Package de.julielab.jules.ae.genemapping.resources

Class UniprotFreeTextHandler

  • All Implemented Interfaces:
    org.xml.sax.ContentHandler, org.xml.sax.DTDHandler, org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler
    public class UniprotFreeTextHandler
extends org.xml.sax.helpers.DefaultHandler

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected java.util.TreeMap<java.lang.String,​java.io.BufferedWriter> freetextFiles  
      protected java.util.HashMap<java.lang.String,​java.lang.String[]> uniprot2EntrezMap  

    • Constructor Summary

      Constructors 
      Constructor Description
      UniprotFreeTextHandler​(java.lang.String output)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void characters​(char[] ch, int start, int length)
      This method holds the text between two tags for modification purposes.
      void endDocument()  
      void endElement​(java.lang.String uri, java.lang.String localName, java.lang.String qName)
      endElement moves data acquired by characters() into storage structure, updates tag hierarchy information (level -1) & resets all switches in case an entry ended
      void startDocument()  
      void startElement​(java.lang.String uri, java.lang.String localName, java.lang.String qName, org.xml.sax.Attributes atts)
      This method sets all necessary switches (tag attributes) and updates tag hierarchy information.

      • Methods inherited from class org.xml.sax.helpers.DefaultHandler

        endPrefixMapping, error, fatalError, ignorableWhitespace, notationDecl, processingInstruction, resolveEntity, setDocumentLocator, skippedEntity, startPrefixMapping, unparsedEntityDecl, warning

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • uniprot2EntrezMap

        protected java.util.HashMap<java.lang.String,​java.lang.String[]> uniprot2EntrezMap

      • freetextFiles

        protected java.util.TreeMap<java.lang.String,​java.io.BufferedWriter> freetextFiles

    • Constructor Detail

      • UniprotFreeTextHandler

        public UniprotFreeTextHandler​(java.lang.String output)

    • Method Detail

      • startDocument

        public void startDocument()
        Specified by:
        startDocument in interface org.xml.sax.ContentHandler
        Overrides:
        startDocument in class org.xml.sax.helpers.DefaultHandler

      • startElement

        public void startElement​(java.lang.String uri,
                         java.lang.String localName,
                         java.lang.String qName,
                         org.xml.sax.Attributes atts)
        This method sets all necessary switches (tag attributes) and updates tag hierarchy information.
        Specified by:
        startElement in interface org.xml.sax.ContentHandler
        Overrides:
        startElement in class org.xml.sax.helpers.DefaultHandler

      • endDocument

        public void endDocument()
        Specified by:
        endDocument in interface org.xml.sax.ContentHandler
        Overrides:
        endDocument in class org.xml.sax.helpers.DefaultHandler

      • endElement

        public void endElement​(java.lang.String uri,
                       java.lang.String localName,
                       java.lang.String qName)
        endElement moves data acquired by characters() into storage structure, updates tag hierarchy information (level -1) & resets all switches in case an entry ended
        Specified by:
        endElement in interface org.xml.sax.ContentHandler
        Overrides:
        endElement in class org.xml.sax.helpers.DefaultHandler

      • characters

        public void characters​(char[] ch,
                       int start,
                       int length)
                throws org.xml.sax.SAXException
        This method holds the text between two tags for modification purposes. (and acquires entry name).
        Specified by:
        characters in interface org.xml.sax.ContentHandler
        Overrides:
        characters in class org.xml.sax.helpers.DefaultHandler
        Throws:
        org.xml.sax.SAXException