A B C D E F G H I L M N O P R S T U V W Z

A

A - Static variable in class HMM
 
A_double_gap - Static variable in class HMM
 
A_gap - Static variable in class HMM
 
addDistributionGroup(LinkedList) - Method in class HMM
 
addDistributionGroup(LinkedList) - Method in class ModelMaker
 
addEndTransition(int) - Method in class Cluster
 
addEndTransition(int) - Method in class Forward_alt
 
addEndTransition(int) - Method in class Forward_std
 
addEndTransition(int) - Method in class Highway
 
addEndTransition(int) - Method in class Module
 
addEndTransition(int) - Method in class Profile7
 
addEndTransition(int) - Method in class Profile9
 
addEndTransition(int) - Method in class SingleLoop
 
addEndTransition(int) - Method in class SingleNode
 
addEndTransition(int) - Method in class U_Turn
 
addEndTransition(int) - Method in class Vertex
 
addPriorfile(String) - Method in class HMM
 
addPriorfile(int, String) - Method in class HMM
 
addPriorfile(String) - Method in class ModelMaker
add methods
addPriorfile(int, String) - Method in class ModelMaker
 
addTransition(int, int) - Method in class Cluster
 
addTransition(int) - Method in class Cluster
 
addTransition(int, int) - Method in class Forward_alt
 
addTransition(int) - Method in class Forward_alt
 
addTransition(int, int) - Method in class Forward_std
 
addTransition(int) - Method in class Forward_std
 
addTransition(int, int) - Method in class Highway
 
addTransition(int) - Method in class Highway
 
addTransition(int, int) - Method in class Module
 
addTransition(int) - Method in class Module
 
addTransition(int, int) - Method in class Profile7
 
addTransition(int) - Method in class Profile7
 
addTransition(int, int) - Method in class Profile9
 
addTransition(int) - Method in class Profile9
 
addTransition(int, int) - Method in class SingleLoop
 
addTransition(int) - Method in class SingleLoop
 
addTransition(int, int) - Method in class SingleNode
 
addTransition(int) - Method in class SingleNode
 
addTransition(int, int) - Method in class U_Turn
 
addTransition(int) - Method in class U_Turn
 
addTransition(int, double, boolean) - Method in class Vertex
 
addTransition(int) - Method in class Vertex
 
addTransPriorfile(String) - Method in class HMM
 
addTransPriorfile(String) - Method in class ModelMaker
 
addTransTieGroup(LinkedList) - Method in class HMM
 
addTransTieGroup(LinkedList) - Method in class ModelMaker
 
addVerticesToVertexHash(Hashtable) - Method in class Cluster
 
addVerticesToVertexHash(Hashtable) - Method in class Forward_alt
 
addVerticesToVertexHash(Hashtable) - Method in class Forward_std
 
addVerticesToVertexHash(Hashtable) - Method in class Highway
 
addVerticesToVertexHash(Hashtable) - Method in class Module
 
addVerticesToVertexHash(Hashtable) - Method in class Profile7
 
addVerticesToVertexHash(Hashtable) - Method in class Profile9
 
addVerticesToVertexHash(Hashtable) - Method in class SingleLoop
 
addVerticesToVertexHash(Hashtable) - Method in class SingleNode
 
addVerticesToVertexHash(Hashtable) - Method in class U_Turn
 
alphabet - Static variable in class HMM
 
alphabet_2 - Static variable in class HMM
 
alphabet_3 - Static variable in class HMM
 
alphabet_4 - Static variable in class HMM
 
AMINO - Static variable in class HMM
 
AMINO_DOUBLE_GAP - Static variable in class HMM
 
AMINO_GAP - Static variable in class HMM
 

B

beta(double, double) - Static method in class BetaGamma
Returns the beta function of the arguments.
BetaGamma - Class in <Unnamed>
Gamma and Beta functions.
BetaGamma() - Constructor for class BetaGamma
Makes this class non instantiable, but still let's others inherit from it.
BI - Variable in class Forward_alt
 
BI - Variable in class Forward_std
 
big - Static variable in class Constants
 
biginv - Static variable in class Constants
 

C

Cluster - Class in <Unnamed>
 
Cluster(String, int, int, int, String) - Constructor for class Cluster
 
Cluster(String, double[], int, int, String) - Constructor for class Cluster
 
CLUSTER - Static variable in class HMM
 
Constants - Class in <Unnamed>
Defines some useful constants.
Constants() - Constructor for class Constants
Makes this class non instantiable, but still let's others inherit from it.
createHMM(String) - Method in class ModelMaker
create-methods
createModule(String, int, int, int, String, boolean) - Method in class HMM
CREATE and ADD methods
createModule(String, int, int, int, int, String) - Method in class HMM
 
createModule(String, int, int, int, String) - Method in class ModelMaker
 
createModule(String, int, int, int, int, String) - Method in class ModelMaker
 
createModule(String, int, int, int, String, boolean) - Method in class ModelMaker
 

