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);
}
}
}
if I plot the output, I see that computation time of each cycle increases with time. This makes this class unusable for my purpose. Thank you for addressing this issue.
Alberto Ambesi
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