public class BioPolymerCharAlignmentModelFactory extends AbstractAlignmentModelFactory<Character> implements AlignmentModelFactory<Character>
PackedAlignmentModel
using a CharacterTokenSet
for
nucleotide or amino acid data.
The token set of the created models (and the maximum number of different tokens supported by the packed model) depends on the character state type and predefined tokens specified in the parameter map. If no such data is provided an instance supporting all amino acid one letter (ambiguity) codes will be created. Such an instance can also take up all nucleotide (ambiguity) codes, since all such characters are also contained in the amino acid set.
In addition to the default molecular tokens, all tokens specified in
NewAlignmentModelParameterMap.getDefinedTokens()
will be added to the token set. Note
that only the first character of each string representation will be added the set. There will
be no warning, if representations get cut off.
In addition the number of supported different tokens by the packed model can be increased by
specifying a value for NewAlignmentModelParameterMap.KEY_CHARACTER_STATE_COUNT
which
is higher than the number of molecular tokens necessary for the specified character state set
type.
Constructor and Description |
---|
BioPolymerCharAlignmentModelFactory()
Creates a new instance of this class without an shared sequence ID manager.
|
BioPolymerCharAlignmentModelFactory(SequenceIDManager sharedIDManager)
Creates a new instance of this class using a shared sequence ID manager.
|
Modifier and Type | Method and Description |
---|---|
AlignmentModel<Character> |
doCreateNewModel(NewAlignmentModelParameterMap parameterMap) |
createNewModel, createToken, getSharedIDManager, hasSharedIDManager
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
createNewModel, createToken
public BioPolymerCharAlignmentModelFactory()
public BioPolymerCharAlignmentModelFactory(SequenceIDManager sharedIDManager)
sharedIDManager
- the sequence ID manager that will be shared by all model instances
created by this factorypublic AlignmentModel<Character> doCreateNewModel(NewAlignmentModelParameterMap parameterMap)
doCreateNewModel
in class AbstractAlignmentModelFactory<Character>