Class Profile7

java.lang.Object
  extended by Module
      extended by Profile7

 class Profile7
extends Module


Field Summary
(package private)  int distribType
           
(package private)  int distribType_2
           
(package private)  int distribType_3
           
(package private)  int distribType_4
           
(package private)  double INIT_A_OPEN_PROB
           
(package private)  double INIT_DD_PROB
           
(package private)  double INIT_DM_PROB
           
(package private)  double INIT_EXIT_PROB
           
(package private)  double INIT_II_PROB
           
(package private)  double INIT_IM_PROB
           
(package private)  double INIT_MD_PROB
           
(package private)  double INIT_MI_PROB
           
(package private)  double INIT_MM_PROB
           
(package private)  double INIT_NA_CLOSE_PROB
           
(package private)  double INIT_NA_LOOP_PROB
           
(package private)  double INIT_NA_OPEN_PROB
           
(package private)  java.lang.String label
           
(package private)  java.lang.String name
           
(package private)  int nrVertices
           
(package private)  java.lang.String priorfile
           
(package private)  java.lang.String priorfile_2
           
(package private)  java.lang.String priorfile_3
           
(package private)  java.lang.String priorfile_4
           
(package private)  int size
           
(package private)  java.util.LinkedList theDeleteVertices
           
(package private)  java.util.LinkedList theInsertVertices
           
(package private)  java.util.LinkedList theMatchVertices
           
(package private)  Vertex[] theOutVertices
           
(package private)  java.util.LinkedList theVertices
           
(package private)  java.lang.String transPriorfile
           
(package private)  int vertexType
           
 
Fields inherited from class Module
inVertices, outVertices
 
Constructor Summary
Profile7(java.lang.String name, double[] initDistrib, int vertexType, int size, java.lang.String label, boolean global)
           
Profile7(java.lang.String name, int distribType, int vertexType, int size, java.lang.String label, boolean global)
           
 
Method Summary
 boolean addEndTransition(int toVertex)
           
 boolean addTransition(int toVertex)
           
 boolean addTransition(int fromVertex, int toVertex)
           
 void addVerticesToVertexHash(java.util.Hashtable theVerticesHash)
           
 int getDistribType()
           
 double[] getEmissionProbs()
           
 int[] getInVertices()
           
 java.lang.String getLabel()
           
 java.lang.String getName()
           
 int getNrOfEndTransitions()
           
 int getNrOfRegularTransitions()
           
 int getNrOfTransitions()
           
 int[] getOutVertices()
           
 java.lang.String getPriorfile()
           
 int getSize()
           
 Vertex getVertex(int nr)
           
 int getVertexType()
           
 java.util.LinkedList getVertices()
           
 void initializeTransitionProbabilities()
           
 void lockVertexEmissions()
           
 void setDistribType(int distribType)
           
 void setDistribType(int distribType, double[] distribution)
           
 void setDistribType(int nr, int distribType)
           
 void setDistribType(int nr, int distribType, double[] distribution)
           
 void setEmissPriorScaler(double d)
           
 void setEmissPriorScaler(int nr, double d)
           
 void setEmissPriorScalerInsert(int nr, double d)
           
 void setInternalInitDistrib(InternalInitDistrib iid)
           
 void setPriorfile(int nr, java.lang.String priorfile)
           
 void setPriorfile(java.lang.String priorfile)
           
 void setTransPriorfile(java.lang.String priorfile)
           
 void setTransPriorScaler(double d)
           
 boolean write(java.io.BufferedWriter writer)
           
 boolean write(int nrOfAlphabets, java.io.BufferedWriter writer)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

