Description: fix numerous issues caught by gcc 14. Author: Étienne Mollier Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075198 Forwarded: no Last-Update: 2024-08-25 --- This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ --- libpsortb.orig/modhmm0.92b/core_algorithms_multialpha.c +++ libpsortb/modhmm0.92b/core_algorithms_multialpha.c @@ -1187,14 +1187,14 @@ if(hmmp->alphabet_type == DISCRETE) { - a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); + a_index = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); if(a_index < 0) { a_index = hmmp->a_size; /* if letter is wild card, use default column in subst matrix */ } } if(hmmp->nr_alphabets > 1) { if(hmmp->alphabet_type_2 == DISCRETE) { - a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, + a_index_2 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, hmmp->alphabet_2, hmmp->a_size_2); if(a_index_2 < 0) { a_index_2 = hmmp->a_size_2; /* if letter is wild card, use default column in subst matrix */ @@ -1203,7 +1203,7 @@ } if(hmmp->nr_alphabets > 2) { if(hmmp->alphabet_type_3 == DISCRETE) { - a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, + a_index_3 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, hmmp->alphabet_3, hmmp->a_size_3); if(a_index_3 < 0) { a_index_3 = hmmp->a_size_3; /* if letter is wild card, use default column in subst matrix */ @@ -1212,7 +1212,7 @@ } if(hmmp->nr_alphabets > 3) { if(hmmp->alphabet_type_4 == DISCRETE) { - a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, + a_index_4 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, hmmp->alphabet_4, hmmp->a_size_4); if(a_index_4 < 0) { a_index_4 = hmmp->a_size_4; /* if letter is wild card, use default column in subst matrix */ @@ -1414,14 +1414,14 @@ a_index_3 = -1; a_index_4 = -1; if(hmmp->alphabet_type == DISCRETE) { - a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); + a_index = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); if(a_index < 0) { a_index = hmmp->a_size; /* if letter is wild card, use default column in subst matrix */ } } if(hmmp->nr_alphabets > 1) { if(hmmp->alphabet_type_2 == DISCRETE) { - a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, + a_index_2 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, hmmp->alphabet_2, hmmp->a_size_2); if(a_index_2 < 0) { a_index_2 = hmmp->a_size_2; /* if letter is wild card, use default column in subst matrix */ @@ -1430,7 +1430,7 @@ } if(hmmp->nr_alphabets > 2) { if(hmmp->alphabet_type_3 == DISCRETE) { - a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, + a_index_3 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, hmmp->alphabet_3, hmmp->a_size_3); if(a_index_3 < 0) { a_index_3 = hmmp->a_size_3; /* if letter is wild card, use default column in subst matrix */ @@ -1439,7 +1439,7 @@ } if(hmmp->nr_alphabets > 3) { if(hmmp->alphabet_type_4 == DISCRETE) { - a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, + a_index_4 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, hmmp->alphabet_4, hmmp->a_size_4); if(a_index_4 < 0) { a_index_4 = hmmp->a_size_4; /* if letter is wild card, use default column in subst matrix */ @@ -1603,14 +1603,14 @@ a_index_3 = -1; a_index_4 = -1; if(hmmp->alphabet_type == DISCRETE) { - a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); + a_index = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); if(a_index < 0) { a_index = hmmp->a_size; /* if letter is wild card, use default column