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MOD: Added a [P]ath option displaying for each taxon its full path

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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@423 60f365c0-8329-0410-b2a4-ec073aeeaa1d
This commit is contained in:
Frédéric Boyer
2012-05-16 11:43:33 +00:00
parent 745d50cfa4
commit 2452df90de
1 changed files with 45 additions and 20 deletions
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65
src/ecofind.c
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@ -9,7 +9,20 @@
/**
* display the result
**/
static void printresult(ecotx_t *taxon,econame_t* name,ecotaxonomy_t *taxonomy)
void displayPath(ecotx_t *taxon, ecotaxonomy_t *taxonomy){
if (taxon != taxon->parent){
displayPath(taxon->parent,taxonomy);
printf(";");
}
if (rank_index("no rank",taxonomy->ranks) != taxon->rank)
printf("%s:", taxonomy->ranks->label[taxon->rank]);
printf("%s", taxon->name);
}
static void printresult(ecotx_t *taxon,econame_t* name,ecotaxonomy_t *taxonomy, int32_t pathDisplay)
{
char* rankname;
char* classname;
@ -24,32 +37,38 @@ static void printresult(ecotx_t *taxon,econame_t* name,ecotaxonomy_t *taxonomy)
rankname= taxonomy->ranks->label[taxon->rank];
printf("%10d \t| %15s \t|\t %-50s \t|\t %15s \t|\t %s\n",
printf("%10d \t| %15s \t|\t %-50s \t|\t %15s \t|\t %s",
taxon->taxid,
rankname,
matchedname,
classname,
taxon->name);
taxon->name);
if (pathDisplay) {
printf("\t|\t");
displayPath(taxon, taxonomy);
}
printf("\n");
}
/**
* display header before printing any result
**/
static void printheader(void)
static void printheader(int32_t pathDisplay)
{
printf("# %12s \t| %15s \t|\t %-50s \t|\t %-15s \t|\t %s\n#\n",
printf("# %12s \t| %15s \t|\t %-50s \t|\t %-15s \t|\t %s%s\n#\n",
"taxonomy id",
"taxonomy rank",
"name",
"class name",
"scientific name");
"scientific name",
pathDisplay ? "\t|\t path":"");
}
/**
* display son's list for given taxon
**/
static void get_son(ecotaxonomy_t *taxonomy, ecotx_t *taxon, int32_t *count, char *rankname)
static void get_son(ecotaxonomy_t *taxonomy, ecotx_t *taxon, int32_t *count, char *rankname, int32_t pathDisplay)
{
int32_t i;
ecotx_t *current_taxon;
@ -63,10 +82,10 @@ static void get_son(ecotaxonomy_t *taxonomy, ecotx_t *taxon, int32_t *count, cha
{
if (rankname == NULL || !strcmp(rankname,taxonomy->ranks->label[current_taxon->rank]))
{
printresult(current_taxon, NULL, taxonomy);
printresult(current_taxon, NULL, taxonomy, pathDisplay);
(*count)++;
}
get_son(taxonomy,current_taxon,count,rankname);
get_son(taxonomy,current_taxon,count,rankname, pathDisplay);
}
}
}
@ -97,23 +116,23 @@ static void listfilteroptions(ecorankidx_t *ranks)
/* get back on given taxid taxonomic parent */
/* and display it */
/* ---------------------------------------- */
void gettaxidparents(int32_t taxid, ecotaxonomy_t *taxonomy, char *rankname)
void gettaxidparents(int32_t taxid, ecotaxonomy_t *taxonomy, char *rankname, int32_t pathDisplay)
{
ecotx_t *next_parent;
int32_t c = 0;
next_parent = eco_findtaxonbytaxid(taxonomy, taxid);
printheader();
printheader(pathDisplay);
printresult(next_parent, NULL,taxonomy);
printresult(next_parent, NULL,taxonomy, pathDisplay);
while ( strcmp(next_parent->name, "root") )
{
next_parent = next_parent->parent;
if (rankname == NULL || !strcmp(rankname,taxonomy->ranks->label[next_parent->rank]))
{
printresult(next_parent, NULL,taxonomy);
printresult(next_parent, NULL,taxonomy, pathDisplay);
c++;
}
}
@ -164,6 +183,7 @@ static void PrintHelp()
PP "-p : [P]arents : specifiying this option displays all parental tree's information for the given taxid.\n\n");
PP "-r : [R]estrict to given taxonomic rank\n\n");
PP "-s : [S]ons: specifiying this option displays all subtree's information for the given taxid.\n\n");
PP "-P : Display taxonomic [P]ath as suplementary column in output\n\n");
PP "arguments:\n");
PP "<taxon> name pattern bearing regular expressions\n\n");
PP "------------------------------------------\n");
@ -199,12 +219,13 @@ int main(int argc, char **argv)
char *rankname = NULL;
int32_t rankfilter = 1;
int32_t list = 0;
int32_t path = 0;
ecotx_t *subtree_parent;
int32_t count_son = 0;
while ((carg = getopt(argc, argv, "had:p:s:r:l")) != -1) {
while ((carg = getopt(argc, argv, "had:p:s:r:lP")) != -1) {
switch (carg) {
case 's': /* path to the database */
sscanf(optarg,"%d",&subtree);
@ -224,6 +245,10 @@ int main(int argc, char **argv)
case 'l': /* list rank filter options */
list = 1;
break;
case 'P': /* Path output option */
path=1;
break;
case 'a': /* allow alternative names */
alternative = 1;
@ -281,7 +306,7 @@ int main(int argc, char **argv)
/* ---------------------------------------- */
if (uptree)
{
gettaxidparents(uptree,taxonomy,rankname);
gettaxidparents(uptree,taxonomy,rankname, path);
return 0;
}
@ -291,10 +316,10 @@ int main(int argc, char **argv)
/* ---------------------------------------- */
if (subtree)
{
printheader();
printheader(path);
subtree_parent = eco_findtaxonbytaxid(taxonomy,subtree);
printresult(subtree_parent, NULL,taxonomy);
get_son(taxonomy, subtree_parent,&count_son,rankname);
printresult(subtree_parent, NULL,taxonomy, path);
get_son(taxonomy, subtree_parent,&count_son,rankname, path);
printf("# %d son(s) found\n#\n",count_son);
return 0;
}
@ -317,7 +342,7 @@ int main(int argc, char **argv)
nummatch=0;
printheader();
printheader(path);
for (j=0,name=taxonomy->names->names;
j < name_count;
@ -331,7 +356,7 @@ int main(int argc, char **argv)
if (!re_match && (alternative || name->is_scientificname) && rankfilter)
{
printresult(name->taxon,name,taxonomy);
printresult(name->taxon,name,taxonomy, path);
nummatch++;
}