Package org.biojava.bio.program.ssbind
Class SeqSimilarityAdapter
- java.lang.Object
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- org.biojava.bio.program.ssbind.SeqSimilarityAdapter
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- All Implemented Interfaces:
org.xml.sax.ContentHandler
public class SeqSimilarityAdapter extends java.lang.Object implements org.xml.sax.ContentHandler
ASeqSimilarityAdapter
converts SAX events into method calls on aSearchContentHandler
implementation. The SAX events should describe elements conforming to the BioJava BlastLikeDataSetCollection DTD. ABlastLikeSearchBuilder
is supplied, implementing theSearchContentHandler
interface, which will createSeqSimilaritySearchResult
s from the stream.- Since:
- 1.2
- Author:
- Keith James
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Constructor Summary
Constructors Constructor Description SeqSimilarityAdapter()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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)
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Method Detail
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getSearchContentHandler
public SearchContentHandler getSearchContentHandler()
getSearchContentHandler
gets the handler which will recieve the method calls generated by the adapter.- Returns:
- a
SearchContentHandler
.
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setSearchContentHandler
public void setSearchContentHandler(SearchContentHandler scHandler)
setSearchContentHandler
sets the handler which will recieve the method calls generated by the adapter.- Parameters:
scHandler
- aSearchContentHandler
.
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startDocument
public void startDocument() throws org.xml.sax.SAXException
- Specified by:
startDocument
in interfaceorg.xml.sax.ContentHandler
- Throws:
org.xml.sax.SAXException
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endDocument
public void endDocument() throws org.xml.sax.SAXException
- Specified by:
endDocument
in interfaceorg.xml.sax.ContentHandler
- Throws:
org.xml.sax.SAXException
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characters
public void characters(char[] ch, int start, int end) throws org.xml.sax.SAXException
- Specified by:
characters
in interfaceorg.xml.sax.ContentHandler
- Throws:
org.xml.sax.SAXException
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ignorableWhitespace
public void ignorableWhitespace(char[] ch, int start, int end) throws org.xml.sax.SAXException
- Specified by:
ignorableWhitespace
in interfaceorg.xml.sax.ContentHandler
- Throws:
org.xml.sax.SAXException
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startPrefixMapping
public void startPrefixMapping(java.lang.String prefix, java.lang.String uri) throws org.xml.sax.SAXException
- Specified by:
startPrefixMapping
in interfaceorg.xml.sax.ContentHandler
- Throws:
org.xml.sax.SAXException
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endPrefixMapping
public void endPrefixMapping(java.lang.String prefix) throws org.xml.sax.SAXException
- Specified by:
endPrefixMapping
in interfaceorg.xml.sax.ContentHandler
- Throws:
org.xml.sax.SAXException
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processingInstruction
public void processingInstruction(java.lang.String target, java.lang.String data) throws org.xml.sax.SAXException
- Specified by:
processingInstruction
in interfaceorg.xml.sax.ContentHandler
- Throws:
org.xml.sax.SAXException
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setDocumentLocator
public void setDocumentLocator(org.xml.sax.Locator locator)
- Specified by:
setDocumentLocator
in interfaceorg.xml.sax.ContentHandler
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skippedEntity
public void skippedEntity(java.lang.String name) throws org.xml.sax.SAXException
- Specified by:
skippedEntity
in interfaceorg.xml.sax.ContentHandler
- Throws:
org.xml.sax.SAXException
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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 interfaceorg.xml.sax.ContentHandler
- Throws:
org.xml.sax.SAXException
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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 interfaceorg.xml.sax.ContentHandler
- Throws:
org.xml.sax.SAXException
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