Serialized Form
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ambig
java.util.Map<K,V> ambig
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sites
java.util.LinkedHashMap<K,V> sites
ambig
Ambiguous ambig
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l
double l
siteLikelihoods
java.util.Map<K,V> siteLikelihoods
missingLikelihoods
java.util.Map<K,V> missingLikelihoods
p
Parameters p
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likelihoods
ToDoubleHashMap<K> likelihoods
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l
double l
nodeLikelihoods
java.util.Map<K,V> nodeLikelihoods
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rateLikelihoods
java.util.Map<K,V> rateLikelihoods
l
double l
rateProbability
java.util.Map<K,V> rateProbability
maxCat
RateCategory maxCat
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n
int n
- Row and column dimension (square matrix).
- matrix dimension.
issymmetric
boolean issymmetric
- Symmetry flag.
- internal symmetry flag.
d
double[] d
- Arrays for internal storage of eigenvalues.
- internal storage of eigenvalues.
e
double[] e
- Arrays for internal storage of eigenvalues.
- internal storage of eigenvalues.
V
double[][] V
- Array for internal storage of eigenvectors.
- internal storage of eigenvectors.
H
double[][] H
- Array for internal storage of nonsymmetric Hessenberg form.
- internal storage of nonsymmetric Hessenberg form.
ort
double[] ort
- Working storage for nonsymmetric algorithm.
- working storage for nonsymmetric algorithm.
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LU
double[][] LU
- Array for internal storage of decomposition.
- internal array storage.
m
int m
- Row and column dimensions, and pivot sign.
- column dimension.
n
int n
- Row and column dimensions, and pivot sign.
- column dimension.
pivsign
int pivsign
- Row and column dimensions, and pivot sign.
- column dimension.
piv
int[] piv
- Internal storage of pivot vector.
- pivot vector.
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m
double[][] m
dim
int dim
p
SquareMatrix p
pi
SquareMatrix pi
d
SquareMatrix d
ed
EigenvalueDecomposition ed
lu
LUDecomposition lu
powers
double[][][] powers
pdiv
int pdiv
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sm
SquareMatrix sm
cache
java.util.Map<K,V> cache
neededParams
java.util.TreeSet<E> neededParams
m
SquareMatrix m
f
double[] f
freq
java.lang.String[] freq
rates
java.lang.String[][] rates
map
java.util.HashMap<K,V> map
freqType
RateCategory.FrequencyType freqType
name
java.lang.String name
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name
java.lang.String name
value
double value
estimate
boolean estimate
lbound
double lbound
ubound
double ubound
matrix
boolean matrix
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params
java.util.ArrayList<E> params
recalc
boolean recalc