Description: Fix implicit declaration
             Please note: Adding two prototypes directly to debug_funcs.c is hackish but
             some declarations in funcs.h are conflicting with the implementation ind
             debug_funcs.c thus it can't be simply included without furtherr changes
Bug-Debian: https://bugs.debian.org/1066475
Author: Andreas Tille <tille@debian.org>
Last-Update: Thu, 11 Apr 2024 15:13:23 +0200
Forwarded: No (orphaned upstream)

--- a/modhmm0.92b/debug_funcs.c
+++ b/modhmm0.92b/debug_funcs.c
@@ -1,11 +1,13 @@
 #include <stdlib.h>
 #include <stdio.h>
 
-
+//there are conflicting definitions remaining.
+//#include "funcs.h"
+int get_mtx_index(int,int,int);
+int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet);
 
 #include "structs.h"
 
-
 void dump_trans_matrix(int nr_rows, int nr_cols, double *mtx)
 {
   int i,j;
--- a/modhmm0.92b/funcs.h
+++ b/modhmm0.92b/funcs.h
@@ -167,6 +167,7 @@ int read_prior_file(struct emission_diri
 int read_frequencies(FILE *freqfile, double **aa_freqs);
 int read_frequencies_multi(FILE *freqfile, double **aa_freqsp, double **aa_freqsp_2, double **aa_freqsp_3, double **aa_freqsp_4);
 int read_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet);
+int read_multi_prior_file_multi(struct emission_dirichlet_s *em_di, struct hmm_multi_s *hmmp, FILE *priorfile, int alphabet);
 int locked_state(struct hmm_s *hmmp, int v);
 int locked_state_multi(struct hmm_multi_s *hmmp, int v);
 int get_best_reliability_score(double reliability_score_1, double reliability_score_2, double reliability_score_3);
@@ -198,6 +199,8 @@ void get_reverse_seq_multi(struct sequen
 			   struct letter_s **reverse_seq_4, struct hmm_multi_s *hmmp, int seq_len);
 
 /* std calculation funcs */
+void add_to_E_continuous(double *E, double Eka_base, struct msa_letter_s *msa_seq, int p,
+                         int k, int a_size, double *emissions);
 double get_single_gaussian_statescore(double mu, double sigma_square, double letter);
 double get_dp_statescore(int a_size, int use_gap_shares, int use_prior_shares, struct msa_letter_s *msa_seq,
 			 int p, double *emissions,  int vertex, int normalize, double *gap_shares);