private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
int[] alignmentIndex
Alignment[] alignmentList
int numAlignments
int[] siteIndex
int[] alignmentIndex
AnnotationAlignment[] alignmentList
boolean mergeByID
int numAlignments
int[][] sequenceIndex
int[] siteIndex
boolean union
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
char[][] data_
boolean anchored
java.util.Vector<E extends java.lang.Object> indel
Alignment rawAlignment
java.lang.String[] sequences
int chromosome
float chromosomePosition
java.lang.String locusName
int[] locusPosition
char[] positionType
float[] weightedLocusPosition
int[] chromosome
float[] chromosomePosition
java.lang.String[] locusName
int[] locusPosition
char[] positionType
DataType[] siteDataType
float[] weightedPosition
char[][] data
FormattedInput fi
int lineLength
java.util.Vector<E extends java.lang.Object> names
java.util.Vector<E extends java.lang.Object> seqs
java.util.Vector<E extends java.lang.Object> sites
char[][] data
FormattedInput fi
int lineLength
java.util.Vector<E extends java.lang.Object> names
java.util.Vector<E extends java.lang.Object> seqs
java.util.Vector<E extends java.lang.Object> sites
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
java.lang.String[] sequences
int chromosome
float chromosomePosition
java.lang.String locusName
char[] positionType
float[] weightedPosition
java.lang.String[] environmentNames
IdGroup idGroup
int numSeqs
int numTraits
java.lang.String[] traitNames
double[][] traitValues
int[] alias
int numPatterns
int[] patSort
byte[][] pattern
int[] weight
int[] alias
boolean[] notDropped
Alignment rawAlignment
int rawNumSites
int firstSite
int lastSite
int minimumCount
double minimumProportion
AnnotationAlignment rawAlignment
int rawNumSites
FormattedOutput fo
double[] intervals
int[] numLineages
int units
double N0
double N0SE
double tx
double txSE
double alpha
double alphaSE
double lx
double N1
double N1SE
int parameterization
DemographicModel model
Binomial binom
FormattedOutput fo
double logL
MersenneTwisterFast rng
int units
double alpha
double alphaSE
double r
double rSE
SimulatedAlignment.Factory alignmentFactory_
DemographicModel demographicModel_
int numberOfTreesToGenerate_
TimeOrderCharacterData tocd_
TreeOperation treeFinisher_
SimpleTree tree
CoalescentIntervals ci
double[] cis
double eps
FormattedOutput fo
double maxTime
int params
double[] populationSize
int size
CodonTable translationTable_
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
char[] conversionTable_
boolean isRNA_
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
char[] conversionTable_
boolean isRNA_
int numberOfNumericStates
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
CodonTable translationTable_
int[] adjustedToOriginal_
int[] originalToAdjusted_
DataType toAdjust_
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
double[][] distance
IdGroup idGroup
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
double distance
double distanceSE
double jcratio
SubstitutionModel model
boolean modelBased
int numPatterns
int numSites
int numStates
SequencePairLikelihood of
DataType patternDataType_
SitePattern sitePattern
UnivariateMinimum um
int[] weight
int[][] fastMatchCount_
boolean isAmbiguous_
double[] logEquilibriumFrequencies_
SubstitutionModel model
int numberOfTransitionCategories_
int numPatterns
int numSites
int numStates
DataType patternDataType_
byte[] seqPat1
byte[] seqPat2
SitePattern sitePattern
double[] transitionCategoryProbabilities_
double[][][] transitionProbabilityStores_
int[] weight
ConditionalProbabilityStore.ExtraProcessor extraProcessor_
boolean fix_
boolean isBasedOnCachedData_
int numberOfCategories_
int numberOfStates_
int patternCapacity_
double[][][] store_
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
double[] categoryProbabilities_
DataType dataType_
double[][] individualLikelihoods_
double overallLogLikelihood_
int[] sitePatternMatchup_
float[] blockBeginPos
int[] blockBeginX
float[] blockEnd
float[] blockEndPos
int[] blockEndX
java.lang.String[] blockNames
float[] blockStart
java.awt.BorderLayout borderLayout1
boolean chromosomalScale
double[][] diseq
int distanceBetweenGraphAndGene
float[] endPos
int h2off
int hoff
int ih
boolean includeBlockSchematic
int iw
java.lang.String lowerLabel
boolean lowerProb
float minimumChromosomeLength
boolean probability
float[] startPos
AnnotationAlignment theAA
java.awt.Color theColor
LinkageDisequilibrium theLD
int totalBlocks
int totalChromosomes
int totalIntervals
int totalLoci
float totalUnits
int totalVariableSites
java.lang.String upperLabel
boolean upperProb
int voff
int[] xEndPos
int[] xPos
int[] yPos
java.util.Hashtable<K extends java.lang.Object,V extends java.lang.Object> displayMappings_
boolean highlight_
Node peer_
double x
TreePainterCircular circlePainter_
boolean circular_
boolean invertCiruclar_
int mode_
TreePainter painter_
java.text.NumberFormat nf
double[] nChoose2
boolean haveNextNextGaussian
int[] mag01
int[] mt
int mti
double nextNextGaussian
int capacity
boolean[] isAvailable
int next
int numDrawn
int numNumbers
MersenneTwisterFast rng
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
double minimumMutationRate_
double mu
double muSE
boolean parameterize_
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
FormattedOutput fo
double maximumMutationRate_
int units
boolean fixedMus
double[] muChanges
double[] mus
double[] muSEs
java.lang.String[] summaryTypes
boolean backgroundFixed
double muBackground
double muBackgroundSE
double muWindow
double muWindowSE
java.lang.String[] summaryTypes
double windowCenter
double windowWidth
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
java.lang.String name