D

D - Static variable in class HMM
 
DataReaderMultiAlpha - Class in <Unnamed>
 
DataReaderMultiAlpha() - Constructor for class DataReaderMultiAlpha
 
DEBUG(String) - Static method in class P
 
DELETE - Static variable in class HMM
 
distrib - Variable in class InternalInitDistrib
 
distribType - Variable in class Cluster
 
distribType - Variable in class Forward_alt
 
distribType - Variable in class Forward_std
 
distribType - Variable in class Highway
 
distribType - Variable in class Profile7
 
distribType - Variable in class Profile9
 
distribType - Variable in class SingleLoop
 
distribType - Variable in class SingleNode
 
distribType - Variable in class U_Turn
 
distribType_2 - Variable in class Cluster
 
distribType_2 - Variable in class Forward_alt
 
distribType_2 - Variable in class Forward_std
 
distribType_2 - Variable in class Highway
 
distribType_2 - Variable in class Profile7
 
distribType_2 - Variable in class Profile9
 
distribType_2 - Variable in class SingleLoop
 
distribType_2 - Variable in class SingleNode
 
distribType_2 - Variable in class U_Turn
 
distribType_3 - Variable in class Cluster
 
distribType_3 - Variable in class Forward_alt
 
distribType_3 - Variable in class Forward_std
 
distribType_3 - Variable in class Highway
 
distribType_3 - Variable in class Profile7
 
distribType_3 - Variable in class Profile9
 
distribType_3 - Variable in class SingleLoop
 
distribType_3 - Variable in class SingleNode
 
distribType_3 - Variable in class U_Turn
 
distribType_4 - Variable in class Cluster
 
distribType_4 - Variable in class Forward_alt
 
distribType_4 - Variable in class Forward_std
 
distribType_4 - Variable in class Highway
 
distribType_4 - Variable in class Profile7
 
distribType_4 - Variable in class Profile9
 
distribType_4 - Variable in class SingleLoop
 
distribType_4 - Variable in class SingleNode
 
distribType_4 - Variable in class U_Turn
 
DNA - Static variable in class HMM
 

E

Emission - Class in <Unnamed>
 
Emission(double, char) - Constructor for class Emission
 
emissions - Variable in class Vertex
 
emissions_2 - Variable in class Vertex
 
emissions_3 - Variable in class Vertex
 
emissions_4 - Variable in class Vertex
 
emissPriorScaler - Variable in class Vertex
 
emissPriorScaler_2 - Variable in class Vertex
 
emissPriorScaler_3 - Variable in class Vertex
 
emissPriorScaler_4 - Variable in class Vertex
 
END - Static variable in class HMM
 
ENDNODE - Static variable in class HMM
 
endTransitionList - Variable in class Vertex
 
endTransitions - Variable in class Vertex
 
EVEN - Static variable in class HMM
 

F

Forward_alt - Class in <Unnamed>
 
Forward_alt(String, int, int, int, int, String) - Constructor for class Forward_alt
 
Forward_alt(String, double[], int, int, int, String) - Constructor for class Forward_alt
 
FORWARD_ALT - Static variable in class HMM
 
Forward_std - Class in <Unnamed>
 
Forward_std(String, int, int, int, int, String) - Constructor for class Forward_std
 
Forward_std(String, double[], int, int, int, String) - Constructor for class Forward_std
 
FORWARD_STD - Static variable in class HMM
 

G

gamma(double) - Static method in class BetaGamma
Returns the Gamma function of the argument.
getAlphabet() - Method in class HMM
 
getAlphabet2() - Method in class HMM
 
getAlphabet3() - Method in class HMM
 
getAlphabet4() - Method in class HMM
 
getAlphabetSize() - Method in class HMM
 
getAlphabetSize() - Method in class ModelMaker
get methods
getAlphabetSize(int) - Method in class ModelMaker
 
