Serialized Form

Package pal.alignment

Class pal.alignment.AbstractAlignment extends java.lang.Object implements Serializable

serialVersionUID: -5197800047652332969l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

numSeqs

int numSeqs

number of sequences

numSites

int numSites

length of each sequence

idGroup

IdGroup idGroup

sequence identifiers

dataType

DataType dataType

data type

Class pal.alignment.AlignmentParseException extends java.lang.Exception implements Serializable

Class pal.alignment.AlignmentReaders.PhylipClustalAlignment extends pal.alignment.AlignmentReaders.StringAlignment implements Serializable

Class pal.alignment.AlignmentReaders.UnalignedAlignment extends pal.alignment.AlignmentReaders.StringAlignment implements Serializable

Class pal.alignment.BootstrappedAlignment extends AbstractAlignment implements Serializable

Serialized Fields

urn

UrnModel urn

rawAlignment

Alignment rawAlignment

alias

int[] alias

Class pal.alignment.ConcatenatedAlignment extends AbstractAlignment implements Serializable

Serialized Fields

alignmentList

Alignment[] alignmentList

numAlignments

int numAlignments

alignmentIndex

int[] alignmentIndex

siteIndex

int[] siteIndex

Class pal.alignment.ConcatenatedAnnotatedAlignment extends AbstractAlignment implements Serializable

Serialized Fields

alignmentList

AnnotationAlignment[] alignmentList

numAlignments

int numAlignments

alignmentIndex

int[] alignmentIndex

siteIndex

int[] siteIndex

sequenceIndex

int[][] sequenceIndex

mergeByID

boolean mergeByID

union

boolean union

Class pal.alignment.GapBalancedAlignment extends AbstractAlignment implements Serializable

serialVersionUID: -1042105658996999207l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

data_

char[][] data_

Just in case we find some Alien DNA

Class pal.alignment.IndelAlignment extends AbstractAlignment implements Serializable

Serialized Fields

sequences

java.lang.String[] sequences

The sequences

anchored

boolean anchored

Indels anchored is true, then indels that share either a left or right side will be combined in the same locus. If false, an indel must share both sides to be scored in this alleles.

indel

java.util.Vector indel

Vector that contains IndelPositions, which has start, end and anchored information.

rawAlignment

Alignment rawAlignment

Class pal.alignment.IndelAnnotatedAlignment extends IndelAlignment implements Serializable

Serialized Fields

chromosomePosition

float chromosomePosition

used to designate position along chromosome

chromosome

int chromosome

used to designate chromosome

weightedLocusPosition

float[] weightedLocusPosition

used to designate weighted position; accounts for gaps

locusPosition

int[] locusPosition

used to designate position; do not account for gaps

positionType

char[] positionType

used to designate position Type

locusName

java.lang.String locusName

used to designate locus name

Class pal.alignment.JumbledAlignment extends AbstractAlignment implements Serializable

Serialized Fields

urn

UrnModel urn

rawAlignment

Alignment rawAlignment

alias

int[] alias

Class pal.alignment.MultiLocusAnnotatedAlignment extends SimpleAlignment implements Serializable

Serialized Fields

chromosomePosition

float[] chromosomePosition

used to designate position along chromosome

chromosome

int[] chromosome

used to designate chromosome

weightedPosition

float[] weightedPosition

used to designate weighted position; accounts for gaps

locusPosition

int[] locusPosition

used to designate position; do not account for gaps

positionType

char[] positionType

used to designate position Type

locusName

java.lang.String[] locusName

used to designate locus name

siteDataType

DataType[] siteDataType

provides datatype for each locus separately

Class pal.alignment.ReadAlignment extends AbstractAlignment implements Serializable

Serialized Fields

lineLength

int lineLength

names

java.util.Vector names

seqs

java.util.Vector seqs

sites

java.util.Vector sites

fi

FormattedInput fi

data

char[][] data

Class pal.alignment.ReadAlignmentOld extends AbstractAlignment implements Serializable

Serialized Fields

lineLength

int lineLength

names

java.util.Vector names

seqs

java.util.Vector seqs

sites

java.util.Vector sites

fi

FormattedInput fi

data

char[][] data

Class pal.alignment.SimpleAlignment extends AbstractAlignment implements Serializable

serialVersionUID: 4303224913340358191l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

sequences

java.lang.String[] sequences

The sequences

Class pal.alignment.SimpleAnnotatedAlignment extends SimpleAlignment implements Serializable

