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# 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

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