INIT_DD_PROB

final double INIT_DD_PROB
See Also:
Constant Field Values

INIT_DM_PROB

final double INIT_DM_PROB
See Also:
Constant Field Values

INIT_MD_PROB

final double INIT_MD_PROB
See Also:
Constant Field Values

INIT_MM_PROB

final double INIT_MM_PROB
See Also:
Constant Field Values

INIT_MI_PROB

final double INIT_MI_PROB
See Also:
Constant Field Values

INIT_EXIT_PROB

final double INIT_EXIT_PROB
See Also:
Constant Field Values

INIT_IM_PROB

final double INIT_IM_PROB
See Also:
Constant Field Values

INIT_II_PROB

final double INIT_II_PROB
See Also:
Constant Field Values

INIT_NA_CLOSE_PROB

final double INIT_NA_CLOSE_PROB
See Also:
Constant Field Values

INIT_NA_LOOP_PROB

final double INIT_NA_LOOP_PROB
See Also:
Constant Field Values

INIT_NA_OPEN_PROB

final double INIT_NA_OPEN_PROB
See Also:
Constant Field Values

INIT_A_OPEN_PROB

final double INIT_A_OPEN_PROB
See Also:
Constant Field Values

name

java.lang.String name

theVertices

java.util.LinkedList theVertices

theMatchVertices

java.util.LinkedList theMatchVertices

theDeleteVertices

java.util.LinkedList theDeleteVertices

theInsertVertices

java.util.LinkedList theInsertVertices

theOutVertices

Vertex[] theOutVertices

nrVertices

int nrVertices

vertexType

int vertexType

distribType

int distribType

distribType_2

int distribType_2

distribType_3

int distribType_3

distribType_4

int distribType_4

label

java.lang.String label

priorfile

java.lang.String priorfile

priorfile_2

java.lang.String priorfile_2

priorfile_3

java.lang.String priorfile_3

priorfile_4

java.lang.String priorfile_4

transPriorfile

java.lang.String transPriorfile

size

int size
Constructor Detail

Profile7

public Profile7(java.lang.String name,
                int distribType,
                int vertexType,
                int size,
                java.lang.String label,
                boolean global)

Profile7

public Profile7(java.lang.String name,
                double[] initDistrib,
                int vertexType,
                int size,
                java.lang.String label,
                boolean global)
Method Detail

getSize

public int getSize()
Specified by:
getSize in class Module

getName

public java.lang.String getName()
Specified by:
getName in class Module

getLabel

public java.lang.String getLabel()

getVertexType

public int getVertexType()
Specified by:
getVertexType in class Module

getDistribType

public int getDistribType()
Specified by:
getDistribType in class Module

getPriorfile

public java.lang.String getPriorfile()
Specified by:
getPriorfile in class Module

getEmissionProbs

public double[] getEmissionProbs()
Specified by:
getEmissionProbs in class Module

getInVertices

public int[] getInVertices()
Specified by:
getInVertices in class Module

getVertices

public java.util.LinkedList getVertices()
Specified by:
getVertices in class Module

getVertex

public Vertex getVertex(int nr)
Specified by:
getVertex in class Module

getNrOfTransitions

public int getNrOfTransitions()
Specified by:
getNrOfTransitions in class Module

getNrOfRegularTransitions

public int getNrOfRegularTransitions()
Specified by:
getNrOfRegularTransitions in class Module

getNrOfEndTransitions

public int getNrOfEndTransitions()
Specified by:
getNrOfEndTransitions in class Module

getOutVertices

public int[] getOutVertices()
Specified by:
getOutVertices in class Module

setTransPriorScaler

public void setTransPriorScaler(double d)
Specified by:
setTransPriorScaler in class Module

setEmissPriorScaler

public void setEmissPriorScaler(double d)
Specified by:
setEmissPriorScaler in class Module

setEmissPriorScaler

public void setEmissPriorScaler(int nr,
                                double d)
Specified by:
setEmissPriorScaler in class Module

setEmissPriorScalerInsert

public void setEmissPriorScalerInsert(int nr,
                                      double d)

lockVertexEmissions

public void lockVertexEmissions()
Specified by:
lockVertexEmissions in class Module

addVerticesToVertexHash

public void addVerticesToVertexHash(java.util.Hashtable theVerticesHash)
Specified by:
addVerticesToVertexHash in class Module

addTransition

public boolean addTransition(int fromVertex,
                             int toVertex)
Specified by:
addTransition in class Module

addTransition

public boolean addTransition(int toVertex)
Specified by:
addTransition in class Module

addEndTransition

public boolean addEndTransition(int toVertex)
Specified by:
addEndTransition in class Module

initializeTransitionProbabilities

public void initializeTransitionProbabilities()
Specified by:
initializeTransitionProbabilities in class Module

setDistribType

public void setDistribType(int distribType,
                           double[] distribution)
Specified by:
setDistribType in class Module

setDistribType

public void setDistribType(int nr,
                           int distribType,
                           double[] distribution)
Specified by:
setDistribType in class Module

setDistribType

public void setDistribType(int distribType)
Specified by:
setDistribType in class Module

setDistribType

public void setDistribType(int nr,
                           int distribType)
Specified by:
setDistribType in class Module

setPriorfile

public void setPriorfile(java.lang.String priorfile)
Specified by:
setPriorfile in class Module

setPriorfile

public void setPriorfile(int nr,
                         java.lang.String priorfile)
Specified by:
setPriorfile in class Module

setTransPriorfile

public void setTransPriorfile(java.lang.String priorfile)
Specified by:
setTransPriorfile in class Module

setInternalInitDistrib

public void setInternalInitDistrib(InternalInitDistrib iid)
Specified by:
setInternalInitDistrib in class Module

write

public boolean write(java.io.BufferedWriter writer)

write

public boolean write(int nrOfAlphabets,
                     java.io.BufferedWriter writer)
Specified by:
write in class Module