Serialized Fields

chromosomePosition

float chromosomePosition

used to designate position along chromosome

chromosome

int chromosome

used to designate chromosome

weightedPosition

float[] weightedPosition

used to designate weighted position; accounts for gaps

positionType

char[] positionType

used to designate position Type

locusName

java.lang.String locusName

used to designate locus name

Class pal.alignment.SimpleCharacterAlignment extends java.lang.Object implements Serializable

Serialized Fields

traitValues

double[][] traitValues

trait values

traitNames

java.lang.String[] traitNames

names of the traits

environmentNames

java.lang.String[] environmentNames

names of the traits

numSeqs

int numSeqs

number of sequences

numTraits

int numTraits

number of traits

idGroup

IdGroup idGroup

sequence identifiers

Class pal.alignment.SitePattern extends AbstractAlignment implements Serializable

Serialized Fields

numPatterns

int numPatterns

number of site patterns

alias

int[] alias

site -> site pattern

weight

int[] weight

weights of each site pattern

pattern

byte[][] pattern

site patterns [sequence][site pattern]

patSort

int[] patSort

Class pal.alignment.StrippedAlignment extends AbstractAlignment implements Serializable

Serialized Fields

rawAlignment

Alignment rawAlignment

rawNumSites

int rawNumSites

alias

int[] alias

notDropped

boolean[] notDropped

Class pal.alignment.StrippedAnnotatedAlignment extends StrippedAlignment implements Serializable

Serialized Fields

rawAlignment

AnnotationAlignment rawAlignment

rawNumSites

int rawNumSites

minimumProportion

double minimumProportion

minimumCount

int minimumCount

firstSite

int firstSite

lastSite

int lastSite

Package pal.coalescent

Class pal.coalescent.CoalescentException extends java.lang.Exception implements Serializable

Class pal.coalescent.CoalescentIntervals extends java.lang.Object implements Serializable

Serialized Fields

intervals

double[] intervals

The widths of the intervals.

numLineages

int[] numLineages

The number of uncoalesced lineages within a particular interval.

units

int units

The units in which the intervals are expressed.

fo

FormattedOutput fo

Class pal.coalescent.ConstantPopulation extends DemographicModel implements Serializable

Serialized Fields

N0

double N0

population size

N0SE

double N0SE

standard error of population size

Class pal.coalescent.ConstExpConst extends ConstExpGrowth implements Serializable

Serialized Fields

tx

double tx

time of end of exponential growth

txSE

double txSE

standard error of time of growth

Class pal.coalescent.ConstExpGrowth extends ExponentialGrowth implements Serializable

Serialized Fields

parameterization

int parameterization

parameterization bit string:
first bit: 0 = ALPHA, 1 = N1
second bit: 0 = GROWTH RATE, 1 = LX

alpha

double alpha

ratio of pop. sizes

alphaSE

double alphaSE

standard error of time alpha

N1

double N1

ancestral pop. size

N1SE

double N1SE

standard error of ancestral pop. size

lx

double lx

the duration of the growth phase

Class pal.coalescent.DemographicClockTree extends ClockTree implements Serializable

Serialized Fields

model

DemographicModel model

Class pal.coalescent.DemographicModel extends java.lang.Object implements Serializable

Serialized Fields

units

int units

Units in which population size is measured.

logL

double logL

rng

MersenneTwisterFast rng

binom

Binomial binom

fo

FormattedOutput fo

Class pal.coalescent.ExpandingPopulation extends ExponentialGrowth implements Serializable

Serialized Fields

alpha

double alpha

ratio of pop. sizes

alphaSE

double alphaSE

standard error of time alpha

Class pal.coalescent.ExponentialGrowth extends ConstantPopulation implements Serializable

Serialized Fields

r

double r

growth rate r

rSE

double rSE

standard error of growth rate r

Class pal.coalescent.SerialCoalescentGenerator extends java.lang.Object implements Serializable

Serialized Fields

tocd_

TimeOrderCharacterData tocd_

demographicModel_

DemographicModel demographicModel_

numberOfTreesToGenerate_

int numberOfTreesToGenerate_

alignmentFactory_

SimulatedAlignment.Factory alignmentFactory_

treeFinisher_

TreeOperation treeFinisher_

Class pal.coalescent.SerialCoalescentSimulator extends java.lang.Object implements Serializable

