info.bioinfweb.libralign.model.factory

Interface AlignmentModelFactory<T>

Type Parameters:

T - the token type of the created alignment model

All Known Implementing Classes:

AbstractAlignmentModelFactory, BioJava3AminoAcidAligmentModelFactory, BioJava3NucleotideAlignmentModelFactory, BioPolymerCharAlignmentModelFactory, DoubleAlignmentModelFactory, FloatAlignmentModelFactory, StringAlignmentModelFactory

public interface AlignmentModelFactory<T>

Interface to be implemented by classes creating instance of implementations of AlignmentModel. Alignment model factories are e.g. needed in combination with AlignmentDataReader to read alignments from files.

Since:

0.4.0

Author:

Ben Stöver

Method Summary

Modifier and Type	Method and Description
AlignmentModel<T>	createNewModel(NewAlignmentModelParameterMap parameterMap) Creates a new instance of an alignment model according to the specified parameters.
T	createToken(AlignmentModel<T> alignmentModel, java.lang.String tokenRepresentation) Creates a token object associated with the specified string representation.

Method Detail

createNewModel

AlignmentModel<T> createNewModel(NewAlignmentModelParameterMap parameterMap)

Creates a new instance of an alignment model according to the specified parameters.

Parameters:

parameterMap - a map with parameters describing the requirements to be met by the returned instance

Returns:

a new instance of an alignment model or null if this factory is not able to create an object that meets the specified requirements

createToken

T createToken(AlignmentModel<T> alignmentModel,
              java.lang.String tokenRepresentation)

Creates a token object associated with the specified string representation. Implementations may use TokenSet.tokenByRepresentation(String) of the token set associated with the specified alignment model to determine the return value, but could also implement a different or extended behavior.

Parameters:

alignmentModel - the alignment model which will hold the returned token

tokenRepresentation - the string representation of the token to be returned (e.g. read from an alignment file)

Returns:

the new token instance or null if no according token could be generated by this factory