Package org.snpeff.nextProt
Class NextProtHandler
- java.lang.Object
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- org.xml.sax.helpers.DefaultHandler
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- org.snpeff.nextProt.NextProtHandler
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- All Implemented Interfaces:
org.xml.sax.ContentHandler
,org.xml.sax.DTDHandler
,org.xml.sax.EntityResolver
,org.xml.sax.ErrorHandler
public class NextProtHandler extends org.xml.sax.helpers.DefaultHandler
Handler used in XML parsing for NextProt database It keeps track of the tags and saves state data to create Markers using NextProtMarkerFactory http://www.nextprot.org/- Author:
- pablocingolani
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Constructor Summary
Constructors Constructor Description NextProtHandler(NextProtMarkerFactory markersFactory)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
characters(char[] ch, int start, int length)
void
countMissingCategory(java.lang.String category)
void
endElement(java.lang.String uri, java.lang.String localName, java.lang.String qName)
Parse XML's element endCountByType
getMissingCategories()
void
startElement(java.lang.String uri, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attributes)
Parse XML's element start
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Constructor Detail
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NextProtHandler
public NextProtHandler(NextProtMarkerFactory markersFactory)
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Method Detail
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characters
public void characters(char[] ch, int start, int length) throws org.xml.sax.SAXException
- Specified by:
characters
in interfaceorg.xml.sax.ContentHandler
- Overrides:
characters
in classorg.xml.sax.helpers.DefaultHandler
- Throws:
org.xml.sax.SAXException
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countMissingCategory
public void countMissingCategory(java.lang.String category)
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endElement
public void endElement(java.lang.String uri, java.lang.String localName, java.lang.String qName) throws org.xml.sax.SAXException
Parse XML's element end- Specified by:
endElement
in interfaceorg.xml.sax.ContentHandler
- Overrides:
endElement
in classorg.xml.sax.helpers.DefaultHandler
- Throws:
org.xml.sax.SAXException
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getMissingCategories
public CountByType getMissingCategories()
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startElement
public void startElement(java.lang.String uri, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes attributes) throws org.xml.sax.SAXException
Parse XML's element start- Specified by:
startElement
in interfaceorg.xml.sax.ContentHandler
- Overrides:
startElement
in classorg.xml.sax.helpers.DefaultHandler
- Throws:
org.xml.sax.SAXException
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