Package org.biojava.bio.program.ssbind
Class SeqSimilarityAdapter
java.lang.Object
org.biojava.bio.program.ssbind.SeqSimilarityAdapter
- All Implemented Interfaces:
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
SeqSimilaritySearchResult
s from the stream.- Since:
- 1.2
- Author:
- Keith James
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
characters
(char[] ch, int start, int end) void
void
endElement
(String nsURI, String localName, String qName) void
endPrefixMapping
(String prefix) 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
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
getSearchContentHandler
gets the handler which will recieve the method calls generated by the adapter.- Returns:
- a
SearchContentHandler
.
-
setSearchContentHandler
setSearchContentHandler
sets the handler which will recieve the method calls generated by the adapter.- Parameters:
scHandler
- aSearchContentHandler
.
-
startDocument
- Specified by:
startDocument
in interfaceContentHandler
- Throws:
SAXException
-
endDocument
- Specified by:
endDocument
in interfaceContentHandler
- Throws:
SAXException
-
characters
- Specified by:
characters
in interfaceContentHandler
- Throws:
SAXException
-
ignorableWhitespace
- Specified by:
ignorableWhitespace
in interfaceContentHandler
- Throws:
SAXException
-
startPrefixMapping
- Specified by:
startPrefixMapping
in interfaceContentHandler
- Throws:
SAXException
-
endPrefixMapping
- Specified by:
endPrefixMapping
in interfaceContentHandler
- Throws:
SAXException
-
processingInstruction
- Specified by:
processingInstruction
in interfaceContentHandler
- Throws:
SAXException
-
setDocumentLocator
- Specified by:
setDocumentLocator
in interfaceContentHandler
-
skippedEntity
- Specified by:
skippedEntity
in interfaceContentHandler
- Throws:
SAXException
-
startElement
public void startElement(String nsURI, String localName, String qName, Attributes attrs) throws SAXException - Specified by:
startElement
in interfaceContentHandler
- Throws:
SAXException
-
endElement
- Specified by:
endElement
in interfaceContentHandler
- Throws:
SAXException
-