--- /dev/null
+struct CL_node
+ {
+
+ int copy_mode;
+ struct CL_node *c;
+ struct CL_node *p;
+ struct CL_node *l;
+ struct CL_node *r;
+ int seq;
+ int res;
+ int free;
+};
+
+typedef struct CL_node CL_node;
+Alignment * add_constraint2aln ( Alignment *A, int s1, int r1, int s2, int r2);
+Alignment * graph_aln (Alignment *A, Constraint_list *CL, Sequence *S);
+Alignment* graph2aln (Alignment *A, CL_node *G, Sequence *S);
+CL_node ***add_constraint2graph_aln (CL_node ***G, int s1, int r1, int s2, int r2);
+CL_node * shift_segment ( CL_node *S, int segL, int shiftL);
+
+int is_graph_gap_column(CL_node *S);
+CL_node * remove_graph_gap_column (CL_node *S);
+CL_node * swap_gap_in_graph ( CL_node*S, CL_node *E);
+
+CL_node * declare_cl_nodes ( int len, int seq);
+CL_node * insert_gap_columns (CL_node *S, int d);
+int get_node_distance ( CL_node *S, CL_node *E);
+CL_node ***aln2graph (Alignment *A);
+CL_node *vfree_graph (CL_node *S);
+CL_node *vfree_cl_node ( CL_node *N);
+
+int gotoh_pair_wise_lalign ( Alignment *A, int*ns, int **l_s,Constraint_list *CL);
+Constraint_list * undefine_sw_aln ( Alignment *A, Constraint_list *CL);
+Constraint_list * undefine_sw_pair ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int sw_pair_is_defined ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+
+int gotoh_pair_wise_sw (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+
+Alignment * get_best_local_aln ( Alignment *IN,Constraint_list *CL,int gop, int gep, int sw_t, int sw_l, int sw_z, int greedy);
+Alignment * get_best_nol_local_aln ( Alignment *IN, Constraint_list *CL, int gop, int gep,int sw_t,int sw_l, int sw_z, int mode);
+double compute_penalty (Constraint_list *CL, char *mode, int len);
+double compute_scale ( Constraint_list *CL,char *mode, int len);
+int evaluate_penalty (Alignment *A, Constraint_list *CL, int *scale,char *scale_mode, int *penalty, char *penalty_mode, int len_seq);
+Alignment ** t_coffee_lalign (Constraint_list *CL, int scale, int penalty,int maximise,Sequence *S, int sw_t, int sw_l, int sw_z,int *sw_n, int sw_io);
+Alignment * add_seq2aln (Constraint_list *CL, Alignment *IN,Sequence *S);
+
+
+
+
+
+
+
+struct Dp_Model
+{
+ int *diag;
+
+ int TG_MODE;
+ int F_TG_MODE;
+ int gop;
+ int gep;
+ int f_gop;
+ int f_gep;
+ int nstate;
+ int START;
+ int END;
+
+ char**model_comments;
+ int **model;
+ int **model_properties;
+ int **bounded_model;
+ int (***model_emission_function)(Alignment*, int **, int, int*, int, int **, int, int*, int, struct Constraint_list *);
+
+ int LEN_I;
+ int LEN_J;
+ int DELTA_I;
+ int DELTA_J;
+ int EMISSION;
+ int START_EMISSION;
+ int TERM_EMISSION;
+
+ int ALN_TYPE;
+ Constraint_list *CL;
+ /*Associated Functions*/
+
+ /*To Deprecate*/
+ int UM;
+
+ int TYPE;
+ int F0;
+ int F1;
+
+
+ int NON_CODING;
+ int INSERTION;
+ int DELETION;
+ int CODING0;
+ int CODING1;
+ int CODING2;
+
+
+};
+typedef struct Dp_Model Dp_Model;
+
+struct Dp_Result
+{
+ int *traceback;
+ int len;
+ int score;
+ Dp_Model *Dp_model;
+};
+typedef struct Dp_Result Dp_Result;
+
+Dp_Result * make_fast_generic_dp_pair_wise (Alignment *A, int*ns, int **l_s,Dp_Model *M);
+
+Constraint_list* free_dp_model (Dp_Model *D);
+Dp_Result * free_dp_result (Dp_Result *D );
+
+typedef struct hseq* SeqHasch;
+
+typedef struct hseq
+{
+ SeqHasch hl[256];
+ int n;
+ int *l;
+} hseq;
+
+int ** ktup_dist_mat ( char **seq, int nseq, int ktup, char *type);
+int ** evaluate_diagonals_for_two_sequences ( char *seq1, char *seq2,int maximise,Constraint_list *CL,int ktup);
+int ** evaluate_diagonals ( Alignment *A, int *ns, int **l_s, Constraint_list *CL,int maximise,int n_groups, char **group_list,int ktup);
+int ** evaluate_segments_with_ktup ( Alignment *A, int *ns, int **l_s, Constraint_list *CL,int maximise,int n_groups, char **group_list,int ktup);
+int ** evaluate_diagonals_with_ktup ( Alignment *A, int *ns, int **l_s, Constraint_list *CL,int maximise,int n_groups, char **group_list,int ktup);
+
+int ** evaluate_diagonals_with_clist ( Alignment *A, int *ns, int **l_s, Constraint_list *CL,int maximise,int n_groups, char **group_list,int ktup);
+
+int * flag_diagonals (int l1, int l2, int **sorted_diag,float T, int window);
+int * extract_N_diag (int l1, int l2, int **sorted_diag, int n_chosen_diag, int window);
+
+int hasch_seq(char *seq1, int **hs, int **lu,int ktup, char *alph);
+int fasta_gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int cfasta_gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int very_fast_gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+
+int make_fasta_gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL, int *diag);
+/*********************************************************************/
+/* */
+/* KTUP_DP */
+/* */
+/* */
+/*********************************************************************/
+
