Package | Description |
---|---|
pal.xml |
Utility classes for converting PAL objects to and from XML documents.
|
Modifier and Type | Method and Description |
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static Alignment |
ElementParser.parseAlignmentElement(org.w3c.dom.Element e)
Parses an alignment element and returns an alignment object.
|
static Attribute |
ElementParser.parseAttributeElement(org.w3c.dom.Element e)
parses an attribute element.
|
static DemographicModel |
ElementParser.parseDemographicModel(org.w3c.dom.Element e)
Parses an element from an DOM document into a DemographicModel.
|
static Node |
ElementParser.parseEdgeNodeElement(org.w3c.dom.Element e) |
static double[] |
ElementParser.parseFrequencies(org.w3c.dom.Element element)
reads XML format of frequencies.
|
static MutationRateModel |
ElementParser.parseMutationRateModel(org.w3c.dom.Element e)
Reads a mutation rate model from a DOM Document element.
|
static Node |
ElementParser.parseNodeElement(org.w3c.dom.Element e) |
static RateDistribution |
ElementParser.parseRateDistribution(org.w3c.dom.Element e) |
static RateMatrix |
ElementParser.parseRateMatrix(org.w3c.dom.Element e)
Reads a rate matrix from a DOM Document element.
|
protected static RateMatrix |
ElementParser.parseRateMatrix(org.w3c.dom.Element e,
Alignment a)
Reads a rate matrix from a DOM Document element.
|
static TimeOrderCharacterData |
ElementParser.parseTimeDataElement(org.w3c.dom.Element e) |
static Tree |
ElementParser.parseTreeElement(org.w3c.dom.Element e) |
static void |
ElementParser.validateTagName(org.w3c.dom.Element e,
java.lang.String name)
Throws a runtime exception if the element does not have
the given name.
|