info.bioinfweb.libralign.model

Interface SequenceAccessAlignmentModel<S,T>

Type Parameters:

S - the type of the sequence objects (e.g. a BioJava sequence type or String)

T - the type of sequence elements (tokens) the implementing provider object works with

All Superinterfaces:

AlignmentModel<T>, SequenceAccess<S>

All Known Implementing Classes:

AbstractUnmodifyableAlignmentModel, BioJava3SequenceAlignmentModel, CharSequenceAlignmentModel

public interface SequenceAccessAlignmentModel<S,T>
extends AlignmentModel<T>, SequenceAccess<S>

Interface for classes implementing AlignmentModel by using sequence objects. Methods to replace a whole sequence are specified for the case that the sequence objects (e.g. Strings or BioJava sequences) do not allow to be modified after creation.

Since:

0.1.0

Author:

Ben Stöver

Method Summary

Modifier and Type	Method and Description
java.lang.String	addSequence(java.lang.String sequenceName, S content) Adds a the specified sequence to the underlying data source and generates an ID for it.
S	replaceSequence(java.lang.String sequenceID, S content) Replaces the sequence object with the specified ID.

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

addSequence, addSequence, appendToken, appendTokens, containsSequence, getChangeListeners, getID, getLabel, getMaxSequenceLength, getSequenceCount, getSequenceLength, getTokenAt, getTokenSet, getWriteType, insertTokenAt, insertTokensAt, isSequencesReadOnly, isTokensReadOnly, removeSequence, removeTokenAt, removeTokensAt, renameSequence, sequenceIDIterator, sequenceIDsByName, sequenceNameByID, setID, setLabel, setTokenAt, setTokensAt, setTokenSet

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

getSequence

Method Detail

addSequence

java.lang.String addSequence(java.lang.String sequenceName,
                             S content)
                      throws AlignmentSourceNotWritableException

Adds a the specified sequence to the underlying data source and generates an ID for it.

Parameters:

sequenceName - the name of the new sequence

content - the sequence object to be added.

Returns:

the unique ID of the new sequence

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for sequences

replaceSequence

S replaceSequence(java.lang.String sequenceID,
                  S content)
           throws AlignmentSourceNotWritableException

Replaces the sequence object with the specified ID.

Parameters:

sequenceID - the ID of the sequence to be replaced

content - the new sequence object

Returns:

the previous sequence identified by the specified ID, or null if there was no sequence with the ID

Throws:

AlignmentSourceNotWritableException - if the underlying data source is not writable for tokens