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protected void compile junction tree throws exception super compile jt new junction tree
compiles this subnetwork in a junction tree structure
protected junction tree get junction tree return junction tree
returns the junctiontree
protected void verify consistency throws exception super verify consistency
verify the local consistency
protected void hyper tree throws exception int nets size nets size if nets size 2 return array list node inters make intersection boolean na arvore new boolean nets size na arvore 0 true for int i 0 i nets size 1 i insert link inters na arvore
makes a hypertree structure from this multi sectioned network
protected list make path sub network net list sub network path new array list sub network make path net path return path
makes the path from this subnetwork to the specified subnetwork
protected boolean elimine sub network adj system out println elimine oe clear array list node inter set toolkit intersection copia nos adj copia nos array list node aux nos set toolkit clone copia nos int size ant aux nos size aux nos remove all inter assert inter size aux nos size size ant boolean inseriu false while minimum weight elimination aux nos inseriu true while minimum weight elimination inter inseriu true make adjacents return inseriu
minimum weight triangulation
public boolean supports string extension boolean is load only returns true if there is no extension file is a folder return extension null extension trim length 0
checks if file extension is compatible to what this i o expects
protected void elimine profundidade sub network caller system out println elimine profundidade for int i adjacents size 1 i 0 i sub network ai sub network adjacents get i if elimine ai update arcs aux ai ai elimine profundidade this if caller null if elimine caller update arcs aux caller
depth first eliminate
protected void distribute arcs system out println distribute arcs for int i adjacents size 1 i 0 i sub network net sub network adjacents get i update arcs bilateral net net distribute arcs
distribute the edges inserted in this subnetwork to the adjacents
public void save msbn file output single agent msbn msbn throws file not found exception ioexception jaxbexception save exception if output is directory throw new save exception resource get string is not directory exception for int i msbn get net count 1 i 0 i single entity network net msbn get net at i file out new file output net get id xml save out net
saves a msbn to the output directory
protected void init visited visited new char node list size
initialize the visited array for the cycle detection
protected void distributed cycle throws exception for int i node list size 1 i 0 i dfs cycle i null
method used to verify cycles in the union graph of sub networks
public jinternal frame get panel return window
gets the msbnwindow associated with this controller
private string generate description from types string title string types string ret title for int i 0 i types length i ret types i if i 1 types length ret return ret
it just creates a string describing a file type
public string get prowl file extension return prowl file extension
this attribute stores the file extension of a normal pr owl file
public string get description owlontology ontology owlindividual individual try return this get description ontology owlentity individual as owlnamed individual catch exception e e print stack trace return null
extracts the comments from a owl individual
public void set prowl file extension string prowl file extension this prowl file extension prowl file extension
this attribute stores the file extension of a normal pr owl file
public boolean is to update mebnname return is to update mebnname
if set to true
public void set to update mebnname boolean is to update mebnname this is to update mebnname is to update mebnname
if set to true
public string get ubffile extension return ubf file extension
this is the
public void set ubffile extension string ubf file extension this ubf file extension ubf file extension
this is the
public prefix manager get ontology prefix manager owlontology ontology value to return prefix manager ret null use cache if available if this get ontology prefix cache null ret this get ontology prefix cache get ontology if ret null found in cache return immediately return ret it was not found in cache just delegate if this get prowl model user delegator null ret this get prowl model user delegator get ontology prefix manager ontology update cache if cache is available if this get ontology prefix cache null this get ontology prefix cache put ontology ret return ret return ret
this method uses cache i
public string get has mfrag object property return has mfrag object property
the name of the has mfrag object property
public void set has mfrag object property string has mfrag object property this has mfrag object property has mfrag object property
the name of the has mfrag object property
public void help throws exception java helper controller get instance open help main screen
used to call the help files
public void j menu help about action performed action event e try java helper controller get instance open help this catch exception evt status bar set text error evt get message this get class get name
help about action performed
public void j menu help about action performed action event e try java helper controller get instance open help this catch exception evt status bar set text resource get string error2 evt get message this get class get name
help about action performed
protected void set map name to type map string type map name to type this map name to type map name to type
a mapping from name to types meta entities
