Serialized Form

Package calhoun.analysis.crf

Class calhoun.analysis.crf.AbstractFeatureManager extends java.lang.Object implements Serializable

Serialized Fields

inputComponent

java.lang.String inputComponent

Class calhoun.analysis.crf.BeanModel extends CompositeFeatureManager implements Serializable

serialVersionUID: -6641426879906871691L

Serialized Fields

nodes

java.util.List<E> nodes

edges

java.util.List<E> edges

Class calhoun.analysis.crf.BeanModel.Edge extends java.lang.Object implements Serializable

serialVersionUID: 5429589777288279645L

Serialized Fields

from

BeanModel.Node from

to

BeanModel.Node to

Class calhoun.analysis.crf.BeanModel.Node extends java.lang.Object implements Serializable

serialVersionUID: 1550966522391566799L

Serialized Fields

index

int index

name

java.lang.String name

Class calhoun.analysis.crf.CompositeFeatureManager extends AbstractFeatureManager implements Serializable

serialVersionUID: 5061912595256694049L

Serialized Fields

allFeatureTypes

java.util.List<E> allFeatureTypes

nodeFeatureTypes

java.util.List<E> nodeFeatureTypes

edgeFeatureTypes

java.util.List<E> edgeFeatureTypes

explicitLengthNodeFeatureTypes

java.util.List<E> explicitLengthNodeFeatureTypes

explicitLengthEdgeFeatureTypes

java.util.List<E> explicitLengthEdgeFeatureTypes

startIndexes

int[] startIndexes

startIx

int startIx

totalFeatures

int totalFeatures

Class calhoun.analysis.crf.CompositeFeatureManager.ComponentList extends java.util.ArrayList<InputSequence<?>> implements Serializable

serialVersionUID: 2954775229926328434L

Serialized Fields

name

java.lang.String name

Class calhoun.analysis.crf.Conrad extends java.lang.Object implements Serializable

serialVersionUID: -5964610632818921236L

Serialized Fields

configXml

byte[] configXml

model

ModelManager model

inputHandler

InputHandler inputHandler

outputHandler

OutputHandler outputHandler

weights

double[] weights

trainingTime

double trainingTime

Class calhoun.analysis.crf.ConstrainedFeatureManager extends CompositeFeatureManager implements Serializable

serialVersionUID: 5061912595256694050L

Package calhoun.analysis.crf.executables.viewer

Class calhoun.analysis.crf.executables.viewer.ViterbiTableModel extends javax.swing.table.AbstractTableModel implements Serializable

serialVersionUID: 4315252264878822897L

Serialized Fields

crfModel

Conrad crfModel

seq

TrainingSequence<A> seq

viterbiPath

int[] viterbiPath

bestScore

double[] bestScore

nStates

int nStates

Class calhoun.analysis.crf.executables.viewer.ViterbiTableModel.ViterbiCellRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable

serialVersionUID: -1156070614840797662L

Class calhoun.analysis.crf.executables.viewer.ViterbiViewerApp extends javax.swing.JFrame implements Serializable

serialVersionUID: -5564046976928448201L

Serialized Fields

recordViewer

calhoun.analysis.crf.executables.viewer.ViterbiViewerApp.ViterbiViewer recordViewer

Package calhoun.analysis.crf.features.generic

Class calhoun.analysis.crf.features.generic.EndFeatures extends AbstractFeatureManager<java.lang.Object> implements Serializable

serialVersionUID: 5206582215565363768L

Serialized Fields

startIx

int startIx

endStates

int[] endStates

names

java.lang.String[] names

configStates

int[] configStates

Class calhoun.analysis.crf.features.generic.IndicatorEdges extends AbstractFeatureManager implements Serializable

serialVersionUID: -2633500053477439285L

Serialized Fields

debug

boolean debug

startIx

int startIx

transitions

DenseIntMatrix2D transitions

names

java.util.List<E> names

Class calhoun.analysis.crf.features.generic.StartFeatures extends AbstractFeatureManager<java.lang.Object> implements Serializable

serialVersionUID: 2578820778300251051L

Serialized Fields

startIx

int startIx

startStates

int[] startStates

names

java.lang.String[] names

configStates

int[] configStates

Class calhoun.analysis.crf.features.generic.WeightedEdges extends AbstractFeatureManager<java.lang.Object> implements Serializable

serialVersionUID: 8477631359065280630L

Serialized Fields

startIx

int startIx

manager

ModelManager manager

transitions

float[][] transitions

Class calhoun.analysis.crf.features.generic.WeightedStateChanges extends AbstractFeatureManager<java.lang.Object> implements Serializable

serialVersionUID: 8477631359065280630L

Serialized Fields

debug

boolean debug

startIx

int startIx

manager

ModelManager manager

transitions

float[][] transitions

Package calhoun.analysis.crf.features.interval13

Class calhoun.analysis.crf.features.interval13.BlastInterval13 extends AbstractFeatureManager<CompositeInput> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

