Class HMM

java.lang.Object
  extended by HMM

 class HMM
extends java.lang.Object


Field Summary
static java.lang.String[] A
           
static java.lang.String[] A_double_gap
           
static java.lang.String[] A_gap
           
static java.lang.String[] alphabet
           
static java.lang.String[] alphabet_2
           
static java.lang.String[] alphabet_3
           
static java.lang.String[] alphabet_4
           
static int AMINO
           
static int AMINO_DOUBLE_GAP
           
static int AMINO_GAP
           
static int CLUSTER
           
static java.lang.String[] D
           
static int DELETE
           
static int DNA
           
static int END
           
static int ENDNODE
           
static int EVEN
           
static int FORWARD_ALT
           
static int FORWARD_STD
           
static int HIGHWAY
           
static int INSERT
           
static int LOCKED
           
static int LOCKED_EVEN
           
static int LOCKED_MANUAL
           
static int MANUAL
           
static int NOTYPE
           
(package private)  int nrOfAlphabets
           
(package private)  int nrOfDistributionGroups
           
(package private)  int nrOfDistributionGroupVertices
           
(package private)  int nrOfTransTieGroups
           
(package private)  int nrOfTransTieGroupVertices
           
static int OWN
           
static int PROFILE7
           
static int PROFILE9
           
static int RANDOM
           
static int SILENT
           
static int SINGLELOOP
           
static int SINGLENODE
           
static int STANDARD
           
static int START
           
static int STARTNODE
           
static int U_TURN
           
static int ZERO
           
 
Constructor Summary
HMM(java.lang.String name)
           
 
Method Summary
 void addDistributionGroup(java.util.LinkedList group)
           
 void addPriorfile(int nr, java.lang.String s)
           
 void addPriorfile(java.lang.String s)
           
 void addTransPriorfile(java.lang.String s)
           
 void addTransTieGroup(java.util.LinkedList group)
           
 int createModule(java.lang.String name, int moduleType, int distribType, int intervalStart, int intervalEnd, java.lang.String label)
           
 int createModule(java.lang.String name, int moduleType, int distribType, int size, java.lang.String label, boolean global)
          CREATE and ADD methods
 java.lang.String getAlphabet()
           
 java.lang.String getAlphabet2()
           
 java.lang.String getAlphabet3()
           
 java.lang.String getAlphabet4()
           
 int getAlphabetSize()
           
 int getAlphabetSize2()
           
 int getAlphabetSize3()
           
 int getAlphabetSize4()
           
 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 getNrOfAlphabets()
           
 int getNrOfDistributionGroups()
           
 int getNrOfDistributionGroupVertices()
           
 int getNrOfPriorfiles()
           
 int getNrOfPriorfiles(int nr)
           
 int getNrOfTransitions()
           
 int getNrOfTransPriorfiles()
           
 int getNrOfTransTieGroups()
           
 int getNrOfTransTieGroupVertices()
           
 int getNrVertices()
           
static int GETNUMBER()
           
 java.util.Iterator getPriorfiles()
           
 java.util.Iterator getPriorfiles(int nr)
           
 java.util.Iterator getTransPriorfiles()
           
 java.util.ListIterator getTransTieGroups()
           
 Vertex getVertex(int nr)
           
 boolean identicalModules(java.lang.String moduleA, java.lang.String moduleB)
           
 void initializeTransitionProbabilities(java.lang.String name)
          MISC methods
static void resetStatics()
           
 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 filename)
           
 void setInternalInitDistrib(java.lang.String name, InternalInitDistrib iid)
           
 void setNrOfAlphabets(int nr)
           
 void setTransition(java.lang.String fromModule, java.lang.String toModule)
           
 boolean transitionExists(int fromNr, int toNr)
           
 boolean writeModule(java.lang.String moduleName, java.io.BufferedWriter writer)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

