info.bioinfweb.libralign.model.adapters

Class CharSequenceAdapter<T>

java.lang.Object

info.bioinfweb.libralign.model.adapters.AbstractBasicAlignmentModelView<T>

info.bioinfweb.libralign.model.adapters.CharSequenceAdapter<T>

Type Parameters:

T - the token type used by the underlying provider

All Implemented Interfaces:

SequenceDataAdapter<java.lang.CharSequence,T>, BasicAlignmentModelView<T>, SequenceAccess<java.lang.CharSequence>

Direct Known Subclasses:

StringAdapter

public class CharSequenceAdapter<T>
extends AbstractBasicAlignmentModelView<T>
implements SequenceDataAdapter<java.lang.CharSequence,T>

Adapter class that allows to access the contents of an implementation of AlignmentModel as a set of CharSequences or Strings.

Since:

0.1.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
CharSequenceAdapter(AlignmentModel<T> underlyingProvider, boolean cutLongRepresentations) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
java.lang.CharSequence	getSequence(java.lang.String sequenceID) Returns an implementation of SingleCharSequenceAdapter<T> that acts as a view to the sequence with the specified ID.
java.lang.CharSequence	getSubSequence(java.lang.String sequenceID, int offset, int length) Returns an implementation of SingleCharSequenceAdapter<T> that acts as a view to a subsequence of the sequence with the specified ID.
boolean	isCutLongRepresentations() Returns true if the first character of string representations (of tokens in the underlying sequence data provider) that are longer than one character shall be used for translations or false if an InvalidUnderlyingTokenException shall be thrown if such a token occurs.
boolean	returnsCopies() Returns false since this class always returns views of the underlying data source.

Methods inherited from class info.bioinfweb.libralign.model.adapters.AbstractBasicAlignmentModelView

getUnderlyingModel, setUnderlyingModel

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.BasicAlignmentModelView

getUnderlyingModel

Constructor Detail

CharSequenceAdapter

public CharSequenceAdapter(AlignmentModel<T> underlyingProvider,
                           boolean cutLongRepresentations)

Creates a new instance of this class.

Parameters:

provider - the sequence data provider that contains the sequences to be viewed

cutLongRepresentations - Specify true here if the first character of string representations (of tokens in the underlying sequence data provider) that are longer than one character shall be used for translations or false if an InvalidUnderlyingTokenException shall be thrown if such a token occurs.

Method Detail

isCutLongRepresentations

public boolean isCutLongRepresentations()

Returns true if the first character of string representations (of tokens in the underlying sequence data provider) that are longer than one character shall be used for translations or false if an InvalidUnderlyingTokenException shall be thrown if such a token occurs.

Returns:

the value that was specified for cutLongRepresentations in the constructor

getSequence

public java.lang.CharSequence getSequence(java.lang.String sequenceID)

Returns an implementation of SingleCharSequenceAdapter<T> that acts as a view to the sequence with the specified ID.

Specified by:

getSequence in interface SequenceAccess<java.lang.CharSequence>

Parameters:

sequenceID - the ID of the sequence to be viewed

Returns:

a sequence as a CharSequence

getSubSequence

public java.lang.CharSequence getSubSequence(java.lang.String sequenceID,
                                             int offset,
                                             int length)

Returns an implementation of SingleCharSequenceAdapter<T> that acts as a view to a subsequence of the sequence with the specified ID.

Specified by:

getSubSequence in interface SequenceDataAdapter<java.lang.CharSequence,T>

Parameters:

sequenceID - the ID of the sequence to be viewed

offset - the start index of the subsequence to be viewed (The first token has the index 0.)

length - the length of the subsequence to be viewed

Returns:

a sequence as a CharSequence

returnsCopies

public boolean returnsCopies()

Returns false since this class always returns views of the underlying data source.

Specified by:

returnsCopies in interface SequenceDataAdapter<java.lang.CharSequence,T>

Returns:

false