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
SeqSimilaritySearchResult
s from the stream.
- Since:
- 1.2
- Author:
- Keith James
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 |
SeqSimilarityAdapter
public SeqSimilarityAdapter()
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