Serialized Fields

tree

SimpleTree tree

Class pal.coalescent.SkylinePlot extends java.lang.Object implements Serializable

Serialized Fields

ci

CoalescentIntervals ci

fo

FormattedOutput fo

size

int size

maxTime

double maxTime

eps

double eps

params

int params

cis

double[] cis

cummulative interval sizes

populationSize

double[] populationSize

estimated population size in a coalescent interval

Package pal.datatype

Class pal.datatype.AminoAcids extends SimpleDataType implements Serializable

serialVersionUID: -466623855742195043l

Class pal.datatype.Codons extends SimpleDataType implements Serializable

serialVersionUID: -2779857947044354950l

Class pal.datatype.GapBalanced extends SimpleDataType implements Serializable

Serialized Fields

translationTable_

CodonTable translationTable_

Class pal.datatype.IUPACNucleotides extends SimpleDataType implements Serializable

serialVersionUID: 8863411606027017687l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

isRNA_

boolean isRNA_

conversionTable_

char[] conversionTable_

Class pal.datatype.Nucleotides extends SimpleDataType implements Serializable

serialVersionUID: -497943046234232204l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

isRNA_

boolean isRNA_

conversionTable_

char[] conversionTable_

Class pal.datatype.NumericDataType extends SimpleDataType implements Serializable

Serialized Fields

numberOfNumericStates

int numberOfNumericStates

Class pal.datatype.SimpleDataType extends java.lang.Object implements Serializable

serialVersionUID: 7902613264354545217l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Class pal.datatype.SpecificAminoAcids extends AminoAcids implements Serializable

Serialized Fields

translationTable_

CodonTable translationTable_

Class pal.datatype.StateRemover extends SimpleDataType implements Serializable

Serialized Fields

toAdjust_

DataType toAdjust_

originalToAdjusted_

int[] originalToAdjusted_

adjustedToOriginal_

int[] adjustedToOriginal_

A translation array -> originalToAdjusted_["original State"] = "adjusted state"

Class pal.datatype.TwoStates extends SimpleDataType implements Serializable

Package pal.distance

Class pal.distance.AlignmentDistanceMatrix extends DistanceMatrix implements Serializable

Class pal.distance.DistanceMatrix extends java.lang.Object implements Serializable

serialVersionUID: 4725925229860707633l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

I like doing things my self!

Serialized Fields

idGroup

IdGroup idGroup

sequence identifiers

distance

double[][] distance

distances [seq1][seq2]

Class pal.distance.DistanceMatrixUtils extends java.lang.Object implements Serializable

Class pal.distance.DistanceParseException extends java.lang.Exception implements Serializable

Class pal.distance.JukesCantorDistanceMatrix extends DistanceMatrix implements Serializable

Class pal.distance.PairwiseDistance extends java.lang.Object implements Serializable

serialVersionUID: 4721062357793106145l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

distance

double distance

last estimated distance

distanceSE

double distanceSE

last estimate standard error of a distance

numSites

int numSites

numPatterns

int numPatterns

numStates

int numStates

weight

int[] weight

jcratio

double jcratio

modelBased

boolean modelBased

sitePattern

SitePattern sitePattern

model

SubstitutionModel model

um

UnivariateMinimum um

of

SequencePairLikelihood of

patternDataType_

DataType patternDataType_

Class pal.distance.ReadDistanceMatrix extends DistanceMatrix implements Serializable

Class pal.distance.SequencePairLikelihood extends java.lang.Object implements Serializable

Serialized Fields

model

SubstitutionModel model

sitePattern

SitePattern sitePattern

patternDataType_

DataType patternDataType_

numPatterns

int numPatterns

numSites

int numSites

numStates

int numStates

numberOfTransitionCategories_

int numberOfTransitionCategories_

weight

int[] weight

logEquilibriumFrequencies_

double[] logEquilibriumFrequencies_

transitionProbabilityStores_

double[][][] transitionProbabilityStores_

transitionCategoryProbabilities_

double[] transitionCategoryProbabilities_

fastMatchCount_

int[][] fastMatchCount_

seqPat1

byte[] seqPat1

seqPat2

byte[] seqPat2

isAmbiguous_

boolean isAmbiguous_

Package pal.eval

Class pal.eval.ConditionalProbabilityStore extends java.lang.Object implements Serializable

