org.biojava.bio.program.sax.blastxml
Class BlastXMLParserFacade

java.lang.Object
  extended by org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
All Implemented Interfaces:
org.xml.sax.XMLReader

public class BlastXMLParserFacade
extends java.lang.Object
implements org.xml.sax.XMLReader

A facade class that wraps the NCBI Blast XML parsing framework in a more user-friendly form. It is identical to BlastlikeSAXParser in use.

Since:
1.3
Author:
David Huen

Constructor Summary
BlastXMLParserFacade()
           
 
Method Summary
 org.xml.sax.ContentHandler getContentHandler()
          correct this later
 org.xml.sax.DTDHandler getDTDHandler()
           
 org.xml.sax.EntityResolver getEntityResolver()
          This class has an EntityResolver that resolves the public ID specifying the NCBI DTDs to resource files within the BioJava libraries.
 org.xml.sax.ErrorHandler getErrorHandler()
           
 boolean getFeature(java.lang.String name)
           
 java.lang.Object getProperty(java.lang.String name)
           
 void parse(org.xml.sax.InputSource is)
           
 void parse(java.lang.String systemId)
           
 void setContentHandler(org.xml.sax.ContentHandler handler)
          this sets the ContentHandler that receives SAX events from the internal Blast XML parser which is the actual ContentHandler.
 void setDTDHandler(org.xml.sax.DTDHandler handler)
           
 void setEntityResolver(org.xml.sax.EntityResolver resolver)
          This class has an EntityResolver that resolves the public ID specifying the NCBI DTDs to resource files within the BioJava libraries.
 void setErrorHandler(org.xml.sax.ErrorHandler handler)
           
 void setFeature(java.lang.String key, boolean value)
          by default, we set the parser to non-validating.
 void setProperty(java.lang.String key, java.lang.Object value)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

BlastXMLParserFacade

public BlastXMLParserFacade()
                     throws BioException
Throws:
BioException
Method Detail

getContentHandler

public org.xml.sax.ContentHandler getContentHandler()
correct this later

Specified by:
getContentHandler in interface org.xml.sax.XMLReader

getDTDHandler

public org.xml.sax.DTDHandler getDTDHandler()
Specified by:
getDTDHandler in interface org.xml.sax.XMLReader

getEntityResolver

public org.xml.sax.EntityResolver getEntityResolver()
This class has an EntityResolver that resolves the public ID specifying the NCBI DTDs to resource files within the BioJava libraries. This call will return that resolver. It you should set your own resolver, ensure you resolve that URN yourself or the parser will blow up on you!.

Specified by:
getEntityResolver in interface org.xml.sax.XMLReader

getErrorHandler

public org.xml.sax.ErrorHandler getErrorHandler()
Specified by:
getErrorHandler in interface org.xml.sax.XMLReader

getFeature

public boolean getFeature(java.lang.String name)
                   throws org.xml.sax.SAXNotRecognizedException,
                          org.xml.sax.SAXNotSupportedException
Specified by:
getFeature in interface org.xml.sax.XMLReader
Throws:
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException

getProperty

public java.lang.Object getProperty(java.lang.String name)
                             throws org.xml.sax.SAXNotRecognizedException,
                                    org.xml.sax.SAXNotSupportedException
Specified by:
getProperty in interface org.xml.sax.XMLReader
Throws:
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException

parse

public void parse(org.xml.sax.InputSource is)
           throws java.io.IOException,
                  org.xml.sax.SAXException
Specified by:
parse in interface org.xml.sax.XMLReader
Throws:
java.io.IOException
org.xml.sax.SAXException

parse

public void parse(java.lang.String systemId)
           throws java.io.IOException,
                  org.xml.sax.SAXException
Specified by:
parse in interface org.xml.sax.XMLReader
Throws:
java.io.IOException
org.xml.sax.SAXException

setContentHandler

public void setContentHandler(org.xml.sax.ContentHandler handler)
this sets the ContentHandler that receives SAX events from the internal Blast XML parser which is the actual ContentHandler. It will not change the internal Blast XML parser.

Specified by:
setContentHandler in interface org.xml.sax.XMLReader

setDTDHandler

public void setDTDHandler(org.xml.sax.DTDHandler handler)
Specified by:
setDTDHandler in interface org.xml.sax.XMLReader

setEntityResolver

public void setEntityResolver(org.xml.sax.EntityResolver resolver)
This class has an EntityResolver that resolves the public ID specifying the NCBI DTDs to resource files within the BioJava libraries. This call will return that resolver. It you should set your own resolver, ensure you resolve that URN yourself or the parser will blow up on you!.

Specified by:
setEntityResolver in interface org.xml.sax.XMLReader

setErrorHandler

public void setErrorHandler(org.xml.sax.ErrorHandler handler)
Specified by:
setErrorHandler in interface org.xml.sax.XMLReader

setFeature

public void setFeature(java.lang.String key,
                       boolean value)
                throws org.xml.sax.SAXNotRecognizedException,
                       org.xml.sax.SAXNotSupportedException
by default, we set the parser to non-validating. change it if you wish/dare! The parser is also set to be namespace aware. DO NOT CHANGE THAT!!!

Specified by:
setFeature in interface org.xml.sax.XMLReader
Throws:
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException

setProperty

public void setProperty(java.lang.String key,
                        java.lang.Object value)
                 throws org.xml.sax.SAXNotRecognizedException,
                        org.xml.sax.SAXNotSupportedException
Specified by:
setProperty in interface org.xml.sax.XMLReader
Throws:
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException