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

Constructors

Constructor

Description

XMLDistributionReader()
Method Summary

Modifier and Type

Method

Description

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

Methods inherited from interface org.xml.sax.ContentHandler
declaration

Constructor Details
- XMLDistributionReader
  
  public XMLDistributionReader()
Method Details
- 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

Class XMLDistributionReader

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Methods inherited from interface org.xml.sax.ContentHandler

Constructor Details

XMLDistributionReader

Method Details

parseXML

startElement