Results 1 to 4 of 4
  1. #1
    BHCluster is offline Member
    Join Date
    Mar 2008
    Posts
    32
    Rep Power
    0

    Smile I am Doing Something Wrong But Don't Know What?

    What I am trying to do is to implement the Hierarchical Clustering algorithm with UPGMA (Average distance between clusters) and various distance metrics (Pearson, Manhattan).
    The results required: plot of data in experiment space showing the clustering according to the various distance metrics and a text file with gene clustering using the notation: (A, ((B,C),D)) meaning B & C are closest and then D etc...
    The code that I have compiles but I can't run it if you know what I am doing wrong please help. The code is below:

    Java Code:
    import java.io.*;
    
    class Numbers
    	{
    public static void Manhattan(double[][] a,double[][] b,int n,int n2)
      {
        int q=n2;
        int c=n;
        for(int m=0;m<q;m++)
        {
          for(int h=0;h<q;h++)
          {
            double d=0;
            double d2=0;
            for(int j=0;j<c;j++)
            {
              d2=a[m][j]-a[h][j];
              if(d2<0)
              d2=d2*-1;
              d=d+d2;
              }
            b[m][h]=d;
    
          }
        }
    
      }
    
    
    public static void main(String[] args)
    	{
    double x1=0;
    double x2;
    double x3;
    double y;
    double y1=0;
    double y2=0;
    double y3=0;
    double z=0;
    double z1=0;
    double z2=0;
    double z3=0;
    double total=0;
    /*x=x1;
    y=x2;*/
    
    z=3-2;
    z1=0;
    if(z1<0)
    {
    	z1=z1*-1;
    }
    
    else
    {
    total=z1+z2+z3;
    }
    String[] s2=new String [9];
    BufferedReader inFile;
    try{
     inFile=new BufferedReader(new FileReader("Data_Set_1.txt"));
    String s=inFile.readLine();
    for (int i=1;i<61;i++)
    {
    
    s2=s.split(" ");
    }
    }
    catch(Exception e){}
    		System.out.println();
    	}
    	}
    Below is the Data_Set_1.txt
    Java Code:
    Gene Number	Gene Name	Experiment 1	Experiment 2	Experiment 3
    1	Y1	-9.30	5.65	-5.02
    2	Y2	-4.10	5.68	0.56
    3	Y3	4.75	0.11	2.86
    4	Y4	-1.54	-10.01	-1.99
    5	Y5	-6.29	5.62	-2.78
    6	Y6	-13.02	1.31	1.61
    7	Y7	-5.85	3.79	-6.56
    8	Y8	-12.71	-0.45	0.62
    9	Y9	-3.05	-12.65	-5.07
    10	Y10	2.18	-5.82	-9.73
    11	Y11	1.74	-0.99	-3.66
    12	Y12	-7.88	0.93	-8.33
    13	Y13	-6.34	-1.85	-4.00
    14	Y14	-0.71	-2.64	-5.64
    15	Y15	2.77	-4.16	-3.83
    16	Y16	-0.25	0.58	0.77
    17	Y17	2.52	-5.80	-8.80
    18	Y18	5.53	-9.11	-1.92
    19	Y19	6.63	2.53	7.94
    20	Y20	-7.11	8.09	-6.47
    21	Y21	-0.30	-6.18	-6.25
    22	Y22	-0.33	4.58	-8.32
    23	Y23	-2.39	1.44	3.94
    24	Y24	7.70	9.39	4.73
    25	Y25	4.89	-6.17	6.98
    26	Y26	6.05	-6.54	-1.94
    27	Y27	6.78	7.83	-7.72
    28	Y28	4.86	2.31	2.33
    29	Y29	6.93	3.95	10.61
    30	Y30	0.04	-7.31	-1.49
    31	Y31	-4.78	3.41	10.69
    32	Y32	5.55	-6.48	-0.56
    33	Y33	-3.18	-4.32	-3.32
    34	Y34	3.67	-9.79	-13.03
    35	Y35	-11.01	-3.69	-5.13
    36	Y36	-2.24	-2.19	-12.74
    37	Y37	8.84	2.10	1.28
    38	Y38	0.69	7.11	-5.35
    39	Y39	-9.19	-6.10	-11.01
    40	Y40	2.37	6.58	2.67
    41	Y41	6.40	6.03	3.58
    42	Y42	-0.54	-1.32	-0.69
    43	Y43	-0.45	0.01	-0.25
    44	Y44	0.52	0.96	0.28
    45	Y45	0.86	1.07	0.96
    46	Y46	-0.47	-1.36	-0.81
    47	Y47	-0.64	-1.47	-0.32
    48	Y48	0.34	-0.47	0.46
    49	Y49	-0.27	-0.62	-0.43
    50	Y50	-0.49	-0.22	-0.01
    51	Y51	-9.80	2.34	-5.95
    52	Y52	6.74	-8.43	4.21
    53	Y53	-7.60	-6.57	-5.13
    54	Y54	-6.53	-2.55	-13.86
    55	Y55	-3.82	7.12	-11.45
    56	Y56	5.49	-7.60	0.40
    57	Y57	6.95	-2.61	-5.14
    58	Y58	0.21	-6.98	0.84
    59	Y59	1.65	3.77	3.33
    60	Y60	6.16	3.25	-14.31
    I would appreciate greatly any help I get.
    Last edited by BHCluster; 04-14-2008 at 06:03 PM. Reason: Forgot the Text File

  2. #2
    Java Tip's Avatar
    Java Tip is offline Moderator
    Join Date
    Nov 2007
    Posts
    1,694
    Blog Entries
    430
    Rep Power
    9

    Default

    The code that I have compiles but I can't run it if you know what I am doing wrong please help.
    What is the result? What do you mean with "i cant run it"?

  3. #3
    BHCluster is offline Member
    Join Date
    Mar 2008
    Posts
    32
    Rep Power
    0

    Default

    When I go jav numbers it doesn't run!

  4. #4
    sukatoa's Avatar
    sukatoa is offline Senior Member
    Join Date
    Jan 2008
    Location
    Cebu City, Philippines
    Posts
    556
    Rep Power
    7

    Default

    take a look at your class that holds the main method, is it a public?

    regards,
    sukatoa

Similar Threads

  1. what is wrong with this code
    By masaka in forum New To Java
    Replies: 5
    Last Post: 04-16-2008, 08:27 AM
  2. What's wrong with this code?
    By Wizard wusa in forum New To Java
    Replies: 14
    Last Post: 01-22-2008, 11:55 PM
  3. Is there somethign wrong with this code?
    By Soda in forum New To Java
    Replies: 1
    Last Post: 12-08-2007, 04:46 PM
  4. Whats wrong with my code???
    By Soda in forum New To Java
    Replies: 2
    Last Post: 12-06-2007, 12:54 PM
  5. Replies: 15
    Last Post: 11-30-2007, 05:19 PM

Posting Permissions

  • You may not post new threads
  • You may not post replies
  • You may not post attachments
  • You may not edit your posts
  •