XMLConstants
public class ElementParser 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 | Description |
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ElementParser() |
Modifier and Type | Method | Description |
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protected static double |
getDoubleValue(org.w3c.dom.Element e) |
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static org.w3c.dom.Element |
getFirstByName(org.w3c.dom.Element parent,
java.lang.String name) |
|
protected static int |
getIntegerValue(org.w3c.dom.Element e) |
|
protected static java.lang.String |
getNameAttr(org.w3c.dom.Element e) |
|
protected static int |
getUnitsAttr(org.w3c.dom.Element e) |
|
protected static boolean |
hasAttribute(org.w3c.dom.Element e,
java.lang.String name) |
This method allows the removeal of e.hasAttribute which is DOM Level 2.
|
static Alignment |
parseAlignmentElement(org.w3c.dom.Element e) |
Parses an alignment element and returns an alignment object.
|
static Attribute |
parseAttributeElement(org.w3c.dom.Element e) |
parses an attribute element.
|
static DemographicModel |
parseDemographicModel(org.w3c.dom.Element e) |
Parses an element from an DOM document into a DemographicModel.
|
static Node |
parseEdgeNodeElement(org.w3c.dom.Element e) |
|
static double[] |
parseFrequencies(org.w3c.dom.Element element) |
reads XML format of frequencies.
|
static MutationRateModel |
parseMutationRateModel(org.w3c.dom.Element e) |
Reads a mutation rate model from a DOM Document element.
|
static Node |
parseNodeElement(org.w3c.dom.Element e) |
|
static RateDistribution |
parseRateDistribution(org.w3c.dom.Element e) |
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static RateMatrix |
parseRateMatrix(org.w3c.dom.Element e) |
Reads a rate matrix from a DOM Document element.
|
protected static RateMatrix |
parseRateMatrix(org.w3c.dom.Element e,
Alignment a) |
Reads a rate matrix from a DOM Document element.
|
static TimeOrderCharacterData |
parseTimeDataElement(org.w3c.dom.Element e) |
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static Tree |
parseTreeElement(org.w3c.dom.Element e) |
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static void |
validateTagName(org.w3c.dom.Element e,
java.lang.String name) |
Throws a runtime exception if the element does not have
the given name.
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public static org.w3c.dom.Element getFirstByName(org.w3c.dom.Element parent, java.lang.String name)
public static Alignment parseAlignmentElement(org.w3c.dom.Element e) throws XmlParseException
XmlParseException
public static Attribute parseAttributeElement(org.w3c.dom.Element e) throws XmlParseException
XmlParseException
public static DemographicModel parseDemographicModel(org.w3c.dom.Element e) throws XmlParseException
XmlParseException
public static Node parseEdgeNodeElement(org.w3c.dom.Element e) throws XmlParseException
XmlParseException
public static final double[] parseFrequencies(org.w3c.dom.Element element) throws XmlParseException
XmlParseException
public static MutationRateModel parseMutationRateModel(org.w3c.dom.Element e) throws XmlParseException
XmlParseException
public static Node parseNodeElement(org.w3c.dom.Element e) throws XmlParseException
XmlParseException
public static RateMatrix parseRateMatrix(org.w3c.dom.Element e) throws XmlParseException
XmlParseException
public static RateDistribution parseRateDistribution(org.w3c.dom.Element e) throws XmlParseException
XmlParseException
protected static RateMatrix parseRateMatrix(org.w3c.dom.Element e, Alignment a) throws XmlParseException
XmlParseException
public static TimeOrderCharacterData parseTimeDataElement(org.w3c.dom.Element e) throws XmlParseException
XmlParseException
public static Tree parseTreeElement(org.w3c.dom.Element e) throws XmlParseException
XmlParseException
public static void validateTagName(org.w3c.dom.Element e, java.lang.String name) throws XmlParseException
XmlParseException
protected static double getDoubleValue(org.w3c.dom.Element e)
protected static int getIntegerValue(org.w3c.dom.Element e)
protected static java.lang.String getNameAttr(org.w3c.dom.Element e)
protected static int getUnitsAttr(org.w3c.dom.Element e)
protected static final boolean hasAttribute(org.w3c.dom.Element e, java.lang.String name)