Constant Field Values

Contents

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.datatype.*

pal.eval.*

pal.gui.*

pal.io.*

pal.math.*

pal.mep.*

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.tree.*

pal.treesearch.*

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"