in subst matrix */ } } if(hmmp->nr_alphabets > 1) { if(hmmp->alphabet_type_2 == DISCRETE) { - a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, + a_index_2 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, hmmp->alphabet_2, hmmp->a_size_2); if(a_index_2 < 0) { a_index_2 = hmmp->a_size_2; /* if letter is wild card, use default column in subst matrix */ @@ -1619,7 +1619,7 @@ } if(hmmp->nr_alphabets > 2) { if(hmmp->alphabet_type_3 == DISCRETE) { - a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, + a_index_3 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, hmmp->alphabet_3, hmmp->a_size_3); if(a_index_3 < 0) { a_index_3 = hmmp->a_size_3; /* if letter is wild card, use default column in subst matrix */ @@ -1628,7 +1628,7 @@ } if(hmmp->nr_alphabets > 3) { if(hmmp->alphabet_type_4 == DISCRETE) { - a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, + a_index_4 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, hmmp->alphabet_4, hmmp->a_size_4); if(a_index_4 < 0) { a_index_4 = hmmp->a_size_4; /* if letter is wild card, use default column in subst matrix */ @@ -1887,14 +1887,14 @@ a_index_3 = -1; a_index_4 = -1; if(hmmp->alphabet_type == DISCRETE) { - a_index = get_alphabet_index((msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); + a_index = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_1 + (c * (hmmp->a_size+1)))->query_letter, hmmp->alphabet, hmmp->a_size); if(a_index < 0) { a_index = hmmp->a_size; /* if letter is wild card, use default column in subst matrix */ } } if(hmmp->nr_alphabets > 1) { if(hmmp->alphabet_type_2 == DISCRETE) { - a_index_2 = get_alphabet_index((msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, + a_index_2 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_2 + (c * (hmmp->a_size_2+1)))->query_letter, hmmp->alphabet_2, hmmp->a_size_2); if(a_index_2 < 0) { a_index_2 = hmmp->a_size_2; /* if letter is wild card, use default column in subst matrix */ @@ -1903,7 +1903,7 @@ } if(hmmp->nr_alphabets > 2) { if(hmmp->alphabet_type_3 == DISCRETE) { - a_index_3 = get_alphabet_index((msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, + a_index_3 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_3 + (c * (hmmp->a_size_3+1)))->query_letter, hmmp->alphabet_3, hmmp->a_size_3); if(a_index_3 < 0) { a_index_3 = hmmp->a_size_3; /* if letter is wild card, use default column in subst matrix */ @@ -1912,7 +1912,7 @@ } if(hmmp->nr_alphabets > 3) { if(hmmp->alphabet_type_4 == DISCRETE) { - a_index_4 = get_alphabet_index((msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, + a_index_4 = get_alphabet_index((struct letter_s*)(msa_seq_infop->msa_seq_4 + (c * (hmmp->a_size_4+1)))->query_letter, hmmp->alphabet_4, hmmp->a_size_4); if(a_index_4 < 0) { a_index_4 = hmmp->a_size_4; /* if letter is wild card, use default column in subst matrix */ --- libpsortb.orig/modhmm0.92b/hmmsearch.c +++ libpsortb/modhmm0.92b/hmmsearch.c @@ -532,7 +532,7 @@ through and record their locations */ if(hSites) { - hSites->helix = (helix_sites *) malloc(sizeof (helix_sites) * helices); + hSites->helix = (struct helix_site *) malloc(sizeof (helix_sites) * helices); helixSite = hSites->helix; hSites->helix_count = helices; --- libpsortb.orig/modhmm0.92b/readhmm.c +++ libpsortb/modhmm0.92b/readhmm.c @@ -118,7 +118,7 @@ /* nr of trans tie groups */ if(fgets(s, MAX_LINE, file) != NULL) { hmmp->nr_ttg = atoi(&s[29]); - hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + hmmp->trans_tie_groups = (struct transition_s*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); } /* nr of emission priorfiles */ if(fgets(s, MAX_LINE, file) != NULL) { @@ -391,7 +391,7 @@ /* nr of trans tie groups */ if(fgets(s, MAX_LINE, file) != NULL) { hmmp->nr_ttg = atoi(&s[29]); - hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + hmmp->trans_tie_groups = (struct transition_s*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); } /* nr of emission priorfiles */ if(fgets(s, MAX_LINE, file) != NULL) { --- libpsortb.orig/modhmm0.92b/readseqs_multialpha.c +++ libpsortb/modhmm0.92b/readseqs_multialpha.c @@ -80,7 +80,7 @@ inside_seq = NO; /* read sequence name */ - (seq_infop->seqs + seq_nr)->name[0] = "s"; + (seq_infop->seqs + seq_nr)->name[0] = 's'; i = 0; while((i <= nr_letters) && (seq[i] != '\0')) { --- libpsortb.orig/modhmm0.92b/readhmm_multialpha.c +++ libpsortb/modhmm0.92b/readhmm_multialpha.c @@ -270,7 +270,7 @@ retrain_hmmp->distrib_groups = (int*)(malloc_or_die((hmmp->nr_d + hmmp->nr_v) * sizeof(int))); memcpy(retrain_hmmp->distrib_groups, hmmp->distrib_groups,(hmmp->nr_d + hmmp->nr_v) * sizeof(int)); - retrain_hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + retrain_hmmp->trans_tie_groups = (struct transition_s*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); memcpy(retrain_hmmp->trans_tie_groups, hmmp->trans_tie_groups,(hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s)); @@ -466,7 +466,7 @@ /* nr of trans tie groups */ if(fgets(s, MAX_LINE, file) != NULL) { hmmp->nr_ttg = atoi(&s[29]); - hmmp->trans_tie_groups = (int*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); + hmmp->trans_tie_groups = (struct transition_s*)(malloc_or_die((hmmp->nr_t + hmmp->nr_ttg) * sizeof(struct transition_s))); } /* nr of emission priorfiles */ --- libpsortb.orig/modhmm0.92b/std_funcs.c +++ libpsortb/modhmm0.92b/std_funcs.c @@ -2068,7 +2068,7 @@ /* get gap data (not implemented) */ for(i = 0; i < msa_seq_infop->msa_seq_length; i++) { - *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; + *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = (int*)END; } for(i = 0; i < msa_seq_infop->msa_seq_length; i++) { *(reverse_msa_seq_infop->gaps + i) = (int*)(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)); @@ -2176,7 +2176,7 @@ /* get gap data (not implemented) */ for(i = 0; i < msa_seq_infop->msa_seq_length; i++) { - *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = END; + *(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)) = (int*)END; } for(i = 0; i < msa_seq_infop->msa_seq_length; i++) { *(reverse_msa_seq_infop->gaps + i) = (int*)(reverse_msa_seq_infop->gaps + (msa_seq_infop->msa_seq_length + i)); @@ -2463,7 +2463,7 @@ if(em_di->nr_components <= 0) { //printf("em_di nr comps = %d\n",em_di->nr_components); //printf("alphabet = %d\n", alphabet); - return; + return YES; // Initially void, so YES, but actual intention is unclear. } /* set a_size and msa_seq according to alphabet */ --- libpsortb.orig/modhmm0.92b/training_algorithms_multialpha.c +++ libpsortb/modhmm0.92b/training_algorithms_multialpha.c @@ -698,7 +698,7 @@ /* loop over the alphabets */ for(alphabet_nr = 1; alphabet_nr <= hmmp->nr_alphabets; alphabet_nr++) { if(alphabet_nr == 1) { - alphabet = hmmp->alphabet; + alphabet = (int)hmmp->alphabet; subst_mtx = hmmp->subst_mtx; a_size = hmmp->a_size; E_cur = E; @@ -707,7 +707,7 @@ tmp_emissions = hmmp->emissions; } else if(alphabet_nr == 2) { - alphabet = hmmp->alphabet_2; + alphabet = (int)hmmp->alphabet_2; subst_mtx = hmmp->subst_mtx_2; a_size = hmmp->a_size_2; E_cur = E_2; @@ -716,7 +716,7 @@ tmp_emissions = hmmp->emissions_2; } else if(alphabet_nr == 3) { - alphabet = hmmp->alphabet_3; + alphabet = (int)hmmp->alphabet_3; subst_mtx = hmmp->subst_mtx_3; a_size = hmmp->a_size_3; E_cur = E_3; @@ -725,7 +725,7 @@ tmp_emissions = hmmp->emissions_3; } else if(alphabet_nr == 4) { - alphabet = hmmp->alphabet_4; + alphabet = (int)hmmp->alphabet_4; subst_mtx = hmmp->subst_mtx_4; a_size = hmmp->a_size_4; E_cur = E_4; @@ -1636,28 +1636,28 @@ /* loop over the alphabets */ for(alphabet_nr = 1; alphabet_nr <= hmmp->nr_alphabets; alphabet_nr++) { if(alphabet_nr == 1) { - alphabet = hmmp->alphabet; + alphabet = (int)hmmp->alphabet; subst_mtx = hmmp->subst_mtx; a_size = hmmp->a_size; E_cur = E_ulab; msa_seq = msa_seq_infop->msa_seq_1; } else if(alphabet_nr == 2) { - alphabet = hmmp->alphabet_2; + alphabet = (int)hmmp->alphabet_2; subst_mtx = hmmp->subst_mtx_2; a_size = hmmp->a_size_2; E_cur = E_ulab_2; msa_seq = msa_seq_infop->msa_seq_2; } else if(alphabet_nr == 3) { - alphabet = hmmp->alphabet_3; + alphabet = (int)hmmp->alphabet_3; subst_mtx = hmmp->subst_mtx_3; a_size = hmmp->a_size_3; E_cur = E_ulab_3; msa_seq = msa_seq_infop->msa_seq_3; } else if(alphabet_nr == 4) { - alphabet = hmmp->alphabet_4; + alphabet = (int)hmmp->alphabet_4; subst_mtx = hmmp->subst_mtx_4; a_size = hmmp->a_size_4; E_cur = E_ulab_4; @@ -1781,28 +1781,28 @@ /* loop over the alphabets */ for(alphabet_nr = 1; alphabet_nr <= hmmp->nr_alphabets; alphabet_nr++) { if(alphabet_nr == 1) { - alphabet = hmmp->alphabet; + alphabet = (int)hmmp->alphabet; subst_mtx = hmmp->subst_mtx; a_size = hmmp->a_size; E_cur = E_lab; msa_seq = msa_seq_infop->msa_seq_1; } else if(alphabet_nr == 2) { - alphabet = hmmp->alphabet_2; + alphabet = (int)hmmp->alphabet_2; subst_mtx = hmmp->subst_mtx_2; a_size = hmmp->a_size_2; E_cur = E_lab_2; msa_seq = msa_seq_infop->msa_seq_2; } else if(alphabet_nr == 3) { - alphabet = hmmp->alphabet_3; + alphabet = (int)hmmp->alphabet_3; subst_mtx = hmmp->subst_mtx_3; a_size = hmmp->a_size_3; E_cur = E_lab_3; msa_seq = msa_seq_infop->msa_seq_3; } else if(alphabet_nr == 4) { - alphabet = hmmp->alphabet_4; + alphabet = (int)hmmp->alphabet_4; subst_mtx = hmmp->subst_mtx_4; a_size = hmmp->a_size_4; E_cur = E_lab_4; @@ -3586,11 +3586,11 @@ } else if(scoring_method == SUBST_MTX_DOT_PRODUCT && use_nr_occ == YES) { add_to_E_subst_mtx_dot_product_nr_occ(E, Eka_base, msa_seq, p, k, a_size, normalize, subst_mtx, - alphabet); + (char*)alphabet); } else if(scoring_method == SUBST_MTX_DOT_PRODUCT_PRIOR && use_nr_occ == YES) { add_to_E_subst_mtx_dot_product_prior_nr_occ(E, Eka_base, msa_seq, p, k, a_size, normalize, subst_mtx, - alphabet); + (char*)alphabet); } else if(scoring_method == DOT_PRODUCT) { add_to_E_dot_product(E, Eka_base, msa_seq, p, k, a_size, normalize); @@ -3615,11 +3615,11 @@ } else if(scoring_method == SUBST_MTX_DOT_PRODUCT) { add_to_E_subst_mtx_dot_product(E, Eka_base, msa_seq, p, k, a_size, normalize, subst_mtx, - alphabet); + (char*)alphabet); } else if(scoring_method == SUBST_MTX_DOT_PRODUCT_PRIOR) { add_to_E_subst_mtx_dot_product_prior(E, Eka_base, msa_seq, p, k, a_size, normalize, subst_mtx, - alphabet); + (char*)alphabet); } else { printf("Error: Unrecognized scoring method\n");