getAlphabetSize2() - Method in class HMM
 
getAlphabetSize3() - Method in class HMM
 
getAlphabetSize4() - Method in class HMM
 
getDistrib() - Method in class InternalInitDistrib
 
getDistribType() - Method in class Cluster
 
getDistribType() - Method in class Forward_alt
 
getDistribType() - Method in class Forward_std
 
getDistribType() - Method in class Highway
 
getDistribType() - Method in class Module
 
getDistribType() - Method in class Profile7
 
getDistribType() - Method in class Profile9
 
getDistribType() - Method in class SingleLoop
 
getDistribType() - Method in class SingleNode
 
getDistribType() - Method in class U_Turn
 
getDistributionGroups() - Method in class HMM
 
getDistributionGroups() - Method in class ModelMaker
 
getEmissionProb(int) - Method in class Vertex
 
getEmissionProb(int, int) - Method in class Vertex
 
getEmissionProbs() - Method in class Cluster
 
getEmissionProbs() - Method in class Forward_alt
 
getEmissionProbs() - Method in class Forward_std
 
getEmissionProbs() - Method in class Highway
 
getEmissionProbs() - Method in class Module
 
getEmissionProbs() - Method in class Profile7
 
getEmissionProbs() - Method in class Profile9
 
getEmissionProbs() - Method in class SingleLoop
 
getEmissionProbs() - Method in class SingleNode
 
getEmissionProbs() - Method in class U_Turn
 
getEmissionProbs() - Method in class Vertex
 
getEmissPriorScaler() - Method in class Vertex
 
getEmissPriorScaler(int) - Method in class Vertex
 
getEndTransitions() - Method in class Vertex
 
getFileName() - Method in class HMM
 
getFileName() - Method in class ModelMaker
 
getInVertices() - Method in class Cluster
 
getInVertices() - Method in class Forward_alt
 
getInVertices() - Method in class Forward_std
 
getInVertices() - Method in class Highway
 
getInVertices() - Method in class Module
 
getInVertices() - Method in class Profile7
 
getInVertices() - Method in class Profile9
 
getInVertices() - Method in class SingleLoop
 
getInVertices() - Method in class SingleNode
 
getInVertices() - Method in class U_Turn
 
getLabel() - Method in class Cluster
 
getLabel() - Method in class Forward_alt
 
getLabel() - Method in class Forward_std
 
getLabel() - Method in class Highway
 
getLabel() - Method in class Profile7
 
getLabel() - Method in class Profile9
 
getLabel() - Method in class SingleLoop
 
getLabel() - Method in class SingleNode
 
getLabel() - Method in class U_Turn
 
getLabel() - Method in class Vertex
 
getLetter() - Method in class Emission
 
getModule(String) - Method in class HMM
 
getModule(String) - Method in class ModelMaker
 
getModuleKeys() - Method in class HMM
 
getModuleKeys() - Method in class ModelMaker
 
getModules() - Method in class HMM
 
getModules() - Method in class ModelMaker
 
getName() - Method in class Cluster
 
getName() - Method in class Forward_alt
 
getName() - Method in class Forward_std
 
getName() - Method in class Highway
 
getName() - Method in class HMM
 
getName() - Method in class ModelMaker
 
getName() - Method in class Module
 
getName() - Method in class Profile7
 
getName() - Method in class Profile9
 
getName() - Method in class SingleLoop
 
getName() - Method in class SingleNode
 
getName() - Method in class U_Turn
 
getNrModules() - Method in class HMM
 
getNrModules() - Method in class ModelMaker
 
getNrOfAlphabets() - Method in class HMM
 
getNrOfDistributionGroups() - Method in class HMM
 
getNrOfDistributionGroupVertices() - Method in class HMM
 
getNrOfEndTransitions() - Method in class Cluster
 
getNrOfEndTransitions() - Method in class Forward_alt
 
getNrOfEndTransitions() - Method in class Forward_std
 
getNrOfEndTransitions() - Method in class Highway
 
getNrOfEndTransitions() - Method in class Module
 
getNrOfEndTransitions() - Method in class Profile7
 
getNrOfEndTransitions() - Method in class Profile9
 
getNrOfEndTransitions() - Method in class SingleLoop
 
getNrOfEndTransitions() - Method in class SingleNode
 
getNrOfEndTransitions() - Method in class U_Turn
 
getNrOfEndTransitions() - Method in class Vertex
 
getNrOfPriorfiles() - Method in class HMM
 
getNrOfPriorfiles(int) - Method in class HMM
 
getNrOfRegularTransitions() - Method in class Cluster
 
getNrOfRegularTransitions() - Method in class Forward_alt
 
getNrOfRegularTransitions() - Method in class Forward_std
 
getNrOfRegularTransitions() - Method in class Highway
 
getNrOfRegularTransitions() - Method in class Module
 
getNrOfRegularTransitions() - Method in class Profile7
 
getNrOfRegularTransitions() - Method in class Profile9
 
getNrOfRegularTransitions() - Method in class SingleLoop
 
getNrOfRegularTransitions() - Method in class SingleNode
 
getNrOfRegularTransitions() - Method in class U_Turn
 
getNrOfTransitions() - Method in class Cluster
 
getNrOfTransitions() - Method in class Forward_alt
 
getNrOfTransitions() - Method in class Forward_std
 
getNrOfTransitions() - Method in class Highway
 
getNrOfTransitions() - Method in class HMM
 
getNrOfTransitions() - Method in class Module
 
getNrOfTransitions() - Method in class Profile7
 
getNrOfTransitions() - Method in class Profile9
 
getNrOfTransitions() - Method in class SingleLoop
 
getNrOfTransitions() - Method in class SingleNode
 
getNrOfTransitions() - Method in class U_Turn
 
getNrOfTransitions() - Method in class Vertex
 
getNrOfTransPriorfiles() - Method in class HMM
 
getNrOfTransTieGroups() - Method in class HMM
 
getNrOfTransTieGroupVertices() - Method in class HMM
 
getNrVertices() - Method in class HMM
 
getNrVertices() - Method in class ModelMaker
 
GETNUMBER() - Static method in class HMM
 
getNumber() - Method in class Vertex
 
getOutVertices() - Method in class Cluster
 
getOutVertices() - Method in class Forward_alt
 
getOutVertices() - Method in class Forward_std
 
getOutVertices() - Method in class Highway
 
getOutVertices() - Method in class Module
 
getOutVertices() - Method in class Profile7
 
getOutVertices() - Method in class Profile9
 
getOutVertices() - Method in class SingleLoop
 
