Constant Field Values
Contents
pal.alignment.*
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pal.alignment.Alignment Modifier and Type Constant Field Value public static final char
GAP
45
public static final java.lang.String
GAP_TLA
"---"
public static final java.lang.String
GAPS
"_-?."
public static final char
UNKNOWN
63
public static final java.lang.String
UNKNOWN_TLA
"???"
-
pal.alignment.CharacterAlignment Modifier and Type Constant Field Value public static final double
MISSING
0d/0d
pal.coalescent.*
-
pal.coalescent.CoalescentIntervals Modifier and Type Constant Field Value public static final int
COALESCENT
0
public static final int
NEW_SAMPLE
1
public static final int
NOTHING
2
-
pal.coalescent.ConstExpGrowth Modifier and Type Constant Field Value public static final int
ALPHA_PARAMETERIZATION
0
public static final int
LX_PARAMETERIZATION
2
public static final int
N1_PARAMETERIZATION
1
pal.datatype.*
-
pal.datatype.AminoAcids Modifier and Type Constant Field Value public static final char
TERMINATE_CHARACTER
42
public static final int
TERMINATE_STATE
21
-
pal.datatype.CodonTable Modifier and Type Constant Field Value public static final int
ALTERNATIVE_YEAST
13
public static final int
ASCIDIAN_MITOCHONDRIAL
9
public static final int
BACTERIAL
12
public static final int
BLEPHARISMA_NUCLEAR
11
public static final int
CILATE
6
public static final int
ECHINODERM_MITOCHONDRIAL
7
public static final int
EUPLOTID_NUCLEAR
8
public static final int
FLATWORM_MITOCHONDRIAL
10
public static final int
INVERTEBRATE_MITOCHONDRIAL
5
public static final int
MOLD_PROTOZOAN_MITOCHONDRIAL
3
public static final int
MYCOPLASMA
4
public static final int
UNIVERSAL
0
public static final int
VERTEBRATE_MITOCHONDRIAL
1
public static final int
YEAST
2
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pal.datatype.DataType Modifier and Type Constant Field Value public static final java.lang.String
AMINO_ACID_DESCRIPTION
"amino acid"
public static final int
AMINOACIDS
1
public static final java.lang.String
CODON_DESCRIPTION
"codon"
public static final int
CODONS
4
public static final int
GAP_BALANCED
5
public static final java.lang.String
GAP_BALANCED_DESCRIPTION
"gap balanced"
public static final java.lang.String
IUPAC_NUCELOTIDES_DESCRIPTION
"nucleotide"
public static final int
IUPACNUCLEOTIDES
3
public static final java.lang.String
NUCLEOTIDE_DESCRIPTION
"nucleotide"
public static final int
NUCLEOTIDES
0
public static final int
NUMERIC
6
public static final char
PRIMARY_SUGGESTED_GAP_CHARACTER
45
public static final int
SUGGESTED_GAP_STATE
-2
public static final int
SUGGESTED_UNKNOWN_STATE
-1
public static final java.lang.String
TWO_STATE_DESCRIPTION
"binary"
public static final int
TWOSTATES
2
public static final int
UNKNOWN
100
public static final char
UNKNOWN_CHARACTER
63
public static final java.lang.String
UNKNOWN_TLA
"???"
