Package pal.xml
Class ElementFactory
- java.lang.Object
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- pal.xml.ElementFactory
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- All Implemented Interfaces:
XMLConstants
public class ElementFactory extends java.lang.Object implements XMLConstants
This class provides static methods for creating DOM Elements from PAL Objects. Arguably each object in PAL should be allowed to generate a DOM Element representation itself -- however I have decided to restrict the PAL's dependence on the DOM specification to this package only.- Version:
- $Id: ElementFactory.java,v 1.9 2003/07/20 04:52:42 matt Exp $
- Author:
- Alexei Drummond
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Field Summary
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Fields inherited from interface pal.util.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
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Constructor Summary
Constructors Constructor Description ElementFactory()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description 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)
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Method Detail
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createAlignmentElement
public static org.w3c.dom.Element createAlignmentElement(Alignment a, org.w3c.dom.Document document)
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createAttributeElement
public static org.w3c.dom.Element createAttributeElement(Attribute a, org.w3c.dom.Document document)
- Returns:
- a DOM element describing an attribute element.
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createDemographicModelElement
public static org.w3c.dom.Element createDemographicModelElement(DemographicModel demo, org.w3c.dom.Document document)
Creates an XML element representing a demographic model.
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createEdgeNodeElement
public static org.w3c.dom.Element createEdgeNodeElement(Node node, org.w3c.dom.Document document)
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createFrequenciesElement
public 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.
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createMutationRateModelElement
public static org.w3c.dom.Element createMutationRateModelElement(MutationRateModel muModel, org.w3c.dom.Document document)
Creates an XML element representing a mutation rate model.
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createNodeElement
public static org.w3c.dom.Element createNodeElement(Node node, org.w3c.dom.Document document)
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createNodeElement
public static org.w3c.dom.Element createNodeElement(Node node, org.w3c.dom.Document document, boolean includeEdges)
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createParameterElement
public static org.w3c.dom.Element createParameterElement(java.lang.String name, double value, org.w3c.dom.Document document)
Creates an XML element representing a parameter.
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createRateMatrixElement
public static org.w3c.dom.Element createRateMatrixElement(RateMatrix matrix, org.w3c.dom.Document d)
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createSequenceElement
public static org.w3c.dom.Element createSequenceElement(Identifier id, java.lang.String sequence, org.w3c.dom.Document document)
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createTimeDataElement
public static org.w3c.dom.Element createTimeDataElement(TimeOrderCharacterData tocd, org.w3c.dom.Document document)
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createTreeElement
public static org.w3c.dom.Element createTreeElement(Tree tree, org.w3c.dom.Document document, boolean includeEdges)
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