+int precomputed_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int ktup_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int ktup_comparison ( char *seq1, char *seq2, int ktup);
+HaschT* hasch_sequence ( char *seq1, int ktup);
+
+SeqHasch * seq2hasch (int i,char *seq, int ktup, SeqHasch *H);
+Constraint_list * hasch2constraint_list (Sequence*S, Constraint_list *CL);
+SeqHasch *cleanhasch (SeqHasch *H);
+int hasch2sim (SeqHasch *H, int nseq);
+int cfasta_gotoh_pair_wise_sw (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int fasta_gotoh_pair_wise_sw (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int make_fasta_gotoh_pair_wise_sw (Alignment *A,int*ns, int **l_s,Constraint_list *CL, int *diag);
+
+/*pair wise aln implementations*/
+
+int idscore_pairseq (char *s1, char *s2, int gop, int gep, int **m, char *mode);
+int idscore_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int gotoh_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int glocal_pair_wise ( Alignment *A, int *ns, int **l_s, Constraint_list *CL);
+int gotoh_pair_wise_lgp ( Alignment *A, int *ns, int **l_s, Constraint_list *CL);
+int test_pair_wise (Alignment *A, int *ns, int **l_s, Constraint_list *CL);
+
+int glocal2_pair_wise (Alignment *A,int*ns, int **ls,Constraint_list *CL);
+int linked_pair_wise ( Alignment *A, int *ns, int **l_s, Constraint_list *CL);
+int linked_pair_wise_collapse ( Alignment *A, int *ns, int **l_s, Constraint_list *CL);
+int cl2pair_list_ecl_ext_pc ( Alignment *A, int *ns, int **ls, Constraint_list *CL, int ***list_in, int *n_in);
+void free_proba_pair_wise();
+
+int subop1_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL);
+int subop2_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL);
+int proba_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL);
+int viterbi_pair_wise ( Alignment *A, int *ns, int **ls, Constraint_list *CL);
+int biphasic_pair_wise ( Alignment *A, int *ns, int **l_s, Constraint_list *CL);
+
+
+
+
+
+
+
+
+int cfasta_cdna_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+int fasta_cdna_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+Dp_Model* initialize_dna_dp_model (Constraint_list *CL);
+Dp_Result * make_fast_dp_pair_wise (Alignment *A,int*ns, int **l_s, Constraint_list *CL,Dp_Model *M);
+int make_fasta_cdna_pair_wise (Alignment *B,Alignment *A,int*ns, int **l_s,Constraint_list *CL, int *diag);
+
+
+
+int ** evaluate_diagonals_cdna ( Alignment *A, int *ns, int **l_s, Constraint_list *CL,int maximise,int n_groups, char **group_list, int ktup);
+int cfasta_cdna_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL);
+Alignment *clean_maln ( Alignment *A, Alignment *I, int T, int n_it);
+Alignment *realign_segment (int seq, int start, int len,Alignment *A, Alignment *C);
+Dp_Model * initialize_seg2prf_model(int left_tg_mode, int right_tg_mode, Constraint_list *CL);
+
+int get_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_start_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_term_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+Dp_Model * initialize_sseq_model(int left_tg_mode, int right_tg_mode, Constraint_list *CL);
+int ssec_pwaln_maln (Alignment *A, int *ns, int **ls, Constraint_list *CL);
+
+
+int get_turn_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_turn_start_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_turn_term_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+int get_alpha_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_alpha_start_gep_cost(Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_alpha_term_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+int get_beta_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_beta_start_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_beta_term_gep_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+int get_alpha_sub_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_beta_sub_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_turn_sub_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+int get_ssec_no_cost (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int sim_pair_wise_lalign (Alignment *in_A, int *in_ns, int **in_l_s, Constraint_list *in_CL);
+
+/*pair wise aln implementations*/
+int myers_miller_pair_wise (Alignment *A, int *ns, int **l_s,Constraint_list *CL);
+int diff (Alignment *A, int *ns, int **ls, int s1, int M,int s2, int N , int tb, int te, Constraint_list *CL, int **pos);
+int evaluate_est_order (Sequence *S, char *concat, Constraint_list *CL, int ktuple);
+
+Constraint_list *prepare_cl_for_moca ( Constraint_list *CL);
+Alignment ** moca_aln ( Constraint_list *CL);
+Alignment * extract_domain ( Constraint_list *CL);
+Alignment * interactive_domain_extraction ( Constraint_list *CL);
+int print_moca_interactive_choices ();
+
