pal.xml
Class ElementFactory
java.lang.Object
|
+--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.
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_GROWTH, CONSTANT_MUTATION_RATE, CONSTANT_POPULATION, CPREV, DATA_TYPE, DATA_TYPE_ID, DAYHOFF, DAYS, DEMOGRAPHIC_MODEL, DIRECTION, EDGE, EXPONENTIAL_GROWTH, F81, F84, FREQUENCIES, G_TO_T, GENERATIONS, 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, OMEGA, ORIGIN, PARAMETER, POPULATION_SIZE, PYRIMIDINE_PURINE_RATIO, RATE_MATRIX, SEQUENCE, SPACES_PER_LEVEL, STEPPED_MUTATION_RATE, TIME, TIME_DATA, TN, TREE, TS_TV_RATIO, TWO_STATE, TYPE, UNIFORM, UNITS, UNKNOWN, VALUE, VT, WAG, YANG_CODON_MODEL, YEARS |
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 |
ElementFactory
public ElementFactory()
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)