Package
Class
Tree
Deprecated
Index
Help
PREV NEXT
FRAMES
NO FRAMES
All Classes
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
Package
Class
Tree
Deprecated
Index
Help
PREV NEXT
FRAMES
NO FRAMES
All Classes