Class GwasCatalog

  • All Implemented Interfaces:
    java.lang.Iterable<GwasCatalogEntry>

    public class GwasCatalog
    extends java.lang.Object
    implements java.lang.Iterable<GwasCatalogEntry>
    GWAS catalog table. It is small enough to fit in memory Refernces: http://www.genome.gov/gwastudies/
    Author:
    pablocingolani
    • Constructor Summary

      Constructors 
      Constructor Description
      GwasCatalog​(java.lang.String fileName)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.util.List<GwasCatalogEntry> get​(java.lang.String key)  
      java.util.List<GwasCatalogEntry> get​(java.lang.String chrName, int pos)
      Get all entries at a given chromosome & position Note: Position is zero based.
      java.util.List<GwasCatalogEntry> getByRs​(java.lang.String rs)
      Get an entry based on 'RS' number
      java.util.Iterator<GwasCatalogEntry> iterator()  
      java.lang.String key​(java.lang.String chrName, int pos)
      Create a 'key' string
      java.lang.String key​(GwasCatalogEntry ge)
      Create a 'key' string
      protected void load​(java.lang.String fileName)
      Load data from file
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
      • Methods inherited from interface java.lang.Iterable

        forEach, spliterator
    • Constructor Detail

      • GwasCatalog

        public GwasCatalog​(java.lang.String fileName)
    • Method Detail

      • get

        public java.util.List<GwasCatalogEntry> get​(java.lang.String chrName,
                                                    int pos)
        Get all entries at a given chromosome & position Note: Position is zero based.
      • getByRs

        public java.util.List<GwasCatalogEntry> getByRs​(java.lang.String rs)
        Get an entry based on 'RS' number
      • key

        public java.lang.String key​(GwasCatalogEntry ge)
        Create a 'key' string
      • key

        public java.lang.String key​(java.lang.String chrName,
                                    int pos)
        Create a 'key' string
      • load

        protected void load​(java.lang.String fileName)
        Load data from file