intergenicState

boolean[] intergenicState

plusExonState

boolean[] plusExonState

minusExonState

boolean[] minusExonState

plusIntronState

boolean[] plusIntronState

minusIntronState

boolean[] minusIntronState

Class calhoun.analysis.crf.features.interval13.ESTInterval13 extends AbstractFeatureManager<CompositeInput> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

intergenicState

boolean[] intergenicState

plusExonState

boolean[] plusExonState

minusExonState

boolean[] minusExonState

plusIntronState

boolean[] plusIntronState

minusIntronState

boolean[] minusIntronState

Class calhoun.analysis.crf.features.interval13.FootprintsInterval13 extends AbstractFeatureManager<MultipleAlignmentInputSequence.MultipleAlignmentColumn> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

speciesNames

java.util.List<E> speciesNames

startIx

int startIx

model

ModelManager model

h

KmerHasher h

maxSeqLength

int maxSeqLength

nFeatures

int nFeatures

isStateCoding

java.lang.Boolean[] isStateCoding

isStateIntronic

java.lang.Boolean[] isStateIntronic

isStateIntergenic

java.lang.Boolean[] isStateIntergenic

Class calhoun.analysis.crf.features.interval13.GapFeaturesInterval13 extends AbstractFeatureManager<MultipleAlignmentInputSequence.MultipleAlignmentColumn> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

featureNames

java.lang.String[] featureNames

startIx

int startIx

model

ModelManager model

h

KmerHasher h

maxSeqLength

int maxSeqLength

nFeatures

int nFeatures

nStates

int nStates

gapboundary

java.lang.Boolean[] gapboundary

frameshifter

java.lang.Boolean[] frameshifter

isStateCoding

java.lang.Boolean[] isStateCoding

isStateIntronic

java.lang.Boolean[] isStateIntronic

isStateIntergenic

java.lang.Boolean[] isStateIntergenic

lastSeqLength

int lastSeqLength

lastpos

int lastpos

Class calhoun.analysis.crf.features.interval13.GeneConstraintsInterval13 extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: 3041359216265032511L

Class calhoun.analysis.crf.features.interval13.Interval13Model extends BeanModel implements Serializable

serialVersionUID: 3959312826759045449L

Class calhoun.analysis.crf.features.interval13.PhylogeneticLogprobInterval13 extends AbstractFeatureManager<MultipleAlignmentInputSequence.MultipleAlignmentColumn> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

startIx

int startIx

model

ModelManager model

multipleFeatures

boolean multipleFeatures

emodelIntergenic

EvolutionaryModel emodelIntergenic

emodelIntronic

EvolutionaryModel emodelIntronic

emodelExonic

java.util.ArrayList<E> emodelExonic

Class calhoun.analysis.crf.features.interval13.PWMInterval13 extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

multipleFeatures

boolean multipleFeatures

startIx

int startIx

model

ModelManager model

start

PWMLookup start

stop

PWMLookup stop

donor

PWMLookup[] donor

acceptor

PWMLookup[] acceptor

pseudoCounts

double pseudoCounts

Class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13 extends ReferenceBasePredictorInterval13Base implements Serializable

serialVersionUID: -8460452348450096338L

Class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13Base extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: 8194502006226691957L

Serialized Fields

model

ModelManager model

startIx

int startIx

multipleFeatures

boolean multipleFeatures

pseudoCounts

double pseudoCounts

lookback

int lookback

intron

LogProbLookup intron

intergenic

LogProbLookup intergenic

exonic

LogProbLookup[] exonic

Class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorNodeOnlyInterval13 extends ReferenceBasePredictorInterval13Base implements Serializable

serialVersionUID: 6351525014233239165L

Class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorZeroPadInterval13 extends ReferenceBasePredictorInterval13Base implements Serializable

serialVersionUID: -1104446043334637758L

Class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13 extends java.lang.Object implements Serializable

serialVersionUID: 8685543199212865835L

Serialized Fields

startIx

int startIx

mi

ModelManager mi

inputComponentName

java.lang.String inputComponentName

intergenicMixGamma

MixtureOfGammas intergenicMixGamma

exonMixGamma

MixtureOfGammas exonMixGamma

intronMixGamma

MixtureOfGammas intronMixGamma

forceExponential

boolean forceExponential

exonExponential

boolean exonExponential

intronExponential

boolean intronExponential

multipleFeatures

boolean multipleFeatures

noIntergenic

boolean noIntergenic

Class calhoun.analysis.crf.features.interval13.StateTransitionsInterval13 extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: -7745853849576425025L

