Serialized Form
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Package pal.algorithmics
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Package pal.alignment
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Class pal.alignment.AbstractAlignment extends java.lang.Object implements Serializable
- serialVersionUID:
- -5197800047652332969L
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Serialization Methods
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readObject
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
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writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
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Class pal.alignment.AlignmentParseException extends java.lang.Exception implements Serializable
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Class pal.alignment.AlignmentReaders.PhylipClustalAlignment extends pal.alignment.AlignmentReaders.StringAlignment implements Serializable
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Class pal.alignment.AlignmentReaders.UnalignedAlignment extends pal.alignment.AlignmentReaders.StringAlignment implements Serializable
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Class pal.alignment.BootstrappedAlignment extends AbstractAlignment implements Serializable
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Class pal.alignment.ConcatenatedAlignment extends AbstractAlignment implements Serializable
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Serialized Fields
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alignmentIndex
int[] alignmentIndex
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alignmentList
Alignment[] alignmentList
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numAlignments
int numAlignments
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siteIndex
int[] siteIndex
-
-
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Class pal.alignment.ConcatenatedAnnotatedAlignment extends AbstractAlignment implements Serializable
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Serialized Fields
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alignmentIndex
int[] alignmentIndex
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alignmentList
AnnotationAlignment[] alignmentList
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mergeByID
boolean mergeByID
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numAlignments
int numAlignments
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sequenceIndex
int[][] sequenceIndex
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siteIndex
int[] siteIndex
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union
boolean union
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-
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Class pal.alignment.GapBalancedAlignment extends AbstractAlignment implements Serializable
- serialVersionUID:
- -1042105658996999207L
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Serialization Methods
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readObject
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
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data_
char[][] data_
Just in case we find some Alien DNA
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Class pal.alignment.IndelAlignment extends AbstractAlignment implements Serializable
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Serialized Fields
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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
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sequences
java.lang.String[] sequences
The sequences
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-
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Class pal.alignment.IndelAnnotatedAlignment extends IndelAlignment implements Serializable
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Serialized Fields
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chromosome
int chromosome
used to designate chromosome -
chromosomePosition
float chromosomePosition
used to designate position along chromosome -
locusName
java.lang.String locusName
used to designate locus name -
locusPosition
int[] locusPosition
used to designate position; do not account for gaps -
positionType
char[] positionType
used to designate position Type -
weightedLocusPosition
float[] weightedLocusPosition
used to designate weighted position; accounts for gaps
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-
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Class pal.alignment.JumbledAlignment extends AbstractAlignment implements Serializable
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Class pal.alignment.MultiLocusAnnotatedAlignment extends SimpleAlignment implements Serializable
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Serialized Fields
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chromosome
int[] chromosome
used to designate chromosome -
chromosomePosition
float[] chromosomePosition
used to designate position along chromosome -
locusName
java.lang.String[] locusName
used to designate locus name -
locusPosition
int[] locusPosition
used to designate position; do not account for gaps -
positionType
char[] positionType
used to designate position Type -
siteDataType
DataType[] siteDataType
provides datatype for each locus separately -
weightedPosition
float[] weightedPosition
used to designate weighted position; accounts for gaps
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-
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Class pal.alignment.ReadAlignment extends AbstractAlignment implements Serializable
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Serialized Fields
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data
char[][] data
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fi
FormattedInput fi
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lineLength
int lineLength
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names
java.util.Vector names
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seqs
java.util.Vector seqs
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sites
java.util.Vector sites
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-
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Class pal.alignment.ReadAlignmentOld extends AbstractAlignment implements Serializable
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Serialized Fields
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data
char[][] data
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fi
FormattedInput fi
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lineLength
int lineLength
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names
java.util.Vector names
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seqs
java.util.Vector seqs
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sites
