charite.christo.strap
Class MultiFromPairAligner

java.lang.Object
  charite.christo.strap.MultiFromPairAligner

All Implemented Interfaces:

CanBeStopped, HasControlPanel, HasSharedControlPanel, NeedsSharedInstance, Progress, SequenceAligner, SequenceAlignerSorting, NeedsProteins

public class MultiFromPairAligner
extends Object
implements Progress, CanBeStopped, NeedsProteins, SequenceAlignerSorting, HasControlPanel, HasSharedControlPanel, NeedsSharedInstance

This class converts SequenceAligner for two proteins into one for many proteins. The utility is used to produce multiple sequence alignments with classes that can align only two proteins.

Nested Class Summary

static class

MultiFromPairAligner.CE_Protein

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

MultiFromPairAligner(Object c)

Method Summary

void	compute() The time consuming computation.
byte[][]	getAlignedSequences()
Class	getClazz()
Container	getControlPanel()
int[]	getIndicesOfSequences()
int	getMaxNumberOfSequences() Multiple aligners are usually not limited in the number of sequences.
int	getProgress()
int	getProgressMaximum()
byte[][]	getSequences() Return the sequences that have been set with setSequences(String[])
Container	getSharedControlPanel()
Object	getSharedInstance()
static byte[]	insertGapsAtColumns(int[] insert, byte[] orig)
boolean	isLocal() Local alignment procedures do not align the entire sequences.
void	log(Object... oo)
void	setOptions(long flags)
void	setProteins(StrapProtein... pp)
void	setSequences(byte[]... ss)
void	setSharedInstance(Object shared)
void	stop()
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

MultiFromPairAligner

public MultiFromPairAligner(Object c)

Method Detail

setSharedInstance

public void setSharedInstance(Object shared)

Specified by:

setSharedInstance in interface NeedsSharedInstance

getSharedInstance

public Object getSharedInstance()

Specified by:

getSharedInstance in interface NeedsSharedInstance

setProteins

public void setProteins(StrapProtein... pp)

Specified by:

setProteins in interface NeedsProteins

log

public void log(Object... oo)

setOptions

public void setOptions(long flags)

Specified by:

setOptions in interface SequenceAligner

stop

public void stop()

Specified by:

stop in interface CanBeStopped

getControlPanel

public Container getControlPanel()

Specified by:

getControlPanel in interface HasControlPanel

getSharedControlPanel

public Container getSharedControlPanel()

Specified by:

getSharedControlPanel in interface HasSharedControlPanel

getClazz

public Class getClazz()

compute

public void compute()

Description copied from interface: SequenceAligner

The time consuming computation.

Specified by:

compute in interface SequenceAligner

getIndicesOfSequences

public int[] getIndicesOfSequences()

Specified by:

getIndicesOfSequences in interface SequenceAlignerSorting

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

toString

public String toString()

Overrides:

toString in class Object

getProgressMaximum

public final int getProgressMaximum()

Specified by:

getProgressMaximum in interface Progress

getProgress

public final int getProgress()

Specified by:

getProgress in interface Progress

insertGapsAtColumns

public static byte[] insertGapsAtColumns(int[] insert,
                                         byte[] orig)

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