org.biojava.bio.program.ssbind

Class SeqSimilarityAdapter

java.lang.Object

org.biojava.bio.program.ssbind.SeqSimilarityAdapter

All Implemented Interfaces:

org.xml.sax.ContentHandler

public class SeqSimilarityAdapter
extends java.lang.Object
implements org.xml.sax.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

Methods

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

Specified by:

startDocument in interface org.xml.sax.ContentHandler

Throws:

org.xml.sax.SAXException

endDocument

public void endDocument()
                 throws org.xml.sax.SAXException

Specified by:

endDocument in interface org.xml.sax.ContentHandler

Throws:

org.xml.sax.SAXException

characters

public void characters(char[] ch,
              int start,
              int end)
                throws org.xml.sax.SAXException

Specified by:

characters in interface org.xml.sax.ContentHandler

Throws:

org.xml.sax.SAXException

ignorableWhitespace

public void ignorableWhitespace(char[] ch,
                       int start,
                       int end)
                         throws org.xml.sax.SAXException

Specified by:

ignorableWhitespace in interface org.xml.sax.ContentHandler

Throws:

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

Throws:

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

Throws:

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

Throws:

org.xml.sax.SAXException

setDocumentLocator

public void setDocumentLocator(org.xml.sax.Locator locator)

Specified by:

setDocumentLocator in interface org.xml.sax.ContentHandler

skippedEntity

public void skippedEntity(java.lang.String name)
                   throws org.xml.sax.SAXException

Specified by:

skippedEntity in interface org.xml.sax.ContentHandler

Throws:

org.xml.sax.SAXException

startElement

public void startElement(java.lang.String nsURI,
                java.lang.String localName,
                java.lang.String qName,
                org.xml.sax.Attributes attrs)
                  throws org.xml.sax.SAXException

Specified by:

startElement in interface org.xml.sax.ContentHandler

Throws:

org.xml.sax.SAXException

endElement

public void endElement(java.lang.String nsURI,
              java.lang.String localName,
              java.lang.String qName)
                throws org.xml.sax.SAXException

Specified by:

endElement in interface org.xml.sax.ContentHandler

Throws:

org.xml.sax.SAXException