                                          Protein[] proteinsNotNeeded)

Specified by:

computeResult in class AbstractAligner