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

Description

SeqSimilarityAdapter()
Method Summary

Modifier and Type

Method

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

Methods inherited from interface org.xml.sax.ContentHandler
declaration

Constructor Details
- SeqSimilarityAdapter
  
  public SeqSimilarityAdapter()
Method Details
- 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

Class SeqSimilarityAdapter

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface org.xml.sax.ContentHandler

Constructor Details

SeqSimilarityAdapter

Method Details

getSearchContentHandler

setSearchContentHandler

startDocument

endDocument

characters

ignorableWhitespace

startPrefixMapping

endPrefixMapping

processingInstruction

setDocumentLocator

skippedEntity

startElement

endElement