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
java.util.Hashtable<K extends java.lang.Object,V extends java.lang.Object> mappings_
double currentValue_
double defaultValue_
double maximumValue_
double minimumValue_
java.lang.String name_
double se_
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
Identifier[] ids
java.util.Hashtable<K extends java.lang.Object,V extends java.lang.Object> indices
java.lang.String name
java.lang.String[] types_
double[] values_
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
java.lang.String name
pal.misc.TimeOrderCharacterData.SubgroupHandler[] subgroups_
IdGroup taxa
int[] timeOrdinals
double[] times
int units
boolean annotated
double currentProgress
double[][] diseq
int numberOfPermutations
double[][] pDiseq
boolean rapidPermute
java.util.Vector<E extends java.lang.Object>[] stateVector
Alignment theAlignment
AnnotationAlignment theAnnotationAlignment
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
DataType dataType
int dimension
FormattedOutput format
double[] frequency
double[] parameterStore_
double[][] rate
DoubleKeyCache cache
int dimension
boolean modelChanged_
pal.substmodel.CachedRateMatrix.Pij pij
RateMatrix rateMatrix
double expectedTsTv
double expectedTsTvSE
double kappa
double r
boolean showSE
double alpha
double alphaSE
boolean showSE
int dimension_
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
DataType dataType_
RateMatrixHandler handler_
int numberOfCategories_
MultiParameterized parameterization_
RateDistribution rateDistribution_
int[] constraints_
double[] defaultParameters_
int dimension_
int numberOfEffectiveParameters_
int numberOfParameters_
int[][] parameterChecks_
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
double a
double aSE
double b
double bSE
double c
double cSE
double d
double dSE
double e
double eSE
boolean showSE
double kappa
double kappaSE
boolean showSE
double frac
double fracSE
boolean showSE
double[][] amat
double ci
double cr
int dimension_
double[] Eval
double[] evali
double[][] Evec
double[][] Ievc
double[][] iexp
int[] ordr
double[][] transProb
int[] baseLookup_
double[] defaultRateParameters_
int dimension_
double[] equilibriumFrequencies_
MatrixExponential[] matrixExps_
double[][][] qMatrixStores_
NeoRateMatrix[] rateMatrices_
int[] rateParameterIndexLookup_
double[] rateParameters_
double[] rateParametersSE_
double[][] relativeRateStore_
boolean reversible_
double[] substitutionClassProbabilities_
boolean updateMatrix_
double[] freqs_
MutableDouble kappaStore_
YangCodonModel neutralModel_
double[] neutralParameters_
YangCodonModel purifyingModel_
double[] purifyingParameters_
double expectedTsTvRatio
double expectedYRTsRatio
YangCodonModel[] allMatrices_
double[] freqs_
MutableDouble kappaStore_
YangCodonModel neutralModel_
double[] neutralParameters_
MutableDouble omegaStore_
YangCodonModel positiveModel_
double[] positiveParameters_
YangCodonModel purifyingModel_
double[] purifyingParameters_
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
FormattedOutput format
int numRates
double[] probability
double[] rate
double[] defaultParameters_
int dimension_
double[] equilibriumFrequencies_
MatrixExponential matrixExp_
double[] parameters_
double[] parametersSE_
double[][] qMatrixStore_
NeoRateMatrix rateMatrix_
double[][] relativeRateStore_
boolean reversible_
boolean updateMatrix_
DataType dataType_
int numberOfRateMatrixParameters_
int numberOfSiteClasses_
MultiRateMatrixHandler rateMatrixHandler_
int totalNumberOfParameters_
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
DataType dataType_
RateMatrixHandler handler_
double kappa
double kappaSE
double r
double rSE
boolean showSE
CodonTable codonTable
double kappa
double kappaSE
double omega
double omegaSE
double[] parameterStore_
byte[] rateMap
boolean showSE
YangCodonModel[] baseMatrixes_
double kappa_
double p_
double[] probabilities_
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
YangCodonModel[] baseMatrixes_
double freeOmega_
double kappa_
double p0_
double p1_
double p2_
double[] probabilities_
TimeOrderCharacterData tocd
double[] parameter
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
double[] logDefaults
double[] logMaxs
double[] logMins
ParameterizedTree params
double lnL
double maxRelativeHeight_
MutationRateModel model
int numParameters
double[] parameter
TimeOrderCharacterData tocd
int abi
int abj
int[] alias
int besti
int bestj
double[][] distance
Node newCluster
int numClusters
double[] r
double scale
Tree tree
FormattedInput fi
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
java.util.Hashtable<K extends java.lang.Object,V extends java.lang.Object> attributes
Node[] child
double height
Identifier identifier
double length
double lengthSE
int number
Node parent
byte[] sequence
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
java.util.Hashtable<K extends java.lang.Object,V extends java.lang.Object>[] attributes
Node[] externalNode
Node[] internalNode
int numExternalNodes
int numInternalNodes
Node root
int units
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
double[] cumFreqs
double[] cumRateProbs
SubstitutionModel model
int numStates
int[] rateAtSite
MersenneTwisterFast rng
byte[][] stateData
Tree tree
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
java.io.IOException
java.lang.ClassNotFoundException
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
java.io.IOException
java.util.Hashtable<K extends java.lang.Object,V extends java.lang.Object>[] attributes
Node[] externalNode
Node[] internalNode
int numExternalNodes
int numInternalNodes
Node root
boolean setupLengthsAndHeights_
int units
int abi
int abj
int[] alias
int besti
int bestj
double[][] distance
double[] height
Node newCluster
int numClusters
int[] oc