pal.util
Interface XMLConstants

All Known Implementing Classes:
BLOSUM62, CPREV, Dayhoff, F81, F84, GTR, HKY, JTT, MTREV24, TN, TwoStateModel, VT, WAG, YangCodonModel, ElementParser, ElementFactory

public interface XMLConstants

constants (strings and numbers) relating to reading and writing XML. These constants should avoid the use of < and > and other special XML characters as much as possible.


Field Summary
static java.lang.String A_TO_C
           
static java.lang.String A_TO_G
           
static java.lang.String A_TO_T
           
static java.lang.String ALIGNMENT
           
static java.lang.String ALPHA
           
static java.lang.String ANCESTRAL_MU_RATE
           
static java.lang.String ANCESTRAL_POP_SIZE
           
static java.lang.String ATTRIBUTE
           
static java.lang.String BACKWARDS
           
static java.lang.String BLOSUM62
           
static java.lang.String C_TO_G
           
static java.lang.String C_TO_T
           
static java.lang.String COALESCENT
           
static java.lang.String CONST_EXP_GROWTH
           
static java.lang.String CONSTANT_MUTATION_RATE
           
static java.lang.String CONSTANT_POPULATION
          constant population demographic model type
static java.lang.String CPREV
           
static java.lang.String DATA_TYPE
           
static java.lang.String DATA_TYPE_ID
           
static java.lang.String DAYHOFF
           
static java.lang.String DAYS
           
static java.lang.String DEMOGRAPHIC_MODEL
           
static java.lang.String DIRECTION
           
static java.lang.String EDGE
           
static java.lang.String EXPONENTIAL_GROWTH
           
static java.lang.String F81
           
static java.lang.String F84
           
static java.lang.String FREQUENCIES
           
static java.lang.String G_TO_T
           
static java.lang.String GENERATIONS
           
static java.lang.String GROWTH_RATE
           
static java.lang.String GTR
           
static java.lang.String HEIGHT
           
static java.lang.String HKY
           
static java.lang.String ID
           
static java.lang.String JC
           
static java.lang.String JTT
           
static java.lang.String KAPPA
           
static java.lang.String LENGTH
           
static java.lang.String MISSING
           
static java.lang.String MODEL
           
static java.lang.String MONTHS
           
static java.lang.String MTREV24
           
static java.lang.String MU_STEP_TIME
           
static java.lang.String MUTATION_RATE
           
static java.lang.String MUTATION_RATE_MODEL
           
static java.lang.String MUTATIONS
           
static java.lang.String NAME
           
static java.lang.String NODE
           
static java.lang.String OMEGA
           
static java.lang.String ORIGIN
           
static java.lang.String PARAMETER
           
static java.lang.String POPULATION_SIZE
           
static java.lang.String PYRIMIDINE_PURINE_RATIO
           
static java.lang.String RATE_MATRIX
           
static java.lang.String SEQUENCE
           
static int SPACES_PER_LEVEL
           
static java.lang.String STEPPED_MUTATION_RATE
           
static java.lang.String TIME
           
static java.lang.String TIME_DATA
           
static java.lang.String TN
           
static java.lang.String TREE
           
static java.lang.String TS_TV_RATIO
           
static java.lang.String TWO_STATE
           
static java.lang.String TYPE
           
static java.lang.String UNIFORM
           
static java.lang.String UNITS
           
static java.lang.String UNKNOWN
           
static java.lang.String VALUE
           
static java.lang.String VT
           
static java.lang.String WAG
           
static java.lang.String YANG_CODON_MODEL
           
static java.lang.String YEARS
           
 