+Alignment * approximate_domain ( int min_start, int max_start, int step_start,int min_len, int max_len, int step_len, int *best_start, int *best_len, int *best_score, Constraint_list *CL);
+
+int measure_domain_length ( Constraint_list *CL,Alignment *IN, int start, int min_size, int max_size, int step);
+Alignment *extract_domain_with_coordinates ( Alignment *RESULT,int start, int len, Constraint_list *CL);
+int get_starting_point ( Constraint_list *CL);
+
+Alignment * find_domain_coordinates (Constraint_list *CL, int *start, int *len);
+Alignment * extend_domain ( Constraint_list *CL, int *start, int *len, int dstart, int dlen);
+Alignment * modify_domain ( Constraint_list *CL, Alignment *IN, int *start, int *len, int dstart, int dlen);
+
+int * analyse_sequence ( Constraint_list *CL);
+
+/****************************************************************************/
+/* */
+/* */
+/* Alignment Methods */
+/* */
+/* */
+/****************************************************************************/
+Alignment * sorted_aln (Alignment *A, Constraint_list *CL);
+Alignment * sorted_aln_seq (int seq, Alignment *A, Constraint_list *CL);
+Alignment * full_sorted_aln (Alignment *A, Constraint_list *CL);
+
+/******************************************************************/
+/* MAIN DRIVER */
+/* */
+/* */
+/******************************************************************/
+
+Constraint_list *profile2list ( Job_TC *job,int nprf);
+Constraint_list *seq2list (Job_TC *Job);
+Constraint_list *method2pw_cl (TC_method *M, Constraint_list *CL);
+int method_uses_structure(TC_method *M);
+int method_uses_profile(TC_method *M);
+
+/******************************************************************/
+/* MULTIPLE ALIGNMENTS */
+/* */
+/* */
+/******************************************************************/
+Alignment * compute_prrp_aln (Alignment *A, Constraint_list *CL);
+Alignment * compute_clustalw_aln (Alignment *A, Constraint_list *CL);
+Alignment * compute_tcoffee_aln_quick (Alignment *A, Constraint_list *CL);
+Alignment * seq2clustalw_aln (Sequence *S);
+Alignment * aln2clustalw_aln (Alignment *A, Constraint_list *CL);
+Alignment * realign_block ( Alignment *A, int col1, int col2, char *pg);
+/******************************************************************/
+/* DNA */
+/* */
+/* */
+/******************************************************************/
+Constraint_list * align_coding_nucleotides (char *seq, char *method, char *weight, char *mem_mode, Constraint_list *CL);
+/******************************************************************/
+/* STRUCTURES */
+/* */
+/* */
+/******************************************************************/
+Constraint_list * seq_msa (TC_method *M , char *in_seq, Constraint_list *CL);
+
+Constraint_list *align_pdb_pair (char *seq_in, char *dp_mode,char *evaluate_mode, char *file, Constraint_list *CL, Job_TC *job);
+Constraint_list * align_pdb_pair_2 (char *seq, Constraint_list *CL);
+
+Constraint_list * pdb_pair ( TC_method*M,char *seq, Constraint_list *CL);
+Constraint_list * pdbid_pair ( TC_method*M,char *seq, Constraint_list *CL);
+Constraint_list * profile_pair ( TC_method*M,char *seq, Constraint_list *CL);
+Constraint_list * thread_pair ( TC_method*M,char *seq, Constraint_list *CL);
+Constraint_list * thread_pair2 ( TC_method *M,int s1, int s2, Constraint_list *CL);
+Constraint_list * sap_pair (char *seq, char *weight, Constraint_list *CL);
+Constraint_list * lsqman_pair (char *seq, Constraint_list *CL);
+Constraint_list * rna_pair (TC_method *M , char *in_seq, Constraint_list *CL);
+
+/******************************************************************/
+/* GENERIC PAIRWISE METHODS */
+/* */
+/* */
+/******************************************************************/
+Constraint_list *best_pair4prot (Job_TC *job);
+Constraint_list *best_pair4rna (Job_TC *job);
+Alignment * fast_pair (Job_TC *job);
+
+void toggle_case_in_align_two_sequences(int value);
+Alignment * align_two_sequences ( char *seq1, char *seq2, char *matrix, int gop, int gep, char *align_mode);
+Alignment * align_two_aln ( Alignment *A1, Alignment *A2, char *in_matrix, int gop, int gep, char *in_align_mode);
+NT_node make_root_tree ( Alignment *A,Constraint_list *CL,int gop, int gep,Sequence *S, char *tree_file,int maximise);
+NT_node ** make_tree ( Alignment *A,Constraint_list *CL,int gop, int gep,Sequence *S, char *tree_file, int maximise);
+int ** get_pw_distances ( Alignment *A,Constraint_list *CL,int gop, int gep, char **out_seq, char **out_seq_name, int out_nseq, char *tree_file, char *tree_mode, int maximise);
+Alignment *stack_progressive_nol_aln_with_seq_coor(Constraint_list *CL,int gop, int gep,Sequence *S, int **seq_coor, int nseq);
+Alignment *stack_progressive_aln_with_seq_coor (Constraint_list*CL,int gop, int gep, Sequence *S, int **coor, int nseq);
+Alignment *stack_progressive_aln(Alignment *A, Constraint_list *CL, int gop, int gep);