Serialized Fields

numberOfCategories_

int numberOfCategories_

numberOfStates_

int numberOfStates_

store_

double[][][] store_

patternCapacity_

int patternCapacity_

extraProcessor_

ConditionalProbabilityStore.ExtraProcessor extraProcessor_

isBasedOnCachedData_

boolean isBasedOnCachedData_

fix_

boolean fix_

Class pal.eval.LikelihoodSummary extends java.lang.Object implements Serializable

serialVersionUID: -37625234234158192l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

overallLogLikelihood_

double overallLogLikelihood_

categoryProbabilities_

double[] categoryProbabilities_

individualLikelihoods_

double[][] individualLikelihoods_

sitePatternMatchup_

int[] sitePatternMatchup_

dataType_

DataType dataType_

Package pal.gui

Class pal.gui.LinkageDisequilibriumComponent extends java.awt.Component implements Serializable

Serialized Fields

minimumChromosomeLength

float minimumChromosomeLength

theLD

LinkageDisequilibrium theLD

theAA

AnnotationAlignment theAA

includeBlockSchematic

boolean includeBlockSchematic

chromosomalScale

boolean chromosomalScale

borderLayout1

java.awt.BorderLayout borderLayout1

totalVariableSites

int totalVariableSites

totalLoci

int totalLoci

totalChromosomes

int totalChromosomes

totalIntervals

int totalIntervals

totalBlocks

int totalBlocks

startPos

float[] startPos

endPos

float[] endPos

blockBeginPos

float[] blockBeginPos

blockEndPos

float[] blockEndPos

blockNames

java.lang.String[] blockNames

xPos

int[] xPos

yPos

int[] yPos

xEndPos

int[] xEndPos

blockBeginX

int[] blockBeginX

blockEndX

int[] blockEndX

ih

int ih

iw

int iw

totalUnits

float totalUnits

blockStart

float[] blockStart

blockEnd

float[] blockEnd

upperLabel

java.lang.String upperLabel

lowerLabel

java.lang.String lowerLabel

diseq

double[][] diseq

theColor

java.awt.Color theColor

distanceBetweenGraphAndGene

int distanceBetweenGraphAndGene

hoff

int hoff

h2off

int h2off

voff

int voff

probability

boolean probability

upperProb

boolean upperProb

lowerProb

boolean lowerProb

Class pal.gui.NameColouriser extends java.lang.Object implements Serializable

Serialized Fields

displayMappings_

java.util.Hashtable displayMappings_

Class pal.gui.PositionedNode extends SimpleNode implements Serializable

Serialized Fields

x

double x

highlight_

boolean highlight_

peer_

Node peer_

Class pal.gui.TreeComponent extends java.awt.Component implements Serializable

Serialized Fields

circular_

boolean circular_

mode_

int mode_

circlePainter_

TreePainterCircular circlePainter_

painter_

TreePainter painter_

invertCiruclar_

boolean invertCiruclar_

Package pal.io

Class pal.io.FormattedInput extends java.lang.Object implements Serializable

Class pal.io.FormattedOutput extends java.lang.Object implements Serializable

Serialized Fields

nf

java.text.NumberFormat nf

Class pal.io.NexusParseException extends java.lang.Exception implements Serializable

Package pal.math

Class pal.math.Binomial extends java.lang.Object implements Serializable

Serialized Fields

nChoose2

double[] nChoose2

Class pal.math.MersenneTwisterFast extends java.lang.Object implements Serializable

Serialized Fields

mt

int[] mt

mti

int mti

mag01

int[] mag01

nextNextGaussian

double nextNextGaussian

haveNextNextGaussian

boolean haveNextNextGaussian

Class pal.math.UrnModel extends java.lang.Object implements Serializable

Serialized Fields

capacity

int capacity

numNumbers

int numNumbers

numDrawn

int numDrawn

next

int next

isAvailable

boolean[] isAvailable

rng

MersenneTwisterFast rng

Package pal.mep

Class pal.mep.ConstantMutationRate extends MutationRateModel implements Serializable

serialVersionUID: -6086097377649319118l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

mu

double mu

mutation rate

muSE

double muSE

minimumMutationRate_

double minimumMutationRate_

parameterize_

boolean parameterize_

Class pal.mep.MutationRateModel extends java.lang.Object implements Serializable

serialVersionUID: -1755051453782951214l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

fo

FormattedOutput fo

units

int units

Units in which time units are measured.

