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Removed some problems for specificity

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/branches/eric-test@196 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2009-03-26 00:22:01 +00:00
parent 75a6dac09a
commit 3c21789533
3 changed files with 27 additions and 26 deletions
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7
src/ecoprimer.c
View File

@ -121,13 +121,13 @@ void printapair(int32_t index,ppair_t pair, poptions_t options)
wellidentifiedtaxa = (pair->intaxa + pair->outtaxa) - pair->notwellidentifiedtaxa;
printf("\t%d", pair->notwellidentifiedtaxa);
//printf("\t%d", pair->notwellidentifiedtaxa);
printf("\t%d", (pair->intaxa + pair->outtaxa));
//printf("\t%d", (pair->intaxa + pair->outtaxa));
//printf("\t%4.3f", (float)wellidentifiedtaxa/(options->intaxa + options->outtaxa));
printf("\t%4.3f", (float)wellidentifiedtaxa/(options->intaxa + options->outtaxa));
printf("\t%d", pair->mind);
@ -164,6 +164,7 @@ uint32_t filterandsortpairs(ppair_t* sortedpairs,uint32_t count, poptions_t opti
qfp < options->false_positive_quorum)
{
(void)taxonomycoverage(sortedpairs[j],options);
taxonomyspecificity(sortedpairs[j]);
j++;
}
}

2
src/libecoprimer/ecoprimer.h
View File

@ -218,8 +218,8 @@ typedef struct {
const char *amplifia;
bool_t strand;
int32_t length;
void *taxontree;
int32_t taxoncount;
void *taxontree;
}amptotaxon_t, *pamptotaxon_t;
typedef struct {

44
src/libecoprimer/taxstats.c
View File

@ -25,18 +25,6 @@ static int cmptaxon(const void *t1, const void* t2)
return 0;
}
static int cmptaxamp (const void *t1, const void* t2)
{
const ptaxontoamp_t taxid1=(ptaxontoamp_t)t1;
const ptaxontoamp_t taxid2=(ptaxontoamp_t)t2;
if (taxid1->taxid < taxid2->taxid)
return -1;
if (taxid1->taxid > taxid2->taxid)
return +1;
return 0;
}
int32_t counttaxon(int32_t taxid)
{
static void* taxontree=NULL;
@ -144,6 +132,7 @@ static int cmpamp(const void *ampf1, const void* ampf2)
char cd1;
char cd2;
int chd = 0;
int len = 0;
pamptotaxon_t pampf1 = (pamptotaxon_t) ampf1;
pamptotaxon_t pampf2 = (pamptotaxon_t) ampf2;
@ -161,7 +150,9 @@ static int cmpamp(const void *ampf1, const void* ampf2)
}
}
for (i = 0; i < pampf1->length; i++, j += incr)
len = (pampf1->length <= pampf2->length)? pampf1->length: pampf2->length;
for (i = 0; i < len; i++, j += incr)
{
cd1 = pampf1->amplifia[i];
if (incr == -1)
@ -172,6 +163,10 @@ static int cmpamp(const void *ampf1, const void* ampf2)
if (cd1 < cd2) return chd ? 1: -1;
if (cd2 < cd1) return chd ? -1: 1;
}
if (pampf1->length > pampf2->length) return chd ? -1: 1;
if (pampf2->length > pampf1->length) return chd ? 1: -1;
return 0;
}
@ -186,11 +181,11 @@ void twalkaction (const void *node, VISIT order, int level)
void taxonomyspecificity (ppair_t pair)
{
uint32_t i;
int32_t j;
int32_t ampfindex = 0;
uint32_t ampfindex = 0;
int32_t taxid;
void *ampftree = NULL;
pamptotaxon_t pcurrentampf;
pamptotaxon_t *ptmp;
pamptotaxon_t ampfwithtaxtree = ECOMALLOC(sizeof(amptotaxon_t) * pair->pcr.ampcount,"Cannot allocate amplifia tree");
@ -203,23 +198,28 @@ void taxonomyspecificity (ppair_t pair)
ampfwithtaxtree[ampfindex].length = pair->pcr.amplifias[i].length;
pcurrentampf = &ampfwithtaxtree[ampfindex];
taxid = pair->pcr.amplifias[i].sequence->ranktaxonid;
if ((pcurrentampf = tfind((void*)pcurrentampf, &ampftree, cmpamp)) == NULL)
ptmp = tfind((const void*)pcurrentampf, &ampftree, cmpamp);
if (ptmp == NULL)
{
pcurrentampf = &ampfwithtaxtree[ampfindex];
tsearch((void*)pcurrentampf,&ampftree,cmpamp);
ampfindex++;
}
if (tfind((void*)((size_t)taxid), &pcurrentampf->taxontree, cmptaxon) == NULL)
else
pcurrentampf = *ptmp;
if (tfind((void*)((size_t)taxid), &(pcurrentampf->taxontree), cmptaxon) == NULL)
{
pcurrentampf->taxoncount++;
tsearch((void*)((size_t)taxid),&pcurrentampf->taxontree,cmptaxon);
tsearch((void*)((size_t)taxid),&(pcurrentampf->taxontree),cmptaxon);
}
}
counttaxon(-1);
for (j = 0; j < ampfindex; j++)
for (i = 0; i < ampfindex; i++)
{
if (ampfwithtaxtree[j].taxoncount > 1)
twalk(ampfwithtaxtree[j].taxontree, twalkaction);
if (ampfwithtaxtree[i].taxoncount > 1)
twalk(ampfwithtaxtree[i].taxontree, twalkaction);
}
pair->notwellidentifiedtaxa = counttaxon(-2);