info.bioinfweb.libralign.model.factory

Class StringAlignmentModelFactory

java.lang.Object

info.bioinfweb.libralign.model.factory.StringAlignmentModelFactory

All Implemented Interfaces:

AlignmentModelFactory<java.lang.String>

public class StringAlignmentModelFactory
extends java.lang.Object
implements AlignmentModelFactory<java.lang.String>

Default factory implementation for creating alignment models. If a modified behavior is needed application developers can overwrite methods of this class to handle respective cases and delegate the remaining to the super implementation.

Since:

0.4.0

Author:

Ben Stöver

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_AMINO_ACID_CHARACTER_STATE_COUNT

Constructor Summary

Constructors

Constructor and Description
StringAlignmentModelFactory()

Method Summary

Modifier and Type	Method and Description
AlignmentModel<java.lang.String>	createNewModel(NewAlignmentModelParameterMap parameterMap) Creates a new instance of PackedAlignmentModel if the number of tokens is specified (using NewAlignmentModelParameterMap.KEY_CHARACTER_STATE_COUNT) or ArrayListAlignmentModel if not.
java.lang.String	createToken(AlignmentModel<java.lang.String> 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

Field Detail

DEFAULT_AMINO_ACID_CHARACTER_STATE_COUNT

public static final int DEFAULT_AMINO_ACID_CHARACTER_STATE_COUNT

See Also:

Constant Field Values

Constructor Detail

StringAlignmentModelFactory

public StringAlignmentModelFactory()

Method Detail

createNewModel

public AlignmentModel<java.lang.String> createNewModel(NewAlignmentModelParameterMap parameterMap)

Creates a new instance of PackedAlignmentModel if the number of tokens is specified (using NewAlignmentModelParameterMap.KEY_CHARACTER_STATE_COUNT) or ArrayListAlignmentModel if not.

Specified by:

createNewModel in interface AlignmentModelFactory<java.lang.String>

Parameters:

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

Returns:

a new instance of an alignment model

createToken

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

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

Overwrite this method to support more or different token string representations than the token set of the alignment model.

Specified by:

createToken in interface AlignmentModelFactory<java.lang.String>

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