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.
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