java.util.Vector sites
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-
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Class pal.alignment.SimpleAlignment extends AbstractAlignment implements Serializable
- serialVersionUID:
- 4303224913340358191L
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Serialization Methods
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readObject
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
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writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
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sequences
java.lang.String[] sequences
The sequences
-
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Class pal.alignment.SimpleAnnotatedAlignment extends SimpleAlignment implements Serializable
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Serialized Fields
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chromosome
int chromosome
used to designate chromosome -
chromosomePosition
float chromosomePosition
used to designate position along chromosome -
locusName
java.lang.String locusName
used to designate locus name -
positionType
char[] positionType
used to designate position Type -
weightedPosition
float[] weightedPosition
used to designate weighted position; accounts for gaps
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-
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Class pal.alignment.SimpleCharacterAlignment extends java.lang.Object implements Serializable
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Serialized Fields
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environmentNames
java.lang.String[] environmentNames
names of the traits -
idGroup
IdGroup idGroup
sequence identifiers -
numSeqs
int numSeqs
number of sequences -
numTraits
int numTraits
number of traits -
traitNames
java.lang.String[] traitNames
names of the traits -
traitValues
double[][] traitValues
trait values
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-
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Class pal.alignment.SitePattern extends AbstractAlignment implements Serializable
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Serialized Fields
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alias
int[] alias
site -> site pattern -
numPatterns
int numPatterns
number of site patterns -
patSort
int[] patSort
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pattern
byte[][] pattern
site patterns [sequence][site pattern] -
weight
int[] weight
weights of each site pattern
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-
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Class pal.alignment.StrippedAlignment extends AbstractAlignment implements Serializable
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Serialized Fields
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alias
int[] alias
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notDropped
boolean[] notDropped
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rawAlignment
Alignment rawAlignment
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rawNumSites
int rawNumSites
-
-
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Class pal.alignment.StrippedAnnotatedAlignment extends StrippedAlignment implements Serializable
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Serialized Fields
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firstSite
int firstSite
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lastSite
int lastSite
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minimumCount
int minimumCount
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minimumProportion
double minimumProportion
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rawAlignment
AnnotationAlignment rawAlignment
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rawNumSites
int rawNumSites
-
-
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Package pal.coalescent
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Class pal.coalescent.CoalescentException extends java.lang.Exception implements Serializable
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Class pal.coalescent.CoalescentIntervals extends java.lang.Object implements Serializable
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Serialized Fields
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fo
FormattedOutput fo
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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.
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-
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Class pal.coalescent.ConstantPopulation extends DemographicModel implements Serializable
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Serialized Fields
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N0
double N0
population size -
N0SE
double N0SE
standard error of population size
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Class pal.coalescent.ConstExpConst extends ConstExpGrowth implements Serializable
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Serialized Fields
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tx
double tx
time of end of exponential growth -
txSE
double txSE
standard error of time of growth
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-
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Class pal.coalescent.ConstExpGrowth extends ExponentialGrowth implements Serializable
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Serialized Fields
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alpha
double alpha
ratio of pop. sizes -
alphaSE
double alphaSE
standard error of time alpha -
lx
double lx
the duration of the growth phase -
N1
double N1
ancestral pop. size -
N1SE
double N1SE
standard error of ancestral pop. size -
parameterization
int parameterization
parameterization bit string:
first bit: 0 = ALPHA, 1 = N1
second bit: 0 = GROWTH RATE, 1 = LX
-
-
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Class pal.coalescent.DemographicClockTree extends ClockTree implements Serializable
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Serialized Fields
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model
DemographicModel model
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-
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Class pal.coalescent.DemographicModel extends java.lang.Object implements Serializable
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Serialized Fields
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binom
Binomial binom
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fo
FormattedOutput fo
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logL
double logL
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rng
MersenneTwisterFast rng
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units
int units
Units in which population size is measured.