maximumMutationRate_

double maximumMutationRate_

Class pal.mep.SteppedMutationRate extends MutationRateModel implements Serializable

Serialized Fields

mus

double[] mus

mutation rates

muSEs

double[] muSEs

mutation rate SEs

muChanges

double[] muChanges

mutation rate change times

fixedMus

boolean fixedMus

whether or not the mu values are optimizable

summaryTypes

java.lang.String[] summaryTypes

Class pal.mep.WindowedMutationRate extends MutationRateModel implements Serializable

Serialized Fields

muBackground

double muBackground

mutation rates

muWindow

double muWindow

muBackgroundSE

double muBackgroundSE

mutation rate SEs

muWindowSE

double muWindowSE

windowCenter

double windowCenter

mutation rate change times

windowWidth

double windowWidth

backgroundFixed

boolean backgroundFixed

summaryTypes

java.lang.String[] summaryTypes

Package pal.misc

Class pal.misc.Identifier extends java.lang.Object implements Serializable

serialVersionUID: -7873729831795750538l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Versioning control... only works with 1.1+ (1.0 should be fine though... this is just pointless that's all)

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Versioning control... only works with 1.1+ (1.0 should be fine though... this is just pointless that's all)

Serialized Fields

name

java.lang.String name

Class pal.misc.LabelMapping extends java.lang.Object implements Serializable

serialVersionUID: -9217142171228146380l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

mappings_

java.util.Hashtable mappings_

Class pal.misc.MutableDouble extends java.lang.Object implements Serializable

Serialized Fields

defaultValue_

double defaultValue_

minimumValue_

double minimumValue_

maximumValue_

double maximumValue_

se_

double se_

currentValue_

double currentValue_

name_

java.lang.String name_

Class pal.misc.PalObjectEvent extends java.util.EventObject implements Serializable

Class pal.misc.ParameterEvent extends java.util.EventObject implements Serializable

Class pal.misc.SimpleIdGroup extends java.lang.Object implements Serializable

serialVersionUID: -4266575329980153075l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

name

java.lang.String name

ids

Identifier[] ids

indices

java.util.Hashtable indices

Class pal.misc.SimpleSummarizable extends java.lang.Object implements Serializable

Serialized Fields

types_

java.lang.String[] types_

values_

double[] values_

Class pal.misc.TimeOrderCharacterData extends java.lang.Object implements Serializable

serialVersionUID: 7672390862755080486l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

timeOrdinals

int[] timeOrdinals

Order of times

times

double[] times

Actual times of each sample

taxa

IdGroup taxa

the identifier group

units

int units

subgroups_

pal.misc.TimeOrderCharacterData.SubgroupHandler[] subgroups_

name

java.lang.String name

Name of this character data

Package pal.popgen

Class pal.popgen.LinkageDisequilibrium extends java.lang.Thread implements Serializable

Serialized Fields

theAlignment

Alignment theAlignment

theAnnotationAlignment

AnnotationAlignment theAnnotationAlignment

annotated

boolean annotated

stateVector

java.util.Vector[] stateVector

rapidPermute

boolean rapidPermute

numberOfPermutations

int numberOfPermutations

diseq

double[][] diseq

pDiseq

double[][] pDiseq

currentProgress

double currentProgress

Package pal.substmodel

Class pal.substmodel.AbstractRateMatrix extends java.lang.Object implements Serializable

serialVersionUID: 7726654175983028192l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

dimension

int dimension

dimension

frequency

double[] frequency

stationary frequencies (sum = 1.0)

rate

double[][] rate

rate matrix (transition: from 1st index to 2nd index)

dataType

DataType dataType

data type

format

FormattedOutput format

parameterStore_

double[] parameterStore_

Class pal.substmodel.AminoAcidModel extends AbstractRateMatrix implements Serializable

Class pal.substmodel.BLOSUM62 extends AminoAcidModel implements Serializable

Class pal.substmodel.CachedRateMatrix extends java.lang.Object implements Serializable

Serialized Fields

cache

DoubleKeyCache cache

pij

CachedRateMatrix.Pij pij

rateMatrix

RateMatrix rateMatrix

dimension

int dimension

modelChanged_

boolean modelChanged_

Class pal.substmodel.CodonModel extends AbstractRateMatrix implements Serializable

