Class Profile9
java.lang.Object
Module
Profile9
class Profile9
- extends Module
Constructor Summary |
Profile9(java.lang.String name,
double[] initDistrib,
int vertexType,
int size,
java.lang.String label,
boolean global)
|
Profile9(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 |
setTransDistribType(int distribType)
|
void |
setTransDistribType(int distribType,
double[] distribution)
|
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 |
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_DI_PROB
final double INIT_DI_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_ID_PROB
final double INIT_ID_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
Profile9
public Profile9(java.lang.String name,
int distribType,
int vertexType,
int size,
java.lang.String label,
boolean global)
Profile9
public Profile9(java.lang.String name,
double[] initDistrib,
int vertexType,
int size,
java.lang.String label,
boolean global)
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
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
getVertex
public Vertex getVertex(int nr)
- Specified by:
getVertex
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
setTransDistribType
public void setTransDistribType(int distribType,
double[] distribution)
setTransDistribType
public void setTransDistribType(int distribType)
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