Hi -
Below is the method that is being called (copied from DistributionTools). I cannot see
anything obvious such as a memory leak but there could be one, can anybody else spot
anything?
Maybe if someone has a fancy profilling utility they could try it and let us know
where the slow down is occuring.
- Mark
public static final Distribution[] distOverAlignment(Alignment a,
boolean countGaps,
double nullWeight)
throws IllegalAlphabetException {
List seqs = a.getLabels();
FiniteAlphabet alpha =
(FiniteAlphabet)((SymbolList)a.symbolListForLabel(seqs.get(0))).getAlphabet();
for(int i = 1; i < seqs.size();i++){
FiniteAlphabet test =
(FiniteAlphabet)((SymbolList)a.symbolListForLabel(seqs.get(i))).getAlphabet();
if(test != alpha){
throw new IllegalAlphabetException("Cannot Calculate distOverAlignment() for
alignments with"+
"mixed alphabets");
}
}
Distribution[] pos = new Distribution[a.length()];
DistributionTrainerContext dtc = new SimpleDistributionTrainerContext();
dtc.setNullModelWeight(nullWeight);
try{
for(int i = 0; i < a.length(); i++){// For each position
pos[i] = DistributionFactory.DEFAULT.createDistribution(alpha);
dtc.registerDistribution(pos[i]);
for(Iterator j = seqs.iterator(); j.hasNext();){// of each sequence
Object seqLabel = j.next();
Symbol s = a.symbolAt(seqLabel,i + 1);
/*If this is working over a flexible alignment there is a possibility
that s could be null if this Sequence is not really preset in this
region of the Alignment. In this case it will be skipped*/
if(s == null)
continue;
Symbol gap = alpha.getGapSymbol();
if(countGaps == false &&
s.equals(gap)){
//do nothing, not counting gaps
}else{
dtc.addCount(pos[i],s,1.0);// count the symbol
}
}
}
dtc.train();
}catch(Exception e){
e.printStackTrace(System.err);
}
return pos;
}
> -----Original Message-----
> From: Alberto Ambesi [mailto:[EMAIL PROTECTED]
> Sent: Wednesday, 3 December 2003 11:01 p.m.
> To: [EMAIL PROTECTED]
> Subject: Re: [Biojava-l] issue in class Distribution
>
>
> 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
> >
>
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>
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