Class pal.substmodel.CPREV extends AminoAcidModel implements Serializable

Class pal.substmodel.Dayhoff extends AminoAcidModel implements Serializable

Class pal.substmodel.F81 extends NucleotideModel implements Serializable

serialVersionUID: -8473405513320987709l

Class pal.substmodel.F84 extends NucleotideModel implements Serializable

Serialized Fields

showSE

boolean showSE

kappa

double kappa

r

double r

expectedTsTv

double expectedTsTv

expectedTsTvSE

double expectedTsTvSE

Class pal.substmodel.GammaRates extends RateDistribution implements Serializable

Serialized Fields

showSE

boolean showSE

alpha

double alpha

alphaSE

double alphaSE

Class pal.substmodel.GeneralPoissonRateMatrix extends java.lang.Object implements Serializable

Serialized Fields

dimension_

int dimension_

Class pal.substmodel.GeneralRateDistributionSubstitutionModel extends Parameterized.ParameterizedUser implements Serializable

serialVersionUID: 34127557628342342l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

handler_

RateMatrixHandler handler_

rateDistribution_

RateDistribution rateDistribution_

dataType_

DataType dataType_

parameterization_

MultiParameterized parameterization_

numberOfCategories_

int numberOfCategories_

Class pal.substmodel.GeneralREVRateMatrix extends java.lang.Object implements Serializable

Serialized Fields

dimension_

int dimension_

parameterChecks_

int[][] parameterChecks_

constraints_

int[] constraints_

numberOfParameters_

int numberOfParameters_

numberOfEffectiveParameters_

int numberOfEffectiveParameters_

defaultParameters_

double[] defaultParameters_

Class pal.substmodel.GTR extends NucleotideModel implements Serializable

serialVersionUID: -8557884770092535699l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

showSE

boolean showSE

a

double a

b

double b

c

double c

d

double d

e

double e

aSE

double aSE

bSE

double bSE

cSE

double cSE

dSE

double dSE

eSE

double eSE

Class pal.substmodel.HKY extends NucleotideModel implements Serializable

Serialized Fields

showSE

boolean showSE

kappa

double kappa

kappaSE

double kappaSE

Class pal.substmodel.InvariableSites extends RateDistribution implements Serializable

Serialized Fields

showSE

boolean showSE

frac

double frac

fracSE

double fracSE

Class pal.substmodel.JTT extends AminoAcidModel implements Serializable

Class pal.substmodel.MatrixExponential extends java.lang.Object implements Serializable

Serialized Fields

Eval

double[] Eval

Evec

double[][] Evec

Ievc

double[][] Ievc

iexp

double[][] iexp

ordr

int[] ordr

evali

double[] evali

amat

double[][] amat

dimension_

int dimension_

dimension of rate matrix

transProb

double[][] transProb

transition probability matrix

cr

double cr

ci

double ci

Class pal.substmodel.MTREV24 extends AminoAcidModel implements Serializable

Class pal.substmodel.MultiRateMatrixHandler extends java.lang.Object implements Serializable

Serialized Fields

rateMatrices_

NeoRateMatrix[] rateMatrices_

rateParameters_

double[] rateParameters_

substitutionClassProbabilities_

double[] substitutionClassProbabilities_

rateParametersSE_

double[] rateParametersSE_

defaultRateParameters_

double[] defaultRateParameters_

updateMatrix_

boolean updateMatrix_

equilibriumFrequencies_

double[] equilibriumFrequencies_

dimension_

int dimension_

relativeRateStore_

double[][] relativeRateStore_

qMatrixStores_

double[][][] qMatrixStores_

matrixExps_

MatrixExponential[] matrixExps_

reversible_

boolean reversible_

baseLookup_

int[] baseLookup_

rateParameterIndexLookup_

int[] rateParameterIndexLookup_

Class pal.substmodel.NeutralSelectionRateMatrixGroup extends java.lang.Object implements Serializable

serialVersionUID: 84829859222352l

Serialized Fields

purifyingModel_

YangCodonModel purifyingModel_

neutralModel_

YangCodonModel neutralModel_

freqs_

double[] freqs_

purifyingParameters_

double[] purifyingParameters_

neutralParameters_

double[] neutralParameters_

kappaStore_

MutableDouble kappaStore_

Class pal.substmodel.NucleotideModel extends AbstractRateMatrix implements Serializable

