Package org.biojava.nbio.core.util

Class XMLHelper

java.lang.Object

org.biojava.nbio.core.util.XMLHelper

public class XMLHelper
extends java.lang.Object

Helper methods to simplify boilerplate XML parsing code for org.w3c.dom XML objects

Author:

Scooter

Constructor Summary

Constructors

Constructor	Description
XMLHelper()

Method Summary

Modifier and Type	Method	Description
static org.w3c.dom.Element	addChildElement(org.w3c.dom.Element parentElement, java.lang.String elementName)	Creates a new element called elementName and adds it to parentElement
static org.w3c.dom.Document	getNewDocument()	Create a new, empty org.w3c.dom.Document
static org.w3c.dom.Document	inputStreamToDocument(java.io.InputStream inputStream)	Creates an org.w3c.dom.Document from the content of the inputStream
static org.w3c.dom.Document	loadXML(java.lang.String fileName)	Given a path to an XML file, parses into an org.w3c.dom.Document
static void	outputToStream(org.w3c.dom.Document document, java.io.OutputStream outputStream)	Given an org.w3c.dom.Document, writes it to the given outputStream
static java.util.ArrayList<org.w3c.dom.Element>	selectElements(org.w3c.dom.Element element, java.lang.String xpathExpression)	Gets a list of elements matching xpathExpression.
static org.w3c.dom.Element	selectParentElement(org.w3c.dom.Element element, java.lang.String parentName)	Given an element, searches upwards through ancestor Elements till the first Element matching the requests parentName is found.
static org.w3c.dom.Element	selectSingleElement(org.w3c.dom.Element element, java.lang.String xpathExpression)	If xpathExpression is a plain string with no '/' characterr, this is interpreted as a child element name to search for.

Methods inherited from class java.lang.Object

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

Constructor Detail

XMLHelper

public XMLHelper()

Method Detail

addChildElement

public static org.w3c.dom.Element addChildElement(org.w3c.dom.Element parentElement,
                                                  java.lang.String elementName)

Creates a new element called elementName and adds it to parentElement

Parameters:

parentElement -

elementName -

Returns:

the new child element

getNewDocument

public static org.w3c.dom.Document getNewDocument()
                                           throws javax.xml.parsers.ParserConfigurationException

Create a new, empty org.w3c.dom.Document

Returns:

a new org.w3c.dom.Document

Throws:

javax.xml.parsers.ParserConfigurationException

loadXML

public static org.w3c.dom.Document loadXML(java.lang.String fileName)
                                    throws org.xml.sax.SAXException,
                                           java.io.IOException,
                                           javax.xml.parsers.ParserConfigurationException

Given a path to an XML file, parses into an org.w3c.dom.Document

Parameters:

fileName - path to a readable XML file

Returns:

Throws:

org.xml.sax.SAXException

java.io.IOException

javax.xml.parsers.ParserConfigurationException

inputStreamToDocument

public static org.w3c.dom.Document inputStreamToDocument(java.io.InputStream inputStream)
                                                  throws org.xml.sax.SAXException,
                                                         java.io.IOException,
                                                         javax.xml.parsers.ParserConfigurationException

Creates an org.w3c.dom.Document from the content of the inputStream

Parameters:

inputStream -

Returns:

a Document

Throws:

org.xml.sax.SAXException

java.io.IOException

javax.xml.parsers.ParserConfigurationException

outputToStream

public static void outputToStream(org.w3c.dom.Document document,
                                  java.io.OutputStream outputStream)
                           throws javax.xml.transform.TransformerException

Given an org.w3c.dom.Document, writes it to the given outputStream

Parameters:

document -

outputStream -

Throws:

javax.xml.transform.TransformerException

selectParentElement

public static org.w3c.dom.Element selectParentElement(org.w3c.dom.Element element,
                                                      java.lang.String parentName)

Given an element, searches upwards through ancestor Elements till the first Element matching the requests parentName is found.

Parameters:

element - The starting element

parentName - The tag name of the requested Element.

Returns:

The found element, or null if no matching element is found,

selectSingleElement

public static org.w3c.dom.Element selectSingleElement(org.w3c.dom.Element element,
                                                      java.lang.String xpathExpression)
                                               throws javax.xml.xpath.XPathExpressionException

If xpathExpression is a plain string with no '/' characterr, this is interpreted as a child element name to search for. If xpathExpression is an XPath expression, this is evaluated and is assumed to identify a single element.

Parameters:

element -

xpathExpression -

Returns:

A single element or null if no match or the 1st match if matches more than 1

Throws:

javax.xml.xpath.XPathExpressionException

selectElements

public static java.util.ArrayList<org.w3c.dom.Element> selectElements(org.w3c.dom.Element element,
                                                                      java.lang.String xpathExpression)
                                                               throws javax.xml.xpath.XPathExpressionException

Gets a list of elements matching xpathExpression. If xpathExpression lacks a '/' character, only immediate children o element are searched over.
If xpathExpression contains an '/' character, a full XPath search is made

Parameters:

element -

xpathExpression -

Returns:

A possibly empty but non-null ArrayList

Throws:

javax.xml.xpath.XPathExpressionException