unbbayes.io
Class NetIO

java.lang.Object
  unbbayes.io.NetIO

All Implemented Interfaces:

BaseIO

public class NetIO
extends Object
implements BaseIO

Manipulates input/output of NET files.

Version:

2.0

Author:

Rommel N. Carvalho, Michael S. Onishi, Mario Henrique Paes Vieira (mariohpv@bol.com.br), Shou Matsumoto

Field Summary

protected long	lineno
static String[]	SUPPORTED_EXTENSIONS Single array containing "net"

Constructor Summary

NetIO()

Method Summary

protected String	formatString(String string)
String	getName() Gets the name of this I/O component.
protected int	getNext(StreamTokenizer st)
String[]	getSupportedFileExtensions(boolean isLoadOnly) Obtains an array of file extensions supported by this network window.
String	getSupportedFilesDescription(boolean isLoadOnly) Gets a description of supported file extensions, which may be shown to the user through file chooser's file filter to explain what file format are supported.
Graph	load(File input) Loads a NET format file using default node/network builder.
ProbabilisticNetwork	load(File input, IProbabilisticNetworkBuilder networkBuilder) Loads a NET format file using network builder
protected void	load(File input, SingleEntityNetwork net, IProbabilisticNetworkBuilder networkBuilder)
protected void	loadContinuousNodeDeclaration(StreamTokenizer st, SingleEntityNetwork net, IProbabilisticNetworkBuilder networkBuilder) If the current declaration is of type "continuous node", loads that node (creating new instances using networkBuilder) and adds it to net.
protected void	loadHierarchicTree(StringBuffer sb, DefaultMutableTreeNode root)
protected void	loadNetHeader(StreamTokenizer st, SingleEntityNetwork net) Start loading net{} header from .net specification file; iterating under loadNetHeaderBody(StreamTokenizer, SingleEntityNetwork) in order to treat each declaration.
protected void	loadNetHeaderBody(StreamTokenizer st, SingleEntityNetwork net) If a declaration inside net header is treatable, treat it.
protected void	loadNodeDeclaration(StreamTokenizer st, SingleEntityNetwork net, IProbabilisticNetworkBuilder networkBuilder) If the current declaration is of type "node" (or "decision" or "utility"), loads that node (creating new instances using networkBuilder) and adds it to net.
protected void	loadNodeDeclarationBody(StreamTokenizer st, Node node) Reads inside the node declaration.
protected void	loadPotentialDataContinuous(StreamTokenizer st, Node node) Loads potential declaration assuming it is declaring continuous distribution
protected void	loadPotentialDataOrdinal(StreamTokenizer st, Node node) Loads potential declaration's content assuming it is declaring ordinal "stateful" probability declaration
protected void	loadPotentialDeclaration(StreamTokenizer st, SingleEntityNetwork net) If the current declaration is "potential", treat that declaration and adds it to a node contained within net.
protected void	processTreeNode(TreeNode node, StringBuffer sb, TreeModel model)
protected void	readTillEOL(StreamTokenizer tokenizer) Reads and skips all tokens before next end of line token.
void	save(File output, Graph graph) Saves a network in basic NET file format.
protected String	saveHierarchicTree(HierarchicTree hierarchicTree)
protected void	saveNetHeader(PrintStream stream, SingleEntityNetwork net) Fills the PrintStream with net{} header, starting with "net {" declaration and closing with "}"
protected void	saveNetHeaderBody(PrintStream stream, SingleEntityNetwork net) Stores the content of net{[CONTENT]} header to a stream.
protected void	saveNodeDeclaration(PrintStream stream, Node node, SingleEntityNetwork net) Writes to a PrintStream a node/decision/utility{} declaration.
protected void	saveNodeDeclarationBody(PrintStream stream, Node node, SingleEntityNetwork net) Writes to a PrintStream the body of node/decision/utility{} declaration.
protected void	saveNodeLabelAndPosition(PrintStream stream, Node node) Stores node's label = "[LABEL]"; and position = ([X], [Y]); declarations inside "node" declaration's body
protected void	savePotentialDeclaration(PrintStream stream, Node node, SingleEntityNetwork net) Stores to PrintStream the potential{} declaration
protected void	savePotentialDeclarationBody(PrintStream stream, Node node, SingleEntityNetwork net) Stores to PrintStream the [BODY] of potential {[BODY]} declaration
void	setName(String name) Sets the name of this I/O component.
protected void	setUpHierarchicTree(SingleEntityNetwork net) Sets up the hierarchic tree after the network is completely loaded
protected void	setUpStreamTokenizer(StreamTokenizer st) Configures valid/invalid character ranges of stream tokenizer.
boolean	supports(File file, boolean isLoadOnly) Returns true if the file is supported by this IO class.
boolean	supports(String extension, boolean isLoadOnly) Checks if file extension is compatible to what this i/o expects.
protected String	unformatString(String string)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

