| Package | Description |
|---|---|
| info.bioinfweb.libralign.model.factory |
Contains factory classes to create instances of implementations of
AlignmentModel. |
| info.bioinfweb.libralign.model.factory.biojava |
Contains alignment models working with BioJava
Compounds. |
| info.bioinfweb.libralign.model.factory.continuous |
Contains factories for alignment models that work with continuous values (e.g.
|
| info.bioinfweb.libralign.model.io |
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractAlignmentModelFactory<T>
Implements shared functionality for alignment model factories.
|
class |
BioPolymerCharAlignmentModelFactory
Creates instances of
PackedAlignmentModel using a CharacterTokenSet for
nucleotide or amino acid data. |
class |
StringAlignmentModelFactory
Default factory implementation for creating alignment models.
|
| Modifier and Type | Class and Description |
|---|---|
class |
BioJava3AminoAcidAligmentModelFactory
Alignment model factory for models representing amino acids as BioJava
AminoAcidCompound objects. |
class |
BioJava3NucleotideAlignmentModelFactory
Alignment model factory for models representing nucleotides as BioJava
NucleotideCompound objects. |
| Modifier and Type | Class and Description |
|---|---|
class |
DoubleAlignmentModelFactory
Factory that creates
ArrayListAlignmentModels with Double values as tokens. |
class |
FloatAlignmentModelFactory
Factory that creates
ArrayListAlignmentModels with Float values as tokens. |
| Modifier and Type | Method and Description |
|---|---|
AlignmentModelFactory<?> |
AlignmentModelEventReader.getDefaultFactory()
Returns the alignment model factory that is used to create new model instances for character state (token)
set types which are not defined in the factory map.
|
| Modifier and Type | Method and Description |
|---|---|
java.util.Map<CharacterStateSetType,AlignmentModelFactory> |
AlignmentModelEventReader.getFactoryMap()
Returns the map of alignment model factories for different character state (token) set types.
|
| Modifier and Type | Method and Description |
|---|---|
void |
AlignmentModelEventReader.setNucleotideFactories(AlignmentModelFactory<?> factory)
Sets the specified map for all nucleotide factories (identified with the keys
CharacterStateSetType.NUCLEOTIDE, CharacterStateSetType.DNA, CharacterStateSetType.RNA). |
| Constructor and Description |
|---|
AlignmentDataReader(java.io.File file,
AlignmentModelFactory<?> alignmentModelFactory)
Creates a new instance of this class.
|
AlignmentDataReader(java.io.InputStream stream,
AlignmentModelFactory<?> alignmentModelFactory)
Creates a new instance of this class.
|
AlignmentDataReader(info.bioinfweb.jphyloio.JPhyloIOEventReader eventReader,
AlignmentModelFactory<?> alignmentModelFactory)
Creates a new instance of this class.
|
AlignmentModelEventReader(AlignmentModelFactory<?> defaultFactory)
Creates a new instance of this class with an empty factory map.
|
AlignmentModelEventReader(AlignmentModelFactory<?> defaultFactory,
java.util.Map<CharacterStateSetType,AlignmentModelFactory> factoryMap)
Creates a new instance of this class.
|
| Constructor and Description |
|---|
AlignmentModelEventReader(AlignmentModelFactory<?> defaultFactory,
java.util.Map<CharacterStateSetType,AlignmentModelFactory> factoryMap)
Creates a new instance of this class.
|