charite.christo.strap.extensions
Class Superimpose3D_TM_align

java.lang.Object
  charite.christo.AbstractExecutable
      charite.christo.AbstractExecutable_Cached
          charite.christo.strap.AbstractSuperpositionExecutable
              charite.christo.strap.extensions.Superimpose3D_TM_align

All Implemented Interfaces:

CacheResult.Cacheable, CanBeStopped, ChRunnable, Disposable, HasControlPanel, HasScore, HasSharedControlPanel, IsEnabled, NeedsSharedInstance, SequenceAligner, Superimpose3D, NeedsProteins, SequenceAligner3D

public class Superimpose3D_TM_align
extends AbstractSuperpositionExecutable
implements HasScore, HasControlPanel, SequenceAligner3D

HELP
Publication: PUBMED:15849316
Home page: HOME_PAGE:Superimpose3D_TM_align
Authors: Yang Zhang and Jeffrey Skolnick

Nested Class Summary

Nested classes/interfaces inherited from interface charite.christo.interfaces.Superimpose3D

Superimpose3D.Result

Field Summary

Fields inherited from class charite.christo.strap.AbstractSuperpositionExecutable

mobileResidues, referenceResidues

Fields inherited from class charite.christo.AbstractExecutable

DEFAULT_BINARY

Fields inherited from interface charite.christo.interfaces.SequenceAligner

OPTION_USE_SECONDARY_STRUCTURE

Fields inherited from interface charite.christo.interfaces.Superimpose3D

NO_BYTE

Fields inherited from interface charite.christo.interfaces.CanBeStopped

vALIGNMENTS

Fields inherited from interface charite.christo.interfaces.ChRunnable

APPEND, DOWNLOAD_FINISHED, INTERPRET_LINE, LOG, SET_ICON_IMAGE

Constructor Summary

Superimpose3D_TM_align()

Method Summary

ByteArray	computeOutput()
Container	getSharedControlPanel() A Container containing GUI controles that are independent of a certain instance.
Superimpose3D.Result	parseSuperpositionOutput(ByteArray output)
static Superimpose3D.Result	superimpose(Protein pM, Protein pR)

Methods inherited from class charite.christo.strap.AbstractSuperpositionExecutable

compute, getAlignedSequences, getCacheKey, getCacheSection, getControlPanel, getFile, getMaxNumberOfSequences, getMobileProtein, getOptions, getProtein, getReferenceProtein, getResult, getRmsd, getScore, getSelectedMobileResidues, getSelectedReferenceResidues, getSequences, isEnabled, isLocal, parseOutput, sayComputing, selectMobileResidues, selectReferenceResidues, setIsCommutative, setMobileProtein, setOptions, setProteins, setProteinWriterOptions, setReferenceProtein, setSequences

Methods inherited from class charite.christo.AbstractExecutable_Cached

getCacheClass, setUseCache

Methods inherited from class charite.christo.AbstractExecutable

checkForUpdates, dirBinaries, dirTmp, dispose, exec, execNZ, failedToLaunch, fileExecutable, fileIn, fileOut, getName, getOptionPanel, getOptionsAsStringArray, getSharedInstance, getStderr, getStdout, iniT, installBioPerl, installPackage, isBioPerlInstalled, isPerlInstalled, isStopped, msgInstallCompilers, perlCommand, run, setBinaryPackageURLs, setCommandLineOptions, setName, setSharedInstance, setSourceInstallationScript, setSourcePackageURLs, stop, toString

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface charite.christo.interfaces.HasScore

getScore

Methods inherited from interface charite.christo.interfaces.HasControlPanel

getControlPanel

Methods inherited from interface charite.christo.interfaces.SequenceAligner

compute, getAlignedSequences, getMaxNumberOfSequences, getSequences, isLocal, setOptions, setSequences

Methods inherited from interface charite.christo.strap.interfaces.NeedsProteins

setProteins

Methods inherited from interface charite.christo.CacheResult.Cacheable

getCacheClass

Constructor Detail

Superimpose3D_TM_align

public Superimpose3D_TM_align()

Method Detail

getSharedControlPanel

public Container getSharedControlPanel()

Description copied from class: AbstractExecutable

A Container containing GUI controles that are independent of a certain instance.

Specified by:

getSharedControlPanel in interface HasSharedControlPanel

Overrides:

getSharedControlPanel in class AbstractExecutable

computeOutput

public ByteArray computeOutput()

Specified by:

computeOutput in class AbstractExecutable_Cached

parseSuperpositionOutput

public Superimpose3D.Result parseSuperpositionOutput(ByteArray output)

Specified by:

parseSuperpositionOutput in class AbstractSuperpositionExecutable

superimpose

public static Superimpose3D.Result superimpose(Protein pM,
                                               Protein pR)