Serialized Form


Package pal.alignment

Class pal.alignment.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

numSeqs

int numSeqs
number of sequences

numSites

int numSites
length of each sequence

idGroup

IdGroup idGroup
sequence identifiers

frequency

double[] frequency
frequencies of the allowed states (scaled to sum to 1.0 and suitable for RateMatrix)

dataType

DataType dataType
data type

Class pal.alignment.AlignmentParseException implements Serializable

Class pal.alignment.AminoAcidAlignment implements Serializable

Serialized Fields

data_

char[][] data_

Class pal.alignment.BootstrappedAlignment implements Serializable

Serialized Fields

urn

UrnModel urn

rawAlignment

Alignment rawAlignment

alias

int[] alias

Class pal.alignment.CodonAlignment implements Serializable

Serialized Fields

data_

char[][] data_

Class pal.alignment.ConcatenatedAlignment implements Serializable

Serialized Fields

alignmentList

Alignment[] alignmentList

numAlignments

int numAlignments

alignmentIndex

int[] alignmentIndex

siteIndex

int[] siteIndex

Class pal.alignment.ConcatenatedAnnotatedAlignment 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 implements Serializable

Serialized Fields

data_

char[][] data_

Class pal.alignment.IndelAlignment 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 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 implements Serializable

Serialized Fields

urn

UrnModel urn

rawAlignment

Alignment rawAlignment

alias

int[] alias

Class pal.alignment.MultiLocusAnnotatedAlignment 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 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 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

sequences

java.lang.String[] sequences
The sequences

Class pal.alignment.SimpleAnnotatedAlignment 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 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 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 implements Serializable

Serialized Fields

rawAlignment

Alignment rawAlignment

rawNumSites

int rawNumSites

alias

int[] alias

notDropped

boolean[] notDropped

Class pal.alignment.StrippedAnnotatedAlignment 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 implements Serializable

Class pal.coalescent.CoalescentIntervals 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 implements Serializable

Serialized Fields

N0

double N0
population size

N0SE

double N0SE
standard error of population size

Class pal.coalescent.ConstExpGrowth implements Serializable

Serialized Fields

parameterization

int parameterization
parameterization

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

Class pal.coalescent.DemographicClockTree implements Serializable

Serialized Fields

model

DemographicModel model

Class pal.coalescent.DemographicModel 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 implements Serializable

Serialized Fields

alpha

double alpha
ratio of pop. sizes

alphaSE

double alphaSE
standard error of time alpha

Class pal.coalescent.ExponentialGrowth implements Serializable

Serialized Fields

r

double r
growth rate r

rSE

double rSE
standard error of growth rate r

Class pal.coalescent.SerialCoalescentSimulator implements Serializable

Serialized Fields

tree

Tree tree

Class pal.coalescent.SkylinePlot 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 implements Serializable

Class pal.datatype.Codons implements Serializable

Class pal.datatype.DataTypeUtils implements Serializable

Class pal.datatype.GeneralizedCodons implements Serializable

Serialized Fields

characterType_

DataType characterType_

numberOfCharacterStates_

int numberOfCharacterStates_

codonLength_

int codonLength_

numberOfCodonStates_

int numberOfCodonStates_

Class pal.datatype.IUPACNucleotides implements Serializable

Class pal.datatype.Nucleotides 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

isRNA_

boolean isRNA_

conversionTable_

char[] conversionTable_

Class pal.datatype.NumericDataType implements Serializable

Serialized Fields

numberOfNumericStates

int numberOfNumericStates

Class pal.datatype.SimpleDataType 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

Class pal.datatype.StateRemover 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 implements Serializable


Package pal.distance

Class pal.distance.AlignmentDistanceMatrix implements Serializable

Serialized Fields

pwd

PairwiseDistance pwd

progress_

double progress_

Class pal.distance.DistanceMatrix implements Serializable

Serialized Fields

numSeqs

int numSeqs
number of sequences. Should be replaced by method that looks directly at size of distance matrix.