getOutVertices() - Method in class SingleNode
 
getOutVertices() - Method in class U_Turn
 
getPar1() - Method in class InternalInitDistrib
 
getPar2() - Method in class InternalInitDistrib
 
getPar3() - Method in class InternalInitDistrib
 
getPriorfile() - Method in class Cluster
 
getPriorfile() - Method in class Forward_alt
 
getPriorfile() - Method in class Forward_std
 
getPriorfile() - Method in class Highway
 
getPriorfile() - Method in class Module
 
getPriorfile() - Method in class Profile7
 
getPriorfile() - Method in class Profile9
 
getPriorfile() - Method in class SingleLoop
 
getPriorfile() - Method in class SingleNode
 
getPriorfile() - Method in class U_Turn
 
getPriorfiles() - Method in class HMM
 
getPriorfiles(int) - Method in class HMM
 
getProbability() - Method in class Emission
 
getProbability() - Method in class Transition
 
getSize() - Method in class Cluster
 
getSize() - Method in class Forward_alt
 
getSize() - Method in class Forward_std
 
getSize() - Method in class Highway
 
getSize() - Method in class Module
 
getSize() - Method in class Profile7
 
getSize() - Method in class Profile9
 
getSize() - Method in class SingleLoop
 
getSize() - Method in class SingleNode
 
getSize() - Method in class U_Turn
 
getToVertex() - Method in class Transition
 
getTransitions() - Method in class Vertex
 
getTransPriorfiles() - Method in class HMM
 
getTransPriorScaler() - Method in class Vertex
 
getTransTieGroups() - Method in class HMM
 
getTransTieGroups() - Method in class ModelMaker
 
getVertex(int) - Method in class Cluster
 
getVertex(int) - Method in class Forward_alt
 
getVertex(int) - Method in class Forward_std
 
getVertex(int) - Method in class Highway
 
getVertex(int) - Method in class HMM
 
getVertex(int) - Method in class ModelMaker
 
getVertex(int) - Method in class Module
 
getVertex(int) - Method in class Profile7
 
getVertex(int) - Method in class Profile9
 
getVertex(int) - Method in class SingleLoop
 
getVertex(int) - Method in class SingleNode
 
getVertex(int) - Method in class U_Turn
 
getVertexType() - Method in class Cluster
 
getVertexType() - Method in class Forward_alt
 
getVertexType() - Method in class Forward_std
 
getVertexType() - Method in class Highway
 
getVertexType() - Method in class Module
 
getVertexType() - Method in class Profile7
 
getVertexType() - Method in class Profile9
 
getVertexType() - Method in class SingleLoop
 
getVertexType() - Method in class SingleNode
 
getVertexType() - Method in class U_Turn
 
getVertexType() - Method in class Vertex
 
getVertices() - Method in class Cluster
 
getVertices() - Method in class Forward_alt
 
getVertices() - Method in class Forward_std
 
getVertices() - Method in class Highway
 
getVertices() - Method in class Module
 
getVertices() - Method in class Profile7
 
getVertices() - Method in class Profile9
 
getVertices() - Method in class SingleLoop
 
getVertices() - Method in class SingleNode
 
getVertices() - Method in class U_Turn
 

H

hasEmissions - Variable in class Vertex
 
hasTransitionTo(int) - Method in class Vertex
 
Highway - Class in <Unnamed>
 
Highway(String, int, int, int, String) - Constructor for class Highway
 
Highway(String, double[], int, int, String) - Constructor for class Highway
 
HIGHWAY - Static variable in class HMM
 
HMM - Class in <Unnamed>
 
HMM(String) - Constructor for class HMM
 
HMMSaver - Class in <Unnamed>
 
HMMSaver(HMM) - Constructor for class HMMSaver
 
hmmsaver - Variable in class ModelMaker
 

I

identicalModules(String, String) - Method in class HMM
 
identicalModules(String, String) - Method in class ModelMaker
misc methods
incompleteBeta(double, double, double) - Static method in class BetaGamma
Returns the Incomplete Beta Function evaluated from zero to xx; formerly named ibeta.
incompleteBetaFraction1(double, double, double) - Static method in class BetaGamma
Continued fraction expansion #1 for incomplete beta integral; formerly named incbcf.
incompleteBetaFraction2(double, double, double) - Static method in class BetaGamma
Continued fraction expansion #2 for incomplete beta integral; formerly named incbd.
incompleteGamma(double, double) - Static method in class BetaGamma
Returns the Incomplete Gamma function; formerly named igamma.
incompleteGammaComplement(double, double) - Static method in class BetaGamma
Returns the Complemented Incomplete Gamma function; formerly named igamc.
INIT_A_OPEN_PROB - Variable in class Profile7
 
INIT_A_OPEN_PROB - Variable in class Profile9
 
INIT_DD_PROB - Variable in class Profile7
 
INIT_DD_PROB - Variable in class Profile9
 
INIT_DI_PROB - Variable in class Profile9
 
INIT_DM_PROB - Variable in class Profile7
 
INIT_DM_PROB - Variable in class Profile9
 
INIT_EXIT_PROB - Variable in class Profile7
 
INIT_EXIT_PROB - Variable in class Profile9
 
INIT_ID_PROB - Variable in class Profile9
 
INIT_II_PROB - Variable in class Profile7
 
INIT_II_PROB - Variable in class Profile9
 
INIT_IM_PROB - Variable in class Profile7
 
INIT_IM_PROB - Variable in class Profile9
 
INIT_MD_PROB - Variable in class Profile7
 
INIT_MD_PROB - Variable in class Profile9
 
INIT_MI_PROB - Variable in class Profile7
 
INIT_MI_PROB - Variable in class Profile9
 
INIT_MM_PROB - Variable in class Profile7
 
INIT_MM_PROB - Variable in class Profile9
 
INIT_NA_CLOSE_PROB - Variable in class Profile7
 
INIT_NA_CLOSE_PROB - Variable in class Profile9
 
INIT_NA_LOOP_PROB - Variable in class Profile7
 
INIT_NA_LOOP_PROB - Variable in class Profile9
 
INIT_NA_OPEN_PROB - Variable in class Profile7
 
INIT_NA_OPEN_PROB - Variable in class Profile9
 
initializeTransitionProbabilities() - Method in class Cluster
 
initializeTransitionProbabilities() - Method in class Forward_alt
 
initializeTransitionProbabilities() - Method in class Forward_std
 
initializeTransitionProbabilities() - Method in class Highway
 
initializeTransitionProbabilities(String) - Method in class HMM
MISC methods
initializeTransitionProbabilities(String) - Method in class ModelMaker
 