+Alignment *est_progressive_aln(Alignment *A, Constraint_list *CL, int gop, int gep);
+void analyse_seq ( Alignment *A, int s);
+
+char ** list_file2dpa_list_file (char **list_file, int *len,int maxnseq, Sequence *S);
+Alignment * seq2aln_group (Alignment *A, int T, Constraint_list *CL);
+
+Alignment *profile_aln (Alignment *A, Constraint_list *CL);
+Alignment * iterative_tree_aln (Alignment *A,int n, Constraint_list *CL);
+Alignment * iterative_aln ( Alignment*A, int nseq, Constraint_list *CL);
+Alignment * seq_aln ( Alignment*A, int nseq, Constraint_list *CL);
+Alignment *tsp_aln (Alignment *A, Constraint_list *iCL, Sequence *S);
+Alignment *iterate_aln ( Alignment*A, int nit, Constraint_list *CL);
+Alignment *realign_aln ( Alignment*A, Constraint_list *CL);
+Alignment *very_fast_aln (Alignment*A, int nseq, Constraint_list *CL);
+Alignment *simple_progressive_aln (Sequence *S, NT_node **T, Constraint_list *CL, char *mat);
+Alignment *frame_aln (Alignment *A, int n,Constraint_list *CL);
+Alignment *dpa_aln (Alignment *A, Constraint_list *CL);
+Alignment *new_dpa_aln (Alignment *A, Constraint_list *CL);
+Alignment * make_delayed_tree_aln (Alignment *A,int n, Constraint_list *CL);
+
+NT_node* delayed_tree_aln ( NT_node LT, NT_node RT, Alignment*A, int nseq, Constraint_list *CL);
+int node2seq_list (NT_node P, int *ns, int *ls);
+Alignment* delayed_tree_aln1 ( NT_node P,Alignment*A,Constraint_list *CL, int threshold);
+Alignment* delayed_tree_aln2 ( NT_node P,Alignment*A,Constraint_list *CL, int threshold);
+
+NT_node* tree2ao (NT_node LT, NT_node RT,Alignment *A, int nseq,Constraint_list *CL);//tree2align_order
+NT_node* tree_aln ( NT_node LT, NT_node RT, Alignment*A, int nseq, Constraint_list *CL);
+NT_node* local_tree_aln ( NT_node LT, NT_node RT, Alignment*A, int nseq, Constraint_list *CL);
+NT_node* seqan_tree_aln ( NT_node LT, NT_node RT, Alignment*A, int nseq, Constraint_list *CL);
+
+
+NT_node* tree_realn ( NT_node LT, NT_node RT, Alignment*A, int nseq, Constraint_list *CL);
+
+int split_condition (int nseq, int score, Constraint_list *CL);
+
+int profile_pair_wise (Alignment *A, int n1, int *l1, int n2, int *l2, Constraint_list *CL);
+int pair_wise (Alignment *A, int*ns, int **l_s,Constraint_list *CL );
+
+int empty_pair_wise ( Alignment *A, int *ns, int **l_s, Constraint_list *CL, int glocal);
+
+
+Pwfunc get_pair_wise_function (Pwfunc func, char *dp_mode, int *glocal);
+
+
+
+char *build_consensus ( char *seq1, char *seq2, char *dp_mode);
+int fastal (int argv, char **arg);
+
+int domain_pair_wise (Alignment *A,int*ns, int **l_s,Constraint_list *CL );
+Alignment *domain_match_list2aln ( Alignment *A,int *ns,int **l_s,int **ml, int nseq, int len);
+Alignment * domain_seq2domain (Constraint_list *CL,int scale,int gop,int gep,Alignment *SEQ_DOMAIN, Alignment *TARGET);
+
+
+int custom_pair_score_function1 (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int custom_pair_score_function2 (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int custom_pair_score_function3 (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int custom_pair_score_function4 (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int custom_pair_score_function5 (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int custom_pair_score_function6 (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int custom_pair_score_function7 (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int custom_pair_score_function8 (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int custom_pair_score_function9 (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int custom_pair_score_function10 (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int apdb (int argc, char *argv[]);
+
+Constraint_list * set_constraint_list4align_pdb (Constraint_list *inCL,int seq, char *dp_mode, char *hasch_mode, char *param_file);
+int evaluate_ca_trace_sap2_bubble (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int evaluate_ca_trace_nb (Constraint_list *CL, int s1, int s2, int r1, int r2);
+int evaluate_ca_trace_bubble (Constraint_list *CL, int s1, int s2, int r1, int r2);
+int evaluate_ca_trace_sap1_bubble (Constraint_list *CL, int s1, int s2, int r1, int r2);
+int evaluate_ca_trace_3D_bubble (Constraint_list *CL, int s1, int s2, int r1, int r2);
+int evaluate_ca_trace_transversal (Constraint_list *CL, int s1, int s2, int r1, int r2);
+int evaluate_ca_trace_bubble_2 (Constraint_list *CL, int s1, int s2, int r1, int r2);
+int evaluate_ca_trace_bubble_3 (Constraint_list *CL, int s1, int s2, int r1, int r2);
+
+
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS FOR COMPARING TWO NEIGHBORHOODS:START */
+/* */
+/*********************************************************************************************/
+float matrix_match (Constraint_list *CL, int s1, int s2, int r1, int r2, Struct_nb *nbs1, Struct_nb *nbs2);
