org.biojava.bio.dist
Class XMLDistributionReader

java.lang.Object
  extended by org.xml.sax.helpers.DefaultHandler
      extended by org.biojava.bio.dist.XMLDistributionReader
All Implemented Interfaces:
ContentHandler, DTDHandler, EntityResolver, ErrorHandler

public class XMLDistributionReader
extends 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
XMLDistributionReader()
           
 
Method Summary
 Distribution parseXML(InputStream is)
          Reads an XML representation of a Distribution from a file.
 void startElement(String nameSpaceURI, String localName, String rawName, 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(InputStream is)
                      throws IOException,
                             SAXException
Reads an XML representation of a Distribution from a file.

Parameters:
is - input in XML format
Returns:
dist the Distribution created.
Throws:
IOException - if an error occurs during reading.
SAXException - if the XML is not as expected.

startElement

public void startElement(String nameSpaceURI,
                         String localName,
                         String rawName,
                         Attributes attributes)
                  throws 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 ContentHandler
Overrides:
startElement in class DefaultHandler
Throws:
SAXException