initializeTransitionProbabilities() - Method in class Module
 
initializeTransitionProbabilities() - Method in class Profile7
 
initializeTransitionProbabilities() - Method in class Profile9
 
initializeTransitionProbabilities() - Method in class SingleLoop
 
initializeTransitionProbabilities() - Method in class SingleNode
 
initializeTransitionProbabilities() - Method in class U_Turn
 
initializeTransitionProbabilities() - Method in class Vertex
 
INSERT - Static variable in class HMM
 
INTERNAL_ERROR(String) - Static method in class P
 
InternalInitDistrib - Class in <Unnamed>
 
InternalInitDistrib() - Constructor for class InternalInitDistrib
 
intervalEnd - Variable in class Forward_alt
 
intervalEnd - Variable in class Forward_std
 
intervalStart - Variable in class Forward_alt
 
intervalStart - Variable in class Forward_std
 
inVertex - Variable in class Forward_alt
 
inVertex - Variable in class Forward_std
 
inVertex - Variable in class Highway
 
inVertex - Variable in class U_Turn
 
inVertices - Variable in class Module
 
isLocked - Variable in class Transition
 
isLocked() - Method in class Transition
 

L

label - Variable in class Cluster
 
label - Variable in class Forward_alt
 
label - Variable in class Forward_std
 
label - Variable in class Highway
 
label - Variable in class Profile7
 
label - Variable in class Profile9
 
label - Variable in class SingleLoop
 
label - Variable in class SingleNode
 
label - Variable in class U_Turn
 
label - Variable in class Vertex
 
length - Variable in class SingleLoop
 
letter - Variable in class Emission
 
lock() - Method in class Transition
 
lock() - Method in class Vertex
 
LOCKED - Static variable in class HMM
 
LOCKED_EVEN - Static variable in class HMM
 
LOCKED_MANUAL - Static variable in class HMM
 
lockVertexEmissions() - Method in class Cluster
 
lockVertexEmissions() - Method in class Forward_alt
 
lockVertexEmissions() - Method in class Forward_std
 
lockVertexEmissions() - Method in class Highway
 
lockVertexEmissions() - Method in class Module
 
lockVertexEmissions() - Method in class Profile7
 
lockVertexEmissions() - Method in class Profile9
 
lockVertexEmissions() - Method in class SingleLoop
 
lockVertexEmissions() - Method in class SingleNode
 
lockVertexEmissions() - Method in class U_Turn
 
logGamma(double) - Static method in class BetaGamma
Returns the natural logarithm of the gamma function; formerly named lgamma.
LOGPI - Static variable in class Constants
 

M

m_Po - Variable in class Forward_std
 
MACHEP - Static variable in class Constants
 
main(String[]) - Static method in class modhmmc
 
MANUAL - Static variable in class HMM
 
MAXGAM - Static variable in class Constants
 
MAXLOG - Static variable in class Constants
 
MESSAGE(String) - Static method in class P
 
MINLOG - Static variable in class Constants
 
modelmaker - Variable in class DataReaderMultiAlpha
 
ModelMaker - Class in <Unnamed>
 
ModelMaker() - Constructor for class ModelMaker
 
modhmmc - Class in <Unnamed>
 
modhmmc() - Constructor for class modhmmc
 
Module - Class in <Unnamed>
 
Module() - Constructor for class Module
 

N

name - Variable in class Cluster
 
name - Variable in class Forward_alt
 
name - Variable in class Forward_std
 
name - Variable in class Highway
 
name - Variable in class Profile7
 
name - Variable in class Profile9
 
name - Variable in class SingleLoop
 
name - Variable in class SingleNode
 
name - Variable in class U_Turn
 
normalizeEmissProbs(int) - Method in class Vertex
 
normalizeTransProbs() - Method in class Vertex
 
NOTYPE - Static variable in class HMM
 
nrOfAlphabets - Variable in class HMM
 
nrOfDistributionGroups - Variable in class HMM
 
nrOfDistributionGroupVertices - Variable in class HMM
 
nrOfEndTransitions - Variable in class Vertex
 
nrOfTransitions - Variable in class Vertex
 
nrOfTransTieGroups - Variable in class HMM
 
nrOfTransTieGroupVertices - Variable in class HMM
 
nrVertices - Variable in class Cluster
 
nrVertices - Variable in class Forward_alt
 
nrVertices - Variable in class Forward_std
 
nrVertices - Variable in class Highway
 
nrVertices - Variable in class Profile7
 
nrVertices - Variable in class Profile9
 
nrVertices - Variable in class U_Turn
 
number - Variable in class Vertex
 

O

outVertex - Variable in class Forward_alt
 
outVertex - Variable in class Forward_std
 
outVertex - Variable in class Highway
 
outVertex_end - Variable in class U_Turn
 
outVertex_start - Variable in class U_Turn
 
outVertices - Variable in class Module
 
OWN - Static variable in class HMM
 

P

P - Class in <Unnamed>
 
P() - Constructor for class P
 
p1evl(double, double[], int) - Static method in class Polynomial
Evaluates the given polynomial of degree N at x, assuming coefficient of N is 1.0.
par1 - Variable in class InternalInitDistrib
 
par2 - Variable in class InternalInitDistrib
 
par3 - Variable in class InternalInitDistrib
 
pathSize - Variable in class U_Turn
 
PO - Variable in class Forward_alt
 
PO - Variable in class Forward_std
 
polevl(double, double[], int) - Static method in class Polynomial
Evaluates the given polynomial of degree N at x.
Polynomial - Class in <Unnamed>
Polynomial functions.
Polynomial() - Constructor for class Polynomial
Makes this class non instantiable, but still let's others inherit from it.
powerSeries(double, double, double) - Static method in class BetaGamma
Power series for incomplete beta integral; formerly named pseries.
priorfile - Variable in class Cluster
 