Serialized Fields

startIx

int startIx

intronProb

double intronProb

endProb

double endProb

Package calhoun.analysis.crf.features.interval29

Class calhoun.analysis.crf.features.interval29.ESTInterval29 extends AbstractFeatureManager<CompositeInput> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

plusExonState

boolean[] plusExonState

minusExonState

boolean[] minusExonState

plusIntronState

boolean[] plusIntronState

minusIntronState

boolean[] minusIntronState

Class calhoun.analysis.crf.features.interval29.FootprintsInterval29 extends AbstractFeatureManager<MultipleAlignmentInputSequence.MultipleAlignmentColumn> implements Serializable

serialVersionUID: -885708304411544895L

Serialized Fields

debug

boolean debug

speciesNames

java.util.List<E> speciesNames

startIx

int startIx

model

ModelManager model

h

KmerHasher h

maxSeqLength

int maxSeqLength

nFeatures

int nFeatures

isStateCoding

java.lang.Boolean[] isStateCoding

isStateIntronic

java.lang.Boolean[] isStateIntronic

isStateIntergenic

java.lang.Boolean[] isStateIntergenic

Class calhoun.analysis.crf.features.interval29.GapFeaturesInterval29 extends AbstractFeatureManager<MultipleAlignmentInputSequence.MultipleAlignmentColumn> implements Serializable

serialVersionUID: 8484623829139711313L

Serialized Fields

debug

boolean debug

featureNames

java.lang.String[] featureNames

startIx

int startIx

model

ModelManager model

h

KmerHasher h

maxSeqLength

int maxSeqLength

nFeatures

int nFeatures

nStates

int nStates

gapboundary

java.lang.Boolean[] gapboundary

frameshifter

java.lang.Boolean[] frameshifter

isStateCoding

java.lang.Boolean[] isStateCoding

isStateIntronic

java.lang.Boolean[] isStateIntronic

isStateIntergenic

java.lang.Boolean[] isStateIntergenic

lastSeqLength

int lastSeqLength

lastpos

int lastpos

Class calhoun.analysis.crf.features.interval29.GeneConstraintsInterval29 extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: 3041359216265032511L

Class calhoun.analysis.crf.features.interval29.Interval29Model extends BeanModel implements Serializable

serialVersionUID: 3959312826759045449L

Class calhoun.analysis.crf.features.interval29.PWMInterval29 extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

multipleFeatures

boolean multipleFeatures

startIx

int startIx

model

ModelManager model

start

PWMLookup start

stop

PWMLookup stop

donor

PWMLookup[] donor

acceptor

PWMLookup[] acceptor

pseudoCounts

double pseudoCounts

Class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29 extends ReferenceBasePredictorInterval29Base implements Serializable

serialVersionUID: -8460452348450096338L

Class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29Base extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: 8194502006226691957L

Serialized Fields

model

ModelManager model

startIx

int startIx

multipleFeatures

boolean multipleFeatures

pseudoCounts

double pseudoCounts

lookback

int lookback

intron

LogProbLookup intron

intergenic

LogProbLookup intergenic

exonic

LogProbLookup[] exonic

Class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorNodeOnlyInterval29 extends ReferenceBasePredictorInterval29Base implements Serializable

serialVersionUID: 118734329852813977L

Class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorZeroPadInterval29 extends ReferenceBasePredictorInterval29Base implements Serializable

serialVersionUID: -1104446043334637758L

Class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29 extends java.lang.Object implements Serializable

serialVersionUID: 8685543199212865835L

Serialized Fields

startIx

int startIx

mi

ModelManager mi

inputComponentName

java.lang.String inputComponentName

intergenicMixGamma

MixtureOfGammas intergenicMixGamma

exonMixGamma

MixtureOfGammas exonMixGamma

intronMixGamma

MixtureOfGammas intronMixGamma

forceExponential

boolean forceExponential

exonExponential

boolean exonExponential

multipleFeatures

boolean multipleFeatures

Class calhoun.analysis.crf.features.interval29.StateTransitionsInterval29 extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: -7745853849576425025L

Serialized Fields

startIx

int startIx

intronProb

double intronProb

endProb

double endProb

Package calhoun.analysis.crf.features.supporting

Class calhoun.analysis.crf.features.supporting.LogProbLookup extends java.lang.Object implements Serializable

serialVersionUID: -9195647924401633963L

Serialized Fields

hashForward

KmerHasher.CharacterHash hashForward

hashReverse

KmerHasher.CharacterHash hashReverse

finalized

boolean finalized

mult

int mult

maxLookBack

int maxLookBack

lookupTable

double[] lookupTable

lookupTableSize

int lookupTableSize

Class calhoun.analysis.crf.features.supporting.MarkovPredictorLogprob extends java.lang.Object implements Serializable