idGroup

IdGroup idGroup
sequence identifiers

distance

double[][] distance
distances [seq1][seq2]

format

FormattedOutput format

Class pal.distance.DistanceMatrixUtils implements Serializable

Class pal.distance.DistanceParseException implements Serializable

Class pal.distance.JukesCantorDistanceMatrix implements Serializable

Serialized Fields

obsDistance

double[][] obsDistance

const1

double const1

const2

double const2

Class pal.distance.PairwiseDistance implements Serializable

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

um

UnivariateMinimum um

of

SequencePairLikelihood of

Class pal.distance.ReadDistanceMatrix implements Serializable

Class pal.distance.SUPGMADistanceMatrix implements Serializable


Package pal.gui

Class pal.gui.LinkageDisequilibriumComponent 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 implements Serializable

Serialized Fields

colourMappings_

java.util.Hashtable colourMappings_

Class pal.gui.PositionedNode implements Serializable

Serialized Fields

x

double x

highlight_

boolean highlight_

peer_

Node peer_

Class pal.gui.TreeComponent 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 implements Serializable

Class pal.io.FormattedOutput implements Serializable

Serialized Fields

nf

java.text.NumberFormat nf


Package pal.math

Class pal.math.Binomial implements Serializable

Serialized Fields

nChoose2

double[] nChoose2

Class pal.math.MersenneTwisterFast implements Serializable

Serialized Fields

mt

int[] mt

mti

int mti

mag01

int[] mag01

nextNextGaussian

double nextNextGaussian

haveNextNextGaussian

boolean haveNextNextGaussian

Class pal.math.UrnModel 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 implements Serializable

Serialized Fields

mu

double mu
mutation rate

muSE

double muSE

Class pal.mep.MutationRateModel implements Serializable

Serialized Fields

units

int units
Units in which time units are measured.

fo

FormattedOutput fo

Class pal.mep.SteppedMutationRate 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 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 implements Serializable

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 implements Serializable

Serialized Fields

mappings_

java.util.Hashtable mappings_

Class pal.misc.PalObjectEvent implements Serializable

Class pal.misc.ParameterEvent implements Serializable

Class pal.misc.ParameterizedDouble implements Serializable

Serialized Fields

defaultValue_

double defaultValue_

currentValue_

double currentValue_

minimumValue_

double minimumValue_

maximumValue_

double maximumValue_

se_

double se_

listeners_

java.util.Vector listeners_

Class pal.misc.SimpleIdGroup 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

name

java.lang.String name

ids

Identifier[] ids

indices

java.util.Hashtable indices

Class pal.misc.SimpleSummarizable implements Serializable

Serialized Fields

types_

java.lang.String[] types_

values_

double[] values_

Class pal.misc.TimeOrderCharacterData 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

timeOrdinals

int[] timeOrdinals
Order of times

times

double[] times
Actual times of each sample

taxa

IdGroup taxa
the identifier group

units

int units

name

java.lang.String name
Name of this character data


Package pal.popgen

Class pal.popgen.LinkageDisequilibrium 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 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