-
pal.datatype.Nucleotides Modifier and Type Constant Field Value public static final int
A_STATE
0
public static final int
C_STATE
1
public static final int
G_STATE
2
public static final int
UT_STATE
3
pal.eval.*
-
pal.eval.ModelParameters Modifier and Type Constant Field Value public static final int
FRACDIGITS
3
pal.gui.*
-
pal.gui.LinkageDisequilibriumComponent Modifier and Type Constant Field Value public static final int
DPRIME
1
public static final int
P_VALUE
0
public static final int
RSQUARE
2
-
pal.gui.TreeComponent Modifier and Type Constant Field Value public static final int
CIRCULAR_BW
1
public static final int
CIRCULAR_COLOR
3
public static final int
NORMAL_BW
0
public static final int
NORMAL_COLOR
2
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pal.gui.TreePainter Modifier and Type Constant Field Value public static final java.lang.String
BOOTSTRAP_ATTRIBUTE_NAME
"bootstrap"
public static final java.lang.String
DEFAULT_FONT_NAME
"times"
public static final int
DEFAULT_FONT_SIZE
15
public static final int
DEFAULT_FONT_STYLE
0
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pal.gui.TreePainterCircular Modifier and Type Constant Field Value public static final int
BOTTOMBORDER
30
public static final int
LEFTBORDER
10
public static final int
RIGHTBORDER
75
public static final int
TOPBORDER
20
public static final int
XSPACER
10
public static final int
YSPACER
20
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pal.gui.TreePainterNormal Modifier and Type Constant Field Value public static final int
BOTTOMBORDER
30
public static final int
FONT_SIZE
15
public static final int
LEFTBORDER
10
public static final int
RIGHTBORDER
10
public static final int
TOPBORDER
20
public static final int
XSPACER
4
public static final int
YSPACER
20
pal.io.*
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pal.io.NexusTokenizer Modifier and Type Constant Field Value public static final char
ADDITION
43
public static final char
ASTERIX
42
public static final char
B_SLASH
92
public static final char
B_TICK
96
public static final char
C_RETURN
13
public static final char
COLON
58
public static final char
COMMA
44
public static final char
D_QUOTE
34
public static final char
DASH
45
public static final char
EQUALS
61
public static final char
F_SLASH
47
public static final char
G_THAN
62
public static final char
HASH
35
public static final int
HEADER_TOKEN
15
public static final char
L_BRACE
123
public static final char
L_BRACKET
91
public static final char
L_FEED
10
public static final char
L_PARENTHESIS
40
public static final char
L_THAN
60
public static final int
NEWLINE_TOKEN
13
public static final char
PERIOD
46
public static final int
PUNCTUATION_TOKEN
12
public static final char
R_BRACE
125
public static final char
R_BRACKET
93
public static final char
R_PARENTHESIS
41
public static final char
S_QUOTE
39
public static final char
SEMI_COLON
59
public static final char
SPACE
32
public static final char
TAB
9
public static final int
UNDEFINED_TOKEN
10
public static final int
WHITESPACE_TOKEN
14
public static final int
WORD_LOWERCASE
1
public static final int
WORD_TOKEN
11
public static final int
WORD_UNMODIFIED
2
public static final int
WORD_UPPERCASE
0
pal.math.*
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pal.math.ConjugateGradientSearch Modifier and Type Constant Field Value public static final int
BEALE_SORENSON_HESTENES_STIEFEL_UPDATE
2
public static final int
FLETCHER_REEVES_UPDATE
0
public static final int
POLAK_RIBIERE_UPDATE
1
pal.mep.*
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pal.mep.SteppedMutationRate Modifier and Type Constant Field Value public static final java.lang.String
INVALID_INTERVALS_TEXT
"Incompatible intervals"
public static final java.lang.String
MAX_TIME_IS_TEXT
"Max time is "
public static final java.lang.String
NEGATIVE_VALUES_TEXT
"Negative values"
public static final java.lang.String
REPEATED_TIMES_TEXT
"Repeated times"
public static final java.lang.String
ZERO_TIME_TEXT
"Zero time"
pal.misc.*
-
pal.misc.Attribute Modifier and Type Constant Field Value public static final java.lang.String
BOOLEAN
"boolean"
public static final java.lang.String
DOUBLE
"double"
public static final java.lang.String
FLOAT
"float"
public static final java.lang.String
INTEGER
"integer"
public static final java.lang.String
STRING
"string"
-
pal.misc.BranchLimits Modifier and Type Constant Field Value public static final double
ABSTOL
5.0E-7
