Class PlinkMap


  • public class PlinkMap
    extends java.lang.Object
    PLINK MAP file References: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
    Author:
    pcingola
    • Field Summary

      Fields 
      Modifier and Type Field Description
      static boolean debug  
    • Constructor Summary

      Constructors 
      Constructor Description
      PlinkMap()  
      PlinkMap​(java.lang.String mapFileName)  
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      java.lang.String getChrName​(int idx)  
      java.util.Collection<java.lang.String> getGenotypeNames()  
      java.lang.Integer getGenotypeNames​(java.lang.String idStr)  
      java.lang.String getId​(int idx)  
      int getPosition​(int idx)  
      protected void read​(java.lang.String mapFileName)
      Reads MAP file MAP file format (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) Space separated or tab columns: chromosome (1-22, X, Y or 0 if unplaced) rs# or snp identifier Genetic distance (morgans) Base-pair position (bp units)
      int size()  
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • debug

        public static boolean debug
    • Constructor Detail

      • PlinkMap

        public PlinkMap()
      • PlinkMap

        public PlinkMap​(java.lang.String mapFileName)
    • Method Detail

      • getChrName

        public java.lang.String getChrName​(int idx)
      • getGenotypeNames

        public java.util.Collection<java.lang.String> getGenotypeNames()
      • getGenotypeNames

        public java.lang.Integer getGenotypeNames​(java.lang.String idStr)
      • getId

        public java.lang.String getId​(int idx)
      • getPosition

        public int getPosition​(int idx)
      • read

        protected void read​(java.lang.String mapFileName)
        Reads MAP file MAP file format (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) Space separated or tab columns: chromosome (1-22, X, Y or 0 if unplaced) rs# or snp identifier Genetic distance (morgans) Base-pair position (bp units)
        Parameters:
        dataFileName -
      • size

        public int size()