obitools/ecoprimers
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Patch taxon example/counterexample selection

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@237 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Eric Coissac
2009-11-09 14:50:35 +00:00
parent 9e6b924c92
commit 89576b96fa
3 changed files with 14 additions and 5 deletions
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2
src/ecoprimer.c
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@ -458,7 +458,7 @@ void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxo
for (i=0;i<seqdbsize;i++) for (i=0;i<seqdbsize;i++)
{ {
seqdb[i]->isexample=isGoodTaxon(taxonomy,seqdb[i]->taxid,options); seqdb[i]->isexample=isExampleTaxon(taxonomy,seqdb[i]->taxid,options);
if (seqdb[i]->isexample) if (seqdb[i]->isexample)
(*insamples)++; (*insamples)++;
else else

15
src/libecoprimer/goodtaxon.c
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@ -12,7 +12,7 @@ int isGoodTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options)
{ {
int result; int result;
result=( (options->r == 0) || (eco_is_taxid_included(taxonomy, result=((options->r == 0) || (eco_is_taxid_included(taxonomy,
options->restricted_taxid, options->restricted_taxid,
options->r, options->r,
taxonomy->taxons->taxon[taxon].taxid) taxonomy->taxons->taxon[taxon].taxid)
@ -34,6 +34,11 @@ int isExampleTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options)
options->restricted_taxid, options->restricted_taxid,
options->r, options->r,
taxonomy->taxons->taxon[taxon].taxid) taxonomy->taxons->taxon[taxon].taxid)
)) &&
((options->e == 0) || !(eco_is_taxid_included(taxonomy,
options->exception_taxid,
options->e,
taxonomy->taxons->taxon[taxon].taxid)
)); ));
return result; return result;
@ -47,8 +52,12 @@ int isCounterExampleTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t optio
result=((options->g != 0) && (eco_is_taxid_included(taxonomy, result=((options->g != 0) && (eco_is_taxid_included(taxonomy,
options->ignored_taxid, options->ignored_taxid,
options->g, options->g,
taxonomy->taxons->taxon[taxon].taxid) taxonomy->taxons->taxon[taxon].taxid))
)); ) || ((options->e != 0) && (eco_is_taxid_included(taxonomy,
options->exception_taxid,
options->e,
taxonomy->taxons->taxon[taxon].taxid))
);
return result; return result;

2
src/libecoprimer/taxstats.c
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@ -64,7 +64,7 @@ int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *tax
for (i=0;i<seqdbsize;i++) for (i=0;i<seqdbsize;i++)
{ {
taxon = &(taxonomy->taxons->taxon[seqdb[i]->taxid]); taxon = &(taxonomy->taxons->taxon[seqdb[i]->taxid]);
seqdb[i]->isexample=isGoodTaxon(taxonomy,seqdb[i]->taxid,options); seqdb[i]->isexample=isExampleTaxon(taxonomy,seqdb[i]->taxid,options);
tmptaxon = eco_findtaxonatrank(taxon, tmptaxon = eco_findtaxonatrank(taxon,
options->taxonrankidx); options->taxonrankidx);