org.biojava.bio.program.ssbind
Class SeqSimilarityAdapter

java.lang.Object
  extended byorg.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
SeqSimilarityAdapter()
           
 
Method Summary
 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