Android Open Source - DIYgenomics_Android Variant

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License

The source code is released under:

/** * Copyright (C) 2010 DIYgenomics diygenomics.org * Copyright (C) 2010 Melanie Swan mxswan@gmail * Copyright (C) 2010 Michael Kolb * Copyright (C) 2010 Lawrence S. Wong * All rights reserved. * * M...

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Java Source Code

package org.diygenomics.pg;
/*  w  ww.ja v  a  2  s.  com*/
import java.io.Serializable;

import org.diygenomics.pg.utils.MLog;


/**
 * holds a variant (formerly known as snip)
 */
public class Variant implements Serializable {

  static final String TAG = "Variant";

  public String RSID;
  public String gene;
  public String genotype;
  public int rank;

  private Locus parsedLocus;
  

  public Variant() {
  }

  public Variant(String id, String l, String g, String gtype, int rank) {
    RSID = id;
    gene = g;
    parsedLocus = new Locus(l);
    genotype = gtype;
    this.rank = rank;
  }

  public static boolean isValidLocus(String locus) {
    return (locus.length() >= 1)
      && (locus.startsWith("X")
        || locus.startsWith("Y")
        || locus.startsWith("chr")
        || Character.isDigit(locus.charAt(0)));
  }

  public String getLocus() {
    if (parsedLocus != null) {
      return parsedLocus.name;
    } else {
      return "";
    }
  }

  public int compareTo(Variant variant2) {

    // int order = this.locus.compareTo(variant2.locus);
    int order = parsedLocus.compareTo(variant2.parsedLocus);
    if (order == 0)
      order = this.gene.compareTo(variant2.gene);
    if (order == 0)
      order = this.RSID.compareTo(variant2.RSID);
    return order;
  }

  class Locus implements Serializable {

    public String name;
    
    public int part1;
    public String part2;
    public String part3;

    public Locus() {
    }

    public Locus(String lstring) {
      name = lstring;
      if (lstring != null) {
        if (lstring.startsWith("chr")) {
          //&& (lstring.length() >= 4)) {
          // extract chromosome number
          // special case for chrX:
          if (lstring.startsWith("chrX")) {
            part1 = 23;
            name = "X";
          } else {
            int ix = lstring.indexOf(":");
            if (ix != -1) {
              part1 = Integer.parseInt(lstring.substring(3,ix));
            } else {
              part1 = Integer.parseInt(lstring.substring(3));
            }
            name = ""+part1;
          }
        } else if (lstring.startsWith("X") || lstring.startsWith("Y")) {
          if (lstring.startsWith("X")) {
            part1 = 23;
          } else {
            part1 = 24;
          }
          lstring = lstring.substring(1);
          int firstLetter = 1;
          int firstDigit = findDigit(lstring, firstLetter + 1);
          if (firstDigit != -1) {
            part2 = lstring.substring(firstLetter, firstDigit);
            part3 = lstring.substring(firstDigit);
          } else {
            if (lstring.length() > 0) {
              part2 = lstring.substring(firstLetter);
            }
          }
        } else {
          int firstLetter = Variant.findLetter(lstring, 0);
          if (firstLetter == -1) {
            part1 = Integer.parseInt(lstring);
          } else {
            part1 = Integer.parseInt(lstring.substring(0,
                firstLetter));
            int firstDigit = findDigit(lstring, firstLetter + 1);
            if (firstDigit != -1) {
              part2 = lstring.substring(firstLetter, firstDigit);
              part3 = lstring.substring(firstDigit);
            } else {
              part2 = lstring.substring(firstLetter);
            }

          }

        }
      }
      MLog.i(TAG, this.toString());
    }

    public int compareTo(Locus other) {
      int res = (part1 > other.part1) ? 1 : ((part1 < other.part1) ? -1
          : 0);
      if (res == 0) {
        if (part2 == null) {
          if (other.part2 == null)
            return 0;
          return -1;
        } else {
          if (other.part2 == null) {
            return 1;
          } else {
            return part2.compareTo(other.part2);
          }
        }
      }
      return res;
    }

    public String toString() {
      return part1 + "/" + part2 + "/" + part3;
    }

  }

  static int findLetter(String s, int start) {
    if (s == null)
      return -1;
    int i = start;
    while (i < s.length()) {
      char c = s.charAt(i);
      if (!Character.isDigit(c)) {
        return i;

      }
      i++;
    }
    return -1;

  }

  static int findDigit(String s, int start) {
    if (s == null)
      return -1;
    int i = start;
    while (i < s.length()) {
      char c = s.charAt(i);
      if (Character.isDigit(c)) {
        return i;

      }
      i++;
    }
    return -1;

  }

}

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