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-
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Class pal.coalescent.ExpandingPopulation extends ExponentialGrowth implements Serializable
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Serialized Fields
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alpha
double alpha
ratio of pop. sizes -
alphaSE
double alphaSE
standard error of time alpha
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-
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Class pal.coalescent.ExponentialGrowth extends ConstantPopulation implements Serializable
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Serialized Fields
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r
double r
growth rate r -
rSE
double rSE
standard error of growth rate r
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-
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Class pal.coalescent.SerialCoalescentGenerator extends java.lang.Object implements Serializable
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Serialized Fields
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alignmentFactory_
SimulatedAlignment.Factory alignmentFactory_
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demographicModel_
DemographicModel demographicModel_
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numberOfTreesToGenerate_
int numberOfTreesToGenerate_
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tocd_
TimeOrderCharacterData tocd_
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treeFinisher_
TreeOperation treeFinisher_
-
-
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Class pal.coalescent.SerialCoalescentSimulator extends java.lang.Object implements Serializable
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Serialized Fields
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tree
SimpleTree tree
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Class pal.coalescent.SkylinePlot extends java.lang.Object implements Serializable
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Serialized Fields
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ci
CoalescentIntervals ci
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cis
double[] cis
cummulative interval sizes -
eps
double eps
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fo
FormattedOutput fo
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maxTime
double maxTime
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params
int params
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populationSize
double[] populationSize
estimated population size in a coalescent interval -
size
int size
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-
-
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Package pal.datatype
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Class pal.datatype.AminoAcids extends SimpleDataType implements Serializable
- serialVersionUID:
- -466623855742195043L
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Class pal.datatype.Codons extends SimpleDataType implements Serializable
- serialVersionUID:
- -2779857947044354950L
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Class pal.datatype.GapBalanced extends SimpleDataType implements Serializable
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Serialized Fields
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translationTable_
CodonTable translationTable_
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-
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Class pal.datatype.IUPACNucleotides extends SimpleDataType implements Serializable
- serialVersionUID:
- 8863411606027017687L
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Serialization Methods
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readObject
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
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writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
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conversionTable_
char[] conversionTable_
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isRNA_
boolean isRNA_
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Class pal.datatype.Nucleotides extends SimpleDataType implements Serializable
- serialVersionUID:
- -497943046234232204L
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Serialization Methods
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readObject
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
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writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
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conversionTable_
char[] conversionTable_
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isRNA_
boolean isRNA_
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Class pal.datatype.NumericDataType extends SimpleDataType implements Serializable
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Serialized Fields
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numberOfNumericStates
int numberOfNumericStates
-
-
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Class pal.datatype.SimpleDataType extends java.lang.Object implements Serializable
- serialVersionUID:
- 7902613264354545217L
