Package pal.xml
Class ElementParser
- java.lang.Object
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- pal.xml.ElementParser
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- All Implemented Interfaces:
XMLConstants
public class ElementParser extends java.lang.Object implements XMLConstants
This class provides static methods for parsing PAL objects from DOM Elements. Methods are ordered in public, protected, private and alphabetic within each group.- Version:
- $Id: ElementParser.java,v 1.14 2003/08/02 01:15:14 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 ElementParser()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description protected static double
getDoubleValue(org.w3c.dom.Element e)
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)
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)
static Tree
parseTreeElement(org.w3c.dom.Element e)
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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Method Detail
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getFirstByName
public static org.w3c.dom.Element getFirstByName(org.w3c.dom.Element parent, java.lang.String name)
- Returns:
- the first child element of the given name.
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parseAlignmentElement
public static Alignment parseAlignmentElement(org.w3c.dom.Element e) throws XmlParseException
Parses an alignment element and returns an alignment object.- Throws:
XmlParseException
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parseAttributeElement
public static Attribute parseAttributeElement(org.w3c.dom.Element e) throws XmlParseException
parses an attribute element.- Throws:
XmlParseException
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parseDemographicModel
public static DemographicModel parseDemographicModel(org.w3c.dom.Element e) throws XmlParseException
Parses an element from an DOM document into a DemographicModel. Recognises ConstantPopulation, ExponentialGrowth, ConstExpGrowth.- Throws:
XmlParseException
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parseEdgeNodeElement
public static Node parseEdgeNodeElement(org.w3c.dom.Element e) throws XmlParseException
- Returns:
- a tree node parsed from an XML element.
- Throws:
XmlParseException
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parseFrequencies
public static final double[] parseFrequencies(org.w3c.dom.Element element) throws XmlParseException
reads XML format of frequencies.
e.g <frequencies>0.19 0.31 0.16 0.34 </frequencies>.- Throws:
XmlParseException
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parseMutationRateModel
public static MutationRateModel parseMutationRateModel(org.w3c.dom.Element e) throws XmlParseException
Reads a mutation rate model from a DOM Document element.- Throws:
XmlParseException
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parseNodeElement
public static Node parseNodeElement(org.w3c.dom.Element e) throws XmlParseException
- Returns:
- a tree node parsed from an XML element.
- Throws:
XmlParseException
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parseRateMatrix
public static RateMatrix parseRateMatrix(org.w3c.dom.Element e) throws XmlParseException
Reads a rate matrix from a DOM Document element. Reads JC, F81, HKY, GTR- Throws:
XmlParseException
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parseRateDistribution
public static RateDistribution parseRateDistribution(org.w3c.dom.Element e) throws XmlParseException
- Throws:
XmlParseException
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parseRateMatrix
protected static RateMatrix parseRateMatrix(org.w3c.dom.Element e, Alignment a) throws XmlParseException
Reads a rate matrix from a DOM Document element. Reads JC, F81, HKY, GTR- Throws:
XmlParseException
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parseTimeDataElement
public static TimeOrderCharacterData parseTimeDataElement(org.w3c.dom.Element e) throws XmlParseException
- Returns:
- a time data object based on the given XML element.
- Throws:
XmlParseException
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parseTreeElement
public static Tree parseTreeElement(org.w3c.dom.Element e) throws XmlParseException
- Returns:
- a tree object based on the XML element it was passed.
- Throws:
XmlParseException
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validateTagName
public static void validateTagName(org.w3c.dom.Element e, java.lang.String name) throws XmlParseException
Throws a runtime exception if the element does not have the given name.- Throws:
XmlParseException
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getDoubleValue
protected static double getDoubleValue(org.w3c.dom.Element e)
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getIntegerValue
protected static int getIntegerValue(org.w3c.dom.Element e)
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getNameAttr
protected static java.lang.String getNameAttr(org.w3c.dom.Element e)
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getUnitsAttr
protected static int getUnitsAttr(org.w3c.dom.Element e)
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hasAttribute
protected static final boolean hasAttribute(org.w3c.dom.Element e, java.lang.String name)
This method allows the removeal of e.hasAttribute which is DOM Level 2. I am trying to keep compliant with DOM level 1 for now.
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