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java.lang.Objectde.jstacs.models.AbstractModel
de.jstacs.models.discrete.DiscreteGraphicalModel
de.jstacs.models.discrete.inhomogeneous.InhomogeneousDGM
public abstract class InhomogeneousDGM
This class is the main class for all inhomgeneous discrete graphical models (IDGM).
New instances, loaded instances, clones and instance reinstantiated by fromParameterSet() have the default output
stream.
IDGMParameterSet
Field Summary | |
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protected static OutputStream |
DEFAULT_STREAM
The default OutputStream |
protected SafeOutputStream |
sostream
This stream is used for comments, ... while the training, ... . |
Fields inherited from class de.jstacs.models.discrete.DiscreteGraphicalModel |
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params, trained |
Fields inherited from class de.jstacs.models.AbstractModel |
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alphabets, length |
Constructor Summary | |
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InhomogeneousDGM(IDGMParameterSet params)
The default constructor. |
|
InhomogeneousDGM(StringBuffer representation)
This is the constructor for Storable . |
Method Summary | |
---|---|
protected void |
check(Sequence sequence,
int startpos,
int endpos)
Checks some conditions on a sequence. |
InhomogeneousDGM |
clone()
Follows the conventions of Object 's clone-method. |
abstract String |
getStructure()
Returns a string representation of the graph. |
protected void |
set(DGMParameterSet parameter,
boolean trained)
Sets the parameters as internal parameters and does some essential computations. |
void |
setOutputStream(OutputStream stream)
Sets the output stream for the model. |
Methods inherited from class de.jstacs.models.discrete.DiscreteGraphicalModel |
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fromXML, getCurrentParameterSet, getDescription, getESS, getFurtherModelInfos, getXMLTag, isTrained, setFurtherModelInfos, toString, toXML |
Methods inherited from class de.jstacs.models.AbstractModel |
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emitSample, getAlphabetContainer, getCharacteristics, getLength, getLogProbFor, getLogProbFor, getLogProbFor, getLogProbFor, getLogProbFor, getMaximalMarkovOrder, getPriorTerm, getProbFor, getProbFor, set, setNewAlphabetContainerInstance, train |
Methods inherited from class java.lang.Object |
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equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Methods inherited from interface de.jstacs.models.Model |
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getInstanceName, getLogPriorTerm, getNumericalCharacteristics, getProbFor, train |
Field Detail |
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protected SafeOutputStream sostream
protected static final OutputStream DEFAULT_STREAM
Constructor Detail |
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public InhomogeneousDGM(IDGMParameterSet params) throws CloneNotSupportedException, IllegalArgumentException, NonParsableException
params
- the parameter set
CloneNotSupportedException
- if the parameter set could not be cloned
IllegalArgumentException
- if the parameter set is not instantiated
NonParsableException
- if the parameter set is not parsablepublic InhomogeneousDGM(StringBuffer representation) throws NonParsableException
Storable
.
representation
- the xml representation
NonParsableException
- if the representation could not be parsed.Method Detail |
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public InhomogeneousDGM clone() throws CloneNotSupportedException
AbstractModel
Object
's clone-method.
clone
in interface Model
clone
in class DiscreteGraphicalModel
AbstractModel
(the member-AlphabetContainer
isn't deeply cloned since it is assumed to be immutable). The type of the returned object is defined by
the class X
directly inherited from AbstractModel
. Hence X
's
clone-method should work as:Object o = (X)super.clone();
2. all additional member variables of o
defined by X
that are not of simple data-types like int, double, ... , have to be deeply
copied 3. return o
CloneNotSupportedException
public abstract String getStructure() throws NotTrainedException
NotTrainedException
- if the structure is not set, this can only be the case if the model is not trainedpublic void setOutputStream(OutputStream stream)
stream
- the output streamprotected void check(Sequence sequence, int startpos, int endpos) throws NotTrainedException, IllegalArgumentException
DiscreteGraphicalModel
check
in class DiscreteGraphicalModel
sequence
- the sequencestartpos
- the startpositionendpos
- the endposition
NotTrainedException
- if the model is not trained
IllegalArgumentException
- if some constraints are not fulfilledprotected void set(DGMParameterSet parameter, boolean trained) throws CloneNotSupportedException, NonParsableException
DiscreteGraphicalModel
set
in class DiscreteGraphicalModel
parameter
- the new ParameterSettrained
- the indicator for the model
CloneNotSupportedException
- if the parmeterSet could not be cloned
NonParsableException
- if the parameters of the model could not be parsed
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