lineno

protected long lineno

SUPPORTED_EXTENSIONS

public static final String[] SUPPORTED_EXTENSIONS

Single array containing "net"

Constructor Detail

NetIO

public NetIO()

Method Detail

load

public Graph load(File input)
           throws LoadException,
                  IOException

Loads a NET format file using default node/network builder. In other words, this method returns exactly instances of ProbabilisticNetwork filled by DecisionNode, ProbabilisticNode and UtilityNode.

Specified by:

load in interface BaseIO

Parameters:

input - file to be read.

Returns:

loaded net.

Throws:

LoadException - when there were errors loading the network

IOException - in case there were errors when manipulating files.

See Also:

DefaultProbabilisticNodeBuilder

load

public ProbabilisticNetwork load(File input,
                                 IProbabilisticNetworkBuilder networkBuilder)
                          throws LoadException,
                                 IOException

Loads a NET format file using network builder

Parameters:

input - file to be read.

networkBuilder: - builder to be used in order to generate expected instances of probabilistic network, probabilistic nodes, decision nodes and utility nodes. This is useful if you want to reuse NetIO for networks/nodes which extends ProbabilisticNetwork, ProbabilisticNode, DecisionNode and UtilityNode (or else NetIO will be bound to those superclasses only).

Returns:

loaded net.

Throws:

LoadException - when there were errors loading the network

IOException - in case there were errors when manipulating files.

See Also:

IProbabilisticNetworkBuilder

save

public void save(File output,
                 Graph graph)
          throws FileNotFoundException

Saves a network in basic NET file format.

Specified by:

save in interface BaseIO

Parameters:

output - file where the net should be saved.

graph - network to be saved.

Throws:

FileNotFoundException

load

protected void load(File input,
                    SingleEntityNetwork net,
                    IProbabilisticNetworkBuilder networkBuilder)
             throws IOException,
                    LoadException

Throws:

IOException

LoadException

getNext

protected int getNext(StreamTokenizer st)
               throws IOException

Throws:

IOException

loadHierarchicTree

protected void loadHierarchicTree(StringBuffer sb,
                                  DefaultMutableTreeNode root)

saveHierarchicTree

protected String saveHierarchicTree(HierarchicTree hierarchicTree)

processTreeNode

protected void processTreeNode(TreeNode node,
                               StringBuffer sb,
                               TreeModel model)

readTillEOL

protected void readTillEOL(StreamTokenizer tokenizer)
                    throws IOException

Reads and skips all tokens before next end of line token.

Parameters:

tokenizer - Stream tokenizer

Throws:

IOException - EOF not found

formatString

protected String formatString(String string)

unformatString

protected String unformatString(String string)

setUpStreamTokenizer

protected void setUpStreamTokenizer(StreamTokenizer st)
                             throws IOException

Configures valid/invalid character ranges of stream tokenizer. By setting up using protected method, it becomes easier to extend this class

Parameters:

st: - StreamTokenizer to set up

Throws:

IOException

loadNetHeader

protected void loadNetHeader(StreamTokenizer st,
                             SingleEntityNetwork net)
                      throws IOException

Start loading net{} header from .net specification file; iterating under loadNetHeaderBody(StreamTokenizer, SingleEntityNetwork) in order to treat each declaration. loadNetHeaderBody(StreamTokenizer, SingleEntityNetwork) must ignore incompatible declaration.

