Constant Field Values

pal.alignment.*

• 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

• 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

• 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

• 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

• 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.*

• 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.*

• 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.*

• 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

• 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.*

• 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

• 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"

• 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.*

• 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

• 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"