charite.christo.strap.extensions
Class MultipleAligner_SPEM

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

All Implemented Interfaces:

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

public final class MultipleAligner_SPEM
extends AbstractAligner
implements SequenceAligner

HELP SPEM aligns multiple sequences using pre-processed sequence profiles and predicted secondary structures for pairwise alignment, consistency-based scoring for refinement of the pairwise alignment and a progressive algorithm for final multiple alignment.
Installation: http://sparks.informatics.iupui.edu/.
Publication: PUBMED:16020471
Authors:Hongyi Zhou and Yaoqi Zhou

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

MultipleAligner_SPEM()

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.SequenceAligner

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

Constructor Detail

MultipleAligner_SPEM

public MultipleAligner_SPEM()

Method Detail

computeResult

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

Specified by:

computeResult in class AbstractAligner