info.bioinfweb.libralign.model.implementations.decorate

Class DNAAlignmentModelDecorator<T,U>

java.lang.Object

info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel<T>

info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator<T,U>

info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator<T,U>

info.bioinfweb.libralign.model.implementations.decorate.DNAAlignmentModelDecorator<T,U>

Type Parameters:

T - the type of sequence elements (tokens) the implementing decorator works with

U - the type of sequence elements (tokens) the underlying model works with

All Implemented Interfaces:

AlignmentModel<T>, AlignmentModelView<T,U>, BasicAlignmentModelView<U>

public class DNAAlignmentModelDecorator<T,U>
extends AbstractTokenReplacementAlignmentModelDecorator<T,U>

Shows the underlying nucleotide data source as a DNA sequence, i.e. replaces all uracil tokens by thymine tokens.

Since:

0.4.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
DNAAlignmentModelDecorator(TokenSet<T> tokenSet, AlignmentModel<U> underlyingModel)

Method Summary

Modifier and Type	Method and Description
protected U	convertDecoratedToken(java.lang.String viewedSequenceID, int viewedIndex, T decoratedToken) Inherited classes should perform the token translation from a viewed to an underlying token by implementing this method.
protected T	convertUnderlyingToken(java.lang.String underlyingSequenceID, int underlyingIndex, U underlyingToken) Inherited classes should perform the token translation from an underlying to a viewed token by implementing this method.
static DNAAlignmentModelDecorator<java.lang.Character,java.lang.Character>	newCharacterInstance(AlignmentModel<java.lang.Character> underlyingModel)

Methods inherited from class info.bioinfweb.libralign.model.implementations.decorate.AbstractTokenReplacementAlignmentModelDecorator

appendToken, appendTokens, convertDecoratedTokens, convertTokenChangeEvent, convertUnderlyingTokens, getChangeListeners, getMaxSequenceLength, getSequenceLength, getTokenAt, getWriteType, insertTokenAt, insertTokensAt, isTokensReadOnly, removeTokenAt, removeTokensAt, renameSequence, setTokenAt, setTokensAt

Methods inherited from class info.bioinfweb.libralign.model.implementations.decorate.AbstractAlignmentModelDecorator

addSequence, addSequence, containsSequence, convertDecoratedSequenceID, convertDecoratedTokenIndex, convertSequenceChangeEvent, convertSequenceRenamedEvent, convertUnderlyingSequenceID, convertUnderlyingTokenIndex, getSequenceCount, getTokenSet, getUnderlyingModel, isSequencesReadOnly, removeSequence, sequenceIDIterator, sequenceIDsByName, sequenceNameByID, setTokenSet, setUnderlyingModel

Methods inherited from class info.bioinfweb.libralign.model.implementations.AbstractAlignmentModel

fireAfterSequenceChange, fireAfterSequenceRenamed, fireAfterTokenChange, getID, getLabel, setID, setLabel

Methods inherited from class java.lang.Object

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

Methods inherited from interface info.bioinfweb.libralign.model.AlignmentModel

getID, getLabel, setID, setLabel

Constructor Detail

DNAAlignmentModelDecorator

public DNAAlignmentModelDecorator(TokenSet<T> tokenSet,
                                  AlignmentModel<U> underlyingModel)

Method Detail

newCharacterInstance

public static DNAAlignmentModelDecorator<java.lang.Character,java.lang.Character> newCharacterInstance(AlignmentModel<java.lang.Character> underlyingModel)

convertUnderlyingToken

protected T convertUnderlyingToken(java.lang.String underlyingSequenceID,
                                   int underlyingIndex,
                                   U underlyingToken)

Description copied from class: AbstractTokenReplacementAlignmentModelDecorator

Inherited classes should perform the token translation from an underlying to a viewed token by implementing this method.

Specified by:

convertUnderlyingToken in class AbstractTokenReplacementAlignmentModelDecorator<T,U>

Parameters:

underlyingSequenceID - the ID of the sequence in the underlying model containing the token to be converted

underlyingIndex - the column index of the token to be converted in the underlying model

underlyingToken - the token stored in (or shown by) the underlying provider

Returns:

the token that shall be shown instead

convertDecoratedToken

protected U convertDecoratedToken(java.lang.String viewedSequenceID,
                                  int viewedIndex,
                                  T decoratedToken)

Description copied from class: AbstractTokenReplacementAlignmentModelDecorator

Inherited classes should perform the token translation from a viewed to an underlying token by implementing this method.

Specified by:

convertDecoratedToken in class AbstractTokenReplacementAlignmentModelDecorator<T,U>

Parameters:

viewedSequenceID - the ID of the sequence in this decorator containing the token to be converted

viewedIndex - the column index of the token to be converted in this view (Note that this index may be behind current end of the sequence, of this method is used to elongate a sequence.)

decoratedToken - the token shown in the view instance

Returns:

the token to be stored in (or shown by) the underlying provider