charite.christo.strap
Class Aligner3D

java.lang.Object
  charite.christo.strap.Aligner3D

All Implemented Interfaces:

CanBeStopped, HasControlPanel, HasSharedControlPanel, NeedsSharedInstance, NeedsProteins, SequenceAligner, SequenceAlignerSorting, java.awt.event.ActionListener, java.util.EventListener

public class Aligner3D
extends java.lang.Object
implements CanBeStopped, NeedsProteins, SequenceAlignerSorting, HasControlPanel, HasSharedControlPanel, java.awt.event.ActionListener

HELP Combining sequence alignment methods and 3D-superposition. If at least for two of the sequences to be aligned have 3D-coordinates and not all sequences have attached 3D-structures, this class combines a sequence alignment method such as ClustalW or T_coffee with a 3D-alignment method such as TM_align or CE. Otherwise only the standard sequence alignment method or 3D-method is run.
Default setting: ClustalW + CE
Program line options to set t_coffee and TM_align: -alignerP=t_coffee -a3d=TM_align

Field Summary

Fields inherited from interface charite.christo.CanBeStopped

vALIGNMENTS

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

Constructor Summary

Aligner3D()

Method Summary

void	actionPerformed(java.awt.event.ActionEvent ev)
void	compute() The time consuming computation.
byte[][]	getAlignedSequences()
javax.swing.JComponent	getControlPanel(boolean real)
int[]	getIndicesOfSequences()
long	getOptions()
long	getPropertyFlags()
float	getScore()
byte[][]	getSequences() Return the sequences that have been set with setSequences(String[])
javax.swing.JComponent	getSharedControlPanel()
java.lang.Object	getSharedInstance()
Aligner3D	setClass3D(java.lang.Class c)
void	setOptions(long flags) Multiple aligners are usually not limited in the number of sequences.
void	setProteins(Protein... proteins)
void	setSequences(byte[]... ss)
void	setSharedInstance(java.lang.Object o)
void	stop()

Methods inherited from class java.lang.Object

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

Constructor Detail

Aligner3D

public Aligner3D()

Method Detail

setOptions

public void setOptions(long flags)

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:

setOptions in interface SequenceAligner

getOptions

public long getOptions()

Specified by:

getOptions in interface SequenceAligner

getPropertyFlags

public long getPropertyFlags()

Specified by:

getPropertyFlags in interface SequenceAligner

getControlPanel

public javax.swing.JComponent getControlPanel(boolean real)

Specified by:

getControlPanel in interface HasControlPanel

getScore

public float getScore()

stop

public void stop()

Specified by:

stop in interface CanBeStopped

setClass3D

public Aligner3D setClass3D(java.lang.Class c)

compute

public void compute()

Description copied from interface: SequenceAligner

The time consuming computation.

Specified by:

compute in interface SequenceAligner

actionPerformed

public void actionPerformed(java.awt.event.ActionEvent ev)

Specified by:

actionPerformed in interface java.awt.event.ActionListener

setProteins

public void setProteins(Protein... proteins)

Specified by:

setProteins in interface NeedsProteins

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

getSharedControlPanel

public javax.swing.JComponent getSharedControlPanel()

Specified by:

getSharedControlPanel in interface HasSharedControlPanel

getSharedInstance

public java.lang.Object getSharedInstance()

Specified by:

getSharedInstance in interface NeedsSharedInstance

setSharedInstance

public void setSharedInstance(java.lang.Object o)

Specified by:

setSharedInstance in interface NeedsSharedInstance