Class BlastXMLParserFacade
- java.lang.Object
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- org.biojava.bio.program.sax.blastxml.BlastXMLParserFacade
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- 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
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Constructor Summary
Constructors Constructor Description BlastXMLParserFacade()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description org.xml.sax.ContentHandler
getContentHandler()
correct this laterorg.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(java.lang.String systemId)
void
parse(org.xml.sax.InputSource is)
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)
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Constructor Detail
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BlastXMLParserFacade
public BlastXMLParserFacade() throws BioException
- Throws:
BioException
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Method Detail
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getContentHandler
public org.xml.sax.ContentHandler getContentHandler()
correct this later- Specified by:
getContentHandler
in interfaceorg.xml.sax.XMLReader
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getDTDHandler
public org.xml.sax.DTDHandler getDTDHandler()
- Specified by:
getDTDHandler
in interfaceorg.xml.sax.XMLReader
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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 interfaceorg.xml.sax.XMLReader
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getErrorHandler
public org.xml.sax.ErrorHandler getErrorHandler()
- Specified by:
getErrorHandler
in interfaceorg.xml.sax.XMLReader
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getFeature
public boolean getFeature(java.lang.String name) throws org.xml.sax.SAXNotRecognizedException, org.xml.sax.SAXNotSupportedException
- Specified by:
getFeature
in interfaceorg.xml.sax.XMLReader
- Throws:
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException
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getProperty
public java.lang.Object getProperty(java.lang.String name) throws org.xml.sax.SAXNotRecognizedException, org.xml.sax.SAXNotSupportedException
- Specified by:
getProperty
in interfaceorg.xml.sax.XMLReader
- Throws:
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException
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parse
public void parse(org.xml.sax.InputSource is) throws java.io.IOException, org.xml.sax.SAXException
- Specified by:
parse
in interfaceorg.xml.sax.XMLReader
- Throws:
java.io.IOException
org.xml.sax.SAXException
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parse
public void parse(java.lang.String systemId) throws java.io.IOException, org.xml.sax.SAXException
- Specified by:
parse
in interfaceorg.xml.sax.XMLReader
- Throws:
java.io.IOException
org.xml.sax.SAXException
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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 interfaceorg.xml.sax.XMLReader
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setDTDHandler
public void setDTDHandler(org.xml.sax.DTDHandler handler)
- Specified by:
setDTDHandler
in interfaceorg.xml.sax.XMLReader
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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 interfaceorg.xml.sax.XMLReader
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setErrorHandler
public void setErrorHandler(org.xml.sax.ErrorHandler handler)
- Specified by:
setErrorHandler
in interfaceorg.xml.sax.XMLReader
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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 interfaceorg.xml.sax.XMLReader
- Throws:
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException
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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 interfaceorg.xml.sax.XMLReader
- Throws:
org.xml.sax.SAXNotRecognizedException
org.xml.sax.SAXNotSupportedException
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