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pal.alignment.*
pal.coalescent.*
pal.datatype.*
pal.eval.*
pal.gui.*
pal.io.*
pal.math.*
pal.mep.*
pal.misc.*
pal.substmodel.*
pal.tree.*
pal.util.*

pal.alignment.*

pal.alignment.Alignment
`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
`public static final double`	`MISSING`	`0d/0d`

pal.coalescent.*

pal.coalescent.CoalescentIntervals
`public static final int`	`COALESCENT`	`0`
`public static final int`	`NEW_SAMPLE`	`1`
`public static final int`	`NOTHING`	`2`

pal.coalescent.ConstExpGrowth
`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
`public static final char`	`TERMINATE_CHARACTER`	`42`
`public static final int`	`TERMINATE_STATE`	`21`

pal.datatype.CodonTable
`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
`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
`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
`public static final int`	`FRACDIGITS`	`3`

pal.gui.*

pal.gui.LinkageDisequilibriumComponent
`public static final int`	`DPRIME`	`1`
`public static final int`	`P_VALUE`	`0`
`public static final int`	`RSQUARE`	`2`

pal.gui.TreeComponent
`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
`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
`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
`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
`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
`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
`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
`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
`public static final double`	`ABSTOL`	`5.0E-7d`
`public static final double`	`DEFAULT_LENGTH`	`0.04d`
`public static final int`	`FRACDIGITS`	`6`
`public static final double`	`MAXARC`	`1.0d`
`public static final double`	`MINARC`	`1.0E-9d`

pal.misc.ReleaseInfo
`public static final java.lang.String`	`RELEASE_DATE`	`"November, 2004"`
`public static final java.lang.String`	`VERSION`	`"PAL 1.51"`

pal.misc.Units
`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
`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
`public static final int`	`EXPECTED_TS_TV_PARAMETER_INDEX`	`0`

pal.substmodel.HKY
`public static final int`	`KAPPA_PARAMETER_INDEX`	`0`

pal.substmodel.NucleotideModelID
`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
`public static final int`	`KAPPA_PARAMETER_INDEX`	`0`
`public static final int`	`R_PARAMETER_INDEX`	`1`

pal.substmodel.YangCodonModel
`public static final double`	`DEFAULT_KAPPA`	`2.0d`
`public static final double`	`DEFAULT_OMEGA`	`1.0d`
`public static final int`	`KAPPA_PARAMETER`	`0`
`public static final double`	`MAXIMUM_KAPPA`	`100.0d`
`public static final double`	`MAXIMUM_OMEGA`	`100.0d`
`public static final double`	`MINIMUM_KAPPA`	`1.0E-6d`
`public static final double`	`MINIMUM_OMEGA`	`0.0d`
`public static final int`	`OMEGA_PARAMETER`	`1`

pal.substmodel.YangCodonModel.SimpleNeutralSelection
`public static final double`	`P_DEFAULT_VALUE`	`0.5d`
`public static final double`	`P_LOWER_LIMIT`	`0.0d`
`public static final double`	`P_UPPER_LIMIT`	`1.0d`

pal.tree.*

pal.tree.AttributeNode
`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
`public static final int`	`EXPAND_CONSTRUCTION`	`200`
`public static final int`	`MIMIC_CONSTRUCTION`	`100`
`public static final int`	`REDUCE_CONSTRUCTION`	`300`

pal.treesearch.Constants
`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`	`0.01d`
`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`	`10.0d`
`public static final double`	`MINIMUM_BRANCH_LENGTH`	`0.0d`
`public static final int`	`PIVOT_COMPONENT_TYPE`	`5`

pal.treesearch.GeneralLikelihoodSearcher
`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
`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"`