# Thread: I am Doing Something Wrong But Don't Know What?

1. Member
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Mar 2008
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## 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];
try{
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. 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. Member
Join Date
Mar 2008
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When I go jav numbers it doesn't run!

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

regards,
sukatoa

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