Serialized Fields

expectedTsTvRatio

double expectedTsTvRatio

expectedYRTsRatio

double expectedYRTsRatio

Class pal.substmodel.PositiveSelectionRateMatrixGroup extends java.lang.Object implements Serializable

serialVersionUID: 4829485859252l

Serialized Fields

purifyingModel_

YangCodonModel purifyingModel_

neutralModel_

YangCodonModel neutralModel_

positiveModel_

YangCodonModel positiveModel_

allMatrices_

YangCodonModel[] allMatrices_

freqs_

double[] freqs_

purifyingParameters_

double[] purifyingParameters_

neutralParameters_

double[] neutralParameters_

positiveParameters_

double[] positiveParameters_

kappaStore_

MutableDouble kappaStore_

omegaStore_

MutableDouble omegaStore_

Class pal.substmodel.RateDistribution extends PalObjectListener.EventGenerator implements Serializable

serialVersionUID: -5584969247361304141l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

numRates

int numRates

number of rate categories

rate

double[] rate

rates of each rate category

probability

double[] probability

probability of each rate

format

FormattedOutput format

Class pal.substmodel.RateMatrixHandler extends java.lang.Object implements Serializable

Serialized Fields

rateMatrix_

NeoRateMatrix rateMatrix_

parameters_

double[] parameters_

parametersSE_

double[] parametersSE_

defaultParameters_

double[] defaultParameters_

updateMatrix_

boolean updateMatrix_

equilibriumFrequencies_

double[] equilibriumFrequencies_

dimension_

int dimension_

relativeRateStore_

double[][] relativeRateStore_

qMatrixStore_

double[][] qMatrixStore_

matrixExp_

MatrixExponential matrixExp_

reversible_

boolean reversible_

Class pal.substmodel.SimpleRateMatrixGroup extends java.lang.Object implements Serializable

Serialized Fields

rateMatrixHandler_

MultiRateMatrixHandler rateMatrixHandler_

numberOfRateMatrixParameters_

int numberOfRateMatrixParameters_

numberOfSiteClasses_

int numberOfSiteClasses_

totalNumberOfParameters_

int totalNumberOfParameters_

dataType_

DataType dataType_

Class pal.substmodel.SingleClassSubstitutionModel extends Parameterized.ParameterizedUser implements Serializable

serialVersionUID: 4938429359234234234l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

handler_

RateMatrixHandler handler_

dataType_

DataType dataType_

Class pal.substmodel.TN extends NucleotideModel implements Serializable

Serialized Fields

showSE

boolean showSE

kappa

double kappa

kappaSE

double kappaSE

r

double r

rSE

double rSE

Class pal.substmodel.TwoStateModel extends AbstractRateMatrix implements Serializable

Class pal.substmodel.UniformRate extends RateDistribution implements Serializable

Class pal.substmodel.VT extends AminoAcidModel implements Serializable

Class pal.substmodel.WAG extends AminoAcidModel implements Serializable

Class pal.substmodel.YangCodonModel extends CodonModel implements Serializable

serialVersionUID: -3955993899328983304l

Serialized Fields

showSE

boolean showSE

kappa

double kappa

omega

double omega

kappaSE

double kappaSE

omegaSE

double omegaSE

rateMap

byte[] rateMap

codonTable

CodonTable codonTable

parameterStore_

double[] parameterStore_

Class pal.substmodel.YangCodonModel.SimpleNeutralSelection extends PalObjectListener.EventGenerator implements Serializable

Serialized Fields

baseMatrixes_

YangCodonModel[] baseMatrixes_

p_

double p_

kappa_

double kappa_

probabilities_

double[] probabilities_

Class pal.substmodel.YangCodonModel.SimplePositiveSelection extends PalObjectListener.EventGenerator implements Serializable

serialVersionUID: -7826700615445839100l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

baseMatrixes_

YangCodonModel[] baseMatrixes_

p0_

double p0_

p1_

double p1_

p2_

double p2_

probabilities_

double[] probabilities_

kappa_

double kappa_

freeOmega_

double freeOmega_

Package pal.supgma

Class pal.supgma.SUPGMADistanceMatrix extends DistanceMatrix implements Serializable

Class pal.supgma.SUPGMATree extends ClusterTree implements Serializable

Serialized Fields

tocd

TimeOrderCharacterData tocd

Package pal.tree

Class pal.tree.ClockTree extends ParameterizedTree.ParameterizedTreeBase implements Serializable

