BIFReader (weka-stable 3.6.14 API)

java.lang.Object
- weka.classifiers.Classifier
- - weka.classifiers.bayes.BayesNet
  - - weka.classifiers.bayes.net.BIFReader

All Implemented Interfaces:: Serializable, Cloneable, AdditionalMeasureProducer, CapabilitiesHandler, Drawable, OptionHandler, RevisionHandler, TechnicalInformationHandler, WeightedInstancesHandler

public class BIFReader
extends BayesNet
implements TechnicalInformationHandler

Builds a description of a Bayes Net classifier stored in XML BIF 0.3 format.

For more details on XML BIF see:

Fabio Cozman, Marek Druzdzel, Daniel Garcia (1998). XML BIF version 0.3. URL http://www-2.cs.cmu.edu/~fgcozman/Research/InterchangeFormat/.

BibTeX:

 @misc{Cozman1998,
    author = {Fabio Cozman and Marek Druzdzel and Daniel Garcia},
    title = {XML BIF version 0.3},
    year = {1998},
    URL = {http://www-2.cs.cmu.edu/\~fgcozman/Research/InterchangeFormat/}
 }

Valid options are:

 -D
  Do not use ADTree data structure

 -B <BIF file>
  BIF file to compare with

 -Q weka.classifiers.bayes.net.search.SearchAlgorithm
  Search algorithm

 -E weka.classifiers.bayes.net.estimate.SimpleEstimator
  Estimator algorithm

Version:: $Revision: 1.15 $
Author:: Remco Bouckaert ([email protected])
See Also:: Serialized Form

Field Summary
- Fields inherited from class weka.classifiers.bayes.BayesNet
  m_Distributions, m_Instances
- Fields inherited from interface weka.core.Drawable
  BayesNet, Newick, NOT_DRAWABLE, TREE

Constructor Summary

Constructors
Constructor and Description

BIFReader()
the default constructor

Constructors
Constructor and Description
`BIFReader()` the default constructor

Method Summary

Methods
Modifier and Type	Method and Description
`double`	`divergence(BayesNet other)` calculates the divergence between the probability distribution represented by this network and that of another, that is, \sum_{x\in X} P(x)log P(x)/Q(x) where X is the set of values the nodes in the network can take, P(x) the probability of this network for configuration x Q(x) the probability of the other network for configuration x
`int`	`extraArcs(BayesNet other)` Count nr of exta arcs from other network compared to current network Note that an arc is not 'extra' if it is reversed.
`String`	`getContent(Element node)` Returns all TEXT children of the given node in one string.
`String`	`getFileName()` returns the current filename
`int`	`getNode(String sNodeName)` getNode finds the index of the node with name sNodeName and throws an exception if no such node can be found.
`String`	`getRevision()` Returns the revision string.
`TechnicalInformation`	`getTechnicalInformation()` Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
`String`	`globalInfo()` This will return a string describing the classifier.
`static void`	`main(String[] args)` Loads the file specified as first parameter and prints it to stdout.
`int`	`missingArcs(BayesNet other)` Count nr of arcs missing from other network compared to current network Note that an arc is not 'missing' if it is reversed.
`BIFReader`	`processFile(String sFile)` processFile reads a BIFXML file and initializes a Bayes Net
`BIFReader`	`processString(String sStr)`
`int`	`reversedArcs(BayesNet other)` Count nr of reversed arcs from other network compared to current network
`void`	`Sync(BayesNet other)` synchronizes the node ordering of this Bayes network with those in the other network (if possible).

Methods inherited from class weka.classifiers.bayes.BayesNet
BIFFileTipText, buildClassifier, buildStructure, countsForInstance, distributionForInstance, enumerateMeasures, estimateCPTs, estimatorTipText, getADTree, getBIFFile, getBIFHeader, getCapabilities, getCardinality, getDistributions, getEstimator, getMeasure, getName, getNodeName, getNodeValue, getNrOfNodes, getNrOfParents, getOptions, getParent, getParentCardinality, getParentSet, getParentSets, getProbability, getSearchAlgorithm, getUseADTree, graph, graphType, initCPTs, initStructure, listOptions, measureAICScore, measureBayesScore, measureBDeuScore, measureDivergence, measureEntropyScore, measureExtraArcs, measureMDLScore, measureMissingArcs, measureReversedArcs, partitionOptions, searchAlgorithmTipText, setBIFFile, setEstimator, setOptions, setSearchAlgorithm, setUseADTree, toString, toXMLBIF03, updateClassifier, useADTreeTipText

Methods inherited from class weka.classifiers.Classifier
classifyInstance, debugTipText, forName, getDebug, makeCopies, makeCopy, setDebug

Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - BIFReader
```
public BIFReader()
```
    the default constructor
- Method Detail
  - globalInfo
```
public String globalInfo()
```
    This will return a string describing the classifier.
    
