Class ModelMaker

java.lang.Object
  extended by ModelMaker

 class ModelMaker
extends java.lang.Object


Field Summary
(package private)  HMMSaver hmmsaver
           
(package private)  HMM theHMM
           
 
Constructor Summary
ModelMaker()
           
 
Method Summary
 void addDistributionGroup(java.util.LinkedList group)
           
 void addPriorfile(int nr, java.lang.String s)
           
 void addPriorfile(java.lang.String s)
          add methods
 void addTransPriorfile(java.lang.String s)
           
 void addTransTieGroup(java.util.LinkedList transTieGroup)
           
 void createHMM(java.lang.String name)
          create-methods
 int createModule(java.lang.String name, int type, int distribType, int intervalStart, int intervalEnd, java.lang.String label)
           
 int createModule(java.lang.String name, int type, int distribType, int size, java.lang.String label)
           
 int createModule(java.lang.String name, int type, int distribType, int size, java.lang.String label, boolean global)
           
 int getAlphabetSize()
          get methods
 int getAlphabetSize(int nr)
           
 java.util.ListIterator getDistributionGroups()
           
 java.lang.String getFileName()
           
 Module getModule(java.lang.String name)
           
 java.util.Enumeration getModuleKeys()
           
 java.util.ListIterator getModules()
           
 java.lang.String getName()
           
 int getNrModules()
           
 int getNrVertices()
           
 java.util.ListIterator getTransTieGroups()
           
 Vertex getVertex(int nr)
           
 boolean identicalModules(java.lang.String moduleA, java.lang.String moduleB)
          misc methods
 void initializeTransitionProbabilities(java.lang.String moduleName)
           
 int saveHMM(java.lang.String outdir)
           
 void setAlphabet(int alphabet)
           
 void setAlphabet(int nr, int alphabet)
           
 void setAlphabet(int nr, java.lang.String[] alphabet)
           
 void setAlphabet(java.lang.String[] alphabet)
           
 void setFileName(java.lang.String s)
           
 void setInternalInitDistrib(java.lang.String name, InternalInitDistrib iid)
           
 void setNrOfAlphabets(int nr)
          set methods
 void setTransition(java.lang.String fromModule, java.lang.String toModule)
           
 boolean transitionExists(int fromNr, int toNr)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

theHMM

HMM theHMM

hmmsaver

HMMSaver hmmsaver
Constructor Detail

ModelMaker

public ModelMaker()
Method Detail

getAlphabetSize

public int getAlphabetSize()
get methods


getAlphabetSize

public int getAlphabetSize(int nr)

getNrVertices

public int getNrVertices()

getNrModules

public int getNrModules()

getName

public java.lang.String getName()

getFileName

public java.lang.String getFileName()

getVertex

public Vertex getVertex(int nr)

getModuleKeys

public java.util.Enumeration getModuleKeys()

getModules

public java.util.ListIterator getModules()

getModule

public Module getModule(java.lang.String name)

getDistributionGroups

public java.util.ListIterator getDistributionGroups()

getTransTieGroups

public java.util.ListIterator getTransTieGroups()

transitionExists

public boolean transitionExists(int fromNr,
                                int toNr)

createHMM

public void createHMM(java.lang.String name)
create-methods


createModule

public int createModule(java.lang.String name,
                        int type,
                        int distribType,
                        int size,
                        java.lang.String label)

createModule

public int createModule(java.lang.String name,
                        int type,
                        int distribType,
                        int intervalStart,
                        int intervalEnd,
                        java.lang.String label)

createModule

public int createModule(java.lang.String name,
                        int type,
                        int distribType,
                        int size,
                        java.lang.String label,
                        boolean global)

setNrOfAlphabets

public void setNrOfAlphabets(int nr)
set methods


setAlphabet

public void setAlphabet(int alphabet)

setAlphabet

public void setAlphabet(java.lang.String[] alphabet)

setAlphabet

public void setAlphabet(int nr,
                        int alphabet)

setAlphabet

public void setAlphabet(int nr,
                        java.lang.String[] alphabet)

setFileName

public void setFileName(java.lang.String s)

setTransition

public void setTransition(java.lang.String fromModule,
                          java.lang.String toModule)

setInternalInitDistrib

public void setInternalInitDistrib(java.lang.String name,
                                   InternalInitDistrib iid)

addPriorfile

public void addPriorfile(java.lang.String s)
add methods


addPriorfile

public void addPriorfile(int nr,
                         java.lang.String s)

addTransPriorfile

public void addTransPriorfile(java.lang.String s)

addDistributionGroup

public void addDistributionGroup(java.util.LinkedList group)

addTransTieGroup

public void addTransTieGroup(java.util.LinkedList transTieGroup)

identicalModules

public boolean identicalModules(java.lang.String moduleA,
                                java.lang.String moduleB)
misc methods


initializeTransitionProbabilities

public void initializeTransitionProbabilities(java.lang.String moduleName)

saveHMM

public int saveHMM(java.lang.String outdir)