priorfile - Variable in class Forward_alt
 
priorfile - Variable in class Forward_std
 
priorfile - Variable in class Highway
 
priorfile - Variable in class Module
 
priorfile - Variable in class Profile7
 
priorfile - Variable in class Profile9
 
priorfile - Variable in class SingleLoop
 
priorfile - Variable in class SingleNode
 
priorfile - Variable in class U_Turn
 
priorfile_2 - Variable in class Cluster
 
priorfile_2 - Variable in class Forward_alt
 
priorfile_2 - Variable in class Forward_std
 
priorfile_2 - Variable in class Highway
 
priorfile_2 - Variable in class Profile7
 
priorfile_2 - Variable in class Profile9
 
priorfile_2 - Variable in class SingleLoop
 
priorfile_2 - Variable in class SingleNode
 
priorfile_2 - Variable in class U_Turn
 
priorfile_3 - Variable in class Cluster
 
priorfile_3 - Variable in class Forward_alt
 
priorfile_3 - Variable in class Forward_std
 
priorfile_3 - Variable in class Highway
 
priorfile_3 - Variable in class Profile7
 
priorfile_3 - Variable in class Profile9
 
priorfile_3 - Variable in class SingleLoop
 
priorfile_3 - Variable in class SingleNode
 
priorfile_3 - Variable in class U_Turn
 
priorfile_4 - Variable in class Cluster
 
priorfile_4 - Variable in class Forward_alt
 
priorfile_4 - Variable in class Forward_std
 
priorfile_4 - Variable in class Highway
 
priorfile_4 - Variable in class Profile7
 
priorfile_4 - Variable in class Profile9
 
priorfile_4 - Variable in class SingleLoop
 
priorfile_4 - Variable in class SingleNode
 
priorfile_4 - Variable in class U_Turn
 
probability - Variable in class Emission
 
probability - Variable in class Transition
 
PROFILE7 - Static variable in class HMM
 
Profile7 - Class in <Unnamed>
 
Profile7(String, int, int, int, String, boolean) - Constructor for class Profile7
 
Profile7(String, double[], int, int, String, boolean) - Constructor for class Profile7
 
PROFILE9 - Static variable in class HMM
 
Profile9 - Class in <Unnamed>
 
Profile9(String, int, int, int, String, boolean) - Constructor for class Profile9
 
Profile9(String, double[], int, int, String, boolean) - Constructor for class Profile9
 

