charite.christo.strap.extensions
Class MultipleAlignerMafft

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

All Implemented Interfaces:

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

public class MultipleAlignerMafft
extends AbstractAligner
implements HasPrgParas, SequenceAlignerSorting

HELP Mafft is an alignment program published in PUBMED:15661851

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

MultipleAlignerMafft()

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.HasPrgParas

defineParameters, getPrgParas

Methods inherited from interface charite.christo.NeedsSharedInstance

getSharedInstance, setSharedInstance

Methods inherited from interface charite.christo.protein.SequenceAlignerSorting

getIndicesOfSequences

Methods inherited from interface charite.christo.protein.SequenceAligner

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

Constructor Detail

MultipleAlignerMafft

public MultipleAlignerMafft()

Method Detail

computeResult

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

Specified by:

computeResult in class AbstractAligner