org.biojava.bio.program.ssbind

Class SeqSimilarityAdapter

java.lang.Object

org.biojava.bio.program.ssbind.SeqSimilarityAdapter

All Implemented Interfaces:

ContentHandler

public class SeqSimilarityAdapter
extends Object
implements ContentHandler

A SeqSimilarityAdapter converts SAX events into method calls on a SearchContentHandler implementation. The SAX events should describe elements conforming to the BioJava BlastLikeDataSetCollection DTD. A BlastLikeSearchBuilder is supplied, implementing the SearchContentHandler interface, which will create SeqSimilaritySearchResults from the stream.

Since:

1.2

Author:

Keith James

Constructor Summary

Constructors

Constructor and Description
SeqSimilarityAdapter()

Method Summary

Modifier and Type	Method and Description
void	characters(char[] ch, int start, int end)
void	endDocument()
void	endElement(String nsURI, String localName, String qName)
void	endPrefixMapping(String prefix)
SearchContentHandler	getSearchContentHandler() getSearchContentHandler gets the handler which will recieve the method calls generated by the adapter.
void	ignorableWhitespace(char[] ch, int start, int end)
void	processingInstruction(String target, String data)
void	setDocumentLocator(Locator locator)
void	setSearchContentHandler(SearchContentHandler scHandler) setSearchContentHandler sets the handler which will recieve the method calls generated by the adapter.
void	skippedEntity(String name)
void	startDocument()
void	startElement(String nsURI, String localName, String qName, Attributes attrs)
void	startPrefixMapping(String prefix, String uri)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SeqSimilarityAdapter

public SeqSimilarityAdapter()

Method Detail

getSearchContentHandler

public SearchContentHandler getSearchContentHandler()

getSearchContentHandler gets the handler which will recieve the method calls generated by the adapter.

Returns:

a SearchContentHandler.

setSearchContentHandler

public void setSearchContentHandler(SearchContentHandler scHandler)

setSearchContentHandler sets the handler which will recieve the method calls generated by the adapter.

Parameters:

scHandler - a SearchContentHandler.

startDocument

public void startDocument()
                   throws SAXException

Specified by:

startDocument in interface ContentHandler

Throws:

SAXException

endDocument

public void endDocument()
                 throws SAXException

Specified by:

endDocument in interface ContentHandler

Throws:

SAXException

characters

public void characters(char[] ch,
                       int start,
                       int end)
                throws SAXException

Specified by:

characters in interface ContentHandler

Throws:

SAXException

ignorableWhitespace

public void ignorableWhitespace(char[] ch,
                                int start,
                                int end)
                         throws SAXException

Specified by:

ignorableWhitespace in interface ContentHandler

Throws:

SAXException

startPrefixMapping

public void startPrefixMapping(String prefix,
                               String uri)
                        throws SAXException

Specified by:

startPrefixMapping in interface ContentHandler

Throws:

SAXException

endPrefixMapping

public void endPrefixMapping(String prefix)
                      throws SAXException

Specified by:

endPrefixMapping in interface ContentHandler

Throws:

SAXException

processingInstruction

public void processingInstruction(String target,
                                  String data)
                           throws SAXException

Specified by:

processingInstruction in interface ContentHandler

Throws:

SAXException

setDocumentLocator

public void setDocumentLocator(Locator locator)

Specified by:

setDocumentLocator in interface ContentHandler

skippedEntity

public void skippedEntity(String name)
                   throws SAXException

Specified by:

skippedEntity in interface ContentHandler

Throws:

SAXException

startElement

public void startElement(String nsURI,
                         String localName,
                         String qName,
                         Attributes attrs)
                  throws SAXException

Specified by:

startElement in interface ContentHandler

Throws:

SAXException

endElement

public void endElement(String nsURI,
                       String localName,
                       String qName)
                throws SAXException

Specified by:

endElement in interface ContentHandler

Throws:

SAXException