info.bioinfweb.libralign.model.adapters

Class AbstractSingleSequenceDataAdapter<T>

java.lang.Object

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

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

Type Parameters:

T -

All Implemented Interfaces:

SingleSequenceDataAdapter<T>, BasicAlignmentModelView<T>

Direct Known Subclasses:

SingleBioJava3SequenceAdapter, SingleCharSequenceAdapter

public class AbstractSingleSequenceDataAdapter<T>
extends AbstractBasicAlignmentModelView<T>
implements SingleSequenceDataAdapter<T>

Implements basic functionality of SingleSequenceDataAdapter. Specifically the sequence ID of the viewed sequence, the index of its first viewed token and the length of the viewed part are stored. Additionally protected setter methods are offered.

Since:

0.1.0

Author:

Ben Stöver

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractSingleSequenceDataAdapter(AlignmentModel<T> underlyingModel, java.lang.String sequenceID) Creates a new instance of this class which views the whole length of a sequence in the underlying data source.
protected	AbstractSingleSequenceDataAdapter(AlignmentModel<T> underlyingModel, java.lang.String sequenceID, int offset, int length) Creates a new instance of this class.

Method Summary

Modifier and Type	Method and Description
int	getLength() Returns the length of this character sequence.
int	getOffset() Returns the index the first character in this sequence corresponds to in the original sequence in the underlying sequence data provider.
java.lang.String	getSequenceID() The ID of the viewed sequence in the underlying sequence data provider.
protected void	setLength(int length)
protected void	setOffset(int offset)
protected void	setSequenceID(java.lang.String sequenceID)

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

AbstractSingleSequenceDataAdapter

protected AbstractSingleSequenceDataAdapter(AlignmentModel<T> underlyingModel,
                                            java.lang.String sequenceID,
                                            int offset,
                                            int length)

Creates a new instance of this class.

Parameters:

underlyingModel - the alignment model that contains the sequence to be viewed

sequenceID - the ID used in provider 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

AbstractSingleSequenceDataAdapter

protected AbstractSingleSequenceDataAdapter(AlignmentModel<T> underlyingModel,
                                            java.lang.String sequenceID)

Creates a new instance of this class which views the whole length of a sequence in the underlying data source.

Parameters:

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

sequenceID - the ID used in provider of the sequence to be viewed

Method Detail

getSequenceID

public java.lang.String getSequenceID()

Description copied from interface: SingleSequenceDataAdapter

The ID of the viewed sequence in the underlying sequence data provider.

Specified by:

getSequenceID in interface SingleSequenceDataAdapter<T>

Returns:

the sequence ID

setSequenceID

protected void setSequenceID(java.lang.String sequenceID)

getOffset

public int getOffset()

Description copied from interface: SingleSequenceDataAdapter

Returns the index the first character in this sequence corresponds to in the original sequence in the underlying sequence data provider.

Specified by:

getOffset in interface SingleSequenceDataAdapter<T>

Returns:

a value >= 0

setOffset

protected void setOffset(int offset)

getLength

public int getLength()

Returns the length of this character sequence. Note that the return value might change if the length of the viewed sequence changes.

Specified by:

getLength in interface SingleSequenceDataAdapter<T>

Returns:

the number of characters in this sequence

setLength

protected void setLength(int length)