Package org.biojava.nbio.genome.parsers.genename

Class GeneNamesParser

  • public class GeneNamesParser
extends java.lang.Object
    Parses a file from the www.genenames.org website that contains a mapping of human gene names to other databases
    Author:
    Andreas Prlic

    • Constructor Summary

      Constructors 
      Constructor Description
      GeneNamesParser()  

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.util.List<GeneName> getGeneNames()  
      static java.util.List<GeneName> getGeneNames​(java.io.InputStream inStream)
      Get a list of GeneNames from an input stream.
      static void main​(java.lang.String[] args)
      parses a file from the genenames website

      • Methods inherited from class java.lang.Object

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

    • Field Detail

      • DEFAULT_GENENAMES_URL

        public static final java.lang.String DEFAULT_GENENAMES_URL
        See Also:
        Constant Field Values

    • Constructor Detail

      • GeneNamesParser

        public GeneNamesParser()

    • Method Detail

      • main

        public static void main​(java.lang.String[] args)
        parses a file from the genenames website
        Parameters:
        args -

      • getGeneNames

        public static java.util.List<GeneName> getGeneNames()
                                             throws java.io.IOException
        Throws:
        java.io.IOException

      • getGeneNames

        public static java.util.List<GeneName> getGeneNames​(java.io.InputStream inStream)
                                             throws java.io.IOException
        Get a list of GeneNames from an input stream.
        Parameters:
        inStream -
        Returns:
        list of geneNames
        Throws:
        java.io.IOException