charite.christo.strap.extensions
Class MultipleAlignerClustalW

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

All Implemented Interfaces:

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

public final class MultipleAlignerClustalW
extends AbstractAligner
implements HasPrgParas, SequenceAlignerTakesProfile, SequenceAlignerSorting, HasScore

HELP ClustalW is a widely applied program to generate multiple sequence alignments automatically.
Publication: PUBMED:18792934
Home: http://www.clustal.org/


NT-sequence: ClustalW treats the letters as nucleotides if 85% or more of the characters in the sequence are A,C,G,T,U or N. See UBIC:clustalw

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

MultipleAlignerClustalW()

Method Summary

java.io.File	computePhFile(byte[][] alignment, java.lang.String tree) option -OUTPUTTREE=nj
Superimpose3D.Result	computeResult(byte[][] seqs, Protein[] proteinsNotNeeded)
int	getMaxNumberOfProfiles()

Methods inherited from class charite.christo.strap.AbstractAligner

addProfile, cbCommutative, compute, defineParameters, dirTemp, dispose, getAlignedSequences, getControlPanel, getIndicesOfSequences, 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

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

Constructor Detail

MultipleAlignerClustalW

public MultipleAlignerClustalW()

Method Detail

computePhFile

public java.io.File computePhFile(byte[][] alignment,
                                  java.lang.String tree)

option -OUTPUTTREE=nj

computeResult

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

Specified by:

computeResult in class AbstractAligner

getMaxNumberOfProfiles

public int getMaxNumberOfProfiles()

Specified by:

getMaxNumberOfProfiles in interface SequenceAlignerTakesProfile

Overrides:

getMaxNumberOfProfiles in class AbstractAligner