Serialized Form
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
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
data_
char[][] data_
urn
UrnModel urn
rawAlignment
Alignment rawAlignment
alias
int[] alias
data_
char[][] data_
alignmentList
Alignment[] alignmentList
numAlignments
int numAlignments
alignmentIndex
int[] alignmentIndex
siteIndex
int[] siteIndex
alignmentList
AnnotationAlignment[] alignmentList
numAlignments
int numAlignments
alignmentIndex
int[] alignmentIndex
siteIndex
int[] siteIndex
sequenceIndex
int[][] sequenceIndex
mergeByID
boolean mergeByID
union
boolean union
data_
char[][] data_
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
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
urn
UrnModel urn
rawAlignment
Alignment rawAlignment
alias
int[] alias
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
lineLength
int lineLength
names
java.util.Vector names
seqs
java.util.Vector seqs
sites
java.util.Vector sites
fi
FormattedInput fi
data
char[][] data
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
sequences
java.lang.String[] sequences
- The sequences
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
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
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
rawAlignment
Alignment rawAlignment
rawNumSites
int rawNumSites
alias
int[] alias
notDropped
boolean[] notDropped
rawAlignment
AnnotationAlignment rawAlignment
rawNumSites
int rawNumSites
minimumProportion
double minimumProportion
minimumCount
int minimumCount
firstSite
int firstSite
lastSite
int lastSite
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
N0
double N0
- population size
N0SE
double N0SE
- standard error of population size
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
model
DemographicModel model
units
int units
- Units in which population size is measured.
logL
double logL
rng
MersenneTwisterFast rng
binom
Binomial binom
fo
FormattedOutput fo
alpha
double alpha
- ratio of pop. sizes
alphaSE
double alphaSE
- standard error of time alpha
r
double r
- growth rate r
rSE
double rSE
- standard error of growth rate r
tree
Tree tree
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
characterType_
DataType characterType_
numberOfCharacterStates_
int numberOfCharacterStates_
codonLength_
int codonLength_
numberOfCodonStates_
int numberOfCodonStates_
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
isRNA_
boolean isRNA_
conversionTable_
char[] conversionTable_
numberOfNumericStates
int numberOfNumericStates
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
toAdjust_
DataType toAdjust_
originalToAdjusted_
int[] originalToAdjusted_
adjustedToOriginal_
int[] adjustedToOriginal_
- A translation array -> originalToAdjusted_["original State"] = "adjusted state"
pwd
PairwiseDistance pwd
progress_
double progress_
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
obsDistance
double[][] obsDistance
const1
double const1
const2
double const2
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
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
colourMappings_
java.util.Hashtable colourMappings_
x
double x
highlight_
boolean highlight_
peer_
Node peer_
circular_
boolean circular_
mode_
int mode_
circlePainter_
TreePainterCircular circlePainter_
painter_
TreePainter painter_
invertCiruclar_
boolean invertCiruclar_
nf
java.text.NumberFormat nf
nChoose2
double[] nChoose2
mt
int[] mt
mti
int mti
mag01
int[] mag01
nextNextGaussian
double nextNextGaussian
haveNextNextGaussian
boolean haveNextNextGaussian
capacity
int capacity
numNumbers
int numNumbers
numDrawn
int numDrawn
next
int next
isAvailable
boolean[] isAvailable
rng
MersenneTwisterFast rng
mu
double mu
- mutation rate
muSE
double muSE
units
int units
- Units in which time units are measured.
fo
FormattedOutput fo
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
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
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)
name
java.lang.String name
mappings_
java.util.Hashtable mappings_
defaultValue_
double defaultValue_
currentValue_
double currentValue_
minimumValue_
double minimumValue_
maximumValue_
double maximumValue_
se_
double se_
listeners_
java.util.Vector listeners_
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
name
java.lang.String name
ids
Identifier[] ids
indices
java.util.Hashtable indices
types_
java.lang.String[] types_
values_
double[] values_
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
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
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
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
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_
cache
DoubleKeyCache cache
pij
pal.substmodel.CachedRateMatrix.Pij pij
rateMatrix
RateMatrix rateMatrix
dimension
int dimension
modelChanged_
boolean modelChanged_
showSE
boolean showSE
kappa
double kappa
r
double r
expectedTsTv
double expectedTsTv
expectedTsTvSE
double expectedTsTvSE
showSE
boolean showSE
alpha
double alpha
alphaSE
double alphaSE
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
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
showSE
boolean showSE
kappa
double kappa
kappaSE
double kappaSE
showSE
boolean showSE
frac
double frac
fracSE
double fracSE
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
expectedTsTvRatio
double expectedTsTvRatio
expectedYRTsRatio
double expectedYRTsRatio
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
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
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
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
showSE
boolean showSE
kappa
double kappa
kappaSE
double kappaSE
r
double r
rSE
double rSE
showSE
boolean showSE
kappa
double kappa
omega
double omega
kappaSE
double kappaSE
omegaSE
double omegaSE
rateMap
byte[] rateMap
codonTable
CodonTable codonTable
parameter
double[] parameter
parameter
double[] parameter
rate
ParameterizedDouble rate
minDate
double minDate
maxDate
double maxDate
date
double[] date
tocd
TimeOrderCharacterData tocd
internalHeightMode_
int internalHeightMode_
rateMode_
int rateMode_
params
ParameterizedTree params
logMins
double[] logMins
logMaxs
double[] logMaxs
logDefaults
double[] logDefaults
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
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
tree
Tree tree
- The non-parameterized tree that this parameterized tree is
based on.
fi
FormattedInput fi
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!
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
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!
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.
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
tree
Tree tree
model
SubstitutionModel model
cumFreqs
double[] cumFreqs
rateAtSite
int[] rateAtSite
cumRateProbs
double[] cumRateProbs
numStates
int numStates
stateData
byte[][] stateData
rng
MersenneTwisterFast rng
tocd
TimeOrderCharacterData tocd
alias
int[] alias
tree
Tree tree
dist
double[] dist
idist
double[] idist
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