pal.xml

Class ElementParser

java.lang.Object

pal.xml.ElementParser

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

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

Constructors

Constructor and Description
ElementParser()

Method Summary

Methods

Modifier and Type	Method and 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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

ElementParser

public ElementParser()

Method Detail

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.

parseAlignmentElement

public static Alignment parseAlignmentElement(org.w3c.dom.Element e)
                                       throws XmlParseException

Parses an alignment element and returns an alignment object.

Throws:

XmlParseException

parseAttributeElement

public static Attribute parseAttributeElement(org.w3c.dom.Element e)
                                       throws XmlParseException

parses an attribute element.

Throws:

XmlParseException

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

parseEdgeNodeElement

public static Node parseEdgeNodeElement(org.w3c.dom.Element e)
                                 throws XmlParseException

Returns:

a tree node parsed from an XML element.

Throws:

XmlParseException

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

parseMutationRateModel

public static MutationRateModel parseMutationRateModel(org.w3c.dom.Element e)
                                                throws XmlParseException

Reads a mutation rate model from a DOM Document element.

Throws:

XmlParseException

parseNodeElement

public static Node parseNodeElement(org.w3c.dom.Element e)
                             throws XmlParseException

Returns:

a tree node parsed from an XML element.

Throws:

XmlParseException

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

parseRateDistribution

public static RateDistribution parseRateDistribution(org.w3c.dom.Element e)
                                              throws XmlParseException

Throws:

XmlParseException

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

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

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

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

getDoubleValue

protected static double getDoubleValue(org.w3c.dom.Element e)

getIntegerValue

protected static int getIntegerValue(org.w3c.dom.Element e)

getNameAttr

protected static java.lang.String getNameAttr(org.w3c.dom.Element e)

getUnitsAttr

protected static int getUnitsAttr(org.w3c.dom.Element e)

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.