R

RANDOM - Static variable in class HMM
 
reader - Variable in class DataReaderMultiAlpha
 
resetStatics() - Static method in class HMM
 

S

saveHMM(String) - Method in class HMMSaver
 
saveHMM(String) - Method in class ModelMaker
 
setAlphabet(int) - Method in class HMM
 
setAlphabet(int, int) - Method in class HMM
 
setAlphabet(String[]) - Method in class HMM
 
setAlphabet(int, String[]) - Method in class HMM
 
setAlphabet(int) - Method in class ModelMaker
 
setAlphabet(String[]) - Method in class ModelMaker
 
setAlphabet(int, int) - Method in class ModelMaker
 
setAlphabet(int, String[]) - Method in class ModelMaker
 
setAndLockTransitionProbability(int, double) - Method in class Vertex
 
setBinomial(int) - Method in class Forward_alt
 
setBinomial(int) - Method in class Forward_std
 
setDistrib(String) - Method in class InternalInitDistrib
 
setDistribType(int, double[]) - Method in class Cluster
 
setDistribType(int, int, double[]) - Method in class Cluster
 
setDistribType(int) - Method in class Cluster
 
setDistribType(int, int) - Method in class Cluster
 
setDistribType(int, double[]) - Method in class Forward_alt
 
setDistribType(int, int, double[]) - Method in class Forward_alt
 
setDistribType(int) - Method in class Forward_alt
 
setDistribType(int, int) - Method in class Forward_alt
 
setDistribType(int, double[]) - Method in class Forward_std
 
setDistribType(int, int, double[]) - Method in class Forward_std
 
setDistribType(int) - Method in class Forward_std
 
setDistribType(int, int) - Method in class Forward_std
 
setDistribType(int, double[]) - Method in class Highway
 
setDistribType(int, int, double[]) - Method in class Highway
 
setDistribType(int) - Method in class Highway
 
setDistribType(int, int) - Method in class Highway
 
setDistribType(int, double[]) - Method in class Module
 
setDistribType(int) - Method in class Module
 
setDistribType(int, int, double[]) - Method in class Module
 
setDistribType(int, int) - Method in class Module
 
setDistribType(int, double[]) - Method in class Profile7
 
setDistribType(int, int, double[]) - Method in class Profile7
 
setDistribType(int) - Method in class Profile7
 
setDistribType(int, int) - Method in class Profile7
 
setDistribType(int, double[]) - Method in class Profile9
 
setDistribType(int, int, double[]) - Method in class Profile9
 
setDistribType(int) - Method in class Profile9
 
setDistribType(int, int) - Method in class Profile9
 
setDistribType(int, double[]) - Method in class SingleLoop
 
setDistribType(int, int, double[]) - Method in class SingleLoop
 
setDistribType(int) - Method in class SingleLoop
 
setDistribType(int, int) - Method in class SingleLoop
 
setDistribType(int, double[]) - Method in class SingleNode
 
setDistribType(int, int, double[]) - Method in class SingleNode
 
setDistribType(int) - Method in class SingleNode
 
setDistribType(int, int) - Method in class SingleNode
 
setDistribType(int, double[]) - Method in class U_Turn
 
setDistribType(int, int, double[]) - Method in class U_Turn
 
setDistribType(int) - Method in class U_Turn
 
setDistribType(int, int) - Method in class U_Turn
 
setEmissPriorScaler(double) - Method in class Cluster
 
setEmissPriorScaler(int, double) - Method in class Cluster
 
setEmissPriorScaler(double) - Method in class Forward_alt
 
setEmissPriorScaler(int, double) - Method in class Forward_alt
 
setEmissPriorScaler(double) - Method in class Forward_std
 
setEmissPriorScaler(int, double) - Method in class Forward_std
 
setEmissPriorScaler(double) - Method in class Highway
 
setEmissPriorScaler(int, double) - Method in class Highway
 
setEmissPriorScaler(double) - Method in class Module
 
setEmissPriorScaler(int, double) - Method in class Module
 
setEmissPriorScaler(double) - Method in class Profile7
 
setEmissPriorScaler(int, double) - Method in class Profile7
 
setEmissPriorScaler(double) - Method in class Profile9
 
setEmissPriorScaler(int, double) - Method in class Profile9
 
setEmissPriorScaler(double) - Method in class SingleLoop
 
setEmissPriorScaler(int, double) - Method in class SingleLoop
 
setEmissPriorScaler(double) - Method in class SingleNode
 
setEmissPriorScaler(int, double) - Method in class SingleNode
 
setEmissPriorScaler(double) - Method in class U_Turn
 
setEmissPriorScaler(int, double) - Method in class U_Turn
 
setEmissPriorScaler(double) - Method in class Vertex
 
setEmissPriorScaler(int, double) - Method in class Vertex
 
setEmissPriorScalerInsert(int, double) - Method in class Profile7
 
setEmissPriorScalerInsert(int, double) - Method in class Profile9
 
setFileName(String) - Method in class HMM
 
setFileName(String) - Method in class ModelMaker
 
setInitialEmissionProbs(double[]) - Method in class Vertex
 
setInitialEmissionProbs(int, double[]) - Method in class Vertex
 
setInitialEmissionProbs(int) - Method in class Vertex
 
setInitialEmissionProbs(int, int) - Method in class Vertex
 
setInternalInitDistrib(InternalInitDistrib) - Method in class Cluster
 
setInternalInitDistrib(InternalInitDistrib) - Method in class Forward_alt
 
setInternalInitDistrib(InternalInitDistrib) - Method in class Forward_std
 
setInternalInitDistrib(InternalInitDistrib) - Method in class Highway
 
setInternalInitDistrib(String, InternalInitDistrib) - Method in class HMM
 
setInternalInitDistrib(String, InternalInitDistrib) - Method in class ModelMaker
 
setInternalInitDistrib(InternalInitDistrib) - Method in class Module
 
setInternalInitDistrib(InternalInitDistrib) - Method in class Profile7
 
setInternalInitDistrib(InternalInitDistrib) - Method in class Profile9
 
setInternalInitDistrib(InternalInitDistrib) - Method in class SingleLoop
 
setInternalInitDistrib(InternalInitDistrib) - Method in class SingleNode
 
setInternalInitDistrib(InternalInitDistrib) - Method in class U_Turn
 
setLabel(String) - Method in class Vertex
 
setNrOfAlphabets(int) - Method in class HMM
 
setNrOfAlphabets(int) - Method in class ModelMaker
set methods
setPar1(double) - Method in class InternalInitDistrib
 
setPar2(double) - Method in class InternalInitDistrib
 
setPar3(double) - Method in class InternalInitDistrib
 
setPoisson(double) - Method in class Forward_alt
 
setPoisson(double, int) - Method in class Forward_alt
 
setPoisson(double) - Method in class Forward_std
 
setPoisson(double, int) - Method in class Forward_std
 
setPreliminaryInitialEmissionProbs(int) - Method in class Vertex
 
setPriorfile(String) - Method in class Cluster
 
setPriorfile(int, String) - Method in class Cluster
 
setPriorfile(String) - Method in class Forward_alt
 
setPriorfile(int, String) - Method in class Forward_alt
 
setPriorfile(String) - Method in class Forward_std
 
setPriorfile(int, String) - Method in class Forward_std
 
setPriorfile(String) - Method in class Highway
 
setPriorfile(int, String) - Method in class Highway
 
setPriorfile(String) - Method in class Module
 
setPriorfile(int, String) - Method in class Module
 
setPriorfile(String) - Method in class Profile7
 
setPriorfile(int, String) - Method in class Profile7
 
setPriorfile(String) - Method in class Profile9
 
setPriorfile(int, String) - Method in class Profile9
 
setPriorfile(String) - Method in class SingleLoop
 
setPriorfile(int, String) - Method in class SingleLoop
 
setPriorfile(String) - Method in class SingleNode
 
setPriorfile(int, String) - Method in class SingleNode
 
setPriorfile(String) - Method in class U_Turn
 
setPriorfile(int, String) - Method in class U_Turn
 
setProbability(double) - Method in class Emission
 
setProbability(double) - Method in class Transition
 
setTransDistribType(int, double[]) - Method in class Profile9
 
setTransDistribType(int) - Method in class Profile9
 
setTransition(String, String) - Method in class HMM
 
setTransition(String, String) - Method in class ModelMaker
 
setTransitionProbability(int, double) - Method in class Vertex
 
setTransPriorfile(String) - Method in class Cluster
 
setTransPriorfile(String) - Method in class Forward_alt
 
setTransPriorfile(String) - Method in class Forward_std
 
setTransPriorfile(String) - Method in class Highway
 
setTransPriorfile(String) - Method in class Module
 
setTransPriorfile(String) - Method in class Profile7
 
setTransPriorfile(String) - Method in class Profile9
 
setTransPriorfile(String) - Method in class SingleLoop
 
setTransPriorfile(String) - Method in class SingleNode
 
setTransPriorfile(String) - Method in class U_Turn
 
setTransPriorScaler(double) - Method in class Cluster
 
setTransPriorScaler(double) - Method in class Forward_alt
 
setTransPriorScaler(double) - Method in class Forward_std
 
setTransPriorScaler(double) - Method in class Highway
 
setTransPriorScaler(double) - Method in class Module
 
setTransPriorScaler(double) - Method in class Profile7
 
setTransPriorScaler(double) - Method in class Profile9
 
setTransPriorScaler(double) - Method in class SingleLoop
 
setTransPriorScaler(double) - Method in class SingleNode
 
setTransPriorScaler(double) - Method in class U_Turn
 
setTransPriorScaler(double) - Method in class Vertex
 
SILENT - Static variable in class HMM
 
SINGLELOOP - Static variable in class HMM
 
SingleLoop - Class in <Unnamed>
 
SingleLoop(String, int, int, int, String) - Constructor for class SingleLoop
 
SingleLoop(String, double[], int, int, String) - Constructor for class SingleLoop
 
