Eric Coissac
6f5f2a16f3
Change 2 : Change the used rules to define example and counter example taxon sets. By default all taxa are example taxa and no counterexample taxa are used. By using -r option (one or several time) you could restict example taxa to a subset of taxa In old version all taxa not in example set are in the counterexample set. Now restrict example set with -r option doesn't define the counter example set. You must use -i to define the conterexample set in a similar way or -r option for example taxa. git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@234 60f365c0-8329-0410-b2a4-ec073aeeaa1d
60 lines
1.1 KiB
C
60 lines
1.1 KiB
C
/*
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* readdnadb.c
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*
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* Created on: 7 nov. 2008
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* Author: coissac
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*/
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#include "ecoprimer.h"
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pecodnadb_t readdnadb(const char *name, ecotaxonomy_t *taxonomy, uint32_t *size,poptions_t options)
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{
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ecoseq_t *seq;
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uint32_t buffsize=100;
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pecodnadb_t db;
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db = ECOMALLOC(buffsize*sizeof(ecoseq_t*),"I cannot allocate db memory");
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for(seq=ecoseq_iterator(name), *size=0;
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seq;
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seq=ecoseq_iterator(NULL)
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)
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{
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if (isExampleTaxon(taxonomy,seq->taxid,options) ||
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isCounterExampleTaxon(taxonomy,seq->taxid,options))
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{
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if (*size==buffsize)
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{
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buffsize*=2;
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db = ECOREALLOC(db,buffsize*sizeof(ecoseq_t*),"I cannot allocate db memory");
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}
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db[*size]=seq;
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(*size)++;
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}
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else
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{
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delete_ecoseq(seq);
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}
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};
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db = ECOREALLOC(db,(*size)*sizeof(ecoseq_t*),"I cannot allocate db memory");
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return db;
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}
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void printSeqTest(pecodnadb_t seqdb,uint32_t seqdbsize)
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{
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uint32_t i;
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char ch[11];
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ch [10] = '\0';
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for (i=0; i < seqdbsize; i++)
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{
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strncpy (ch, seqdb[i]->SQ, 10);
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fprintf (stderr, "seq %d = %s\n", i, ch);
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}
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exit (0);
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}
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