serialVersionUID: -3801967331270040642L

Serialized Fields

trainedYet

boolean trainedYet

history

java.util.List<E> history

nStates

int nStates

kmerLengths

int[] kmerLengths

hashers

KmerHasher[] hashers

logProb

float[][][] logProb

maxLength

int maxLength

h

KmerHasher h

currentHash

int[] currentHash

scratch

char[] scratch

lastPos

int lastPos

lastChar

char lastChar

singleHash

int singleHash

Class calhoun.analysis.crf.features.supporting.PWMLookup extends java.lang.Object implements Serializable

serialVersionUID: 5353716408013134581L

Serialized Fields

hashForward

KmerHasher.CharacterHash hashForward

hashReverse

KmerHasher.CharacterHash hashReverse

finalized

boolean finalized

mult

int mult

left

int left

right

int right

span

int span

lookupTable

double[] lookupTable

Package calhoun.analysis.crf.features.supporting.phylogenetic

Class calhoun.analysis.crf.features.supporting.phylogenetic.BinaryTreeNode extends java.lang.Object implements Serializable

serialVersionUID: -2109391655262800568L

Serialized Fields

p

int p

l

int l

r

int r

d

double d

n

java.lang.String n

lm

java.lang.Boolean lm

rm

java.lang.Boolean rm

Class calhoun.analysis.crf.features.supporting.phylogenetic.ColumnConditionalLogProbability extends java.lang.Object implements Serializable

serialVersionUID: 5837909206967310115L

Serialized Fields

lastSeq

InputSequence<A> lastSeq

lastPos

int lastPos

vals

double[] vals

clusters

java.util.List<E> clusters

state2cluster

int[] state2cluster

emodels

java.util.List<E> emodels

model

ModelManager model

columnCache

java.util.Map<K,V> columnCache

eModelNum

int eModelNum

Class calhoun.analysis.crf.features.supporting.phylogenetic.EvolutionaryModel extends java.lang.Object implements Serializable

serialVersionUID: -4531626481183209673L

Serialized Fields

T

PhylogeneticTreeFelsensteinOrder T

pi

double[] pi

R

NucleotideSubstitutionModel R

numSpecies

int numSpecies

ileft

int[] ileft

iright

int[] iright

Tleft

double[][] Tleft

Tright

double[][] Tright

P

double[][] P

Class calhoun.analysis.crf.features.supporting.phylogenetic.HKY85Model extends NucleotideSubstitutionModel implements Serializable

serialVersionUID: -1555350959092722736L

Serialized Fields

ts

double ts

tv

double tv

piA

double piA

piC

double piC

piG

double piG

piT

double piT

Class calhoun.analysis.crf.features.supporting.phylogenetic.Kimura80Model extends NucleotideSubstitutionModel implements Serializable

serialVersionUID: 4075281397219042249L

Serialized Fields

ts

double ts

tv

double tv

Class calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModel extends java.lang.Object implements Serializable

Serialized Fields

R

cern.colt.matrix.DoubleMatrix2D R

Class calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder extends java.lang.Object implements Serializable

serialVersionUID: -2394371116379001213L

Serialized Fields

ileft

int[] ileft

iright

int[] iright

bleft

double[] bleft

bright

double[] bright

nSpecies

int nSpecies

nSteps

int nSteps

nNodes

int nNodes

Class calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree extends java.lang.Object implements Serializable

serialVersionUID: 4800435332663788163L

Serialized Fields

T

java.util.ArrayList<E> T

Package calhoun.analysis.crf.features.tricycle13

Class calhoun.analysis.crf.features.tricycle13.CodingStopFeature extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

h

KmerHasher h

pluslogprob

float[][] pluslogprob

minuslogprob

float[][] minuslogprob

pc

int[][] pc

mc

int[][] mc

stateIntergenic

int stateIntergenic

stateExon3

int stateExon3

stateExon3m

int stateExon3m

predictorlp

MarkovPredictorLogprob predictorlp

Class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

predictorlp

MarkovPredictorLogprob predictorlp

tieFlag

boolean tieFlag

Class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature.MarkovHistory extends java.lang.Object implements Serializable

serialVersionUID: 8731309130784681776L

Serialized Fields

states

java.util.List<E> states

Class calhoun.analysis.crf.features.tricycle13.ESTEdge extends AbstractFeatureManager<CompositeInput> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

plusExonState

boolean[] plusExonState

minusExonState

boolean[] minusExonState

plusIntronState

boolean[] plusIntronState

minusIntronState

boolean[] minusIntronState

Class calhoun.analysis.crf.features.tricycle13.ESTExon extends AbstractFeatureManager<CompositeInput> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

plusExonState

boolean[] plusExonState

minusExonState

boolean[] minusExonState

plusIntronState

boolean[] plusIntronState

minusIntronState

boolean[] minusIntronState

Class calhoun.analysis.crf.features.tricycle13.ESTIntron extends AbstractFeatureManager<CompositeInput> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