SINGLENODE - Static variable in class HMM
 
SingleNode - Class in <Unnamed>
 
SingleNode(String, int, int, String) - Constructor for class SingleNode
 
SingleNode(String, double[], int, String) - Constructor for class SingleNode
 
size - Variable in class Cluster
 
size - Variable in class Forward_alt
 
size - Variable in class Forward_std
 
size - Variable in class Highway
 
size - Variable in class Profile7
 
size - Variable in class Profile9
 
size - Variable in class SingleLoop
 
size - Variable in class SingleNode
 
size - Variable in class U_Turn
 
SQRTH - Static variable in class Constants
 
SQTPI - Static variable in class Constants
 
STANDARD - Static variable in class HMM
 
START - Static variable in class HMM
 
STARTNODE - Static variable in class HMM
 
stirlingFormula(double) - Static method in class BetaGamma
Returns the Gamma function computed by Stirling's formula; formerly named stirf.

T

theDeleteVertices - Variable in class Profile7
 
theDeleteVertices - Variable in class Profile9
 
theHMM - Variable in class HMMSaver
 
theHMM - Variable in class ModelMaker
 
theInsertVertices - Variable in class Profile7
 
theInsertVertices - Variable in class Profile9
 
theMatchVertices - Variable in class Profile7
 
theMatchVertices - Variable in class Profile9
 
theOutVertices - Variable in class Profile7
 
theOutVertices - Variable in class Profile9
 
theVertex - Variable in class SingleLoop
 
theVertex - Variable in class SingleNode
 
theVertices - Variable in class Cluster
 
theVertices - Variable in class Forward_alt
 
theVertices - Variable in class Forward_std
 
theVertices - Variable in class Highway
 
theVertices - Variable in class Profile7
 
theVertices - Variable in class Profile9
 
theVertices - Variable in class U_Turn
 
toVertex - Variable in class Transition
 
transDistribType - Variable in class Forward_alt
 
transDistribType - Variable in class Forward_std
 
Transition - Class in <Unnamed>
 
Transition(int, double) - Constructor for class Transition
 
Transition(int, double, boolean) - Constructor for class Transition
 
transitionExists(int, int) - Method in class HMM
 
transitionExists(int, int) - Method in class ModelMaker
 
transitionList - Variable in class Vertex
 
transitions - Variable in class Vertex
 
transPriorfile - Variable in class Cluster
 
transPriorfile - Variable in class Forward_alt
 
transPriorfile - Variable in class Forward_std
 
transPriorfile - Variable in class Highway
 
transPriorfile - Variable in class Profile7
 
transPriorfile - Variable in class Profile9
 
transPriorfile - Variable in class SingleLoop
 
transPriorfile - Variable in class SingleNode
 
transPriorfile - Variable in class U_Turn
 
transPriorScaler - Variable in class Vertex
 
typeAsString() - Method in class Vertex
 

U

U - Variable in class Forward_alt
 
U - Variable in class Forward_std
 
U_TURN - Static variable in class HMM
 
U_Turn - Class in <Unnamed>
 
U_Turn(String, int, int, int, String) - Constructor for class U_Turn
 
U_Turn(String, double[], int, int, String) - Constructor for class U_Turn
 
unLock() - Method in class Transition
 

V

Vertex - Class in <Unnamed>
 
Vertex(String, int, int, String) - Constructor for class Vertex
 
Vertex(String, int, double[], String) - Constructor for class Vertex
 
vertexType - Variable in class Cluster
 
vertexType - Variable in class Forward_alt
 
vertexType - Variable in class Forward_std
 
vertexType - Variable in class Highway
 
vertexType - Variable in class Profile7
 
vertexType - Variable in class Profile9
 
vertexType - Variable in class SingleLoop
 
vertexType - Variable in class SingleNode
 
vertexType - Variable in class U_Turn
 
vertexType - Variable in class Vertex
 

W

write(int, BufferedWriter) - Method in class Cluster
 
write(BufferedWriter) - Method in class Forward_alt
 
write(int, BufferedWriter) - Method in class Forward_alt
 
write(BufferedWriter) - Method in class Forward_std
 
write(int, BufferedWriter) - Method in class Forward_std
 
write(int, BufferedWriter) - Method in class Highway
 
write(int, BufferedWriter) - Method in class Module
 
write(BufferedWriter) - Method in class Profile7
 
write(int, BufferedWriter) - Method in class Profile7
 
write(BufferedWriter) - Method in class Profile9
 
write(int, BufferedWriter) - Method in class Profile9
 
write(BufferedWriter) - Method in class SingleLoop
 
write(int, BufferedWriter) - Method in class SingleLoop
 
write(BufferedWriter) - Method in class SingleNode
 
write(int, BufferedWriter) - Method in class SingleNode
 
write(BufferedWriter) - Method in class U_Turn
 
write(int, BufferedWriter) - Method in class U_Turn
 
writeModule(String, BufferedWriter) - Method in class HMM
 
writer - Variable in class HMMSaver
 

Z

ZERO - Static variable in class HMM
 

A B C D E F G H I L M N O P R S T U V W Z