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 Description

ElementParser()

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.

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.

Class ElementParser

Field Summary

Fields inherited from interface pal.util.XMLConstants

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ElementParser

Method Detail

getFirstByName

parseAlignmentElement

parseAttributeElement

parseDemographicModel

parseEdgeNodeElement

parseFrequencies

parseMutationRateModel

parseNodeElement

parseRateMatrix

parseRateDistribution

parseRateMatrix

parseTimeDataElement

parseTreeElement

validateTagName

getDoubleValue

getIntegerValue

getNameAttr

getUnitsAttr

hasAttribute