public void j menu help about action performed action event e try java helper controller get instance open help this catch exception evt status bar set text resource get string error exception evt get message this get class get name
help about action performed
protected leaf classify instance aux instance instance nominal node node node tree node x root node int index while tree node children get 0 instanceof leaf node nominal node tree node children get 0 atributo nominal index int instance get value node get attribute tree node nominal node tree node children get index return leaf tree node children get 0
classifies a given test instance using the decision tree
public node get root node return x root node
returns the root of the tree created
public void evaluate model classifier classifier instance set test data throws exception if classifier instanceof distribution classifier propagation results new float num instances num classes propagation new byte num instances 2 int num instances test data num instances for int i 0 i num instances i evaluate model once classifier test data get instance i
evaluates the classifier on a given set of instances
public void compute rocpoints roc points1 compute rocpoints probs1 ground truth roc points2 compute rocpoints probs2 ground truth system out println roc points 1 for int i 0 i roc points1 length i system out println roc points1 i 0 roc points1 i 1 system out println system out println system out println system out println roc points 2 for int i 0 i roc points2 length i system out println roc points2 i 0 roc points2 i 1
assuming the probabilities loaded were in ascending order
protected void set map boolean states map string entity map boolean states this map boolean states map boolean states
a mapping from names to boolean state entities
protected void set entity cache map entity iri entity cache this entity cache entity cache
this is a cache for entities loaded by this knowledge base
protected void set map loaded nodes map string inode map loaded nodes this map loaded nodes map loaded nodes
a mapping from names to nodes resident input context or ordinary variables
public void set clear kbcommand list list iclear kbcommand clear kbcommand list this clear kbcommand list clear kbcommand list
this is a list of commmands to be executed by
public void undo clear knowledge base if this get clear kbcommand list null for iclear kbcommand command this get clear kbcommand list try command undo command catch exception e debug println this get class e get message e
this method just calls
public boolean is to reset cache return is to reset cache
if set to false calls to
public void set is to reset cache boolean is to reset cache try debug println get class requests for resetting cache is is to reset cache enabled blocked catch throwable t t print stack trace this is to reset cache is to reset cache
if set to false calls to
public void set type int type if type type input if this get oobnparents size 0 input node of a class must not have parents throw new illegal argument exception resource get string input node has no parents this type type
this method also tests consistency for basic node types input output private
protected void set map argument map string argument map argument this map argument map argument
a mapping from argument name to argument
public void set expression cache map string owlclass expression expression cache this expression cache expression cache
this is a cache for
public boolean is ignorable node node node nodes will become alone if they have no parents and no children at all if node get parents null node get parents size 0 there is at least 1 parent so it is not alone return false there are no parents if node get children null node get children size 1 no parents and no children return true there are at least one child return false
note this method is not used by
public void set up button listeners this get tb edition get btn add probabilistic node add action listener new action listener public void action performed action event ae get linked window get graph pane set action graph action create probabilistic node debug println this get class hey yo i m gonna add a node from oobnedition pane
alters the behavior of superclass pnedition pane edition buttons
public void set up oobnspecific buttons setting up button to change node type jbutton button new jbutton this get icon controller get change node type icon this set change node type button button button set tool tip text resource get string change node type this get change node type button add action listener new action listener public void action performed action event e get linked window get graph pane show node type change popup get change node type button get change node type button get x get change node type button get y super get tb edition add button
sets up the buttons for oobn edition
public boolean is immutable node return is immutable node
if this nodes visual should not be changed anymore
public void set immutable node boolean is immutable node this is immutable node is immutable node
if this nodes visual should not be changed anymore
private container build status bar status panel new jpanel status bar new jlabel status panel set layout new border layout status panel set border new titled border resource get string status status bar set text resource get string status ready label status panel add status bar return this status panel
builds up the status bar
public single entity network get single entity network try return single entity network controller get network catch exception e return null
retorna a rede probabil stica code probabilistic network code
protected void save rvdefault probability distribution owlindividual rv individual resident node resident multi entity bayesian network mebn owlontology ontology todo auto generated method stub debug println get class save rvdefault probability distribution is not implemented yet
