java.lang.Object

org.xml.sax.helpers.DefaultHandler

org.snpeff.nextProt.NextProtHandler

All Implemented Interfaces:: ContentHandler, DTDHandler, EntityResolver, ErrorHandler

public class NextProtHandler extends DefaultHandler

Handler used in XML parsing for NextProt database It keeps track of the tags and saves state data to create Markers using NextProtMarkerFactory http://www.nextprot.org/

Author:: pablocingolani

Constructor Summary

Constructors

Constructor

Description

NextProtHandler(NextProtMarkerFactory markersFactory)
Method Summary

Modifier and Type

Method

Description

void

characters(char[] ch, int start, int length)

void

countMissingCategory(String category)

void

endElement(String uri, String localName, String qName)

Parse XML's element end

CountByType

getMissingCategories()

void

startElement(String uri, String localName, String qName, Attributes attributes)

Parse XML's element start

Methods inherited from class org.xml.sax.helpers.DefaultHandler
endDocument, 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
- NextProtHandler
  
  public NextProtHandler(NextProtMarkerFactory markersFactory)
Method Details
- characters
  
  public void characters(char[] ch, int start, int length) throws SAXException
  
  Specified by:
  
  characters in interface ContentHandler
  
  Overrides:
  
  characters in class DefaultHandler
  
  Throws:
  
  SAXException
- countMissingCategory
  
  public void countMissingCategory(String category)
- endElement
  
  public void endElement(String uri, String localName, String qName) throws SAXException
  
  Parse XML's element end
  
  Specified by:
  
  endElement in interface ContentHandler
  
  Overrides:
  
  endElement in class DefaultHandler
  
  Throws:
  
  SAXException
- getMissingCategories
  
  public CountByType getMissingCategories()
- startElement
  
  public void startElement(String uri, String localName, String qName, Attributes attributes) throws SAXException
  
  Parse XML's element start
  
  Specified by:
  
  startElement in interface ContentHandler
  
  Overrides:
  
  startElement in class DefaultHandler
  
  Throws:
  
  SAXException

Class NextProtHandler

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

NextProtHandler

Method Details

characters

countMissingCategory

endElement

getMissingCategories

startElement