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Serialization Methods
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readObject
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
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writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
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Class pal.datatype.SpecificAminoAcids extends AminoAcids implements Serializable
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Serialized Fields
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translationTable_
CodonTable translationTable_
-
-
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Class pal.datatype.StateRemover extends SimpleDataType implements Serializable
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Serialized Fields
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adjustedToOriginal_
int[] adjustedToOriginal_
A translation array -> originalToAdjusted_["original State"] = "adjusted state" -
originalToAdjusted_
int[] originalToAdjusted_
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toAdjust_
DataType toAdjust_
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-
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Class pal.datatype.TwoStates extends SimpleDataType implements Serializable
-
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Package pal.distance
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Class pal.distance.AlignmentDistanceMatrix extends DistanceMatrix implements Serializable
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Class pal.distance.DistanceMatrix extends java.lang.Object implements Serializable
- serialVersionUID:
- 4725925229860707633L
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Serialization Methods
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readObject
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
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writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
I like doing things my self!- Throws:
java.io.IOException
-
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Serialized Fields
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distance
double[][] distance
distances [seq1][seq2] -
idGroup
IdGroup idGroup
sequence identifiers
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Class pal.distance.DistanceMatrixUtils extends java.lang.Object implements Serializable
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Class pal.distance.DistanceParseException extends java.lang.Exception implements Serializable
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Class pal.distance.JukesCantorDistanceMatrix extends DistanceMatrix implements Serializable
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Class pal.distance.PairwiseDistance extends java.lang.Object implements Serializable
- serialVersionUID:
- 4721062357793106145L
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Serialization Methods
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readObject
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
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writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
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distance
double distance
last estimated distance -
distanceSE
double distanceSE
last estimate standard error of a distance -
jcratio
double jcratio
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model
SubstitutionModel model
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modelBased
boolean modelBased
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numPatterns
int numPatterns
-
numSites
int numSites
-
numStates
int numStates
-
of
SequencePairLikelihood of
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patternDataType_
DataType patternDataType_
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sitePattern
SitePattern sitePattern
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um
UnivariateMinimum um
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weight
int[] weight
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Class pal.distance.ReadDistanceMatrix extends DistanceMatrix implements Serializable
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Class pal.distance.SequencePairLikelihood extends java.lang.Object implements Serializable
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Serialized Fields
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fastMatchCount_
int[][] fastMatchCount_
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isAmbiguous_
boolean isAmbiguous_
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logEquilibriumFrequencies_
double[] logEquilibriumFrequencies_
-
model
SubstitutionModel model
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numberOfTransitionCategories_
int numberOfTransitionCategories_
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numPatterns
int numPatterns
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numSites
int numSites
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numStates
int numStates
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patternDataType_
DataType patternDataType_
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seqPat1
byte[] seqPat1
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seqPat2