Parameters:

st -

net -

Throws:

IOException

loadNetHeaderBody

protected void loadNetHeaderBody(StreamTokenizer st,
                                 SingleEntityNetwork net)
                          throws IOException

If a declaration inside net header is treatable, treat it. The currently compatible declarations are: name, node_size, tree, UnBBayes_Color_Utility, UnBBayes_Color_Decision, UnBBayes_Color_Probabilistic_Description, UnBBayes_Color_Probabilistic_Explanation. If declaration is not compatible, it will be ignored.

Parameters:

st -

net -

Throws:

IOException

loadNodeDeclaration

protected void loadNodeDeclaration(StreamTokenizer st,
                                   SingleEntityNetwork net,
                                   IProbabilisticNetworkBuilder networkBuilder)
                            throws IOException,
                                   LoadException

If the current declaration is of type "node" (or "decision" or "utility"), loads that node (creating new instances using networkBuilder) and adds it to net. If declaration is not "node" (or "decision" or "utility"), it will not move the token index from st.

Parameters:

st -

net -

networkBuilder -

Throws:

IOException

LoadException

loadContinuousNodeDeclaration

protected void loadContinuousNodeDeclaration(StreamTokenizer st,
                                             SingleEntityNetwork net,
                                             IProbabilisticNetworkBuilder networkBuilder)
                                      throws IOException,
                                             LoadException

If the current declaration is of type "continuous node", loads that node (creating new instances using networkBuilder) and adds it to net. If declaration is not "continuous node", it will not move the token index from st.

Parameters:

st -

net -

networkBuilder -

Throws:

IOException

LoadException

loadPotentialDeclaration

protected void loadPotentialDeclaration(StreamTokenizer st,
                                        SingleEntityNetwork net)
                                 throws IOException,
                                        LoadException

If the current declaration is "potential", treat that declaration and adds it to a node contained within net. If current declaration is not "potential", this method ignores it and remains the st untouched

Parameters:

st -

net -

Throws:

IOException

LoadException

setUpHierarchicTree

protected void setUpHierarchicTree(SingleEntityNetwork net)

Sets up the hierarchic tree after the network is completely loaded

Parameters:

net -

loadNodeDeclarationBody

protected void loadNodeDeclarationBody(StreamTokenizer st,
                                       Node node)
                                throws IOException,
                                       LoadException

Reads inside the node declaration. node {[READS THIS CONTENT]}

Parameters:

st -

node: - node to be filled

Throws:

IOException

LoadException

loadPotentialDataOrdinal

protected void loadPotentialDataOrdinal(StreamTokenizer st,
                                        Node node)
                                 throws LoadException,
                                        IOException

Loads potential declaration's content assuming it is declaring ordinal "stateful" probability declaration

Parameters:

st -

node -

Throws:

LoadException

IOException

loadPotentialDataContinuous

protected void loadPotentialDataContinuous(StreamTokenizer st,
                                           Node node)
                                    throws LoadException,
                                           IOException

Loads potential declaration assuming it is declaring continuous distribution

Parameters:

st -

node -

Throws:

LoadException

IOException

saveNetHeader

protected void saveNetHeader(PrintStream stream,
                             SingleEntityNetwork net)

Fills the PrintStream with net{} header, starting with "net {" declaration and closing with "}"

Parameters:

stream: - stream to write to

net: - network to be saved to stream

saveNetHeaderBody

protected void saveNetHeaderBody(PrintStream stream,
                                 SingleEntityNetwork net)

Stores the content of net{[CONTENT]} header to a stream. the informations are: node_size, name, tree, UnBBayes_Color_Probabilistic_Description, UnBBayes_Color_Probabilistic_Explanation, UnBBayes_Color_Utility, UnBBayes_Color_Decision.