+float transversal_match (Constraint_list *CL, int s1, int s2, int r1, int r2, Struct_nb *nbs1, Struct_nb *nbs2);
+float neighborhood_match (Constraint_list *CL, int s1, int s2, int r1, int r2,Struct_nb *nbs1, Struct_nb *nbs2);
+float sap1_neighborhood_match (Constraint_list *CL, int s1, int s2, int r1, int r2, Struct_nb *nbs1, Struct_nb *nbs2);
+float sap2_neighborhood_match (Constraint_list *CL, int s1, int s2, int r1, int r2, Struct_nb *nbs1, Struct_nb *nbs2);
+
+
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS FOR COMPARING TWO NEIGHBORHOODS:END */
+/* */
+/*********************************************************************************************/
+Alignment * analyse_pdb ( Alignment *A, Alignment *ST, char *filename);
+Alignment * msa2struc_dist ( Alignment *A, Alignment *ST, char *filename, int gapped, int min_ncol);
+float **** analyse_pdb_residues ( Alignment *A, Constraint_list *CL, Pdb_param *pdb_param);
+
+float square_atom ( Atom *X);
+Atom* reframe_atom ( Atom *X, Atom*Y, Atom *Z, Atom *IN, Atom *R);
+Atom* add_atom ( Atom *A, Atom*B, Atom *R);
+Atom* diff_atom ( Atom *A, Atom*B, Atom *R);
+Atom * copy_atom ( Atom *A, Atom*R);
+/************************************************************************/
+/* */
+/* NUSSINOV */
+/* */
+/************************************************************************/
+char *nussinov (char *S, int min_dist);
+char * rna_struc2rna_lib ( char *seq_name, char *seq, char *name);
+int display_rna_ss ( int pos, char *seq, char *struc, FILE *fp);
+int evaluate_aln_gibbs ( Alignment *A, Constraint_list *CL);
+int evaluate_moca_domain ( Alignment *A, Constraint_list *CL);
+int moca_residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int moca_evaluate_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int moca_slow_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+int **cache_cl_with_moca_domain (Alignment *A, Constraint_list *CL);
+Alignment *make_moca_nol_aln ( Alignment *A, Constraint_list *CL);
+/*********************************************************************************************/
+/* */
+/* DOMAIN Z SCORE EVALUATION */
+/* */
+/*********************************************************************************************/
+
+int evaluate_domain_aln_z_score (Alignment *A, int start, int end,Constraint_list *CL, char *alphabet);
+int evaluate_domain_aln ( Alignment *A, int start, int end,Constraint_list *CL);
+
+
+
+int unpack_seq_residues ( int *s1, int *r1, int *s2, int *r2, int **packed_seq_lu);
+Alignment * unpack_seq_aln ( Alignment *A,Constraint_list *C);
+typedef struct
+{
+ int N_COMPONENT;
+ double *double_logB_alpha;
+ double *exponant_list;
+ double **ALPHA;
+ double *DM_Q;
+ double *alpha_tot;
+ int n_aa;
+ int tot_n;
+}
+Mixture;
+
+double int_logB (int *i, int n);
+double float_logB (float *i, int n);
+double double_logB (double *x, int n);
+double *** make_lup_table ( Mixture *D);
+double double_logB2(int j, double *n,Mixture *D);
+double compute_exponant ( double *n, int j, Mixture *D);
+
+double *compute_matrix_p ( double *n,int Nseq);
+double* compute_dirichlet_p ( double *n,int Nseq);
+void precompute_log_B ( double *table,Mixture *D);
+double compute_X (double *n,int i,Mixture *D);
+Mixture *read_dirichlet ( char *name);
+int dirichlet_code( char aa);
+
+double lgamma2 ( double x);
+double lgamma_r(double x, int *signgamp);
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS FOR EVALUATING THE CONSISTENCY BETWEEN ALN AND CL */
+/* */
+/*********************************************************************************************/
+Alignment * overlay_alignment_evaluation ( Alignment *I, Alignment *O);
+Alignment * main_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL, const char *mode );
+int aln2ecl_raw_score (Alignment *A, Constraint_list *C);
+int sub_aln2ecl_raw_score (Alignment *A, Constraint_list *CL, int ns, int *ls);
+int sub_aln2sub_aln_raw_score ( Alignment *IN,Constraint_list *CL, const char *mode, int *ns, int **ls);
+int node2sub_aln_score(Alignment *A,Constraint_list *CL, char *mode, NT_node T);
+int sub_aln2sub_aln_score ( Alignment *IN,Constraint_list *CL, const char *mode, int *ns, int **ls);
+Alignment * main_coffee_evaluate_output_sub_aln ( Alignment *IN,Constraint_list *CL, const char *mode, int *ns, int **ls);
+
+Alignment * categories_evaluate_output ( Alignment *IN,Constraint_list *CL);
+Alignment * matrix_evaluate_output ( Alignment *IN,Constraint_list *CL);
+Alignment * sar_evaluate_output ( Alignment *IN,Constraint_list *CL);
+Alignment * boxshade_evaluate_output ( Alignment *IN,Constraint_list *CL, int T);
+Alignment * triplet_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL);
+Alignment * fast_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL);
+
+int slow_coffee_evaluate_sub_aln ( Alignment *IN,int *ns, int **ls, Constraint_list *CL);