byte[] seqPat2
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sitePattern
SitePattern sitePattern
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transitionCategoryProbabilities_
double[] transitionCategoryProbabilities_
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transitionProbabilityStores_
double[][][] transitionProbabilityStores_
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weight
int[] weight
-
-
-
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Package pal.eval
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Class pal.eval.ConditionalProbabilityStore extends java.lang.Object implements Serializable
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Serialized Fields
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extraProcessor_
ConditionalProbabilityStore.ExtraProcessor extraProcessor_
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fix_
boolean fix_
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isBasedOnCachedData_
boolean isBasedOnCachedData_
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numberOfCategories_
int numberOfCategories_
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numberOfStates_
int numberOfStates_
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patternCapacity_
int patternCapacity_
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store_
double[][][] store_
-
-
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Class pal.eval.LikelihoodSummary extends java.lang.Object implements Serializable
- serialVersionUID:
- -37625234234158192L
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Serialization Methods
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readObject
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
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categoryProbabilities_
double[] categoryProbabilities_
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dataType_
DataType dataType_
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individualLikelihoods_
double[][] individualLikelihoods_
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overallLogLikelihood_
double overallLogLikelihood_
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sitePatternMatchup_
int[] sitePatternMatchup_
-
-
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Package pal.gui
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Class pal.gui.LinkageDisequilibriumComponent extends java.awt.Component implements Serializable
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Serialized Fields
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blockBeginPos
float[] blockBeginPos
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blockBeginX
int[] blockBeginX
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blockEnd
float[] blockEnd
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blockEndPos
float[] blockEndPos
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blockEndX
int[] blockEndX
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blockNames
java.lang.String[] blockNames
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blockStart
float[] blockStart
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borderLayout1
java.awt.BorderLayout borderLayout1
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chromosomalScale
boolean chromosomalScale
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diseq
double[][] diseq
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distanceBetweenGraphAndGene
int distanceBetweenGraphAndGene
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endPos
float[] endPos
-
h2off
int h2off
-
hoff
int hoff
-
ih
int ih
-
includeBlockSchematic
boolean includeBlockSchematic
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iw
int iw
-
lowerLabel
java.lang.String lowerLabel
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lowerProb
boolean lowerProb
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minimumChromosomeLength
float minimumChromosomeLength
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probability
boolean probability
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startPos
float[] startPos
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theAA
AnnotationAlignment theAA
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theColor
java.awt.Color theColor
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theLD
LinkageDisequilibrium theLD
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totalBlocks
int totalBlocks
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totalChromosomes
int totalChromosomes
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totalIntervals
int totalIntervals
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totalLoci
int totalLoci
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totalUnits
float totalUnits
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totalVariableSites
int totalVariableSites
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upperLabel
java.lang.String upperLabel
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upperProb
boolean upperProb
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voff
int voff
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xEndPos
int[] xEndPos
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xPos
int[] xPos