Parameters:

stream -

net -

saveNodeDeclaration

protected void saveNodeDeclaration(PrintStream stream,
                                   Node node,
                                   SingleEntityNetwork net)

Writes to a PrintStream a node/decision/utility{} declaration. node|decision|utility [NAME] {[CONTENT]}

Parameters:

stream -

node -

net -

saveNodeDeclarationBody

protected void saveNodeDeclarationBody(PrintStream stream,
                                       Node node,
                                       SingleEntityNetwork net)

Writes to a PrintStream the body of node/decision/utility{} declaration. node|decision|utility [NAME] {[THIS_CONTENT_IS_WRITTEN]}

Parameters:

stream -

node -

net -

savePotentialDeclaration

protected void savePotentialDeclaration(PrintStream stream,
                                        Node node,
                                        SingleEntityNetwork net)

Stores to PrintStream the potential{} declaration

Parameters:

stream -

node -

net -

savePotentialDeclarationBody

protected void savePotentialDeclarationBody(PrintStream stream,
                                            Node node,
                                            SingleEntityNetwork net)

Stores to PrintStream the [BODY] of potential {[BODY]} declaration

Parameters:

stream -

node -

net -

saveNodeLabelAndPosition

protected void saveNodeLabelAndPosition(PrintStream stream,
                                        Node node)

Stores node's label = "[LABEL]"; and position = ([X], [Y]); declarations inside "node" declaration's body

Parameters:

stream -

node -

supports

public boolean supports(String extension,
                        boolean isLoadOnly)

Checks if file extension is compatible to what this i/o expects.

Parameters:

extension -

isLoadOnly -

Returns:

See Also:

supports(File, boolean)

getSupportedFileExtensions

public String[] getSupportedFileExtensions(boolean isLoadOnly)

Description copied from interface: BaseIO

Obtains an array of file extensions supported by this network window. The file extensions should come without the dot

Specified by:

getSupportedFileExtensions in interface BaseIO

Parameters:

isLoadOnly - : if set to true, it should consider file extensions for file loading (input). If set to false, it should consider both saving and loading. Note that not every module/plugin can implement both loading and saving, and this parameter may separate such special behaviors.

Returns:

getSupportedFilesDescription

public String getSupportedFilesDescription(boolean isLoadOnly)

Description copied from interface: BaseIO

Gets a description of supported file extensions, which may be shown to the user through file chooser's file filter to explain what file format are supported. E.g. "Net (.net), XMLBIF(.xml), UnBBayes File (.ubf)"

Specified by:

getSupportedFilesDescription in interface BaseIO

Parameters:

isLoadOnly - : if set to true, it should consider file extensions for file loading (input). If set to false, it should consider both saving and loading. Note that not every module/plugin can implement both loading and saving, and this parameter may separate such special behaviors.

supports

public boolean supports(File file,
                        boolean isLoadOnly)

Description copied from interface: BaseIO

Returns true if the file is supported by this IO class. It may be implemented as simple extension check. False otherwise.

Specified by:

supports in interface BaseIO

Parameters:

file - : the file to analyze extension.

isLoadOnly - : if set to true, it should consider file extensions for file loading (input). If set to false, it should consider both saving and loading. Note that not every I/O class can implement both loading and saving, and this parameter may separate such special behaviors.

Returns:

getName

public String getName()

Description copied from interface: BaseIO

Gets the name of this I/O component. This name may be displayed to a user when there is a need to choose a specific I/O class to use.

Specified by:

getName in interface BaseIO

Returns:

the name

setName

public void setName(String name)

Description copied from interface: BaseIO

Sets the name of this I/O component. This name may be displayed to a user when there is a need to choose a specific I/O class to use.

Specified by:

setName in interface BaseIO

Parameters:

name - the name to set