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Add a small patch for performances

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This commit is contained in:
Eric Coissac
2010-09-23 09:40:03 +00:00
parent 9507f488c5
commit 6d01d73ac9
1 changed files with 3 additions and 1 deletions
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4
src/ecoTag.py
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@@ -107,14 +107,16 @@ def lcsIterator(entries,db,options):
for seq in entries: for seq in entries:
results = [] results = []
maxid = (None,0.0) maxid = (None,0.0)
minid = options.minimum
for d in db: for d in db:
lcs = lenlcs(seq,d,options.minimum,normalized=True, large=options.large) lcs = lenlcs(seq,d,minid,normalized=True, large=options.large)
if lcs > maxid[1]: if lcs > maxid[1]:
# try: # try:
# print "@@@@@@@@@@@>>>>>>",(maxid[0].id,maxid[1]),(d.id,lcs) # print "@@@@@@@@@@@>>>>>>",(maxid[0].id,maxid[1]),(d.id,lcs)
# except: # except:
# print "@@@@@@@@@@@>>>>>>",(None,maxid[1]),(d.id,lcs) # print "@@@@@@@@@@@>>>>>>",(None,maxid[1]),(d.id,lcs)
maxid = (d,lcs) maxid = (d,lcs)
minid = maxid[1] ** options.shape
results.append((d,lcs)) results.append((d,lcs))
minid = maxid[1] ** options.shape minid = maxid[1] ** options.shape
results = [x for x in results if x[1]>=minid] results = [x for x in results if x[1]>=minid]