pal.util
Interface XMLConstants

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

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.

Version:
$Id: XMLConstants.java,v 1.11 2002/06/03 09:18:04 alexi Exp $
Author:
Alexei Drummond

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_CONST
           
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 CURRENT_POP_SIZE_DURATION
           
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 EXPANDING_POPULATION
           
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 GAMMA_ALPHA
           
static java.lang.String GAMMA_DISTRIBUTION
           
static java.lang.String GENERATIONS
           
static java.lang.String GROWTH_PHASE_DURATION
           
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 NUMBER_CATEGORIES
           
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_DISTRIBUTION
           
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 UNIFORM_RATE_DISTRIBUTION
           
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

static final int SPACES_PER_LEVEL
See Also:
Constant Field Values

DEMOGRAPHIC_MODEL

static final java.lang.String DEMOGRAPHIC_MODEL
See Also:
Constant Field Values

MUTATION_RATE_MODEL

static final java.lang.String MUTATION_RATE_MODEL
See Also:
Constant Field Values

RATE_MATRIX

static final java.lang.String RATE_MATRIX
See Also:
Constant Field Values

TREE

static final java.lang.String TREE
See Also:
Constant Field Values

FREQUENCIES

static final java.lang.String FREQUENCIES
See Also:
Constant Field Values

PARAMETER

static final java.lang.String PARAMETER
See Also:
Constant Field Values

NODE

static final java.lang.String NODE
See Also:
Constant Field Values

EDGE

static final java.lang.String EDGE
See Also:
Constant Field Values

ALIGNMENT

static final java.lang.String ALIGNMENT
See Also:
Constant Field Values

SEQUENCE

static final java.lang.String SEQUENCE
See Also:
Constant Field Values

TIME

static final java.lang.String TIME
See Also:
Constant Field Values

TIME_DATA

static final java.lang.String TIME_DATA
See Also:
Constant Field Values

ATTRIBUTE

static final java.lang.String ATTRIBUTE
See Also:
Constant Field Values

TYPE

static final java.lang.String TYPE
See Also:
Constant Field Values

NAME

static final java.lang.String NAME
See Also:
Constant Field Values

VALUE

static final java.lang.String VALUE
See Also:
Constant Field Values

UNITS

static final java.lang.String UNITS
See Also:
Constant Field Values

MODEL

static final java.lang.String MODEL
See Also:
Constant Field Values

ID

static final java.lang.String ID
See Also:
Constant Field Values

HEIGHT

static final java.lang.String HEIGHT
See Also:
Constant Field Values

LENGTH

static final java.lang.String LENGTH
See Also:
Constant Field Values

DATA_TYPE

static final java.lang.String DATA_TYPE
See Also:
Constant Field Values

DATA_TYPE_ID

static final java.lang.String DATA_TYPE_ID
See Also:
Constant Field Values

DIRECTION

static final java.lang.String DIRECTION
See Also:
Constant Field Values

ORIGIN

static final java.lang.String ORIGIN
See Also:
Constant Field Values

MISSING

static final java.lang.String MISSING
See Also:
Constant Field Values

COALESCENT

static final java.lang.String COALESCENT
See Also:
Constant Field Values

CONSTANT_POPULATION

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

See Also:
Constant Field Values

EXPONENTIAL_GROWTH

static final java.lang.String EXPONENTIAL_GROWTH
See Also:
Constant Field Values

CONST_EXP_GROWTH

static final java.lang.String CONST_EXP_GROWTH
See Also:
Constant Field Values

EXPANDING_POPULATION

static final java.lang.String EXPANDING_POPULATION
See Also:
Constant Field Values

CONST_EXP_CONST

static final java.lang.String CONST_EXP_CONST
See Also:
Constant Field Values

CONSTANT_MUTATION_RATE

static final java.lang.String CONSTANT_MUTATION_RATE
See Also:
Constant Field Values

STEPPED_MUTATION_RATE

static final java.lang.String STEPPED_MUTATION_RATE
See Also:
Constant Field Values

