void gt_checkgreedyunitedist(GT_UNUSED bool forward, const GtUchar *useq, GtUword ulen, const GtUchar *vseq, GtUword vlen) { GtUword edist1, edist2; GtFrontResource *frontresource = gt_frontresource_new(10UL); GtSeqabstract *greedyedistuseq = gt_seqabstract_new_gtuchar(useq,ulen,0), *greedyedistvseq = gt_seqabstract_new_gtuchar(vseq,vlen,0); edist1 = greedyunitedist(frontresource,greedyedistuseq,greedyedistvseq); edist2 = gt_squarededistunit (useq,ulen,vseq,vlen); #ifdef SKDEBUG printf("edist = "GT_WU"\n",edist1); #endif if (edist1 != edist2) { fprintf(stderr,"greedyunitedist = "GT_WU" != "GT_WU " = gt_squarededistunit\n", edist1,edist2); exit(GT_EXIT_PROGRAMMING_ERROR); } gt_seqabstract_delete(greedyedistuseq); gt_seqabstract_delete(greedyedistvseq); gt_frontresource_delete(frontresource); }
GtUword gt_computegreedyunitedist(const GtUchar *useq, GtUword ulen, const GtUchar *vseq, GtUword vlen) { GtUword edist; GtFrontResource *frontresource = gt_frontresource_new(10UL); GtSeqabstract *greedyedistuseq = gt_seqabstract_new_gtuchar(useq,ulen,0), *greedyedistvseq = gt_seqabstract_new_gtuchar(vseq,vlen,0); edist = greedyunitedist(frontresource,greedyedistuseq,greedyedistvseq); gt_seqabstract_delete(greedyedistuseq); gt_seqabstract_delete(greedyedistvseq); gt_frontresource_delete(frontresource); return edist; }
int gt_xdrop_unit_test(GT_UNUSED GtError *err) { int had_err = 0, i, j, s; const GtUchar *strings[GT_XDROP_NUM_OF_TESTS] = {(const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCCCAAAGGGTTTCCCTTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTTTTTGGGGCCCCAAAATTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTNNNNTTTTGGGGCCCCAAAATTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCGCAAAGGGTTTCCCTTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCCAAAGGGTTTCCCCTTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTAAAGGGTTTCCTCAAAGGGTTTCCTTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTAAACAGATCACCCGCTTTTTTTTTTTTTTTT", (const GtUchar*) "TTTTTTTTTTTTTTTAAACGGGTTTCTCAAAGGGTTCCCTTTTTTTTTTTTTTT"}; GtUword lengths[GT_XDROP_NUM_OF_TESTS] = {54UL, 46UL, 50UL, 54UL, 54UL, 54UL, 46UL, 54UL}, eval_scores[GT_XDROP_NUM_OF_TESTS * GT_XDROP_NUM_OF_TESTS * GT_XDROP_NUM_OF_TESTS] = {0, 13UL, 0, 1UL, 4UL, 1UL, 0, 7UL, 13UL, 0, 0, 14UL, 15UL, 14UL, 0, 15UL, 0, 0, 0, 0, 0, 0, 0, 0, 1UL, 14UL, 0, 0, 1UL, 2UL, 0, 1UL, 4UL, 15UL, 0, 1UL, 0, 8UL, 0, 1UL, 1UL, 14UL, 0, 2UL, 8UL, 0, 0, 4UL, 0, 0, 0, 0, 0, 0, 0, 0, 7UL, 15UL, 0, 1UL, 1UL, 4UL, 0, 0, 0, 13UL, 0, 1UL, 4UL, 5UL, 14UL, 7UL, 13UL, 0, 0, 14UL, 15UL, 14UL, 12UL, 15UL, 0, 0, 0, 20UL, 0, 19UL, 17UL, 0, 1UL, 14UL, 20UL, 0, 5UL, 6UL, 15UL, 8UL, 4UL, 15UL, 0, 5UL, 0, 8UL, 15UL, 10UL, 5UL, 14UL, 19UL, 6UL, 8UL, 0, 14UL, 4UL, 14UL, 12UL, 17UL, 15UL, 15UL, 14UL, 0, 14UL, 7UL, 15UL, 0, 8UL, 10UL, 4UL, 14UL, 0, 0, 13UL, 19UL, 1UL, 2UL, 2UL, 13UL, 3UL, 13UL, 0, 9UL, 14UL, 14UL, 13UL, 12UL, 14UL, 17UL, 4UL, 0, 18UL, 19UL, 16UL, 16UL, 18UL, 1UL, 14UL, 18UL, 0, 2UL, 3UL, 13UL, 3UL, 2UL, 14UL, 18UL, 2UL, 0, 4UL, 13UL, 4UL, 2UL, 13UL, 19UL, 3UL, 4UL, 0, 13UL, 3UL, 14UL, 12UL, 17UL, 13UL, 13UL, 14UL, 0, 14UL, 3UL, 14UL, 18UL, 3UL, 4UL, 3UL, 13UL, 0, 0, 13UL, 17UL, 1UL, 2UL, 2UL, 14UL, 