+Alignment * slow_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL);
+Alignment * non_extended_t_coffee_evaluate_output( Alignment *IN,Constraint_list *CL);
+Alignment * heuristic_coffee_evaluate_output ( Alignment *IN,Constraint_list *CL);
+Alignment *coffee_seq_evaluate_output ( Alignment *IN, Constraint_list *CL);
+/*Old Function: To deprecate*/
+Alignment * coffee_evaluate_output ( Alignment *IN,Constraint_list *CL);
+
+/*********************************************************************************************/
+/* */
+/* PROFILE/PRofile Functions */
+/* */
+/*********************************************************************************************/
+Profile_cost_func get_profile_mode_function (char *name, Profile_cost_func func);
+int generic_evaluate_profile_score (Constraint_list *CL,Alignment *Prf1, int s1, int r1, Alignment *Prf2, int s2, int r2, Profile_cost_func prf_prf);
+int cw_profile_profile (int *prf1, int *prf2, Constraint_list *CL);
+int muscle_profile_profile (int *prf1, int *prf2, Constraint_list *CL);
+
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS FOR GETING THE COST : (Sequences) ->evaluate_residue_pair */
+/* */
+/*********************************************************************************************/
+int initialize_scoring_scheme (Constraint_list *CL);
+int evaluate_blast_profile_score (Constraint_list *CL, int s1, int r1, int s2, int r2);
+int evaluate_aln_profile_score (Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+int evaluate_profile_score ( Constraint_list *CL,Alignment *Prf1, int s1, int r1, Alignment *Prf2, int s2, int r2);
+int evaluate_cdna_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int evaluate_diaa_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int evaluate_monoaa_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int evaluate_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int evaluate_tm_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int evaluate_ssp_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int evaluate_curvature_score ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+int evaluate_combined_matrix_score ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int evaluate_physico_score ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int residue_pair_non_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+int residue_pair_extended_list4rna1 ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int residue_pair_extended_list4rna2 ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int residue_pair_extended_list4rna3 ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int residue_pair_extended_list4rna4 ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int residue_pair_extended_list4rna ( Constraint_list *CL, Constraint_list *R, int s1, int r1, int s2, int r2);
+
+int residue_pair_extended_list_raw ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int residue_pair_extended_list_pc ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int residue_pair_extended_list_4gp ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int residue_pair_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+
+
+
+int residue_pair_extended_list_g_coffee_quadruplet ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int residue_pair_extended_list_g_coffee ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int residue_pair_extended_list_quadruplet ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int residue_pair_extended_list_mixt ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int residue_pair_test_function ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+int extend_residue_pair ( Constraint_list *CL, int s1, int r1, int s2, int r2);
+
+int residue_pair_relative_extended_list ( Constraint_list *CL, int s1, int r1, int s2, int r2 );
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS FOR GETTING THE PW COST : CL->get_dp_cost */
+/* */
+/*********************************************************************************************/
+int get_dp_cost_blosum_matrix (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_dp_cost_pam_matrix (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_dp_cost_pw_matrix (Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+int get_cdna_best_frame_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_dp_cost_quadruplet ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+
+int very_fast_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+int cw_profile_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int cw_profile_get_dp_cost_window ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+int consensus_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+int fast_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int fast_get_dp_cost_2 ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int fast_get_dp_cost_3 ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+int fast_get_dp_cost_quadruplet ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+int check_fast_profile_mode (Alignment *A, int ns1,int *list1,int ns2, int *list2, Constraint_list *CL);