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

matrixExp_

MatrixExponential matrixExp_

Class pal.substmodel.AminoAcidModel implements Serializable

Class pal.substmodel.BLOSUM62 implements Serializable

Class pal.substmodel.CachedRateMatrix implements Serializable

Serialized Fields

cache

DoubleKeyCache cache

pij

pal.substmodel.CachedRateMatrix.Pij pij

rateMatrix

RateMatrix rateMatrix

dimension

int dimension

modelChanged_

boolean modelChanged_

Class pal.substmodel.CodonModel implements Serializable

Class pal.substmodel.CPREV implements Serializable

Class pal.substmodel.Dayhoff implements Serializable

Class pal.substmodel.F81 implements Serializable

Class pal.substmodel.F84 implements Serializable

Serialized Fields

showSE

boolean showSE

kappa

double kappa

r

double r

expectedTsTv

double expectedTsTv

expectedTsTvSE

double expectedTsTvSE

Class pal.substmodel.GammaRates implements Serializable

Serialized Fields

showSE

boolean showSE

alpha

double alpha

alphaSE

double alphaSE

Class pal.substmodel.GTR 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

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 implements Serializable

Serialized Fields

showSE

boolean showSE

kappa

double kappa

kappaSE

double kappaSE

Class pal.substmodel.InvariableSites implements Serializable

Serialized Fields

showSE

boolean showSE

frac

double frac

fracSE

double fracSE

Class pal.substmodel.JTT implements Serializable

Class pal.substmodel.MatrixExponential implements Serializable

Serialized Fields

dimension

int dimension
dimension of rate matrix

transProb

double[][] transProb
transition probability matrix

lastDistance

double lastDistance

Eval

double[] Eval

Evec

double[][] Evec

Ievc

double[][] Ievc

iexp

double[][] iexp

ordr

int[] ordr

evali

double[] evali

amat

double[][] amat

cr

double cr

ci

double ci

Class pal.substmodel.MTREV24 implements Serializable

Class pal.substmodel.NucleotideModel implements Serializable

Serialized Fields

expectedTsTvRatio

double expectedTsTvRatio

expectedYRTsRatio

double expectedYRTsRatio

Class pal.substmodel.RateDistribution 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

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.SimpleSubstitutionModel 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

rateMatrix

RateMatrix rateMatrix
rate matrix

rateDistribution

RateDistribution rateDistribution
rate distribution

dimension

int dimension
dimension of rate matrix

numRates

int numRates
number of categories in discrete rate distribution

probs

double[][][] probs

numRmatParams

int numRmatParams

numRdistParams

int numRdistParams

numParams

int numParams

Class pal.substmodel.TN implements Serializable

Serialized Fields

showSE

boolean showSE

kappa

double kappa

kappaSE

double kappaSE

r

double r

rSE

double rSE

Class pal.substmodel.TwoStateModel implements Serializable

Class pal.substmodel.UniformRate implements Serializable

Class pal.substmodel.VT implements Serializable

Class pal.substmodel.WAG implements Serializable

Class pal.substmodel.YangCodonModel implements Serializable

Serialized Fields

showSE

boolean showSE

kappa

double kappa

omega

double omega

kappaSE

double kappaSE

omegaSE

double omegaSE

rateMap

byte[] rateMap

codonTable

CodonTable codonTable


Package pal.tree

Class pal.tree.ClockTree implements Serializable

Serialized Fields

parameter

double[] parameter

Class pal.tree.DatedTipsClockTree implements Serializable

Serialized Fields

parameter

double[] parameter

rate

ParameterizedDouble rate

minDate

double minDate

maxDate

double maxDate

date

double[] date

tocd

TimeOrderCharacterData tocd

internalHeightMode_

int internalHeightMode_

rateMode_

int rateMode_

Class pal.tree.LogParameterizedTree implements Serializable

Serialized Fields

params

ParameterizedTree params

logMins

double[] logMins

logMaxs

double[] logMaxs

logDefaults

double[] logDefaults

Class pal.tree.MutationRateModelTree implements Serializable

Serialized Fields

tocd

TimeOrderCharacterData tocd

model

MutationRateModel model

numParameters

int numParameters

MIN_MU

double MIN_MU

MIN_DELTA

double MIN_DELTA

lnL

double lnL

parameter

double[] parameter

Class pal.tree.NeighborJoiningTree 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 implements Serializable

Serialized Fields

tree

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

Class pal.tree.ReadTree implements Serializable

Serialized Fields

fi

FormattedInput fi

Class pal.tree.SimpleNode 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

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 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.

Class pal.tree.SimulatedAlignment 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.SUPGMATree implements Serializable

Serialized Fields

tocd

TimeOrderCharacterData tocd

Class pal.tree.TreeDistanceMatrix implements Serializable

Serialized Fields

alias

int[] alias

tree

Tree tree

dist

double[] dist

idist

double[] idist

Class pal.tree.TreeParseException implements Serializable

Class pal.tree.UnconstrainedTree implements Serializable

Class pal.tree.UPGMATree 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

height

double[] height

oc

int[] oc


Package pal.xml

Class pal.xml.XmlParseException implements Serializable