info.bioinfweb.libralign.model.adapters

Class StringAdapter<T>

java.lang.Object

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

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

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

Type Parameters:

T - the token type of the underlying data source

All Implemented Interfaces:

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

public class StringAdapter<T>
extends CharSequenceAdapter<T>

Returns the sequences contained in the underlying data source as strings. Note that the returned string sequences are copies of the data, whereas CharSequenceAdapter returns views. Therefore CharSequenceAdapter should be used instead if possible for large sequences to save memory.

Since:

0.1.0

Author:

Ben Stöver

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
java.lang.String	getSequence(java.lang.String sequenceID) Returns a string copy of the sequence with the specified ID in the underlying data source.
java.lang.String	getSubSequence(java.lang.String sequenceID, int offset, int length) Returns a string copy of a subsequence of the sequence with the specified ID in the underlying data source.
boolean	returnsCopies() Returns true since this class always returns copies of the data in the underlying data source.

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

isCutLongRepresentations

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

StringAdapter

public StringAdapter(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

getSequence

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

Returns a string copy of the sequence with the specified ID in the underlying data source.

Specified by:

getSequence in interface SequenceAccess<java.lang.CharSequence>

Overrides:

getSequence in class CharSequenceAdapter<T>

Parameters:

sequenceID - the ID of the sequence to be viewed

Returns:

a string object

getSubSequence

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

Returns a string copy of a subsequence of the sequence with the specified ID in the underlying data source.

Specified by:

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

Overrides:

getSubSequence in class CharSequenceAdapter<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 string object

returnsCopies

public boolean returnsCopies()

Returns true since this class always returns copies of the data in the underlying data source.

Specified by:

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

Overrides:

returnsCopies in class CharSequenceAdapter<T>

Returns:

true