3UL, 13UL, 0, 4UL, 14UL, 15UL, 13UL, 12UL, 14UL, 19UL, 9UL, 0, 18UL, 18UL, 19UL, 17UL, 18UL, 1UL, 14UL, 18UL, 0, 2UL, 3UL, 13UL, 3UL, 2UL, 14UL, 19UL, 2UL, 0, 4UL, 13UL, 4UL, 2UL, 13UL, 16UL, 3UL, 4UL, 0, 14UL, 3UL, 13UL, 12UL, 16UL, 13UL, 13UL, 13UL, 0, 13UL, 3UL, 14UL, 18UL, 3UL, 4UL, 3UL, 14UL, 0, 0, 0, 0, 1UL, 1UL, 1UL, 0, 1UL, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1UL, 0, 0, 0, 1UL, 0, 0, 1UL, 1UL, 0, 0, 1UL, 0, 0, 0, 1UL, 1UL, 0, 0, 0, 0, 0, 0, 1UL, 0, 0, 0, 0, 0, 0, 0, 0, 1UL, 0, 0, 1UL, 1UL, 1UL, 0, 0, 0, 0, 0, 1UL, 1UL, 1UL, 0, 1UL, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1UL, 0, 0, 0, 1UL, 2UL, 0, 1UL, 1UL, 0, 0, 1UL, 0, 0, 0, 1UL, 1UL, 0, 0, 2UL, 0, 0, 0, 1UL, 0, 0, 0, 0, 0, 0, 0, 0, 1UL, 0, 0, 1UL, 1UL, 1UL, 0, 0, 0, 13UL, 17UL, 1UL, 2UL, 2UL, 13UL, 3UL, 13UL, 0, 4UL, 14UL, 14UL, 13UL, 12UL, 14UL, 17UL, 4UL, 0, 18UL, 19UL, 16UL, 16UL, 19UL, 1UL, 14UL, 18UL, 0, 2UL, 3UL, 13UL, 3UL, 2UL, 14UL, 19UL, 2UL, 0, 4UL, 13UL, 4UL, 2UL, 13UL, 16UL, 3UL, 4UL, 0, 13UL, 3UL, 13UL, 12UL, 16UL, 13UL, 13UL, 13UL, 0, 13UL, 3UL, 14UL, 19UL, 3UL, 4UL, 3UL, 13UL, 0, 0, 13UL, 0, 1UL, 2UL, 2UL, 5UL, 3UL, 13UL, 0, 0, 14UL, 15UL, 13UL, 0, 14UL, 0, 0, 0, 0, 0, 0, 0, 0, 1UL, 14UL, 0, 0, 2UL, 3UL, 5UL, 3UL, 2UL, 15UL, 0, 2UL, 0, 4UL, 5UL, 4UL, 2UL, 13UL, 0, 3UL, 4UL, 0, 6UL, 3UL, 5UL, 0, 0, 5UL, 5UL, 6UL, 0, 5UL, 3UL, 14UL, 0, 3UL, 4UL, 3UL, 5UL, 0}; GtSeqabstract *useq, *vseq; GtXdropArbitraryscores score[GT_XDROP_NUM_OF_TESTS] = {{2, -2, -2, -2}, {2, -1, -1, -1}, {2, -1, -5, -2}, {2, -1, -2, -5}, {3, -2, -3, -3}, {3, -1, -1, -1}, {4, -1, -3, -3}, {10, -3, -8, -8}}; GtXdropresources *resources; GtXdropbest best; GtXdropscore dropscore = (GtXdropscore) 12; GtMultieoplist *edit_ops = NULL; GtAlignment *alignment; bool rightextension = true; gt_error_check(err); for (s = 0; s < GT_XDROP_NUM_OF_TESTS; ++s) { resources = gt_xdrop_resources_new(&score[s]); for (i = 0; i < GT_XDROP_NUM_OF_TESTS && !had_err; ++i) { for (j = 0; j < GT_XDROP_NUM_OF_TESTS; ++j) { useq = gt_seqabstract_new_gtuchar(rightextension,GT_READMODE_FORWARD, strings[i], lengths[i], 0,lengths[i]); vseq = gt_seqabstract_new_gtuchar(rightextension, GT_READMODE_FORWARD, strings[j], lengths[j], 0,lengths[j]); gt_evalxdroparbitscoresextend(true, &best, resources, useq, vseq, dropscore); edit_ops = gt_xdrop_backtrack(resources, &best); gt_ensure(edit_ops != NULL); alignment = gt_alignment_new_with_seqs(strings[i], best.ivalue, strings[j], best.jvalue); gt_alignment_set_multieop_list(alignment, edit_ops); gt_ensure(eval_scores[s*64+i*8+j] == gt_alignment_eval(alignment)); gt_multieoplist_delete(edit_ops); gt_alignment_delete(alignment); if (i == j) { gt_evalxdroparbitscoresextend(false, &best, resources, useq, vseq, dropscore); edit_ops = gt_xdrop_backtrack(resources, &best); alignment = gt_alignment_new_with_seqs(strings[i], best.ivalue, strings[j], best.jvalue); gt_alignment_set_multieop_list(alignment, edit_ops); gt_ensure(eval_scores[s*64+i*8+j] == gt_alignment_eval(alignment)); gt_multieoplist_delete(edit_ops); gt_alignment_delete(alignment); } gt_seqabstract_delete(useq); gt_seqabstract_delete(vseq); } } gt_xdrop_resources_delete(resources); } return had_err; }