edu.hust.go.model
Class XmlGoParser

java.lang.Object
  |
  +--edu.hust.go.model.GoParser
        |
        +--edu.hust.go.model.XmlGoParser
All Implemented Interfaces:
org.xml.sax.ContentHandler, org.xml.sax.ext.DeclHandler, org.xml.sax.DTDHandler, org.xml.sax.ErrorHandler, org.xml.sax.ext.LexicalHandler
Direct Known Subclasses:
OboXmlGoParser, OwlGoParser, RdfXmlGoParser

public abstract class XmlGoParser
extends GoParser
implements org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.ErrorHandler, org.xml.sax.ext.DeclHandler, org.xml.sax.ext.LexicalHandler


Field Summary
(package private)  org.w3c.dom.Document curDocument
           
(package private)  org.w3c.dom.Element curElement
           
(package private)  org.xml.sax.XMLReader parser
           
(package private)  java.lang.String targetElementName
           
 
Fields inherited from class edu.hust.go.model.GoParser
dataPool, defaultPoolSize, defaultThreadNumber, m_ParserActive, OBO, OBOXML, OWL, poolSize, RDFXML, target, termMap, threadNumber, threadPool
 
Constructor Summary
XmlGoParser(java.lang.String _target)
           
XmlGoParser(java.lang.String _target, int _maxThreadNumber)
           
XmlGoParser(java.lang.String _target, int _maxThreadNumber, int _maxPoolSize)
           
 
Method Summary
 void attributeDecl(java.lang.String elementName, java.lang.String attributeName, java.lang.String type, java.lang.String valueDefault, java.lang.String value)
           
 void characters(char[] ch, int offset, int length)
           
 void comment(char[] ch, int offset, int length)
           
 void elementDecl(java.lang.String name, java.lang.String contentModel)
           
 void endCDATA()
           
 void endDocument()
           
 void endDTD()
           
 void endElement(java.lang.String uri, java.lang.String localName, java.lang.String qname)
           
 void endEntity(java.lang.String name)
           
 void endPrefixMapping(java.lang.String prefix)
           
 void error(org.xml.sax.SAXParseException ex)
           
 void externalEntityDecl(java.lang.String name, java.lang.String publicId, java.lang.String systemId)
           
 void fatalError(org.xml.sax.SAXParseException ex)
           
 java.lang.String getTargetElementName()
           
 void ignorableWhitespace(char[] ch, int offset, int length)
           
(package private)  void init()
           
 void internalEntityDecl(java.lang.String name, java.lang.String text)
           
 void notationDecl(java.lang.String name, java.lang.String publicId, java.lang.String systemId)
           
protected  void parseTarget()
           
protected  void printError(java.lang.String type, org.xml.sax.SAXParseException ex)
           
 void processingInstruction(java.lang.String target, java.lang.String data)
           
 void setDocumentLocator(org.xml.sax.Locator locator)
           
 void setTargetElementName(java.lang.String _targetElementName)
           
 void skippedEntity(java.lang.String name)
           
 void startCDATA()
           
 void startDocument()
           
 void startDTD(java.lang.String name, java.lang.String publicId, java.lang.String systemId)
           
 void startElement(java.lang.String uri, java.lang.String localName, java.lang.String qname, org.xml.sax.Attributes attributes)
           
 void startEntity(java.lang.String name)
           
 void startPrefixMapping(java.lang.String prefix, java.lang.String uri)
           
 void unparsedEntityDecl(java.lang.String name, java.lang.String publicId, java.lang.String systemId, java.lang.String notationName)
           
 void warning(org.xml.sax.SAXParseException ex)
           
 
Methods inherited from class edu.hust.go.model.GoParser
addDataToPool, addTermToMap, getDataFromPool, getGoTermById, getTermMap, parse, parsingInProgress, queueProcessed, removeThread, setParserActive, setParsingComplete, threadActive
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

parser

org.xml.sax.XMLReader parser

curDocument

org.w3c.dom.Document curDocument

curElement

org.w3c.dom.Element curElement

targetElementName

java.lang.String targetElementName
Constructor Detail

XmlGoParser

public XmlGoParser(java.lang.String _target)

XmlGoParser

public XmlGoParser(java.lang.String _target,
                   int _maxThreadNumber)

XmlGoParser

public XmlGoParser(java.lang.String _target,
                   int _maxThreadNumber,
                   int _maxPoolSize)
Parameters:
_target - GO definition file
_maxThreadNumber - thread number
_maxPoolSize - GO term parse speed may slower than read thread, if the number of unparsed terms greater than maxPoolSize, new term has to wait until old terms have been parsed.
Method Detail

getTargetElementName

public java.lang.String getTargetElementName()

setTargetElementName

public void setTargetElementName(java.lang.String _targetElementName)

init

void init()

parseTarget

protected void parseTarget()
Specified by:
parseTarget in class GoParser

setDocumentLocator

public void setDocumentLocator(org.xml.sax.Locator locator)
Specified by:
setDocumentLocator in interface org.xml.sax.ContentHandler

startDocument

public void startDocument()
                   throws org.xml.sax.SAXException
Specified by:
startDocument in interface org.xml.sax.ContentHandler
org.xml.sax.SAXException

processingInstruction

public void processingInstruction(java.lang.String target,
                                  java.lang.String data)
                           throws org.xml.sax.SAXException
Specified by:
processingInstruction in interface org.xml.sax.ContentHandler
org.xml.sax.SAXException

ignorableWhitespace

public void ignorableWhitespace(char[] ch,
                                int offset,
                                int length)
                         throws org.xml.sax.SAXException
Specified by:
ignorableWhitespace in interface org.xml.sax.ContentHandler
org.xml.sax.SAXException