public static final double
DEFAULT_LENGTH
0.04
public static final int
FRACDIGITS
6
public static final double
MAXARC
1.0
public static final double
MINARC
1.0E-9
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pal.misc.ReleaseInfo Modifier and Type Constant Field Value public static final java.lang.String
RELEASE_DATE
"November, 2004"
public static final java.lang.String
VERSION
"PAL 1.51"
-
pal.misc.Units Modifier and Type Constant Field Value public static final int
DAYS
2
public static final int
EXPECTED_SUBSTITUTIONS
0
public static final int
GENERATIONS
1
public static final int
MONTHS
3
public static final int
SAMPLE
5
public static final int
UNKNOWN
6
public static final int
YEARS
4
pal.substmodel.*
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pal.substmodel.AminoAcidModelID Modifier and Type Constant Field Value public static final int
BLOSUM62
3
public static final int
CPREV
6
public static final int
DAYHOFF
0
public static final int
JTT
1
public static final int
MODELCOUNT
7
public static final int
MTREV24
2
public static final int
VT
4
public static final int
WAG
5
-
pal.substmodel.F84 Modifier and Type Constant Field Value public static final int
EXPECTED_TS_TV_PARAMETER_INDEX
0
-
pal.substmodel.HKY Modifier and Type Constant Field Value public static final int
KAPPA_PARAMETER_INDEX
0
-
pal.substmodel.NucleotideModelID Modifier and Type Constant Field Value public static final int
F81
4
public static final int
F84
3
public static final int
GTR
0
public static final int
HKY
2
public static final int
MODELCOUNT
5
public static final int
TN
1
-
pal.substmodel.TN Modifier and Type Constant Field Value public static final int
KAPPA_PARAMETER_INDEX
0
public static final int
R_PARAMETER_INDEX
1
-
pal.substmodel.YangCodonModel Modifier and Type Constant Field Value public static final double
DEFAULT_KAPPA
2.0
public static final double
DEFAULT_OMEGA
1.0
public static final int
KAPPA_PARAMETER
0
public static final double
MAXIMUM_KAPPA
100.0
public static final double
MAXIMUM_OMEGA
100.0
public static final double
MINIMUM_KAPPA
1.0E-6
public static final double
MINIMUM_OMEGA
0.0
public static final int
OMEGA_PARAMETER
1
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pal.substmodel.YangCodonModel.SimpleNeutralSelection Modifier and Type Constant Field Value public static final double
P_DEFAULT_VALUE
0.5
public static final double
P_LOWER_LIMIT
0.0
public static final double
P_UPPER_LIMIT
1.0
pal.tree.*
-
pal.tree.AttributeNode Modifier and Type Constant Field Value public static final java.lang.String
CLADE_PROBABILITY
"clade probability"
public static final java.lang.String
MEAN_CLADE_HEIGHT
"mean clade height"
public static final java.lang.String
NODE_HEIGHT_SE
"node height SE"
public static final java.lang.String
SUBTREE_PROBABILITY
"subtree probability"
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pal.tree.TreeManipulator Modifier and Type Constant Field Value public static final int
EXPAND_CONSTRUCTION
200
public static final int
MIMIC_CONSTRUCTION
100
public static final int
REDUCE_CONSTRUCTION
300
pal.treesearch.*
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pal.treesearch.Constants Modifier and Type Constant Field Value public static final int
CONSTRAINED_LEAF_COMPONENT_TYPE
4
public static final int
CONSTRAINED_NODE_COMPONENT_TYPE
0
public static final double
CONSTRUCTED_BRANCH_LENGTH
0.01
public static final int
FREE_BRANCH_COMPONENT_TYPE
2
public static final int
FREE_LEAF_COMPONENT_TYPE
3
public static final int
FREE_NODE_COMPONENT_TYPE
1
public static final int
GENERAL_OPTIMISABLE_TYPE
6
public static final double
MAXIMUM_BRANCH_LENGTH
10.0
public static final double
MINIMUM_BRANCH_LENGTH
0.0
public static final int
PIVOT_COMPONENT_TYPE
5
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pal.treesearch.GeneralLikelihoodSearcher Modifier and Type Constant Field Value public static final int
NO_OPTIMISE
3
public static final int
OPTIMISE_ALL
0
public static final int
OPTIMISE_PRIMARY
1
public static final int
OPTIMISE_SECONDARY
2
pal.util.*
-
pal.util.XMLConstants Modifier and Type Constant Field Value public static final java.lang.String
A_TO_C
"A-C"
public static final java.lang.String
A_TO_G
"A-G"
public static final java.lang.String
A_TO_T
"A-T"
public static final java.lang.String
ALIGNMENT
"alignment"
public static final java.lang.String
ALPHA
"alpha"
public static final java.lang.String
ANCESTRAL_MU_RATE
"ancestral mutation rate"