+int check_fast_mode (Alignment *A, int ns1,int *list1,int ns2, int *list2, Constraint_list *CL);
+
+
+int slow_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int slow_get_dp_cost_pc ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int slow_get_dp_cost_test ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+
+int sw_get_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2, Constraint_list *CL);
+int get_domain_dp_cost ( Alignment *A, int**pos1, int ns1, int*list1, int col1, int**pos2, int ns2, int*list2, int col2,Constraint_list *CL , int scale , int gop, int gep);
+
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS FOR ANALYSING AL OR MATRIX */
+/* */
+/*********************************************************************************************/
+float ** initialise_aa_physico_chemical_property_table (int *n);
+int aln2n_res ( Alignment *A, int start, int end);
+float get_gop_scaling_factor ( int **matrix,float id, int l1, int l2);
+float get_avg_matrix_mm ( int **matrix, char *alphabet);
+float get_avg_matrix_match ( int **matrix, char *alphabet);
+float get_avg_matrix_diff ( int **matrix1,int **matrix2, char *alphabet);
+float measure_matrix_enthropy (int **matrix,char *alphabet);
+float measure_matrix_pos_avg (int **matrix,char *alphabet);
+float evaluate_random_match (char *matrix, int n, int len,char *alp);
+float compare_two_mat (char *mat1,char*mat2, int n, int len,char *alp);
+float compare_two_mat_array (int **matrix1,int **matrix2, int n, int len,char *alp);
+int ** rescale_two_mat (char *mat1,char*mat2, int n, int len,char *alp);
+int ** rescale_matrix ( int **mat, float lambda, char *alp);
+int **mat2inverted_mat (int **matrix, char *alp);
+void output_matrix_header ( char *name, int **matrix, char *alp);
+float evaluate_random_match2 (int **matrix, int n, int len,char *alp);
+float measure_lambda2(char *mat1,char*mat2, int n, int len,char *alp);
+float measure_lambda(char *mat1,char*mat2, int n, int len,char *alp);
+Constraint_list * choose_extension_mode ( char *extend_mode, Constraint_list *CL);
+int ** combine_two_matrices ( int **mat1, int **mat2);
+/*********************************************************************************************/
+/* */
+/* OFF THE SHELVES EVALUATION */
+/* */
+/*********************************************************************************************/
+float sum_pair ( Alignment*A,char *mat_name, int gap_op, int gap_ext);
+int lat_sum_pair (Alignment *A, char *mat);
+int ** show_pair(int istart, int iend, int jstart, int jend, int *seqlen_array, char **seq_array, int dna_ktup, int dna_window, int dna_wind_gap, int dna_signif,int prot_ktup, int prot_window,int prot_wind_gap,int prot_signif, int nseqs,int dnaflag, int max_aa, int max_aln_length );
+/*By convention, 0: START, 1: END*/
+
+struct Hmm
+{
+
+ double freeT; /*Free transition*/
+ double forbiden; /*Forbiden transition*/
+ int start; /*start, by convention: 0*/
+ int end; /*end, by convention: 1*/
+
+ int nS; /*Number of states*/
+ int order;
+ struct HmmState **S; /*State List*/
+
+ /*Bounded HMM*/
+ double **T; /*Transition matrix*/
+ int **fromM; /*For any sate s, fromM[0]->number of states leading to s*/
+ int **toM; /*For any sate s, toM[0]->number of s can go to*/
+ /*End and Start are NOT included in toM and FromM*/
+
+
+};
+typedef struct Hmm Hmm;
+
+struct HmmAln
+{
+ Hmm *H;
+ int *state_list;
+};
+typedef struct HmmAln HmmAln;
+
+typedef double (*Generic_em_func)(struct Hmm*, struct HmmState*, int);
+
+struct HmmState
+{
+char name[100];
+int state;
+int DJ;
+int DI;
+
+ /*Pair HMM*/
+double em;
+Col_cost_func em_func;
+
+ /*Linear HMM*/
+double *em2;
+Generic_em_func em_func2;
+int nT;
+struct StateTrans **T;
+};
+typedef struct HmmState HmmState;
+
+struct StateTrans
+{
+ char name[101];
+ double tr;
+};
+typedef struct StateTrans StateTrans;
+
+struct MatState
+{
+ int i;
+ int j;
+ int st;
+ int pst;
+ double sc;
+ struct MatState *n;
+ struct MatState *p;
+ struct MatState *m; /*memory*/
+ struct MatState *s; /*memory of the start point*/
+ /*Heap Mamagement: Never copy*/
+ struct MatState *Hn;/*Heap Next*/
+ struct MatState *Hp;/*Heap Previous*/
+
+ struct MatState *Mn;/*Marked Heap section*/
+ struct MatState *Mp;/*Marked Heap Section*/
+ int free;
+};
+typedef struct MatState MatState;
+
+
+/*********************************************************************************/
+/* */
+/* */
+/* simple HMM: Viterbi */
+/* */
+/* */
+/*********************************************************************************/
+int seq_viterbi_pair_wise (Alignment *A,int*ns, int **ls,Constraint_list *CL);