Serialized Fields

parameter

double[] parameter

Class pal.tree.ClusterTree extends SimpleTree implements Serializable

serialVersionUID: 677888847384253321l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Class pal.tree.LogParameterizedTree extends ParameterizedTree.ParameterizedTreeBase implements Serializable

Serialized Fields

params

ParameterizedTree params

logMins

double[] logMins

logMaxs

double[] logMaxs

logDefaults

double[] logDefaults

Class pal.tree.MutationRateModelTree extends ParameterizedTree.ParameterizedTreeBase implements Serializable

Serialized Fields

tocd

TimeOrderCharacterData tocd

model

MutationRateModel model

numParameters

int numParameters

maxRelativeHeight_

double maxRelativeHeight_

parameter

double[] parameter

lnL

double lnL

Class pal.tree.NeighborJoiningTree extends SimpleTree implements Serializable

Serialized Fields

numClusters

int numClusters

newCluster

Node newCluster

besti

int besti

abi

int abi

bestj

int bestj

abj

int abj

alias

int[] alias

distance

double[][] distance

r

double[] r

scale

double scale

Class pal.tree.ParameterizedTree.ParameterizedTreeBase extends java.lang.Object implements Serializable

Serialized Fields

tree

Tree tree

The non-parameterized tree that this parameterized tree is based on.

Class pal.tree.ReadTree extends SimpleTree implements Serializable

Serialized Fields

fi

FormattedInput fi

Class pal.tree.SimpleNode extends java.lang.Object implements Serializable

serialVersionUID: 3472432765038556717l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

I like doing things my self!

Serialized Fields

parent

Node parent

parent node

number

int number

number of node as displayed

sequence

byte[] sequence

sequences associated with node

length

double length

length of branch to parent node

lengthSE

double lengthSE

standard error of length of branch to parent node

height

double height

height of this node

identifier

Identifier identifier

identifier of node/associated branch

attributes

java.util.Hashtable attributes

the attributes associated with this node.

child

Node[] child

Class pal.tree.SimpleTree extends java.lang.Object implements Serializable

serialVersionUID: -7330318631600898531l

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

I like doing things my self!

Serialized Fields

root

Node root

root node

internalNode

Node[] internalNode

list of internal nodes (including root)

numInternalNodes

int numInternalNodes

number of internal nodes (including root)

externalNode

Node[] externalNode

list of external nodes

numExternalNodes

int numExternalNodes

number of external nodes

attributes

java.util.Hashtable[] attributes

attributes attached to this tree.

units

int units

holds the units of the trees branches.

Class pal.tree.SimulatedAlignment extends AbstractAlignment implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

Serialized Fields

tree

Tree tree

model

SubstitutionModel model

cumFreqs

double[] cumFreqs

rateAtSite

int[] rateAtSite

cumRateProbs

double[] cumRateProbs

numStates

int numStates

stateData

byte[][] stateData

rng

MersenneTwisterFast rng

Class pal.tree.Tree.TreeBase extends java.lang.Object implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

writeObject

private void writeObject(java.io.ObjectOutputStream out)
                  throws java.io.IOException

I like doing things my self!

Serialized Fields

root

Node root

root node

internalNode

Node[] internalNode

list of internal nodes (including root)

numInternalNodes

int numInternalNodes

number of internal nodes (including root)

externalNode

Node[] externalNode

list of external nodes

numExternalNodes

int numExternalNodes

number of external nodes

attributes

java.util.Hashtable[] attributes

attributes attached to this tree.

units

int units

holds the units of the trees branches.

setupLengthsAndHeights_

boolean setupLengthsAndHeights_

Class pal.tree.TreeDistanceMatrix extends DistanceMatrix implements Serializable

Class pal.tree.TreeParseException extends java.lang.Exception implements Serializable

Class pal.tree.UnconstrainedTree extends ParameterizedTree.ParameterizedTreeBase implements Serializable

Class pal.tree.UPGMATree extends SimpleTree implements Serializable

Serialized Fields

numClusters

int numClusters

Deprecated.

newCluster

Node newCluster

Deprecated.

besti

int besti

Deprecated.

abi

int abi

Deprecated.

bestj

int bestj

Deprecated.

abj

int abj

Deprecated.

alias

int[] alias

Deprecated.

distance

double[][] distance

Deprecated.

height

double[] height

Deprecated.

oc

int[] oc

Deprecated.

Package pal.xml

Class pal.xml.XmlParseException extends java.lang.Exception implements Serializable