plusIntronState

boolean[] plusIntronState

minusIntronState

boolean[] minusIntronState

Class calhoun.analysis.crf.features.tricycle13.FelsensteinFeatures extends AbstractFeatureManager<MultipleAlignmentInputSequence.MultipleAlignmentColumn> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

mo

ColumnConditionalLogProbability mo

tieFlag

boolean tieFlag

clusterIndices

java.util.List<E> clusterIndices

eModelNum

int eModelNum

Class calhoun.analysis.crf.features.tricycle13.GapConjunctionFeatures extends AbstractFeatureManager<MultipleAlignmentInputSequence.MultipleAlignmentColumn> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

h

KmerHasher h

maxSeqLength

int maxSeqLength

nFeatures

int nFeatures

nStates

int nStates

gapboundary

java.lang.Boolean[] gapboundary

frameshifter

java.lang.Boolean[] frameshifter

isStateCoding

java.lang.Boolean[] isStateCoding

isStateIntronic

java.lang.Boolean[] isStateIntronic

isStateIntergenic

java.lang.Boolean[] isStateIntergenic

lastSeqLength

int lastSeqLength

lastpos

int lastpos

lastSeq

InputSequence<A> lastSeq

Class calhoun.analysis.crf.features.tricycle13.GeneConstraints extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: -3045999729941973608L

Serialized Fields

constraints

calhoun.analysis.crf.features.tricycle13.GeneConstraints.Constraint[] constraints

numStates

int numStates

Class calhoun.analysis.crf.features.tricycle13.IntervalPresenceFeatures extends AbstractFeatureManager<IntervalInputSequence.IntervalPosition> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

plusExonState

boolean[] plusExonState

minusExonState

boolean[] minusExonState

plusIntronState

boolean[] plusIntronState

minusIntronState

boolean[] minusIntronState

Class calhoun.analysis.crf.features.tricycle13.IntronLengthFeature extends AbstractFeatureManager implements Serializable

serialVersionUID: 8477631359065280630L

Serialized Fields

debug

boolean debug

startIx

int startIx

logProbExtend

double[] logProbExtend

explicitLengthFlag

boolean[] explicitLengthFlag

isIntron

boolean[] isIntron

Class calhoun.analysis.crf.features.tricycle13.KmerFeatures extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: 5959560033335736926L

Serialized Fields

startIx

int startIx

model

ModelManager model

nStates

int nStates

kmerDefs

java.util.List<E> kmerDefs

counts

java.util.Map<K,V>[] counts

kmerIds

java.util.Map<K,V>[] kmerIds

cardinality

KmerFeatures.Cardinality cardinality

rareThreshold

int rareThreshold

kmers

java.lang.String[] kmers

vals

double[][] vals

Class calhoun.analysis.crf.features.tricycle13.MaxentMotifFeatures extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

h

KmerHasher h

tieFlag

boolean tieFlag

nFeatures

int nFeatures

spanLimit

int spanLimit

span

int[] span

offset

int[] offset

tranfrom

int[] tranfrom

tranto

int[] tranto

dcflag

boolean dcflag

dcc

java.util.List<E> dcc

predictorlp

MarkovPredictorLogprob predictorlp

lastSeq

InputSequence<A> lastSeq

lastPos

int lastPos

vals

float[] vals

listprob

java.util.List<E> listprob

Class calhoun.analysis.crf.features.tricycle13.PfamGenic extends AbstractFeatureManager<CompositeInput> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

plusGenic

boolean[] plusGenic

minusGenic

boolean[] minusGenic

Class calhoun.analysis.crf.features.tricycle13.PfamPhase extends AbstractFeatureManager<CompositeInput> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

exon1S

int exon1S

exon2S

int exon2S

exon3S

int exon3S

exon1mS

int exon1mS

exon2mS

int exon2mS

exon3mS

int exon3mS

Class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

nFeatures

int nFeatures

span

int[] span

offset

int[] offset

nTrans

int[] nTrans

h

KmerHasher h

transitions

DenseBooleanMatrix2D[] transitions

geometry

java.util.List<E> geometry

logprob

java.util.List<E> logprob

dcflag

boolean dcflag

dcc

java.util.List<E> dcc

predictorlp

MarkovPredictorLogprob predictorlp

lastPos

int lastPos

vals

float[] vals

tieFlag

boolean tieFlag

UVCount

int UVCount

pwmGeometry

java.util.List<E> pwmGeometry

markovHistory

EmissionMarkovFeature.MarkovHistory markovHistory

Class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry extends java.lang.Object implements Serializable

serialVersionUID: 4896358213027322167L

Serialized Fields

size

int size

transition

int transition

prev

BeanModel.Node prev

current

BeanModel.Node current

overlapCorrections

java.util.List<E> overlapCorrections

Class calhoun.analysis.crf.features.tricycle13.PWM_evolution extends AbstractFeatureManager<CompositeInput> implements Serializable

