charite.christo.strap.extensions
Class ClustalW_3D

java.lang.Object
  charite.christo.strap.extensions.ClustalW_3D

All Implemented Interfaces:

CanBeStopped, HasControlPanel, HasScore, Progress, SequenceAligner, SequenceAlignerSorting, NeedsProteins

public class ClustalW_3D
extends Object
implements CanBeStopped, Progress, NeedsProteins, SequenceAlignerSorting, HasScore, HasControlPanel

HELP This is a combination of ClustalW and TM_align. If there are two or more 3D structures, they are superimposed with TM_align (PUBMED:15849316). Subsequently, clustalW is called with all sequences taking the 3D alignment as a profile.

Field Summary

Fields inherited from interface charite.christo.interfaces.CanBeStopped

vALIGNMENTS

Fields inherited from interface charite.christo.interfaces.SequenceAligner

OPTION_USE_SECONDARY_STRUCTURE

Constructor Summary

ClustalW_3D()

Method Summary

void	compute() The time consuming computation.
byte[][]	getAlignedSequences()
Container	getControlPanel()
int[]	getIndicesOfSequences()
int	getMaxNumberOfSequences() Multiple aligners are usually not limited in the number of sequences.
int	getProgress()
int	getProgressMaximum()
float	getScore()
byte[][]	getSequences() Return the sequences that have been set with setSequences(String[])
boolean	isLocal() Local alignment procedures do not align the entire sequences.
void	setOptions(long flags)
void	setProteins(StrapProtein... proteins)
void	setSequences(byte[]... ss)
void	stop()

Methods inherited from class java.lang.Object

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

Constructor Detail

ClustalW_3D

public ClustalW_3D()

Method Detail

setOptions

public void setOptions(long flags)

Specified by:

setOptions in interface SequenceAligner

getControlPanel

public Container getControlPanel()

Specified by:

getControlPanel in interface HasControlPanel

getScore

public float getScore()

Specified by:

getScore in interface HasScore

stop

public void stop()

Specified by:

stop in interface CanBeStopped

compute

public void compute()

Description copied from interface: SequenceAligner

The time consuming computation.

Specified by:

compute in interface SequenceAligner

getProgressMaximum

public final int getProgressMaximum()

Specified by:

getProgressMaximum in interface Progress

getProgress

public final int getProgress()

Specified by:

getProgress in interface Progress

setProteins

public void setProteins(StrapProtein... proteins)

Specified by:

setProteins in interface NeedsProteins

getMaxNumberOfSequences

public int getMaxNumberOfSequences()

Description copied from interface: SequenceAligner

Multiple aligners are usually not limited in the number of sequences. Pair aligners should return "2". See JAVADOC:charite.christo.strap.extensions.MultiFromPairAligner

Specified by:

getMaxNumberOfSequences in interface SequenceAligner

isLocal

public boolean isLocal()

Description copied from interface: SequenceAligner

Local alignment procedures do not align the entire sequences. They identify sequence regions which match best.

Specified by:

isLocal in interface SequenceAligner

getIndicesOfSequences

public int[] getIndicesOfSequences()

Specified by:

getIndicesOfSequences in interface SequenceAlignerSorting

getSequences

public byte[][] getSequences()

Description copied from interface: SequenceAligner

Return the sequences that have been set with setSequences(String[])

Specified by:

getSequences in interface SequenceAligner

getAlignedSequences

public byte[][] getAlignedSequences()

Specified by:

getAlignedSequences in interface SequenceAligner

setSequences

public void setSequences(byte[]... ss)

Specified by:

setSequences in interface SequenceAligner