this method saves the default probability distribution of a random variable
public owlontology get last owlontology return last owlontology
this is the ontology used by this class in the last time
public jinternal frame get panel return this window
gets the oobnwindow associated with this controller
private void init this window set controller this this window get net list set selected index 0 if this get oobn get oobnclass count 0 this change active oobnclass oobnclass window new instance this get oobn get oobnclass list get first network index
initializes the controller
public abstract msbn compile active oobnclass to msbn ioobncompiler compiler oobnto single agent msbncompiler new instance abstract msbn msbn abstract msbn compiler compile this get oobn oobnclass single entity network wrapper new instance single entity network this get active get network controller get network return msbn
compiles the currently active oobn class
public boolean contains oobnclass by name string class name for ioobnclass oobn class this get oobn get oobnclass list if class name equals oobn class get class name return true return false
searches for classes and detects if there is a class with same name
public oobnnode graphical wrapper get oobnnode from names string class name string node name for ioobnclass oobn class this get oobn get oobnclass list if node name equals oobn class get class name for ioobnnode node oobn class get all nodes if node name equals node get name return oobnnode graphical wrapper new instance node return null
searches for a oobnnode by giving class name and node name
public jpopup menu get oobn on node popup return oobn on node popup
this popupmenu is used by this pane to edit an
public void set oobn on node popup jpopup menu oobn on node popup this oobn on node popup oobn on node popup
this popupmenu is used by this pane to edit an
public ioobnclass get selected class return selected class
gets the currently selected class by the oobn class list
public void set selected class ioobnclass selected class debug println this get class the currently selected class was set to selected class get class name this selected class selected class
sets the currently selected class by the oobn class list
public jlist get net list return this oobn class list
returns the oobn class list
protected void renew class list index try single entity network active network get controller get active get controller get single entity network int index of active network get controller get oobn get oobnclass list index of active network get oobn class list set selected index index of active network get oobn class list update ui debug println this get class setted active class list index to index of active network catch exception exc debug println this get class could not treat event in order to change selected oobn class exc
this method resets the currently selected class list element
public void initialize this reload plugins
this method will initialize this manager
public void add domain mfrag mfrag domain mfrag m frag list add domain mfrag domain mfrag list add domain mfrag current mfrag domain mfrag domain mfrag num
method responsible for adding a new domain mfrag
public plugin manager get plugin manager return this plugin manager
obtains the currently used plugin manager
public void set plugin manager plugin manager manager this plugin manager manager
sets the plugin manager to use
protected int get next without ignoring chars stream tokenizer st char not to ignore throws ioexception do st next token if st ttype stream tokenizer tt eol super lineno for char c not to ignore if st ttype int c return st ttype while st ttype stream tokenizer tt word st ttype st ttype stream tokenizer tt eof return st ttype
does the same as get next but doesnt ignore some chars
public void remove domain mfrag mfrag domain mfrag domain mfrag delete m frag list remove domain mfrag domain mfrag list remove domain mfrag current mfrag null
method responsible for removing the given domain mfrag
public mfrag get mfrag by name string name for mfrag test domain mfrag list if test get name equals name return test return null
return a mfrag with the name if it exists or null otherwise
public int get ordinary variable index ordinary variable ov int result 1 for int i 0 i ordinary variable list length i if ordinary variable list i equals ov result i break return result
return the index of a ordinary variable
public ordinary variable get correspondent ordinary variable ordinary variable input node ov int index index get ordinary variable index input node ov return this resident node get ordinary variable by index index
return the ordinary variable at the resident node that corresponds to
public void set input instance of built in rv rv input instance of node null input instance of rv rv rv add input instance this update label resident node pointer null
set the input instance of this node for the built in rv
public void set name string name this name name for node node is ovariable of list if node instanceof iresident node iresident node node update label
turn the name of the ordinary variable
public void set input instance of input instance of rv null input instance of node null update label resident node pointer null
set the input instance of propriety for null
public void remove resident node child resident node node resident node child list remove node node remove input node father list this
remove the node of the resident node child list
public ordinary variable get ordinary variable bound to resident node string input ov name try ordinary variable input ov this get ordinary variable by name input ov name return this get resident node pointer get resident node get ordinary variable by index this get ordinary variable list index of input ov catch exception e debug println this get class e get message e return null