serialVersionUID: -7659288739348604129L

Serialized Fields

debug

boolean debug

startIx

int startIx

model

ModelManager model

nFeatures

int nFeatures

span

int[] span

offset

int[] offset

nTrans

int[] nTrans

transitions

DenseBooleanMatrix2D[] transitions

geometry

java.util.List<E> geometry

logprob

java.util.List<E> logprob

dcc

java.util.List<E> dcc

predictorlp

MarkovPredictorLogprob predictorlp

clusters

java.util.List<E> clusters

emodels

java.util.List<E> emodels

state2cluster

int[] state2cluster

mo

ColumnConditionalLogProbability mo

tieFlag

boolean tieFlag

lastSeq

InputSequence<A> lastSeq

lastPos

int lastPos

vals

float[] vals

nUpdate

int nUpdate

Package calhoun.analysis.crf.io

Class calhoun.analysis.crf.io.AlignmentTree extends java.lang.Object implements Serializable

serialVersionUID: 760405914814389112L

Serialized Fields

component

java.lang.String component

Class calhoun.analysis.crf.io.AllIntergenicHiddenStateReader extends java.lang.Object implements Serializable

serialVersionUID: 4413724139445660884L

Class calhoun.analysis.crf.io.BooleanInput extends InterleavedInputComponentBase implements Serializable

serialVersionUID: 4922000330136279956L

Class calhoun.analysis.crf.io.CompositeInput extends java.lang.Object implements Serializable

serialVersionUID: -5179361895471860850L

Serialized Fields

components

java.util.List<E> components

Deprecated.

hiddenSequenceFile

java.lang.String hiddenSequenceFile

Deprecated.

hiddenSequenceReader

TrainingSequenceIO hiddenSequenceReader

Deprecated.

Class calhoun.analysis.crf.io.CompositeInput.InputComponent extends java.lang.Object implements Serializable

serialVersionUID: -652343588509377034L

Serialized Fields

name

java.lang.String name

inputSequence

InterleavedInputComponentBase inputSequence

filename

java.lang.String filename

Class calhoun.analysis.crf.io.CompositeInput.LegacyInputHandler extends java.lang.Object implements Serializable

serialVersionUID: -5031580949745955877L

Serialized Fields

inputComponent

java.lang.Object inputComponent

handler

InputHandler handler

Class calhoun.analysis.crf.io.FastaAlignmentInput extends java.lang.Object implements Serializable

serialVersionUID: 760405914814389112L

Serialized Fields

component

java.lang.String component

Class calhoun.analysis.crf.io.FastaInput extends java.lang.Object implements Serializable

serialVersionUID: 760405914814389112L

Serialized Fields

header

java.lang.String header

sequence

java.lang.String sequence

numSeqCap

java.lang.Integer numSeqCap

Class calhoun.analysis.crf.io.GTFInputInterval13 extends java.lang.Object implements Serializable

serialVersionUID: 4413724139445660883L

Serialized Fields

nameComponent

java.lang.String nameComponent

Class calhoun.analysis.crf.io.GTFInputInterval29 extends GTFInputInterval13 implements Serializable

serialVersionUID: 4413724139445660884L

Class calhoun.analysis.crf.io.InputHandlerBase extends java.lang.Object implements Serializable

serialVersionUID: 4002620265503458109L

Class calhoun.analysis.crf.io.InputHandlerDirectory extends InputHandlerBase implements Serializable

serialVersionUID: -2969140424776995686L

Serialized Fields

inputReaders

java.util.Map<K,V> inputReaders

hiddenStateReader

TrainingSequenceIO hiddenStateReader

hiddenSequenceFile

java.lang.String hiddenSequenceFile

Class calhoun.analysis.crf.io.InputHandlerFile extends InputHandlerBase implements Serializable

serialVersionUID: -2969140424776995686L

Serialized Fields

inputReader

InputComponentIO inputReader

mapper

FilenameMapper mapper

hiddenStateReader

TrainingSequenceIO hiddenStateReader

Class calhoun.analysis.crf.io.InputHandlerInterleaved extends java.lang.Object implements Serializable

serialVersionUID: -2969140424776995686L

Serialized Fields

components

java.util.List<E> components

hiddenStateReader

IntInput hiddenStateReader

locationIsLiteral

boolean locationIsLiteral

singleComponent

boolean singleComponent

componentName

java.lang.String componentName

Class calhoun.analysis.crf.io.InterleavedInputComponentBase extends java.lang.Object implements Serializable

serialVersionUID: 2972885935425621520L

Serialized Fields

name

java.lang.String name

Class calhoun.analysis.crf.io.Interval21HiddenSequenceTranslator extends IntInput implements Serializable

