pal.xml
Class ElementFactory

java.lang.Object
  extended by pal.xml.ElementFactory
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

Field Summary
 
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
 
Constructor Summary
ElementFactory()
           
 
Method Summary
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)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ElementFactory

public ElementFactory()
Method Detail

createAlignmentElement

public static org.w3c.dom.Element createAlignmentElement(Alignment a,
                                                         org.w3c.dom.Document document)

createAttributeElement

public static org.w3c.dom.Element createAttributeElement(Attribute a,
                                                         org.w3c.dom.Document document)
Returns:
a DOM element describing an attribute element.

createDemographicModelElement

public static org.w3c.dom.Element createDemographicModelElement(DemographicModel demo,
                                                                org.w3c.dom.Document document)
Creates an XML element representing a demographic model.


createEdgeNodeElement

public static org.w3c.dom.Element createEdgeNodeElement(Node node,
                                                        org.w3c.dom.Document document)

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.


createMutationRateModelElement

public static org.w3c.dom.Element createMutationRateModelElement(MutationRateModel muModel,
                                                                 org.w3c.dom.Document document)
Creates an XML element representing a mutation rate model.


createNodeElement

public static org.w3c.dom.Element createNodeElement(Node node,
                                                    org.w3c.dom.Document document)

createNodeElement

public static org.w3c.dom.Element createNodeElement(Node node,
                                                    org.w3c.dom.Document document,
                                                    boolean includeEdges)

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.


createRateMatrixElement

public static org.w3c.dom.Element createRateMatrixElement(RateMatrix matrix,
                                                          org.w3c.dom.Document d)

createSequenceElement

public static org.w3c.dom.Element createSequenceElement(Identifier id,
                                                        java.lang.String sequence,
                                                        org.w3c.dom.Document document)

createTimeDataElement

public static org.w3c.dom.Element createTimeDataElement(TimeOrderCharacterData tocd,
                                                        org.w3c.dom.Document document)

createTreeElement

public static org.w3c.dom.Element createTreeElement(Tree tree,
                                                    org.w3c.dom.Document document,
                                                    boolean includeEdges)