charite.christo.protein
Class MultiFromPairAligner

java.lang.Object
  charite.christo.protein.MultiFromPairAligner

All Implemented Interfaces:

CanBeStopped, HasControlPanel, NeedsProteins, SequenceAligner, SequenceAlignerSorting

public class MultiFromPairAligner
extends java.lang.Object
implements CanBeStopped, NeedsProteins, SequenceAlignerSorting, HasControlPanel

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.

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

MultiFromPairAligner(java.lang.Object c)

Method Summary

void	compute() The time consuming computation.
byte[][]	getAlignedSequences()
java.lang.Object[]	getClasses()
javax.swing.JComponent	getControlPanel(boolean real)
int[]	getIndicesOfSequences()
long	getOptions()
long	getPropertyFlags()
byte[][]	getSequences() Return the sequences that have been set with setSequences(String[])
static byte[]	insertGapsAtColumns(int[] insert, byte[] orig)
BA	log()
MultiFromPairAligner	set3dMethod(java.lang.Class c)
void	setIsInterrupted(boolean[] boolArraySize1)
void	setOptions(long flags) Multiple aligners are usually not limited in the number of sequences.
void	setProteins(Protein... pp)
void	setSequences(byte[]... ss)
void	stop()

Methods inherited from class java.lang.Object

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

Constructor Detail

MultiFromPairAligner

public MultiFromPairAligner(java.lang.Object c)

Method Detail

set3dMethod

public MultiFromPairAligner set3dMethod(java.lang.Class c)

getClasses

public java.lang.Object[] getClasses()

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

setProteins

public void setProteins(Protein... pp)

Specified by:

setProteins in interface NeedsProteins

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

getPropertyFlags

public long getPropertyFlags()

Specified by:

getPropertyFlags in interface SequenceAligner

getOptions

public long getOptions()

Specified by:

getOptions in interface SequenceAligner

getIndicesOfSequences

public int[] getIndicesOfSequences()

Specified by:

getIndicesOfSequences in interface SequenceAlignerSorting

log

public BA log()

getControlPanel

public javax.swing.JComponent getControlPanel(boolean real)

Specified by:

getControlPanel in interface HasControlPanel

compute

public void compute()

Description copied from interface: SequenceAligner

The time consuming computation.

Specified by:

compute in interface SequenceAligner

stop

public void stop()

Specified by:

stop in interface CanBeStopped

setIsInterrupted

public void setIsInterrupted(boolean[] boolArraySize1)

insertGapsAtColumns

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