info.bioinfweb.libralign.model

Interface SequenceAccess<S>

Type Parameters:

S - the class of the sequence objects representing a row in the alignment

All Known Subinterfaces:

SequenceAccessAlignmentModel<S,T>, SequenceDataAdapter<S,T>

All Known Implementing Classes:

AbstractUnmodifyableAlignmentModel, BioJava3SequenceAdapter, BioJava3SequenceAlignmentModel, CharSequenceAdapter, CharSequenceAlignmentModel, StringAdapter

public interface SequenceAccess<S>

Implementations of AlignmentModel or SequenceDataAdapter that provide access to a sequence object representing a row in the alignment should implement this interface.

This interface can be considered as the overlap between SequenceAccessAlignmentModel and SequenceDataAdapter, but could also be implemented by classes not implementing one of these interfaces.

Since:

0.1.0

Author:

Ben Stöver

Method Summary

Modifier and Type	Method and Description
S	getSequence(java.lang.String sequenceID) Returns the sequence object with the specified ID.

Method Detail

getSequence

S getSequence(java.lang.String sequenceID)

Returns the sequence object with the specified ID.

If the implementing class also implements SequenceDataAdapter the returned object can be a view or copy of a sequence in the underlying data source depending in the return value of SequenceDataAdapter.returnsCopies(). If SequenceAccessAlignmentModel is implemented the object used to store the sequence data is returned.

Parameters:

sequenceID - the ID of the sequence to be returned

Returns:

the sequence object as described above