[Biojava-l] issue in class Distribution

[Alberto Ambesi]

I apologize, the line:
Distribution[] dists = distOverAlignment2(align, false, 0.01);

should actually be:
Distribution[] dists = DistributionTools.distOverAlignment(align, 
false, 0.01);

Thank you.

Alberto Ambesi


On 3 Dec 2003, at 09:55, David Huen wrote:

> On Tuesday 02 Dec 2003 4:49 pm, Alberto Ambesi wrote:
>> hi, I found this bug when using Distrubutions iteratively many times.
>> The problem is that when creating Distrubution objects iteratively
>> computation time for each iteration increases with time.
>>
>> this is a piece of code that demonstrates the issue:
>>
>> public class DistributionTest {
>>      public static void main(String[] args) throws Exception{
>>          long timePoint = System.currentTimeMillis();
>>          for (int i=0; i<2500; i++) {
>>              Map map = new HashMap();
>>              map.put("seq0", DNATools.createDNA("aggag"));
>>              map.put("seq1", DNATools.createDNA("aggaa"));
>>              map.put("seq2", DNATools.createDNA("aggag"));
>>              map.put("seq3", DNATools.createDNA("aagag"));
>>              Alignment align = new SimpleAlignment(map);
>>              Distribution[] dists = distOverAlignment2(align, false,
>> 0.01);
>>              long previousPoint = timePoint;
>>              timePoint = System.currentTimeMillis();
>>              System.out.println(timePoint - previousPoint);
>>          }
>>      }
>> }
>>
>
> Could you provide the source to distOverAlignment2 so it becomes clear 
> what
> it is doing?
>
> Thanks,
> David Huen
>