serialVersionUID: 4413724139445660883L

Class calhoun.analysis.crf.io.IntervalInput extends InterleavedInputComponentBase implements Serializable

serialVersionUID: 8110670530135286052L

Class calhoun.analysis.crf.io.IntInput extends InterleavedInputComponentBase implements Serializable

serialVersionUID: 4413724139445660883L

Class calhoun.analysis.crf.io.IntInputInterval29 extends IntInput implements Serializable

serialVersionUID: -2301269002866688631L

Class calhoun.analysis.crf.io.MultipleAlignmentInput extends InterleavedInputComponentBase implements Serializable

serialVersionUID: 1796622784861590659L

Class calhoun.analysis.crf.io.NameInput extends InterleavedInputComponentBase implements Serializable

serialVersionUID: -2944973705715162476L

Class calhoun.analysis.crf.io.OutputHandlerComposite extends java.lang.Object implements Serializable

serialVersionUID: 7923868199821973396L

Serialized Fields

handlers

java.util.List<E> handlers

Class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict extends java.lang.Object implements Serializable

serialVersionUID: 2014487490985409134L

Serialized Fields

manager

ModelManager manager

inputHandler

InputHandler inputHandler

location

java.lang.String location

writeTrainingData

boolean writeTrainingData

labeled

java.util.List<E> labeled

correct

int correct

incorrect

int incorrect

perfect

int perfect

imperfect

int imperfect

lla

double lla

llv

double llv

nStates

int nStates

nTransitions

int nTransitions

fromInd

java.util.List<E> fromInd

toInd

java.util.List<E> toInd

ctCodingNucleotide

PredictedActualBinaryContingencyTable ctCodingNucleotide

ctExons

PredictedActualBinaryContingencyTable ctExons

ctStates

java.util.List<E> ctStates

ctTransitions

java.util.List<E> ctTransitions

seqName

java.lang.String seqName

genePrefix

java.lang.String genePrefix

offset

long offset

Class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict.Results extends java.lang.Object implements Serializable

serialVersionUID: 9082449588200635355L

Serialized Fields

ctCodingNucleotide

PredictedActualBinaryContingencyTable ctCodingNucleotide

ctExons

PredictedActualBinaryContingencyTable ctExons

ctStates

java.util.List<E> ctStates

ctTransitions

java.util.List<E> ctTransitions

correct

int correct

incorrect

int incorrect

perfect

int perfect

imperfect

int imperfect

Class calhoun.analysis.crf.io.OutputHandlerGeneCallStats extends java.lang.Object implements Serializable

serialVersionUID: -1506791895658464225L

Serialized Fields

manager

ModelManager manager

inputHandler

InputHandler inputHandler

location

java.lang.String location

writeTrainingData

boolean writeTrainingData

labeled

java.util.List<E> labeled

correct

int correct

incorrect

int incorrect

perfect

int perfect

imperfect

int imperfect

lla

double lla

llv

double llv

nStates

int nStates

nTransitions

int nTransitions

fromInd

java.util.List<E> fromInd

toInd

java.util.List<E> toInd

ctCodingNucleotide

PredictedActualBinaryContingencyTable ctCodingNucleotide

ctExons

PredictedActualBinaryContingencyTable ctExons

ctStates

java.util.List<E> ctStates

ctTransitions

java.util.List<E> ctTransitions

seqName

java.lang.String seqName

genePrefix

java.lang.String genePrefix

offset

long offset

Class calhoun.analysis.crf.io.OutputHandlerGeneCallStats.Results extends java.lang.Object implements Serializable

serialVersionUID: 9082449588200635355L

Serialized Fields

ctCodingNucleotide

PredictedActualBinaryContingencyTable ctCodingNucleotide

ctExons

PredictedActualBinaryContingencyTable ctExons

ctStates

java.util.List<E> ctStates

ctTransitions

java.util.List<E> ctTransitions

correct

int correct

incorrect

int incorrect

perfect

int perfect

imperfect

int imperfect

Class calhoun.analysis.crf.io.OutputHandlerGeneCallStatsInterval29 extends OutputHandlerGeneCallStats implements Serializable

serialVersionUID: 5955650475684210702L

Class calhoun.analysis.crf.io.OutputHandlerWriter extends java.lang.Object implements Serializable

serialVersionUID: -3039234501926777322L

Serialized Fields

filenameMapper

FilenameMapper filenameMapper

resultHandler

TrainingSequenceIO resultHandler

location

java.lang.String location

Class calhoun.analysis.crf.io.StringInput extends InterleavedInputComponentBase implements Serializable

serialVersionUID: -2944973705715162476L

Package calhoun.analysis.crf.statistics

Class calhoun.analysis.crf.statistics.MixtureOfGammas extends java.lang.Object implements Serializable

