Package org.biojava.bio.dist

Class XMLDistributionReader

java.lang.Object

org.xml.sax.helpers.DefaultHandler

org.biojava.bio.dist.XMLDistributionReader

All Implemented Interfaces:

org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler

public class XMLDistributionReader
extends org.xml.sax.helpers.DefaultHandler

A SAX parser that reads an XML representation of a Distribution from a file and recreates it as a Distribution Object. Handles OrderNDistributions and Simple Distributions but ensure the OrderNDistributions being read in was made using conditioning and conditioned Alphabets.

Since:

1.3

Author:

Russell Smithies, Mark Schreiber, Matthew Pocock

Constructor Summary

Constructors

Constructor	Description
XMLDistributionReader()

Method Summary

Modifier and Type	Method	Description
Distribution	parseXML(java.io.InputStream is)	Reads an XML representation of a Distribution from a file.
void	startElement(java.lang.String nameSpaceURI, java.lang.String localName, java.lang.String rawName, org.xml.sax.Attributes attributes)	Required by SAXParser to be public.

Methods inherited from class org.xml.sax.helpers.DefaultHandler

characters, endDocument, endElement, endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startDocument, startPrefixMapping, unparsedEntityDecl, warning

Methods inherited from class java.lang.Object

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

Constructor Detail

XMLDistributionReader

public XMLDistributionReader()

Method Detail

parseXML

public Distribution parseXML(java.io.InputStream is)
                      throws java.io.IOException,
                             org.xml.sax.SAXException

Reads an XML representation of a Distribution from a file.

Parameters:

is - input in XML format

Returns:

dist the Distribution created.

Throws:

java.io.IOException - if an error occurs during reading.

org.xml.sax.SAXException - if the XML is not as expected.

startElement

public void startElement(java.lang.String nameSpaceURI,
                         java.lang.String localName,
                         java.lang.String rawName,
                         org.xml.sax.Attributes attributes)
                  throws org.xml.sax.SAXException

Required by SAXParser to be public.

It is not reccomended that you use this method directly. Use ParseXML instead.

Specified by:

startElement in interface org.xml.sax.ContentHandler

Overrides:

startElement in class org.xml.sax.helpers.DefaultHandler

Throws:

org.xml.sax.SAXException