info.bioinfweb.libralign.model.adapters

Interface SingleSequenceDataAdapter<T>

Type Parameters:

T - the token type used by the underlying alignment model

All Superinterfaces:

BasicAlignmentModelView<T>

All Known Implementing Classes:

AbstractSingleSequenceDataAdapter, SingleBioJava3SequenceAdapter, SingleCharSequenceAdapter

public interface SingleSequenceDataAdapter<T>
extends BasicAlignmentModelView<T>

Adapter classes providing views of (sub-) sequences of single rows of an implementation of AlignmentModel should implement this interface.

Since:

0.1.0

Author:

Ben Stöver

Method Summary

Modifier and Type	Method and Description
int	getLength() Returns the number of tokens (sequence elements) that make up this view.
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.

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

getUnderlyingModel

Method Detail

getSequenceID

java.lang.String getSequenceID()

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

Returns:

the sequence ID

getOffset

int getOffset()

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

Returns:

a value >= 0

getLength

int getLength()

Returns the number of tokens (sequence elements) that make up this view. Depending on the implementation this might differ from the length of the viewed (sub-) sequence (e.g. if a nucleotide sequence would be viewed as an amino acid sequence).

Returns:

a value >= 0