Class Vertex

java.lang.Object
  extended by Vertex

 class Vertex
extends java.lang.Object


Field Summary
(package private)  double[] emissions
           
(package private)  double[] emissions_2
           
(package private)  double[] emissions_3
           
(package private)  double[] emissions_4
           
(package private)  double emissPriorScaler
           
(package private)  double emissPriorScaler_2
           
(package private)  double emissPriorScaler_3
           
(package private)  double emissPriorScaler_4
           
(package private)  java.util.LinkedList endTransitionList
           
(package private)  java.util.Hashtable endTransitions
           
(package private)  boolean hasEmissions
           
(package private)  java.lang.String label
           
(package private)  int nrOfEndTransitions
           
(package private)  int nrOfTransitions
           
(package private)  int number
           
(package private)  java.util.LinkedList transitionList
           
(package private)  java.util.Hashtable transitions
           
(package private)  double transPriorScaler
           
(package private)  int vertexType
           
 
Constructor Summary
Vertex(java.lang.String moduleName, int vertexType, double[] initDistrib, java.lang.String label)
           
Vertex(java.lang.String moduleName, int vertexType, int distribType, java.lang.String label)
           
 
Method Summary
 boolean addEndTransition(int toVertex)
           
 boolean addTransition(int toVertex)
           
 boolean addTransition(int toVertex, double probability, boolean isLocked)
           
 double getEmissionProb(int pos)
           
 double getEmissionProb(int nr, int pos)
           
 double[] getEmissionProbs()
           
 double getEmissPriorScaler()
           
 double getEmissPriorScaler(int nr)
           
 java.util.ListIterator getEndTransitions()
           
 java.lang.String getLabel()
           
 int getNrOfEndTransitions()
           
 int getNrOfTransitions()
           
 int getNumber()
           
 java.util.ListIterator getTransitions()
           
 double getTransPriorScaler()
           
 int getVertexType()
           
 boolean hasTransitionTo(int vNr)
           
 void initializeTransitionProbabilities()
           
 void lock()
           
 void normalizeEmissProbs(int alphabet)
           
 void normalizeTransProbs()
           
 void setAndLockTransitionProbability(int toVertex, double probability)
           
 void setEmissPriorScaler(double d)
           
 void setEmissPriorScaler(int nr, double d)
           
 void setInitialEmissionProbs(double[] initDistrib)
           
 void setInitialEmissionProbs(int distribType)
           
 void setInitialEmissionProbs(int nr, double[] initDistrib)
           
 void setInitialEmissionProbs(int nr, int distribType)
           
 void setLabel(java.lang.String label)
           
 void setPreliminaryInitialEmissionProbs(int distribType)
           
 void setTransitionProbability(int toVertex, double probability)
           
 void setTransPriorScaler(double d)
           
 java.lang.String typeAsString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

transitions

java.util.Hashtable transitions

endTransitions

java.util.Hashtable endTransitions

transitionList

java.util.LinkedList transitionList

endTransitionList

java.util.LinkedList endTransitionList

emissions

double[] emissions

emissions_2

double[] emissions_2

emissions_3

double[] emissions_3

emissions_4

double[] emissions_4

hasEmissions

boolean hasEmissions

number

int number

nrOfTransitions

int nrOfTransitions

nrOfEndTransitions

int nrOfEndTransitions

vertexType

int vertexType

transPriorScaler

double transPriorScaler

emissPriorScaler

double emissPriorScaler

emissPriorScaler_2

double emissPriorScaler_2

emissPriorScaler_3

double emissPriorScaler_3

emissPriorScaler_4

double emissPriorScaler_4

label

java.lang.String label
Constructor Detail

Vertex

public Vertex(java.lang.String moduleName,
              int vertexType,
              int distribType,
              java.lang.String label)

Vertex

public Vertex(java.lang.String moduleName,
              int vertexType,
              double[] initDistrib,
              java.lang.String label)
Method Detail

hasTransitionTo

public boolean hasTransitionTo(int vNr)

getNumber

public int getNumber()

getLabel

public java.lang.String getLabel()

getVertexType

public int getVertexType()

typeAsString

public java.lang.String typeAsString()

getTransPriorScaler

public double getTransPriorScaler()

getEmissPriorScaler

public double getEmissPriorScaler()

getEmissPriorScaler

public double getEmissPriorScaler(int nr)

getTransitions

public java.util.ListIterator getTransitions()

getEndTransitions

public java.util.ListIterator getEndTransitions()

getNrOfTransitions

public int getNrOfTransitions()

getNrOfEndTransitions

public int getNrOfEndTransitions()

getEmissionProb

public double getEmissionProb(int pos)

getEmissionProb

public double getEmissionProb(int nr,
                              int pos)

getEmissionProbs

public double[] getEmissionProbs()

setLabel

public void setLabel(java.lang.String label)

setTransPriorScaler

public void setTransPriorScaler(double d)

setEmissPriorScaler

public void setEmissPriorScaler(double d)

setEmissPriorScaler

public void setEmissPriorScaler(int nr,
                                double d)

setTransitionProbability

public void setTransitionProbability(int toVertex,
                                     double probability)

setAndLockTransitionProbability

public void setAndLockTransitionProbability(int toVertex,
                                            double probability)

addTransition

public boolean addTransition(int toVertex,
                             double probability,
                             boolean isLocked)

addTransition

public boolean addTransition(int toVertex)

addEndTransition

public boolean addEndTransition(int toVertex)

initializeTransitionProbabilities

public void initializeTransitionProbabilities()

setInitialEmissionProbs

public void setInitialEmissionProbs(double[] initDistrib)

setInitialEmissionProbs

public void setInitialEmissionProbs(int nr,
                                    double[] initDistrib)

lock

public void lock()

normalizeEmissProbs

public void normalizeEmissProbs(int alphabet)

normalizeTransProbs

public void normalizeTransProbs()

setInitialEmissionProbs

public void setInitialEmissionProbs(int distribType)

setInitialEmissionProbs

public void setInitialEmissionProbs(int nr,
                                    int distribType)

setPreliminaryInitialEmissionProbs

public void setPreliminaryInitialEmissionProbs(int distribType)