info.bioinfweb.libralign.model.utils.indextranslation

Class AbstractIndexTranslator<T,D>

java.lang.Object

info.bioinfweb.libralign.model.utils.indextranslation.AbstractIndexTranslator<T,D>

All Implemented Interfaces:

IndexTranslator<T>

Direct Known Subclasses:

RandomAccessIndexTranslator

public abstract class AbstractIndexTranslator<T,D>
extends java.lang.Object
implements IndexTranslator<T>

Constructor Summary

Constructors

Constructor and Description
AbstractIndexTranslator(AlignmentModel<T> model, java.util.Set<T> gapTokens)

Method Summary

Modifier and Type	Method and Description
protected abstract D	createSequenceData(java.lang.String sequenceID)
protected void	finalize()
abstract int	getAlignedIndex(java.lang.String sequenceID, int unalignedIndex) Returns the column in the alignment, the specified token is contained in
java.util.Set<T>	getGapTokens() Returns the set of gap tokens used by this instance.
AlignmentModel<T>	getModel() Returns the alignment model this instance works on.
protected D	getSequenceData(java.lang.String sequenceID)
abstract IndexRelation	getUnalignedIndex(java.lang.String sequenceID, int alignedIndex) Returns the index of the sequence token at the specified alignment column.

Methods inherited from class java.lang.Object

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

Methods inherited from interface info.bioinfweb.libralign.model.utils.indextranslation.IndexTranslator

getUnalignedLength

Constructor Detail

AbstractIndexTranslator

public AbstractIndexTranslator(AlignmentModel<T> model,
                               java.util.Set<T> gapTokens)

Method Detail

getModel

public AlignmentModel<T> getModel()

Description copied from interface: IndexTranslator

Returns the alignment model this instance works on.

Specified by:

getModel in interface IndexTranslator<T>

Returns:

the associated alignment model

getGapTokens

public java.util.Set<T> getGapTokens()

Description copied from interface: IndexTranslator

Returns the set of gap tokens used by this instance.

Specified by:

getGapTokens in interface IndexTranslator<T>

Returns:

a set of tokens to be considered as gaps

getUnalignedIndex

public abstract IndexRelation getUnalignedIndex(java.lang.String sequenceID,
                                                int alignedIndex)

Description copied from interface: IndexTranslator

Returns the index of the sequence token at the specified alignment column.

Specified by:

getUnalignedIndex in interface IndexTranslator<T>

Parameters:

sequenceID - the ID of the sequence which contains the token to be located

alignedIndex - the column index in the alignment

Returns:

an index relation object describing the position of respective sequence tokens (If the specified alignment columns contains a gap, the IndexRelation.getCorresponding() will return IndexRelation.GAP, and IndexRelation.getBefore() and {IndexRelation#getAfter()} the positions of the neighboring tokens, if present. If the specified column contains a token, IndexRelation.getCorresponding() will return the index of that token in the unaligned sequence.)

getAlignedIndex

public abstract int getAlignedIndex(java.lang.String sequenceID,
                                    int unalignedIndex)

Description copied from interface: IndexTranslator

Returns the column in the alignment, the specified token is contained in

Specified by:

getAlignedIndex in interface IndexTranslator<T>

Parameters:

sequenceID - the ID of the sequence which contains the token to be located

unalignedIndex - the index of the token in the unaligned sequence

Returns:

the column index in the alignment

createSequenceData

protected abstract D createSequenceData(java.lang.String sequenceID)

getSequenceData

protected D getSequenceData(java.lang.String sequenceID)

finalize

protected void finalize()
                 throws java.lang.Throwable

Overrides:

finalize in class java.lang.Object

Throws:

java.lang.Throwable