endDocument

public void endDocument()
                 throws org.xml.sax.SAXException
Specified by:
endDocument in interface org.xml.sax.ContentHandler
org.xml.sax.SAXException

characters

public void characters(char[] ch,
                       int offset,
                       int length)
                throws org.xml.sax.SAXException
Specified by:
characters in interface org.xml.sax.ContentHandler
org.xml.sax.SAXException

startElement

public void startElement(java.lang.String uri,
                         java.lang.String localName,
                         java.lang.String qname,
                         org.xml.sax.Attributes attributes)
                  throws org.xml.sax.SAXException
Specified by:
startElement in interface org.xml.sax.ContentHandler
org.xml.sax.SAXException

endElement

public void endElement(java.lang.String uri,
                       java.lang.String localName,
                       java.lang.String qname)
                throws org.xml.sax.SAXException
Specified by:
endElement in interface org.xml.sax.ContentHandler
org.xml.sax.SAXException

notationDecl

public void notationDecl(java.lang.String name,
                         java.lang.String publicId,
                         java.lang.String systemId)
                  throws org.xml.sax.SAXException
Specified by:
notationDecl in interface org.xml.sax.DTDHandler
org.xml.sax.SAXException

unparsedEntityDecl

public void unparsedEntityDecl(java.lang.String name,
                               java.lang.String publicId,
                               java.lang.String systemId,
                               java.lang.String notationName)
                        throws org.xml.sax.SAXException
Specified by:
unparsedEntityDecl in interface org.xml.sax.DTDHandler
org.xml.sax.SAXException

startPrefixMapping

public void startPrefixMapping(java.lang.String prefix,
                               java.lang.String uri)
                        throws org.xml.sax.SAXException
Specified by:
startPrefixMapping in interface org.xml.sax.ContentHandler
org.xml.sax.SAXException

endPrefixMapping

public void endPrefixMapping(java.lang.String prefix)
                      throws org.xml.sax.SAXException
Specified by:
endPrefixMapping in interface org.xml.sax.ContentHandler
org.xml.sax.SAXException

skippedEntity

public void skippedEntity(java.lang.String name)
                   throws org.xml.sax.SAXException
Specified by:
skippedEntity in interface org.xml.sax.ContentHandler
org.xml.sax.SAXException

startDTD

public void startDTD(java.lang.String name,
                     java.lang.String publicId,
                     java.lang.String systemId)
              throws org.xml.sax.SAXException
Specified by:
startDTD in interface org.xml.sax.ext.LexicalHandler
org.xml.sax.SAXException

startEntity

public void startEntity(java.lang.String name)
                 throws org.xml.sax.SAXException
Specified by:
startEntity in interface org.xml.sax.ext.LexicalHandler
org.xml.sax.SAXException

startCDATA

public void startCDATA()
                throws org.xml.sax.SAXException
Specified by:
startCDATA in interface org.xml.sax.ext.LexicalHandler
org.xml.sax.SAXException

endCDATA

public void endCDATA()
              throws org.xml.sax.SAXException
Specified by:
endCDATA in interface org.xml.sax.ext.LexicalHandler
org.xml.sax.SAXException

comment

public void comment(char[] ch,
                    int offset,
                    int length)
             throws org.xml.sax.SAXException
Specified by:
comment in interface org.xml.sax.ext.LexicalHandler
org.xml.sax.SAXException

endEntity

public void endEntity(java.lang.String name)
               throws org.xml.sax.SAXException
Specified by:
endEntity in interface org.xml.sax.ext.LexicalHandler
org.xml.sax.SAXException

endDTD

public void endDTD()
            throws org.xml.sax.SAXException
Specified by:
endDTD in interface org.xml.sax.ext.LexicalHandler
org.xml.sax.SAXException

elementDecl

public void elementDecl(java.lang.String name,
                        java.lang.String contentModel)
                 throws org.xml.sax.SAXException
Specified by:
elementDecl in interface org.xml.sax.ext.DeclHandler
org.xml.sax.SAXException

attributeDecl

public void attributeDecl(java.lang.String elementName,
                          java.lang.String attributeName,
                          java.lang.String type,
                          java.lang.String valueDefault,
                          java.lang.String value)
                   throws org.xml.sax.SAXException
Specified by:
attributeDecl in interface org.xml.sax.ext.DeclHandler
org.xml.sax.SAXException

internalEntityDecl

public void internalEntityDecl(java.lang.String name,
                               java.lang.String text)
                        throws org.xml.sax.SAXException
Specified by:
internalEntityDecl in interface org.xml.sax.ext.DeclHandler
org.xml.sax.SAXException

externalEntityDecl

public void externalEntityDecl(java.lang.String name,
                               java.lang.String publicId,
                               java.lang.String systemId)
                        throws org.xml.sax.SAXException
Specified by:
externalEntityDecl in interface org.xml.sax.ext.DeclHandler
org.xml.sax.SAXException

warning

public void warning(org.xml.sax.SAXParseException ex)
             throws org.xml.sax.SAXException
Specified by:
warning in interface org.xml.sax.ErrorHandler
org.xml.sax.SAXException

error

public void error(org.xml.sax.SAXParseException ex)
           throws org.xml.sax.SAXException
Specified by:
error in interface org.xml.sax.ErrorHandler
org.xml.sax.SAXException

fatalError

public void fatalError(org.xml.sax.SAXParseException ex)
                throws org.xml.sax.SAXException
Specified by:
fatalError in interface org.xml.sax.ErrorHandler
org.xml.sax.SAXException

printError

protected void printError(java.lang.String type,
                          org.xml.sax.SAXParseException ex)