info.bioinfweb.libralign.model.utils.indextranslation

Class RandomAccessIndexTranslator<T>

java.lang.Object

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

info.bioinfweb.libralign.model.utils.indextranslation.RandomAccessIndexTranslator<T>

All Implemented Interfaces:

IndexTranslator<T>

public class RandomAccessIndexTranslator<T>
extends AbstractIndexTranslator<T,RandomAccessIndexTranslator.IndexTranslations>

Instance of this tool class allow fast translation between aligned and unaligned indices of tokens in an AlignmentModel. A set of tokens to be considered as gaps can be defined using the gapTokens constructor parameter.

In contrast to SequentialAccessIndexTranslator this class stores the mapping for all positions of all sequences to allow fast random access, while SequentialAccessIndexTranslator calculates the mapping in each call with a runtime proportional to the distance between the indices used in two subsequent calls. Therefore this implementation is faster for random access but uses more memory.

Since:

0.5.0

Author:

Ben Stöver

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	RandomAccessIndexTranslator.IndexTranslations

Constructor Summary

Constructors

Constructor and Description
RandomAccessIndexTranslator(AlignmentModel<T> model) Creates a new instance of this class using a HashSet containing the gap token specified by the token set of model.
RandomAccessIndexTranslator(AlignmentModel<T> model, java.util.Set<T> gapTokens)

Method Summary

Modifier and Type	Method and Description
protected RandomAccessIndexTranslator.IndexTranslations	createSequenceData(java.lang.String sequenceID)
int	getAlignedIndex(java.lang.String sequenceID, int unalignedIndex) Returns the column in the alignment, the specified token is contained in
IndexRelation	getUnalignedIndex(java.lang.String sequenceID, int alignedIndex) Returns the index of the sequence token at the specified alignment column.
int	getUnalignedLength(java.lang.String sequenceID)

Methods inherited from class info.bioinfweb.libralign.model.utils.indextranslation.AbstractIndexTranslator

finalize, getGapTokens, getModel, getSequenceData

Methods inherited from class java.lang.Object

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

Constructor Detail

RandomAccessIndexTranslator

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

RandomAccessIndexTranslator

public RandomAccessIndexTranslator(AlignmentModel<T> model)

Creates a new instance of this class using a HashSet containing the gap token specified by the token set of model. Additional gap tokens can be added using AbstractIndexTranslator.getGapTokens() later on.

Parameters:

model - the alignment model to calculate ungapped indices in

Method Detail

createSequenceData

protected RandomAccessIndexTranslator.IndexTranslations createSequenceData(java.lang.String sequenceID)

Specified by:

createSequenceData in class AbstractIndexTranslator<T,RandomAccessIndexTranslator.IndexTranslations>

getUnalignedIndex

public 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>

Specified by:

getUnalignedIndex in class AbstractIndexTranslator<T,RandomAccessIndexTranslator.IndexTranslations>

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 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>

Specified by:

getAlignedIndex in class AbstractIndexTranslator<T,RandomAccessIndexTranslator.IndexTranslations>

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

getUnalignedLength

public int getUnalignedLength(java.lang.String sequenceID)