info.bioinfweb.libralign.model.factory.biojava

Class BioJava3AminoAcidAligmentModelFactory

java.lang.Object

info.bioinfweb.libralign.model.factory.biojava.BioJava3AminoAcidAligmentModelFactory

All Implemented Interfaces:

AlignmentModelFactory<org.biojava3.core.sequence.compound.AminoAcidCompound>

public class BioJava3AminoAcidAligmentModelFactory
extends java.lang.Object
implements AlignmentModelFactory<org.biojava3.core.sequence.compound.AminoAcidCompound>

Alignment model factory for models representing amino acids as BioJava AminoAcidCompound objects.

Author:

Ben Stöver

Module:

info.bioinfweb.libralign.biojava3

Constructor Summary

Constructors

Constructor and Description
BioJava3AminoAcidAligmentModelFactory()

Method Summary

Modifier and Type	Method and Description
AlignmentModel<org.biojava3.core.sequence.compound.AminoAcidCompound>	createNewModel(NewAlignmentModelParameterMap parameterMap) Creates a new instance of an alignment model according to the specified parameters.
org.biojava3.core.sequence.compound.AminoAcidCompound	createToken(AlignmentModel<org.biojava3.core.sequence.compound.AminoAcidCompound> alignmentModel, java.lang.String tokenRepresentation) Creates the token using the token set of the specified alignment model.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BioJava3AminoAcidAligmentModelFactory

public BioJava3AminoAcidAligmentModelFactory()

Method Detail

createNewModel

public AlignmentModel<org.biojava3.core.sequence.compound.AminoAcidCompound> createNewModel(NewAlignmentModelParameterMap parameterMap)

Description copied from interface: AlignmentModelFactory

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

Specified by:

createNewModel in interface AlignmentModelFactory<org.biojava3.core.sequence.compound.AminoAcidCompound>

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

public org.biojava3.core.sequence.compound.AminoAcidCompound createToken(AlignmentModel<org.biojava3.core.sequence.compound.AminoAcidCompound> alignmentModel,
                                                                         java.lang.String tokenRepresentation)

Creates the token using the token set of the specified alignment model.

Specified by:

createToken in interface AlignmentModelFactory<org.biojava3.core.sequence.compound.AminoAcidCompound>

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

Throws:

InvalidTokenException - if no token for the specified representation could be found in the token set of the specified alignment model