Commit 73236c72 by Celine Mercier

version 0.5: ecoPrimers can now read *.ldx files (local taxa)

parent eb8d4452
0.4
\ No newline at end of file
0.5
\ No newline at end of file
......@@ -20,7 +20,7 @@
#include"libthermo/thermostats.h"
#define VERSION "0.4"
#define VERSION "0.5"
/* TR: by default, statistics are made on species level*/
#define DEFAULTTAXONRANK "species"
......
......@@ -219,7 +219,7 @@ econameidx_t *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy);
* @return pointer to a taxonomy index structure
*/
ecotxidx_t *read_taxonomyidx(const char *filename);
ecotxidx_t *read_taxonomyidx(const char *filename,const char *filename2);
ecotaxonomy_t *read_taxonomy(const char *prefix,int32_t readAlternativeName);
......
......@@ -10,23 +10,41 @@ static ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon);
* @param pointer to the database (.tdx file)
* @return a ecotxidx_t structure
*/
ecotxidx_t *read_taxonomyidx(const char *filename)
ecotxidx_t *read_taxonomyidx(const char *filename,const char *filename2)
{
int32_t count;
int32_t count2;
FILE *f;
FILE *f2;
ecotxidx_t *index;
int32_t i;
f = open_ecorecorddb(filename,&count,1);
f = open_ecorecorddb(filename,&count,1);
f2 = open_ecorecorddb(filename2,&count2,0);
index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count-1),
index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count+count2-1),
"Allocate taxonomy");
index->count=count;
index->count=count+count2;
fprintf(stderr,"Reading %d taxa...\n",count);
for (i=0; i < count; i++){
readnext_ecotaxon(f,&(index->taxon[i]));
index->taxon[i].parent=index->taxon + (size_t)index->taxon[i].parent;
index->taxon[i].parent=index->taxon + (int32_t)index->taxon[i].parent;
}
if (count2>0)
fprintf(stderr,"Reading %d local taxa...\n",count2);
else
fprintf(stderr,"No local taxon\n");
for (i=0; i < count2; i++){
readnext_ecotaxon(f2,&(index->taxon[count+i]));
index->taxon[count+i].parent=index->taxon + (int32_t)index->taxon[count+i].parent;
}
return index;
}
......@@ -111,33 +129,36 @@ ecotaxonomy_t *read_taxonomy(const char *prefix,int32_t readAlternativeName)
{
ecotaxonomy_t *tax;
char *filename;
char *filename2;
int buffsize;
tax = ECOMALLOC(sizeof(ecotaxonomy_t),
"Allocate taxonomy structure");
"Allocate taxonomy structure");
buffsize = strlen(prefix)+10;
filename = ECOMALLOC(buffsize,
"Allocate filename");
"Allocate filename");
filename2= ECOMALLOC(buffsize,
"Allocate filename");
snprintf(filename,buffsize,"%s.rdx",prefix);
tax->ranks = read_rankidx(filename);
snprintf(filename,buffsize,"%s.tdx",prefix);
snprintf(filename2,buffsize,"%s.ldx",prefix);
tax->taxons = read_taxonomyidx(filename);
tax->taxons = read_taxonomyidx(filename,filename2);
if (readAlternativeName)
{
snprintf(filename,buffsize,"%s.ndx",prefix);
snprintf(filename,buffsize,"%s.ndx",prefix);
tax->names=read_nameidx(filename,tax);
}
else
tax->names=NULL;
return tax;
}
......
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