UNIFORM

static final java.lang.String UNIFORM
See Also:
Constant Field Values

MUTATION_RATE

static final java.lang.String MUTATION_RATE
See Also:
Constant Field Values

ANCESTRAL_MU_RATE

static final java.lang.String ANCESTRAL_MU_RATE
See Also:
Constant Field Values

MU_STEP_TIME

static final java.lang.String MU_STEP_TIME
See Also:
Constant Field Values

POPULATION_SIZE

static final java.lang.String POPULATION_SIZE
See Also:
Constant Field Values

GROWTH_RATE

static final java.lang.String GROWTH_RATE
See Also:
Constant Field Values

ALPHA

static final java.lang.String ALPHA
See Also:
Constant Field Values

ANCESTRAL_POP_SIZE

static final java.lang.String ANCESTRAL_POP_SIZE
See Also:
Constant Field Values

CURRENT_POP_SIZE_DURATION

static final java.lang.String CURRENT_POP_SIZE_DURATION
See Also:
Constant Field Values

GROWTH_PHASE_DURATION

static final java.lang.String GROWTH_PHASE_DURATION
See Also:
Constant Field Values

GENERATIONS

static final java.lang.String GENERATIONS
See Also:
Constant Field Values

DAYS

static final java.lang.String DAYS
See Also:
Constant Field Values

MONTHS

static final java.lang.String MONTHS
See Also:
Constant Field Values

YEARS

static final java.lang.String YEARS
See Also:
Constant Field Values

MUTATIONS

static final java.lang.String MUTATIONS
See Also:
Constant Field Values

TWO_STATE

static final java.lang.String TWO_STATE
See Also:
Constant Field Values

JC

static final java.lang.String JC
See Also:
Constant Field Values

F81

static final java.lang.String F81
See Also:
Constant Field Values

F84

static final java.lang.String F84
See Also:
Constant Field Values

HKY

static final java.lang.String HKY
See Also:
Constant Field Values

GTR

static final java.lang.String GTR
See Also:
Constant Field Values

TN

static final java.lang.String TN
See Also:
Constant Field Values

WAG

static final java.lang.String WAG
See Also:
Constant Field Values

JTT

static final java.lang.String JTT
See Also:
Constant Field Values

VT

static final java.lang.String VT
See Also:
Constant Field Values

CPREV

static final java.lang.String CPREV
See Also:
Constant Field Values

BLOSUM62

static final java.lang.String BLOSUM62
See Also:
Constant Field Values

MTREV24

static final java.lang.String MTREV24
See Also:
Constant Field Values

DAYHOFF

static final java.lang.String DAYHOFF
See Also:
Constant Field Values

YANG_CODON_MODEL

static final java.lang.String YANG_CODON_MODEL
See Also:
Constant Field Values

A_TO_C

static final java.lang.String A_TO_C
See Also:
Constant Field Values

A_TO_G

static final java.lang.String A_TO_G
See Also:
Constant Field Values

A_TO_T

static final java.lang.String A_TO_T
See Also:
Constant Field Values

C_TO_G

static final java.lang.String C_TO_G
See Also:
Constant Field Values

C_TO_T

static final java.lang.String C_TO_T
See Also:
Constant Field Values

G_TO_T

static final java.lang.String G_TO_T
See Also:
Constant Field Values

KAPPA

static final java.lang.String KAPPA
See Also:
Constant Field Values

OMEGA

static final java.lang.String OMEGA
See Also:
Constant Field Values

PYRIMIDINE_PURINE_RATIO

static final java.lang.String PYRIMIDINE_PURINE_RATIO
See Also:
Constant Field Values

TS_TV_RATIO

static final java.lang.String TS_TV_RATIO
See Also:
Constant Field Values

UNKNOWN

static final java.lang.String UNKNOWN
See Also:
Constant Field Values

BACKWARDS

static final java.lang.String BACKWARDS
See Also:
Constant Field Values

UNIFORM_RATE_DISTRIBUTION

static final java.lang.String UNIFORM_RATE_DISTRIBUTION
See Also:
Constant Field Values

GAMMA_DISTRIBUTION

static final java.lang.String GAMMA_DISTRIBUTION
See Also:
Constant Field Values

RATE_DISTRIBUTION

static final java.lang.String RATE_DISTRIBUTION
See Also:
Constant Field Values

NUMBER_CATEGORIES

static final java.lang.String NUMBER_CATEGORIES
See Also:
Constant Field Values

GAMMA_ALPHA

static final java.lang.String GAMMA_ALPHA
See Also:
Constant Field Values