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yPos
int[] yPos
-
-
-
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
-
highlight_
boolean highlight_
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peer_
Node peer_
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x
double x
-
-
-
Class pal.gui.TreeComponent extends java.awt.Component implements Serializable
-
Serialized Fields
-
circlePainter_
TreePainterCircular circlePainter_
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circular_
boolean circular_
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invertCiruclar_
boolean invertCiruclar_
-
mode_
int mode_
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painter_
TreePainter painter_
-
-
-
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Package pal.io
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Class pal.io.FormattedInput extends java.lang.Object implements Serializable
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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
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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
-
haveNextNextGaussian
boolean haveNextNextGaussian
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mag01
int[] mag01
-
mt
int[] mt
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mti
int mti
-
nextNextGaussian
double nextNextGaussian
-
-
-
Class pal.math.UrnModel extends java.lang.Object implements Serializable
-
Serialized Fields
-
capacity
int capacity
-
isAvailable
boolean[] isAvailable
-
next
int next
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numDrawn
int numDrawn
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numNumbers
int numNumbers
-
rng
MersenneTwisterFast rng
-
-
-
-
Package pal.mep
-
Class pal.mep.ConstantMutationRate extends MutationRateModel implements Serializable
- serialVersionUID:
- -6086097377649319118L
-
Serialization Methods
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readObject
private void readObject(java.io.ObjectInputStream in) throws java.io.IOException, java.lang.ClassNotFoundException
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
minimumMutationRate_
double minimumMutationRate_
-
mu
double mu
mutation rate -
muSE
double muSE
-
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
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
fo
FormattedOutput fo
-
maximumMutationRate_
double maximumMutationRate_
-
units
int units
Units in which time units are measured.
-
-
Class pal.mep.SteppedMutationRate extends MutationRateModel implements Serializable
-
Serialized Fields
-
fixedMus
boolean fixedMus
whether or not the mu values are optimizable -
muChanges
double[] muChanges
mutation rate change times -
mus
double[] mus
mutation rates -
muSEs
double[] muSEs
mutation rate SEs -
summaryTypes
java.lang.String[] summaryTypes
-
-
-
Class pal.mep.WindowedMutationRate extends MutationRateModel implements Serializable
-
Serialized Fields
-
backgroundFixed
boolean backgroundFixed
-
muBackground
double muBackground
mutation rates -
muBackgroundSE
double muBackgroundSE
mutation rate SEs -
muWindow
double muWindow
-
muWindowSE
double muWindowSE
-
summaryTypes
java.lang.String[] summaryTypes
-
windowCenter
double windowCenter
mutation rate change times -
windowWidth
double windowWidth
-
-
-
-
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)- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
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)- Throws:
java.io.IOException
-
-
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
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
mappings_
java.util.Hashtable mappings_
-
-
Class pal.misc.MutableDouble extends java.lang.Object implements Serializable
-
Serialized Fields
-
currentValue_
double currentValue_
-
defaultValue_
double defaultValue_
-
maximumValue_
double maximumValue_
-
minimumValue_
double minimumValue_
-
name_
java.lang.String name_
-
se_
double se_
-
-
-
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
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
ids
Identifier[] ids
-
indices
java.util.Hashtable indices
-
name
java.lang.String name
-
-
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
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
name
java.lang.String name
Name of this character data -
subgroups_
pal.misc.TimeOrderCharacterData.SubgroupHandler[] subgroups_
-
taxa
IdGroup taxa
the identifier group -
timeOrdinals
int[] timeOrdinals
Order of times -
times
double[] times
Actual times of each sample -
units
int units
-
-
-
Package pal.popgen
-
Class pal.popgen.LinkageDisequilibrium extends java.lang.Thread implements Serializable
-
Serialized Fields
-
annotated
boolean annotated
-
currentProgress
double currentProgress
-
diseq
double[][] diseq
-
numberOfPermutations
int numberOfPermutations
-
pDiseq
double[][] pDiseq
-
rapidPermute
boolean rapidPermute
-
stateVector
java.util.Vector[] stateVector
-
theAlignment
Alignment theAlignment
-
theAnnotationAlignment
AnnotationAlignment theAnnotationAlignment
-
-
-
-
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
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
dataType
DataType dataType
data type -
dimension
int dimension
dimension -
format
FormattedOutput format
-
frequency
double[] frequency
