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