charite.christo.strap.extensions
Class MultipleAlignerT_Coffee

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

All Implemented Interfaces:

CanBeStopped, Disposable, HasControlPanel, HasNativeExec, HasPrgParas, HasPropertyMap, HasScore, IsEnabled, NeedsSharedInstance, NeedsProteins, SequenceAligner, SequenceAlignerSorting, SequenceAlignerTakesProfile

public final class MultipleAlignerT_Coffee
extends AbstractAligner
implements HasPrgParas, SequenceAlignerTakesProfile, SequenceAlignerSorting, HasScore, NeedsProteins

HELP
Publication: PUBMED:10964570
Author: Cedric Notredame

Field Summary

Fields inherited from class charite.christo.strap.AbstractAligner

MFA_FILE, PFX_DPKG, RPLC_WIN_DOT_EXE

Fields inherited from interface charite.christo.HasPrgParas

FURTHER_PARAMETERS

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

MultipleAlignerT_Coffee()

Method Summary

Superimpose3D.Result	computeResult(byte[][] seq, Protein[] proteins)
void	setSequencesWithoutFixed(byte[][] ss)

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.HasPrgParas

defineParameters, getPrgParas

Methods inherited from interface charite.christo.NeedsSharedInstance

getSharedInstance, setSharedInstance

Methods inherited from interface charite.christo.protein.SequenceAlignerTakesProfile

addProfile, getMaxNumberOfProfiles

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.HasScore

getScore

Methods inherited from interface charite.christo.protein.NeedsProteins

setProteins

Constructor Detail

MultipleAlignerT_Coffee

public MultipleAlignerT_Coffee()

Method Detail

computeResult

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

Specified by:

computeResult in class AbstractAligner

setSequencesWithoutFixed

public void setSequencesWithoutFixed(byte[][] ss)