stationary frequencies (sum = 1.0) -
parameterStore_
double[] parameterStore_
-
rate
double[][] rate
rate matrix (transition: from 1st index to 2nd index)
-
-
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
-
dimension
int dimension
-
modelChanged_
boolean modelChanged_
-
pij
pal.substmodel.CachedRateMatrix.Pij pij
-
rateMatrix
RateMatrix rateMatrix
-
-
-
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
-
expectedTsTv
double expectedTsTv
-
expectedTsTvSE
double expectedTsTvSE
-
kappa
double kappa
-
r
double r
-
showSE
boolean showSE
-
-
-
Class pal.substmodel.GammaRates extends RateDistribution implements Serializable
-
Serialized Fields
-
alpha
double alpha
-
alphaSE
double alphaSE
-
showSE
boolean showSE
-
-
-
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
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
dataType_
DataType dataType_
-
handler_
RateMatrixHandler handler_
-
numberOfCategories_
int numberOfCategories_
-
parameterization_
MultiParameterized parameterization_
-
rateDistribution_
RateDistribution rateDistribution_
-
-
Class pal.substmodel.GeneralREVRateMatrix extends java.lang.Object implements Serializable
-
Serialized Fields
-
constraints_
int[] constraints_
-
defaultParameters_
double[] defaultParameters_
-
dimension_
int dimension_
-
numberOfEffectiveParameters_
int numberOfEffectiveParameters_
-
numberOfParameters_
int numberOfParameters_
-
parameterChecks_
int[][] parameterChecks_
-
-
-
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
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
a
double a
-
aSE
double aSE
-
b
double b
-
bSE
double bSE
-
c
double c
-
cSE
double cSE
-
d
double d
-
dSE
double dSE
-
e
double e
-
eSE
double eSE
-
showSE
boolean showSE
-
-
Class pal.substmodel.HKY extends NucleotideModel implements Serializable
-
Serialized Fields
-
kappa
double kappa
-
kappaSE
double kappaSE
-
showSE
boolean showSE
-
-
-
Class pal.substmodel.InvariableSites extends RateDistribution implements Serializable
-
Serialized Fields
-
frac
double frac
-
fracSE
double fracSE
-
showSE
boolean showSE
-
-
-
Class pal.substmodel.JTT extends AminoAcidModel implements Serializable
-
Class pal.substmodel.MatrixExponential extends java.lang.Object implements Serializable
-
Serialized Fields
-
amat
double[][] amat
-
ci
double ci
-
cr
double cr
-
dimension_
int dimension_
dimension of rate matrix -
Eval
double[] Eval
-
evali
double[] evali
-
Evec
double[][] Evec
-
Ievc
double[][] Ievc
-
iexp
double[][] iexp
-
ordr
int[] ordr
-
transProb
double[][] transProb
transition probability matrix
-
-
-
Class pal.substmodel.MTREV24 extends AminoAcidModel implements Serializable
-
Class pal.substmodel.MultiRateMatrixHandler extends java.lang.Object implements Serializable
-
Serialized Fields
-
baseLookup_
int[] baseLookup_
-
defaultRateParameters_
double[] defaultRateParameters_
-
dimension_
int dimension_
-
equilibriumFrequencies_
double[] equilibriumFrequencies_
-
matrixExps_
MatrixExponential[] matrixExps_
-
qMatrixStores_
double[][][] qMatrixStores_
-
rateMatrices_
NeoRateMatrix[] rateMatrices_
-
rateParameterIndexLookup_
int[] rateParameterIndexLookup_
-
rateParameters_
double[] rateParameters_
-
rateParametersSE_
double[] rateParametersSE_
-
relativeRateStore_
double[][] relativeRateStore_
-
reversible_
boolean reversible_
-
substitutionClassProbabilities_
double[] substitutionClassProbabilities_
-
updateMatrix_
boolean updateMatrix_
-
-
-
Class pal.substmodel.NeutralSelectionRateMatrixGroup extends java.lang.Object implements Serializable
- serialVersionUID:
- 84829859222352L
-
Serialized Fields
-
freqs_
double[] freqs_
-
kappaStore_
MutableDouble kappaStore_
-
neutralModel_
YangCodonModel neutralModel_
-
neutralParameters_
double[] neutralParameters_
-
purifyingModel_
YangCodonModel purifyingModel_
-
purifyingParameters_
double[] purifyingParameters_
-
-
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
-
allMatrices_
YangCodonModel[] allMatrices_
-
freqs_
double[] freqs_
-
kappaStore_
MutableDouble kappaStore_
-
neutralModel_
YangCodonModel neutralModel_
-
neutralParameters_
double[] neutralParameters_
-
omegaStore_
MutableDouble omegaStore_
-
positiveModel_
YangCodonModel positiveModel_
-
positiveParameters_
double[] positiveParameters_
-
purifyingModel_
YangCodonModel purifyingModel_
-
purifyingParameters_
double[] purifyingParameters_
-
-
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
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
format
FormattedOutput format
-
numRates
int numRates
number of rate categories -
probability
double[] probability
probability of each rate -
rate
double[] rate
rates of each rate category
-
-
Class pal.substmodel.RateMatrixHandler extends java.lang.Object implements Serializable
-
Serialized Fields
-
defaultParameters_
double[] defaultParameters_
-
dimension_
int dimension_
-
equilibriumFrequencies_
double[] equilibriumFrequencies_
-
matrixExp_
MatrixExponential matrixExp_
-
parameters_
double[] parameters_
-
parametersSE_
double[] parametersSE_
-
qMatrixStore_
double[][] qMatrixStore_
-
rateMatrix_
NeoRateMatrix rateMatrix_
-
relativeRateStore_
double[][] relativeRateStore_
-
reversible_
boolean reversible_
-
updateMatrix_
boolean updateMatrix_
-
-
-
Class pal.substmodel.SimpleRateMatrixGroup extends java.lang.Object implements Serializable
-
Serialized Fields