public static final java.lang.String
ANCESTRAL_POP_SIZE
"ancestral population size"
public static final java.lang.String
ATTRIBUTE
"att"
public static final java.lang.String
BACKWARDS
"backwards"
public static final java.lang.String
BLOSUM62
"BLOSUM62"
public static final java.lang.String
C_TO_G
"C-G"
public static final java.lang.String
C_TO_T
"C-T"
public static final java.lang.String
COALESCENT
"coalescent"
public static final java.lang.String
CONST_EXP_CONST
"constexpconst"
public static final java.lang.String
CONST_EXP_GROWTH
"constexp"
public static final java.lang.String
CONSTANT_MUTATION_RATE
"constant"
public static final java.lang.String
CONSTANT_POPULATION
"constant"
public static final java.lang.String
CPREV
"CPREV"
public static final java.lang.String
CURRENT_POP_SIZE_DURATION
"tx"
public static final java.lang.String
DATA_TYPE
"datatype"
public static final java.lang.String
DATA_TYPE_ID
"datatypeid"
public static final java.lang.String
DAYHOFF
"Dayhoff"
public static final java.lang.String
DAYS
"days"
public static final java.lang.String
DEMOGRAPHIC_MODEL
"demographicmodel"
public static final java.lang.String
DIRECTION
"direction"
public static final java.lang.String
EDGE
"edge"
public static final java.lang.String
EXPANDING_POPULATION
"expanding"
public static final java.lang.String
EXPONENTIAL_GROWTH
"exponential"
public static final java.lang.String
F81
"F81"
public static final java.lang.String
F84
"F84"
public static final java.lang.String
FREQUENCIES
"frequencies"
public static final java.lang.String
G_TO_T
"G-T"
public static final java.lang.String
GAMMA_ALPHA
"shape"
public static final java.lang.String
GAMMA_DISTRIBUTION
"gamma"
public static final java.lang.String
GENERATIONS
"generations"
public static final java.lang.String
GROWTH_PHASE_DURATION
"lx"
public static final java.lang.String
GROWTH_RATE
"growth rate"
public static final java.lang.String
GTR
"GTR"
public static final java.lang.String
HEIGHT
"height"
public static final java.lang.String
HKY
"HKY"
public static final java.lang.String
ID
"id"
public static final java.lang.String
JC
"JC"
public static final java.lang.String
JTT
"JTT"
public static final java.lang.String
KAPPA
"kappa"
public static final java.lang.String
LENGTH
"length"
public static final java.lang.String
MISSING
"missing"
public static final java.lang.String
MODEL
"model"
public static final java.lang.String
MONTHS
"months"
public static final java.lang.String
MTREV24
"MTREV24"
public static final java.lang.String
MU_STEP_TIME
"step time"
public static final java.lang.String
MUTATION_RATE
"current mutation rate"
public static final java.lang.String
MUTATION_RATE_MODEL
"mutationratemodel"
public static final java.lang.String
MUTATIONS
"mutations"
public static final java.lang.String
NAME
"name"
public static final java.lang.String
NODE
"node"
public static final java.lang.String
NUMBER_CATEGORIES
"ncat"
public static final java.lang.String
OMEGA
"omega"
public static final java.lang.String
ORIGIN
"origin"
public static final java.lang.String
PARAMETER
"parameter"
public static final java.lang.String
POPULATION_SIZE
"current population size"
public static final java.lang.String
PYRIMIDINE_PURINE_RATIO
"prymidine/purine transition ratio"
public static final java.lang.String
RATE_DISTRIBUTION
"ratedistribution"
public static final java.lang.String
RATE_MATRIX
"ratematrix"
public static final java.lang.String
SEQUENCE
"sequence"
public static final int
SPACES_PER_LEVEL
4
public static final java.lang.String
STEPPED_MUTATION_RATE
"stepped"
public static final java.lang.String
TIME
"time"
public static final java.lang.String
TIME_DATA
"timedata"
public static final java.lang.String
TN
"Tamura-Nei"
public static final java.lang.String
TREE
"tree"
public static final java.lang.String
TS_TV_RATIO
"transition/transversion ratio"
public static final java.lang.String
TWO_STATE
"binary"
public static final java.lang.String
TYPE
"type"
public static final java.lang.String
UNIFORM
"uniform"
public static final java.lang.String
UNIFORM_RATE_DISTRIBUTION
"uniform"
public static final java.lang.String
UNITS
"units"
public static final java.lang.String
UNKNOWN
"unknown"
public static final java.lang.String
VALUE
"value"
public static final java.lang.String
VT
"VT"
public static final java.lang.String
WAG
"WAG"
public static final java.lang.String
YANG_CODON_MODEL
"Yang codon model"
public static final java.lang.String
YEARS
"years"