AMINO

public static final int AMINO
See Also:
Constant Field Values

DNA

public static final int DNA
See Also:
Constant Field Values

AMINO_GAP

public static final int AMINO_GAP
See Also:
Constant Field Values

AMINO_DOUBLE_GAP

public static final int AMINO_DOUBLE_GAP
See Also:
Constant Field Values

OWN

public static final int OWN
See Also:
Constant Field Values

A

public static final java.lang.String[] A

D

public static final java.lang.String[] D

A_gap

public static final java.lang.String[] A_gap

A_double_gap

public static final java.lang.String[] A_double_gap

NOTYPE

public static final int NOTYPE
See Also:
Constant Field Values

SINGLENODE

public static final int SINGLENODE
See Also:
Constant Field Values

CLUSTER

public static final int CLUSTER
See Also:
Constant Field Values

HIGHWAY

public static final int HIGHWAY
See Also:
Constant Field Values

PROFILE7

public static final int PROFILE7
See Also:
Constant Field Values

PROFILE9

public static final int PROFILE9
See Also:
Constant Field Values

SINGLELOOP

public static final int SINGLELOOP
See Also:
Constant Field Values

FORWARD_STD

public static final int FORWARD_STD
See Also:
Constant Field Values

FORWARD_ALT

public static final int FORWARD_ALT
See Also:
Constant Field Values

U_TURN

public static final int U_TURN
See Also:
Constant Field Values

STARTNODE

public static final int STARTNODE
See Also:
Constant Field Values

ENDNODE

public static final int ENDNODE
See Also:
Constant Field Values

EVEN

public static final int EVEN
See Also:
Constant Field Values

ZERO

public static final int ZERO
See Also:
Constant Field Values

RANDOM

public static final int RANDOM
See Also:
Constant Field Values

MANUAL

public static final int MANUAL
See Also:
Constant Field Values

LOCKED_EVEN

public static final int LOCKED_EVEN
See Also:
Constant Field Values

LOCKED_MANUAL

public static final int LOCKED_MANUAL
See Also:
Constant Field Values

STANDARD

public static final int STANDARD
See Also:
Constant Field Values

SILENT

public static final int SILENT
See Also:
Constant Field Values

LOCKED

public static final int LOCKED
See Also:
Constant Field Values

INSERT

public static final int INSERT
See Also:
Constant Field Values

DELETE

public static final int DELETE
See Also:
Constant Field Values

START

public static final int START
See Also:
Constant Field Values

END

public static final int END
See Also:
Constant Field Values

alphabet

public static java.lang.String[] alphabet

alphabet_2

public static java.lang.String[] alphabet_2

alphabet_3

public static java.lang.String[] alphabet_3

alphabet_4

public static java.lang.String[] alphabet_4

nrOfDistributionGroups

int nrOfDistributionGroups

nrOfDistributionGroupVertices

int nrOfDistributionGroupVertices

nrOfTransTieGroups

int nrOfTransTieGroups

nrOfTransTieGroupVertices

int nrOfTransTieGroupVertices

nrOfAlphabets

int nrOfAlphabets
Constructor Detail

HMM

public HMM(java.lang.String name)
Method Detail

GETNUMBER

public static int GETNUMBER()

resetStatics

public static void resetStatics()

transitionExists

public boolean transitionExists(int fromNr,
                                int toNr)

getNrModules

public int getNrModules()

getNrOfDistributionGroups

public int getNrOfDistributionGroups()

getNrOfDistributionGroupVertices

public int getNrOfDistributionGroupVertices()

getNrOfTransTieGroups

public int getNrOfTransTieGroups()

getNrOfTransTieGroupVertices

public int getNrOfTransTieGroupVertices()

getNrVertices

public int getNrVertices()

getNrOfTransitions

public int getNrOfTransitions()

getName

public java.lang.String getName()

getFileName

public java.lang.String getFileName()

getNrOfAlphabets

public int getNrOfAlphabets()

getAlphabet

public java.lang.String getAlphabet()

getAlphabetSize

public int getAlphabetSize()

getAlphabet2

public java.lang.String getAlphabet2()

getAlphabetSize2

public int getAlphabetSize2()

getAlphabet3

public java.lang.String getAlphabet3()

getAlphabetSize3

public int getAlphabetSize3()

getAlphabet4

public java.lang.String getAlphabet4()

getAlphabetSize4

public int getAlphabetSize4()

getModuleKeys

public java.util.Enumeration getModuleKeys()

getModule

public Module getModule(java.lang.String name)

getVertex

public Vertex getVertex(int nr)

getModules

public java.util.ListIterator getModules()

getDistributionGroups

public java.util.ListIterator getDistributionGroups()

getTransTieGroups

public java.util.ListIterator getTransTieGroups()

getNrOfPriorfiles

public int getNrOfPriorfiles()

getNrOfPriorfiles

public int getNrOfPriorfiles(int nr)

getNrOfTransPriorfiles

public int getNrOfTransPriorfiles()

getPriorfiles

public java.util.Iterator getPriorfiles()

getPriorfiles

public java.util.Iterator getPriorfiles(int nr)

getTransPriorfiles

public java.util.Iterator getTransPriorfiles()

setFileName

public void setFileName(java.lang.String filename)

setNrOfAlphabets

public void setNrOfAlphabets(int nr)

setAlphabet

public void setAlphabet(int alphabet)

setAlphabet

public void setAlphabet(int nr,
                        int alphabet)

setAlphabet

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

setAlphabet

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

setTransition

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

setInternalInitDistrib

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

createModule

public int createModule(java.lang.String name,
                        int moduleType,
                        int distribType,
                        int size,
                        java.lang.String label,
                        boolean global)
CREATE and ADD methods


createModule

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

addDistributionGroup

public void addDistributionGroup(java.util.LinkedList group)

addPriorfile

public void addPriorfile(java.lang.String s)

addPriorfile

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

addTransPriorfile

public void addTransPriorfile(java.lang.String s)

addTransTieGroup

public void addTransTieGroup(java.util.LinkedList group)

initializeTransitionProbabilities

public void initializeTransitionProbabilities(java.lang.String name)
MISC methods


writeModule

public boolean writeModule(java.lang.String moduleName,
                           java.io.BufferedWriter writer)

identicalModules

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