search by name
public void delete m frag remove ordinary variable this type remove user object this for node node is ovariable of list if node instanceof iresident node iresident node node remove argument this else if node instanceof input node for resident node pointer pointer this is argument of list pointer remove ordinary variable this
delete the ordinary variable removing it from the respective mfrag
public void delete while resident node child list is empty resident node resident resident node child list get 0 remove resident node child resident m frag remove edge by nodes this resident m frag remove input node this
method responsible for deleting this input node
public void init string text this init text true
this method just calls
protected void show ssbn ssbn ssbn if this get mediator null if there is no mediator we cannot go on return network window window new network window ssbn get network this get mediator get screen get unbbayes frame add window window window set size window get preferred size window set visible true
uses mediator to display the ssbn
public void create entity definition object entity entity logic object lo pli s create concept entity get type get name null module generative name environment debug println lo to string pli s evaluate assert closed entity get type module name environment
p syntax example
public void add ovvalue ordinary variable ov string entity throws mfrag context fail exception this entity tree update tree for new information ov entity
add a value of a ov that is instanciated for a unique value
protected void remove not permanent nodes collection ssbnnode list ssbnnode log manager appendln removing not permanent nodes begin list ssbnnode nodes to delete new array list ssbnnode for ssbnnode node list ssbnnode if node is permanent nodes to delete add node for ssbnnode node nodes to delete log manager appendln removing node node get name node delete list ssbnnode remove node log manager appendln removing not permanent nodes end
remove of the network all nodes in what the attribute permanent false
public void init ssbnnode ssbnnode this set ssbnnode ssbnnode this node ssbnnode get resident set ssbnnode already does it this mebn this node get mfrag get multi entity bayesian network string pseudocode this node get table function if this ssbnnode get prob node null this set potential table this ssbnnode get prob node get probability function do not clar cache this init pseudocode false
use this method to initialize this parser on ssbn generation step
public context node get context node string name for mfrag mfrag domain mfrag list for context node node mfrag get context node list if node get name equals name return node return null
search the context node with the name
public resident node get domain resident node string name for mfrag mfrag domain mfrag list for resident node node mfrag get resident node list if node get name equals ignore case name return node return null
search the domain resident node node with the name
public iprowl2 individuals extractor get prowl2 individuals extractor return prowl2 individuals extractor
requests for pr owl2 specific individuals will be delegated to this object
public input node get input node string name for mfrag mfrag domain mfrag list for input node node mfrag get input node list if node get name equals name return node return null
search the generative input node with the name
public string get unique name return get unique name for this resident node this get arguments
this unique name is
public iprobability function generate linear distro cpt probabilistic node prob node float value 1 0 f prob node get states size potential table table prob node get probability function for int i 0 i prob node get probability function table size i todo in float operation since 1 3 1 3 1 3 might not be 1 implement some precision control table set value i value return table
this method just fills the nodes probabilistic tables w equal values
public void add argument ordinary variable ov string entity instance name throws ssbnnode general exception if entity instance name length 0 return ovinstance ov instance ovinstance get instance ov literal entity instance get instance entity instance name ov get value type this arguments add ov instance this arguments resident mfrag add ov instance update probabilistic node name
adds an argument
public void add argument ovinstance ov instance this arguments add ov instance this arguments resident mfrag add ov instance update probabilistic node name
adds an argument
public void add argument ordinary variable ov string entity instance name int pos throws ssbnnode general exception if entity instance name length 0 return ovinstance ov instance ovinstance get instance ov literal entity instance get instance entity instance name ov get value type this arguments add pos ov instance this arguments resident mfrag add ov instance update probabilistic node name
adds an argument at a particular position
public void set status bar text string text this get status bar set text text
setts the status bars message
public void remove all arguments this arguments clear this arguments resident mfrag clear update probabilistic node name
remove all the arguments
public icptfor ssbnnode generator builder get cpt for ssbnnode generator builder return cpt for ssbnnode generator builder
this is used in
public void set list of pruners list ipruner list of pruners this list of pruners list of pruners
this list of pruners are called by this class sequencially
public idseparation utility get dseparation utility return d separation utility
the behavior of this class can be customized by using different
public void set dseparation utility idseparation utility separation utility d separation utility separation utility
the behavior of this class can be customized by using different