    Overrides:
    
    globalInfo in class BayesNet
    
    Returns:
    The string.
  - processFile
```
public BIFReader processFile(String sFile)
                      throws Exception
```
    processFile reads a BIFXML file and initializes a Bayes Net
    
    Parameters:
    sFile - name of the file to parse
    
    Returns:
    the BIFReader
    
    Throws:
    
    Exception - if processing fails
  - processString
```
public BIFReader processString(String sStr)
                        throws Exception
```
    Throws:
    
    Exception
  - getFileName
```
public String getFileName()
```
    returns the current filename
    
    Returns:
    the current filename
  - getTechnicalInformation
```
public TechnicalInformation getTechnicalInformation()
```
    Returns an instance of a TechnicalInformation object, containing detailed information about the technical background of this class, e.g., paper reference or book this class is based on.
    
    Specified by:
    
    getTechnicalInformation in interface TechnicalInformationHandler
    
    Returns:
    the technical information about this class
  - Sync
```
public void Sync(BayesNet other)
          throws Exception
```
    synchronizes the node ordering of this Bayes network with those in the other network (if possible).
    
    Parameters:
    other - Bayes network to synchronize with
    
    Throws:
    
    Exception - if nr of attributes differs or not all of the variables have the same name.
  - getContent
```
public String getContent(Element node)
```
    Returns all TEXT children of the given node in one string. Between the node values new lines are inserted.
    
    Parameters:
    node - the node to return the content for
    
    Returns:
    the content of the node
  - missingArcs
```
public int missingArcs(BayesNet other)
```
    Count nr of arcs missing from other network compared to current network Note that an arc is not 'missing' if it is reversed.
    
    Parameters:
    other - network to compare with
    
    Returns:
    nr of missing arcs
  - extraArcs
```
public int extraArcs(BayesNet other)
```
    Count nr of exta arcs from other network compared to current network Note that an arc is not 'extra' if it is reversed.
    
    Parameters:
    other - network to compare with
    
    Returns:
    nr of missing arcs
  - divergence
```
public double divergence(BayesNet other)
```
    calculates the divergence between the probability distribution represented by this network and that of another, that is, \sum_{x\in X} P(x)log P(x)/Q(x) where X is the set of values the nodes in the network can take, P(x) the probability of this network for configuration x Q(x) the probability of the other network for configuration x
    
    Parameters:
    other - network to compare with
    
    Returns:
    divergence between this and other Bayes Network
  - reversedArcs
```
public int reversedArcs(BayesNet other)
```
    Count nr of reversed arcs from other network compared to current network
    
    Parameters:
    other - network to compare with
    
    Returns:
    nr of missing arcs
  - getNode
```
public int getNode(String sNodeName)
            throws Exception
```
    getNode finds the index of the node with name sNodeName and throws an exception if no such node can be found.
    
    Parameters:
    sNodeName - name of the node to get the index from
    
    Returns:
    index of the node with name sNodeName
    
    Throws:
    
    Exception - if node cannot be found
  - getRevision
```
public String getRevision()
```
    Returns the revision string.
    
    Specified by:
    
    getRevision in interface RevisionHandler
    
    Overrides:
    
    getRevision in class BayesNet
    
    Returns:
    the revision
  - main
```
public static void main(String[] args)
```
    Loads the file specified as first parameter and prints it to stdout.
    
    Parameters:
    args - the command line parameters

Class BIFReader

Field Summary

Fields inherited from class weka.classifiers.bayes.BayesNet

Fields inherited from interface weka.core.Drawable

Constructor Summary

Method Summary

Methods inherited from class weka.classifiers.bayes.BayesNet

Methods inherited from class weka.classifiers.Classifier

Methods inherited from class java.lang.Object

Constructor Detail

BIFReader

Method Detail

globalInfo

processFile

processString

getFileName

getTechnicalInformation

Sync

getContent

missingArcs

extraArcs

divergence

reversedArcs

getNode

getRevision

main