+
+/*********************************************************************************/
+/* */
+/* */
+/* HMM: Viterbi */
+/* */
+/* */
+/*********************************************************************************/
+
+int viterbi_pair_wise_OLD (Alignment *A,int*ns, int **ls,Constraint_list *CL);
+Alignment * viterbipath2aln (Alignment *A, int *ns,int **ls,int *tb, Hmm *H);
+double*** viterbi_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL);
+int * viterbi2path (int l1,int l2, Hmm *H, double ***M);
+/*********************************************************************************/
+/* */
+/* */
+/* HMM modeling */
+/* */
+/* */
+/*********************************************************************************/
+int viterbiL_pair_wise (Alignment *A,int*ns, int **ls,Constraint_list *CL);
+MatState* RviterbiL_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E);
+MatState* viterbiL_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL, MatState *S, MatState *E);
+
+int viterbiD_pair_wise (Alignment *A,int*ns, int **ls,Constraint_list *CL);
+double lu_RviterbiD_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E, int **seg_list);
+MatState* RviterbiD_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E, int **seg_list);
+MatState* viterbiD_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL, MatState *S, MatState *E, int **seg_list);
+int **seglist2table ( int **seglist,int l1, int l2);
+int *seglist2line ( int **seglist, int line, int start, int end);
+int * traceback (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E, int **seg_list);
+
+int viterbiDGL_pair_wise (Alignment *A,int*ns, int **ls,Constraint_list *CL);
+double lu_RviterbiDGL_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E, int **seg_list);
+MatState* RviterbiDGL_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E, int **seg_list);
+MatState* viterbiDGL_hmm (Alignment *A,int *ns, int **ls, Hmm *H, Constraint_list *CL,MatState *S, MatState *E, int **seg_list);
+
+
+/*********************************************************************************/
+/* */
+/* */
+/* HMM modeling */
+/* */
+/* */
+/*********************************************************************************/
+int MatStateAreIdentical (MatState*I, MatState*O);
+int MaxDeltaMatState (MatState*I, MatState*O);
+int MinDeltaMatState (MatState*I, MatState*O);
+
+MatState * ManageMatState(int Mode, MatState *C);
+MatState* CopyMatState ( MatState*I, MatState*O);
+
+Hmm* read_hmm(char *file);
+Hmm* declare_hmm(int n);
+Hmm* free_Hmm(Hmm*H);
+void DisplayHmm ( Hmm *H);
+
+/*********************************************************************************/
+/* */
+/* */
+/* HMM Models */
+/* */
+/* */
+/*********************************************************************************/
+Hmm* define_two_mat_model(Constraint_list *CL);
+Hmm* define_probcons_model(Constraint_list *CL);
+Hmm* define_simple_model(Constraint_list *CL);
+
+Hmm * bound_hmm ( Hmm *H);
+Sequence *pavie_seq2random_seq (Sequence *S, char *subst);
+double **pavie_seq2pavie_aln(Sequence *S,char *mat, char *mode);
+Alignment *pavie_seq2pavie_sort ( Sequence *S, char *mat, char *mode);
+Alignment* pavie_seq2pavie_msa ( Sequence *S, char *mat, char *mode);
+NT_node pavie_seq2pavie_tree ( Sequence *S, char *mat, char *mode);
+int **pavie_seq2trained_pavie_mat(Sequence *S, char *param);
+int pavie_pair_wise (Alignment *A,int *ns, int **l_s,Constraint_list *CL );
+Sequence *pavie_seq2noisy_seq (Sequence *S, int val,char *subst);
+/******************************COPYRIGHT NOTICE*******************************/
+/*© Centro de Regulacio Genomica */
+/*and */
+/*Cedric Notredame */
+/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
+/*All rights reserved.*/
+/*This file is part of T-COFFEE.*/
+/**/
+/* T-COFFEE is free software; you can redistribute it and/or modify*/
+/* it under the terms of the GNU General Public License as published by*/
+/* the Free Software Foundation; either version 2 of the License, or*/
+/* (at your option) any later version.*/
+/**/
+/* T-COFFEE is distributed in the hope that it will be useful,*/
+/* but WITHOUT ANY WARRANTY; without even the implied warranty of*/
+/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the*/
+/* GNU General Public License for more details.*/
+/**/
+/* You should have received a copy of the GNU General Public License*/
+/* along with Foobar; if not, write to the Free Software*/
+/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
+/*............................................... |*/
+/* If you need some more information*/
+/* cedric.notredame@europe.com*/
+/*............................................... |*/
+/**/
+/**/
+/* */
+/******************************COPYRIGHT NOTICE*******************************/
git://source.jalview.org / jabaws.git / blobdiff