pal.xml
public class ElementFactory extends java.lang.Object implements XMLConstants
A_TO_C, A_TO_G, A_TO_T, ALIGNMENT, ALPHA, ANCESTRAL_MU_RATE, ANCESTRAL_POP_SIZE, ATTRIBUTE, BACKWARDS, BLOSUM62, C_TO_G, C_TO_T, COALESCENT, CONST_EXP_CONST, CONST_EXP_GROWTH, CONSTANT_MUTATION_RATE, CONSTANT_POPULATION, CPREV, CURRENT_POP_SIZE_DURATION, DATA_TYPE, DATA_TYPE_ID, DAYHOFF, DAYS, DEMOGRAPHIC_MODEL, DIRECTION, EDGE, EXPANDING_POPULATION, EXPONENTIAL_GROWTH, F81, F84, FREQUENCIES, G_TO_T, GAMMA_ALPHA, GAMMA_DISTRIBUTION, GENERATIONS, GROWTH_PHASE_DURATION, GROWTH_RATE, GTR, HEIGHT, HKY, ID, JC, JTT, KAPPA, LENGTH, MISSING, MODEL, MONTHS, MTREV24, MU_STEP_TIME, MUTATION_RATE, MUTATION_RATE_MODEL, MUTATIONS, NAME, NODE, NUMBER_CATEGORIES, OMEGA, ORIGIN, PARAMETER, POPULATION_SIZE, PYRIMIDINE_PURINE_RATIO, RATE_DISTRIBUTION, RATE_MATRIX, SEQUENCE, SPACES_PER_LEVEL, STEPPED_MUTATION_RATE, TIME, TIME_DATA, TN, TREE, TS_TV_RATIO, TWO_STATE, TYPE, UNIFORM, UNIFORM_RATE_DISTRIBUTION, UNITS, UNKNOWN, VALUE, VT, WAG, YANG_CODON_MODEL, YEARS
Constructor and Description |
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ElementFactory() |
Modifier and Type | Method and Description |
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static org.w3c.dom.Element |
createAlignmentElement(Alignment a,
org.w3c.dom.Document document) |
static org.w3c.dom.Element |
createAttributeElement(Attribute a,
org.w3c.dom.Document document) |
static org.w3c.dom.Element |
createDemographicModelElement(DemographicModel demo,
org.w3c.dom.Document document)
Creates an XML element representing a demographic model.
|
static org.w3c.dom.Element |
createEdgeNodeElement(Node node,
org.w3c.dom.Document document) |
static org.w3c.dom.Element |
createFrequenciesElement(double[] frequencies,
org.w3c.dom.Document d)
Creates a DOM element associated with the given document representing
the given equilibrium frequencies of a rate matrix.
|
static org.w3c.dom.Element |
createMutationRateModelElement(MutationRateModel muModel,
org.w3c.dom.Document document)
Creates an XML element representing a mutation rate model.
|
static org.w3c.dom.Element |
createNodeElement(Node node,
org.w3c.dom.Document document) |
static org.w3c.dom.Element |
createNodeElement(Node node,
org.w3c.dom.Document document,
boolean includeEdges) |
static org.w3c.dom.Element |
createParameterElement(java.lang.String name,
double value,
org.w3c.dom.Document document)
Creates an XML element representing a parameter.
|
static org.w3c.dom.Element |
createRateMatrixElement(RateMatrix matrix,
org.w3c.dom.Document d) |
static org.w3c.dom.Element |
createSequenceElement(Identifier id,
java.lang.String sequence,
org.w3c.dom.Document document) |
static org.w3c.dom.Element |
createTimeDataElement(TimeOrderCharacterData tocd,
org.w3c.dom.Document document) |
static org.w3c.dom.Element |
createTreeElement(Tree tree,
org.w3c.dom.Document document,
boolean includeEdges) |
public static org.w3c.dom.Element createAlignmentElement(Alignment a, org.w3c.dom.Document document)
public static org.w3c.dom.Element createAttributeElement(Attribute a, org.w3c.dom.Document document)
public static org.w3c.dom.Element createDemographicModelElement(DemographicModel demo, org.w3c.dom.Document document)
public static org.w3c.dom.Element createEdgeNodeElement(Node node, org.w3c.dom.Document document)
public static org.w3c.dom.Element createFrequenciesElement(double[] frequencies, org.w3c.dom.Document d)
public static org.w3c.dom.Element createMutationRateModelElement(MutationRateModel muModel, org.w3c.dom.Document document)
public static org.w3c.dom.Element createNodeElement(Node node, org.w3c.dom.Document document)
public static org.w3c.dom.Element createNodeElement(Node node, org.w3c.dom.Document document, boolean includeEdges)
public static org.w3c.dom.Element createParameterElement(java.lang.String name, double value, org.w3c.dom.Document document)
public static org.w3c.dom.Element createRateMatrixElement(RateMatrix matrix, org.w3c.dom.Document d)
public static org.w3c.dom.Element createSequenceElement(Identifier id, java.lang.String sequence, org.w3c.dom.Document document)
public static org.w3c.dom.Element createTimeDataElement(TimeOrderCharacterData tocd, org.w3c.dom.Document document)
public static org.w3c.dom.Element createTreeElement(Tree tree, org.w3c.dom.Document document, boolean includeEdges)