info.bioinfweb.libralign.model.factory.biojava

Class BioJava3NucleotideAlignmentModelFactory

java.lang.Object

info.bioinfweb.libralign.model.factory.biojava.BioJava3NucleotideAlignmentModelFactory

All Implemented Interfaces:

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

public class BioJava3NucleotideAlignmentModelFactory
extends java.lang.Object
implements AlignmentModelFactory<org.biojava3.core.sequence.compound.NucleotideCompound>

Alignment model factory for models representing nucleotides as BioJava NucleotideCompound objects.

Author:

Ben Stöver

Module:

info.bioinfweb.libralign.biojava3

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_NUCLEOTIDE_CHARACTER_STATE_COUNT

Constructor Summary

Constructors

Constructor and Description
BioJava3NucleotideAlignmentModelFactory()

Method Summary

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

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_NUCLEOTIDE_CHARACTER_STATE_COUNT

public static final int DEFAULT_NUCLEOTIDE_CHARACTER_STATE_COUNT

See Also:

Constant Field Values

Constructor Detail

BioJava3NucleotideAlignmentModelFactory

public BioJava3NucleotideAlignmentModelFactory()

Method Detail

createNewModel

public AlignmentModel<org.biojava3.core.sequence.compound.NucleotideCompound> 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.NucleotideCompound>

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

Description copied from interface: AlignmentModelFactory

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.

Specified by:

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

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