serialVersionUID: 6269582005717276381L

Serialized Fields

pdist1

double pdist1

shape1

double shape1

lambda1

double lambda1

shape2

double shape2

lambda2

double lambda2

Class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable extends java.lang.Object implements Serializable

serialVersionUID: 557844841355570852L

Serialized Fields

tp

int tp

fp

int fp

fn

int fn

tn

int tn

frozen

boolean frozen

Package calhoun.analysis.crf.test

Class calhoun.analysis.crf.test.ConstraintTest.FixedEdges extends AbstractFeatureManager implements Serializable

serialVersionUID: 5995552526733022868L

Serialized Fields

startIx

int startIx

clusters

int[] clusters

Class calhoun.analysis.crf.test.GeneConstraintsToy extends AbstractFeatureManager<java.lang.Character> implements Serializable

serialVersionUID: -3753476830756229273L

Class calhoun.analysis.crf.test.TestFeatures.EmissionFeature extends TestFeatures.TestFeature implements Serializable

serialVersionUID: 8039479168741225007L

Class calhoun.analysis.crf.test.TestFeatures.ExplicitHalfExponentialLengthFeature extends TestFeatures.TestFeature implements Serializable

serialVersionUID: 6050417482057409153L

Serialized Fields

vals

float[] vals

Class calhoun.analysis.crf.test.TestFeatures.ExponentialLengthFeature extends TestFeatures.TestFeature implements Serializable

serialVersionUID: 290546936098017942L

Serialized Fields

vals

float[] vals

Class calhoun.analysis.crf.test.TestFeatures.GaussianLengthFeature extends TestFeatures.TestFeature implements Serializable

serialVersionUID: 6050417482057409153L

Class calhoun.analysis.crf.test.TestFeatures.HalfExponentialLengthFeature extends TestFeatures.TestFeature implements Serializable

serialVersionUID: 290546936098017942L

Serialized Fields

vals

float[] vals

Class calhoun.analysis.crf.test.TestFeatures.TestFeature extends AbstractFeatureManager<java.lang.Character> implements Serializable

Serialized Fields

startIx

int startIx

Class calhoun.analysis.crf.test.ZeroOrderManager extends ZeroOrderModel implements Serializable

serialVersionUID: 3959312826759045449L

Class calhoun.analysis.crf.test.ZeroOrderModel extends BeanModel implements Serializable

serialVersionUID: 3959312826759045449L

Package calhoun.seq

Class calhoun.seq.FastaIterator.ReaderSequence extends SimpleFastaSequence implements Serializable

serialVersionUID: -637754971987954577L

Serialized Fields

file

java.io.File file

Class calhoun.seq.KmerHasher extends java.lang.Object implements Serializable

serialVersionUID: -3402947063680917230L

Serialized Fields

charHash

KmerHasher.CharacterHash charHash

length

int length

mscMult

int mscMult

lscMult

int lscMult

Class calhoun.seq.SimpleFastaSequence extends java.lang.Object implements Serializable

serialVersionUID: 3541355741077645447L

Serialized Fields

header

java.lang.String header

sequence

java.lang.String sequence

quality

byte[] quality

Package calhoun.util

Class calhoun.util.CheckException extends java.lang.RuntimeException implements Serializable

serialVersionUID: 4225964190101139621L

Class calhoun.util.ConfigException extends java.lang.RuntimeException implements Serializable

serialVersionUID: -5371694423739150838L

Class calhoun.util.DataException extends ConfigException implements Serializable

serialVersionUID: 1993656669514976055L

Class calhoun.util.DenseBooleanMatrix2D extends java.lang.Object implements Serializable

serialVersionUID: 8033567052720988542L

Serialized Fields

array

boolean[] array

length

int length

Class calhoun.util.DenseIntMatrix2D extends java.lang.Object implements Serializable

serialVersionUID: 993972669435690618L

Serialized Fields

array

int[] array

length

int length

Class calhoun.util.ErrorException extends java.lang.RuntimeException implements Serializable

serialVersionUID: -7560596902065799827L

Class calhoun.util.RangeMap extends java.lang.Object implements Serializable

serialVersionUID: 413339879647819935L

Serialized Fields

map

java.util.SortedMap<K,V> map

Imagine a number line. Take the set of start and stop coordinates for each object in the RangeMap and place them on the number line. This divides the number line into a series of intervals. Each interval can be associated with a distinct list of objects that contain all points in that interval. The RangeMap is a sorted map that keys the start of the interval to this distinct list of objects.

Objects that fully contain the points in more than one interval will be contained in multiple lists. One list for each interval they contain.

objectList

java.util.Map<K,V> objectList

Keeps track of the start and end for each object in the map so we can remove them easily if necessary. Maps Object -> int[2]. the first element in the array is the start of the key and the second element is the end of the key.

Class calhoun.util.TypedProperties extends java.util.Properties implements Serializable

serialVersionUID: 8275327757663063251L