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