info.bioinfweb.libralign.model.adapters

Interface SequenceDataAdapter<S,T>

Type Parameters:

S - the type of sequence object that is returned by the implementation of this interface

T - the token type used by the underlying provider

All Superinterfaces:

BasicAlignmentModelView<T>, SequenceAccess<S>

All Known Implementing Classes:

BioJava3SequenceAdapter, CharSequenceAdapter, StringAdapter

public interface SequenceDataAdapter<S,T>
extends BasicAlignmentModelView<T>, SequenceAccess<S>

Classes implementing this interface provide access to the data provided by an implementation of AlignmentModel in a different way (e.g. as a set of CharSequences or BioJava sequences).

Since:

0.1.0

Author:

Ben Stöver

Method Summary

Modifier and Type	Method and Description
S	getSubSequence(java.lang.String sequenceID, int offset, int length) Returns a view or copy of a subsequence in the underlying data source.
boolean	returnsCopies() Specifies if the instances returned by #getSequence(int) are views of the underlying data source or independent copies of the sequences.

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

getUnderlyingModel

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

getSequence

Method Detail

getSubSequence

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

Returns a view or copy of a subsequence in the underlying data source.

Parameters:

sequenceID - the ID of the sequence in the underlying AlignmentModel 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 copy or view depending on the return value of returnsCopies()

returnsCopies

boolean returnsCopies()

Specifies if the instances returned by #getSequence(int) are views of the underlying data source or independent copies of the sequences.

Returns:

true if copies are returned, false if views are returned