-
dataType_
DataType dataType_
-
numberOfRateMatrixParameters_
int numberOfRateMatrixParameters_
-
numberOfSiteClasses_
int numberOfSiteClasses_
-
rateMatrixHandler_
MultiRateMatrixHandler rateMatrixHandler_
-
totalNumberOfParameters_
int totalNumberOfParameters_
-
-
-
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
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
dataType_
DataType dataType_
-
handler_
RateMatrixHandler handler_
-
-
Class pal.substmodel.TN extends NucleotideModel implements Serializable
-
Serialized Fields
-
kappa
double kappa
-
kappaSE
double kappaSE
-
r
double r
-
rSE
double rSE
-
showSE
boolean showSE
-
-
-
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
-
codonTable
CodonTable codonTable
-
kappa
double kappa
-
kappaSE
double kappaSE
-
omega
double omega
-
omegaSE
double omegaSE
-
parameterStore_
double[] parameterStore_
-
rateMap
byte[] rateMap
-
showSE
boolean showSE
-
-
Class pal.substmodel.YangCodonModel.SimpleNeutralSelection extends PalObjectListener.EventGenerator implements Serializable
-
Serialized Fields
-
baseMatrixes_
YangCodonModel[] baseMatrixes_
-
kappa_
double kappa_
-
p_
double p_
-
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
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
baseMatrixes_
YangCodonModel[] baseMatrixes_
-
freeOmega_
double freeOmega_
-
kappa_
double kappa_
-
p0_
double p0_
-
p1_
double p1_
-
p2_
double p2_
-
probabilities_
double[] probabilities_
-
-
-
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
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Class pal.tree.LogParameterizedTree extends ParameterizedTree.ParameterizedTreeBase implements Serializable
-
Serialized Fields
-
logDefaults
double[] logDefaults
-
logMaxs
double[] logMaxs
-
logMins
double[] logMins
-
params
ParameterizedTree params
-
-
-
Class pal.tree.MutationRateModelTree extends ParameterizedTree.ParameterizedTreeBase implements Serializable
-
Serialized Fields
-
lnL
double lnL
-
maxRelativeHeight_
double maxRelativeHeight_
-
model
MutationRateModel model
-
numParameters
int numParameters
-
parameter
double[] parameter
-
tocd
TimeOrderCharacterData tocd
-
-
-
Class pal.tree.NeighborJoiningTree extends SimpleTree implements Serializable
-
Serialized Fields
-
abi
int abi
-
abj
int abj
-
alias
int[] alias
-
besti
int besti
-
bestj
int bestj
-
distance
double[][] distance
-
newCluster
Node newCluster
-
numClusters
int numClusters
-
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
- 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!- Throws:
java.io.IOException
-
-
Serialized Fields
-
attributes
java.util.Hashtable attributes
the attributes associated with this node. -
child
Node[] child
-
height
double height
height of this node -
identifier
Identifier identifier
identifier of node/associated branch -
length
double length
length of branch to parent node -
lengthSE
double lengthSE
standard error of length of branch to parent node -
number
int number
number of node as displayed -
parent
Node parent
parent node -
sequence
byte[] sequence
sequences associated with node
-
-
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
- 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!- Throws:
java.io.IOException
-
-
Serialized Fields
-
attributes
java.util.Hashtable[] attributes
attributes attached to this tree. -
externalNode
Node[] externalNode
list of external nodes -
internalNode
Node[] internalNode
list of internal nodes (including root) -
numExternalNodes
int numExternalNodes
number of external nodes -
numInternalNodes
int numInternalNodes
number of internal nodes (including root) -
root
Node root
root node -
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
- Throws:
java.io.IOException
java.lang.ClassNotFoundException
-
writeObject
private void writeObject(java.io.ObjectOutputStream out) throws java.io.IOException
- Throws:
java.io.IOException
-
-
Serialized Fields
-
cumFreqs
double[] cumFreqs
-
cumRateProbs
double[] cumRateProbs
-
model
SubstitutionModel model
-
numStates
int numStates
-
rateAtSite
int[] rateAtSite
-
rng
MersenneTwisterFast rng
-
stateData
byte[][] stateData
-
tree
Tree tree
-
-
-
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
- 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!- Throws:
java.io.IOException
-
-
Serialized Fields
-
attributes
java.util.Hashtable[] attributes
attributes attached to this tree. -
externalNode
Node[] externalNode
list of external nodes -
internalNode
Node[] internalNode
list of internal nodes (including root) -
numExternalNodes
int numExternalNodes
number of external nodes -
numInternalNodes
int numInternalNodes
number of internal nodes (including root) -
root
Node root
root node -
setupLengthsAndHeights_
boolean setupLengthsAndHeights_
-
units
int units
holds the units of the trees branches.
-
-
-
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
-
abi
int abi
Deprecated. -
abj
int abj
Deprecated. -
alias
int[] alias
Deprecated. -
besti
int besti
Deprecated. -
bestj
int bestj
Deprecated. -
distance
double[][] distance
Deprecated. -
height
double[] height
Deprecated. -
newCluster
Node newCluster
Deprecated. -
numClusters
int numClusters
Deprecated. -
oc
int[] oc
Deprecated.
-
-
-
-
Package pal.xml
-
Class pal.xml.XmlParseException extends java.lang.Exception implements Serializable
-