Field Detail

SPACES_PER_LEVEL

public static final int SPACES_PER_LEVEL

DEMOGRAPHIC_MODEL

public static final java.lang.String DEMOGRAPHIC_MODEL

MUTATION_RATE_MODEL

public static final java.lang.String MUTATION_RATE_MODEL

RATE_MATRIX

public static final java.lang.String RATE_MATRIX

TREE

public static final java.lang.String TREE

FREQUENCIES

public static final java.lang.String FREQUENCIES

PARAMETER

public static final java.lang.String PARAMETER

NODE

public static final java.lang.String NODE

EDGE

public static final java.lang.String EDGE

ALIGNMENT

public static final java.lang.String ALIGNMENT

SEQUENCE

public static final java.lang.String SEQUENCE

TIME

public static final java.lang.String TIME

TIME_DATA

public static final java.lang.String TIME_DATA

ATTRIBUTE

public static final java.lang.String ATTRIBUTE

TYPE

public static final java.lang.String TYPE

NAME

public static final java.lang.String NAME

VALUE

public static final java.lang.String VALUE

UNITS

public static final java.lang.String UNITS

MODEL

public static final java.lang.String MODEL

ID

public static final java.lang.String ID

HEIGHT

public static final java.lang.String HEIGHT

LENGTH

public static final java.lang.String LENGTH

DATA_TYPE

public static final java.lang.String DATA_TYPE

DATA_TYPE_ID

public static final java.lang.String DATA_TYPE_ID

DIRECTION

public static final java.lang.String DIRECTION

ORIGIN

public static final java.lang.String ORIGIN

MISSING

public static final java.lang.String MISSING

COALESCENT

public static final java.lang.String COALESCENT

CONSTANT_POPULATION

public static final java.lang.String CONSTANT_POPULATION
constant population demographic model type

EXPONENTIAL_GROWTH

public static final java.lang.String EXPONENTIAL_GROWTH

CONST_EXP_GROWTH

public static final java.lang.String CONST_EXP_GROWTH

CONSTANT_MUTATION_RATE

public static final java.lang.String CONSTANT_MUTATION_RATE

STEPPED_MUTATION_RATE

public static final java.lang.String STEPPED_MUTATION_RATE

UNIFORM

public static final java.lang.String UNIFORM

MUTATION_RATE

public static final java.lang.String MUTATION_RATE

ANCESTRAL_MU_RATE

public static final java.lang.String ANCESTRAL_MU_RATE

MU_STEP_TIME

public static final java.lang.String MU_STEP_TIME

POPULATION_SIZE

public static final java.lang.String POPULATION_SIZE

GROWTH_RATE

public static final java.lang.String GROWTH_RATE

ALPHA

public static final java.lang.String ALPHA

ANCESTRAL_POP_SIZE

public static final java.lang.String ANCESTRAL_POP_SIZE

GENERATIONS

public static final java.lang.String GENERATIONS

DAYS

public static final java.lang.String DAYS

MONTHS

public static final java.lang.String MONTHS

YEARS

public static final java.lang.String YEARS

MUTATIONS

public static final java.lang.String MUTATIONS

TWO_STATE

public static final java.lang.String TWO_STATE

JC

public static final java.lang.String JC

F81

public static final java.lang.String F81

F84

public static final java.lang.String F84

HKY

public static final java.lang.String HKY

GTR

public static final java.lang.String GTR

TN

public static final java.lang.String TN

WAG

public static final java.lang.String WAG

JTT

public static final java.lang.String JTT

VT

public static final java.lang.String VT

CPREV

public static final java.lang.String CPREV

BLOSUM62

public static final java.lang.String BLOSUM62

MTREV24

public static final java.lang.String MTREV24

DAYHOFF

public static final java.lang.String DAYHOFF

YANG_CODON_MODEL

public static final java.lang.String YANG_CODON_MODEL

A_TO_C

public static final java.lang.String A_TO_C

A_TO_G

public static final java.lang.String A_TO_G

A_TO_T

public static final java.lang.String A_TO_T

C_TO_G

public static final java.lang.String C_TO_G

C_TO_T

public static final java.lang.String C_TO_T

G_TO_T

public static final java.lang.String G_TO_T

KAPPA

public static final java.lang.String KAPPA

OMEGA

public static final java.lang.String OMEGA

PYRIMIDINE_PURINE_RATIO

public static final java.lang.String PYRIMIDINE_PURINE_RATIO

TS_TV_RATIO

public static final java.lang.String TS_TV_RATIO

UNKNOWN

public static final java.lang.String UNKNOWN

BACKWARDS

public static final java.lang.String BACKWARDS