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git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@79 60f365c0-8329-0410-b2a4-ec073aeeaa1d

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This commit is contained in:
Eric Coissac
2007-06-21 13:58:06 +00:00
parent 36d536305e
commit 24f958ce1f
1 changed files with 34 additions and 27 deletions
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61
src/ecofind.c
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@ -48,8 +48,7 @@ static void printheader(void)
/**
* display son's list for given taxon
**/
static void get_son(ecotaxonomy_t *taxonomy, ecotx_t *taxon, int32_t *count)
static void get_son(ecotaxonomy_t *taxonomy, ecotx_t *taxon, int32_t *count, char *rankname)
{
int32_t i;
ecotx_t *current_taxon;
@ -60,9 +59,12 @@ static void get_son(ecotaxonomy_t *taxonomy, ecotx_t *taxon, int32_t *count)
{
if (taxon->taxid == current_taxon->parent->taxid)
{
(*count)++;
printresult(current_taxon, NULL, taxonomy);
get_son(taxonomy,current_taxon,count);
if (rankname == NULL || !strcmp(rankname,taxonomy->ranks->label[current_taxon->rank]))
{
printresult(current_taxon, NULL, taxonomy);
(*count)++;
}
get_son(taxonomy,current_taxon,count,rankname);
}
}
}
@ -93,7 +95,7 @@ static void listfilteroptions(ecorankidx_t *ranks)
/* get back on given taxid taxonomic parent */
/* and display it */
/* ---------------------------------------- */
void gettaxidparents(int32_t taxid, ecotaxonomy_t *taxonomy)
void gettaxidparents(int32_t taxid, ecotaxonomy_t *taxonomy, char *rankname)
{
ecotx_t *next_parent;
int32_t c = 0;
@ -101,12 +103,17 @@ void gettaxidparents(int32_t taxid, ecotaxonomy_t *taxonomy)
next_parent = eco_findtaxonbytaxid(taxonomy, taxid);
printheader();
printresult(next_parent, NULL,taxonomy);
while ( strcmp(next_parent->name, "root") )
{
printresult(next_parent, NULL,taxonomy);
next_parent = next_parent->parent;
c++;
if (rankname == NULL || !strcmp(rankname,taxonomy->ranks->label[next_parent->rank]))
{
printresult(next_parent, NULL,taxonomy);
c++;
}
}
printf("# %d parent(s) found\n#\n",c);
@ -139,27 +146,26 @@ static void PrintHelp()
PP "------------------------------------------\n");
PP " ecofind Version %s\n", VERSION);
PP "------------------------------------------\n");
PP "synopsis : searching for scientific name, taxonomic\n");
PP " rank and taxonomy id for given regular\n");
PP " expression patterns\n");
PP "usage: ecofind [options] pattern\n");
PP "synopsis : searching for taxonomic and rank and\n");
PP " taxonomy id for given regular expression patterns\n\n");
PP "usage: ecofind [options] <patterns>\n");
PP "------------------------------------------\n");
PP "options:\n");
PP "-d : [D]atabase containing the taxonomy\n");
PP " to match the expected format, the database\n");
PP " has to be formated first by the ecoPCRFormat.py\n");
PP " program located in the tools directory.\n");
PP " Write the database radical without any extension.\n\n");
PP "-h : [H]elp - print <this> help\n\n");
PP "-l : [L]ist all taxonomic rank available for -r option\n\n");
PP "-p : [P]arent's taxonomic id. Specifiying this option will display ");
PP " all parent's information for the given taxid.\n\n");
PP "-a : [A]ll enable the search on all alternative names and not only scientific names.\n\n");
PP "-d : [D]atabase containing the taxonomy.\n");
PP " To match the expected format, the database\n");
PP " has to be formated first by the ecoPCRFormat.py\n");
PP " program located in the tools directory.\n");
PP " Write the database radical without any extension.\n\n");
PP "-h : [H]elp - print <this> help\n\n");
PP "-l : [L]ist all taxonomic rank available for -r option\n\n");
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]on's taxonomic id. Specifiying this option will display ");
PP " all son's information for the given taxid.\n\n");
PP "-s : [S]ons: specifiying this option displays all subtree's information for the given taxid.\n\n");
PP "arguments:\n");
PP "<taxon> name pattern bearing regular expressions\n\n");
PP "------------------------------------------\n");
PP " https://www.grenoble.prabi.fr/trac/ecoPCR/wiki\n");
PP " http://www.grenoble.prabi.fr/trac/ecoPCR/\n");
PP "------------------------------------------\n\n");
}
@ -245,7 +251,7 @@ int main(int argc, char **argv)
errflag++;
}
if (errflag && !uptree && !rankname && !subtree)
if (errflag && !uptree && !rankname && !subtree && !list)
ExitUsage(errflag);
/**
@ -274,7 +280,7 @@ int main(int argc, char **argv)
/* ---------------------------------------- */
if (uptree)
{
gettaxidparents(uptree,taxonomy);
gettaxidparents(uptree,taxonomy,rankname);
return 0;
}
@ -286,7 +292,8 @@ int main(int argc, char **argv)
{
printheader();
subtree_parent = eco_findtaxonbytaxid(taxonomy,subtree);
get_son(taxonomy, subtree_parent,&count_son);
printresult(subtree_parent, NULL,taxonomy);
get_son(taxonomy, subtree_parent,&count_son,rankname);
printf("# %d son(s) found\n#\n",count_son);
return 0;
}