--- /dev/null
+/******************************COPYRIGHT NOTICE*******************************/
+/* (c) Centro de Regulacio Genomica */
+/* and */
+/* Cedric Notredame */
+/* 12 Aug 2014 - 22:07. */
+/*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*******************************/
+typedef struct
+ {
+ int p1;
+ int p2;
+ int p3;
+ int p4;
+ int t;
+ int f;
+ char mode[20];//lower, unalign
+ char model[20];//fsa1 fsa2
+}
+OveralnP;
+
+//RNA
+Constraint_list * seq2contacts (Sequence *S, Sequence *T,Constraint_list *CL, char *mode);
+Constraint_list * pdb2contacts (Sequence *S, Sequence *T,Constraint_list *CL, char *mode, float maxD);
+int vienna2template_file (char *outfile, Sequence *R, Sequence *ST);
+Constraint_list * vienna2tc_lib (char *outfile, Sequence *R, Sequence *ST);
+
+
+int ** alifold_list2cov_list (Alignment *A, int **list);
+int ** update_RNAfold_list (Alignment *A, int **pos, int s, int **l);
+int ** vienna2list ( char *seq);
+Alignment *compare_RNA_fold ( Alignment *A, Alignment *B);
+Alignment *trim_RNA (Alignment *RNA, Sequence *ST, int max);
+Alignment *sp3_evaluate (Alignment *A, Sequence *S);
+Alignment *alifold2analyze (Alignment *A, Alignment *ST, char *mode);
+Alignment *alifold2cov_aln (Alignment *A, int **l, int ug);
+Alignment *alifold2cov_stat (Alignment *A, int **l, int ug);
+Alignment *alifold2cov_list (Alignment *A, int **l, int ug);
+Alignment *alifold2cov_cache (Alignment *inA, int **l, int ug);
+
+
+Alignment *add_alifold2aln (Alignment *A, Alignment *ST);
+Alignment *aln2alifold(Alignment *A);
+
+//end
+Alignment * aln2bootstrap (Alignment *A, int n);
+Alignment * aln2sample (Alignment *A, int n);
+Alignment * aln2random_aln(Alignment *A, char *mode);
+Alignment * aln2scale (Alignment *A, char *offset);
+Alignment * aln2case_aln (Alignment *A, char *upper, char *lower);
+Alignment * aln2gap_cache (Alignment *A, int val);
+Alignment * score_aln2score_ascii_aln (Alignment *A, Alignment *C);
+int **aln2resindex ( Alignment *A, Alignment *B, FILE *fp);
+int **index_seq_res ( Sequence *S1, Sequence *S2, int **name_index);
+int **index_seq_name ( Sequence *S1, Sequence *S2);
+int *get_name_index (char **l1, int n1, char **l2, int n2);
+
+int* get_res_index (char *seq1, char *seq2);
+int * pos2list (int * pos, int len, int *nl);
+ int *list2pos (int *list, int nl, int len);
+
+
+int change_residue_coordinate ( char *in_seq1, char *in_seq2, int v);
+
+int ** minimise_repeat_coor (int **coor, int nseq, Sequence *S);
+int ** get_nol_seq( Constraint_list *CL,int **coor, int nseq, Sequence *S);
+
+
+int compare_pos_column( int **pos1,int p1, int **pos2,int p2, int nseq);
+char * seq2alphabet (Sequence *S);
+double* seq2diaa (char *buf, double *v);
+double* seq2triaa(char *buf, double *v);
+double* seq2tetraa(char *buf, double *v);
+
+char *aln2alphabet (Alignment *A);
+char *array2alphabet (char **array, int n, char *forbiden);
+
+
+
+
+//TM Predictions
+char* alnpos2hmmtop_pred (Alignment *A, Alignment *Pred, int pos, int mode);
+Alignment * aln2hmmtop_pred (Alignment *A);
+char * seq2tmstruc ( char *seq);
+
+void set_blast_default_values();
+char * seq2pdb ( Sequence *S);
+Alignment * seq2blast ( Sequence *S);
+
+Sequence * seq2unique_name_seq ( Sequence *S);
+Alignment * aln2unique_name_aln ( Alignment *S);
+int name_list2unique_name_list (int n, char **name);
+Sequence *seq2clean_seq ( Sequence *S, char *alp);//remove all alp characters from seq
+char**gene2exons (char **seq, int nseq);
+
+int ** seq2aln_pos (Alignment *A, int *n, int **ls);
+Alignment *padd_aln ( Alignment *A);
+char **padd_string ( char **string, int n,char pad);
+
+Alignment *local_maln2global_maln (char *seq, Alignment *A);
+
+Alignment * seq2profile (Sequence *S, int index);
+
+Sequence *remove_empty_sequence (Sequence *S);
+Alignment * aln2profile (Alignment * A);
+Alignment * aln2collapsed_aln (Alignment * A, int n, char **string);
+Alignment* remove_seq_from_aln (Alignment *A, char *seq);
+
+Alignment* aln2sub_aln_file (Alignment *A, int n, char **string);
+Alignment* aln2sub_seq (Alignment *A, int n, char **string);
+
+int ** aln2inv_pos (Alignment *A);
+int * seq2inv_pos ( char *seq);
+int ** aln2pos_simple (Alignment *A, int n_nseq, ...);
+int ** aln2pos_simple_2 (Alignment *A);
+Alignment ** split_seq_in_aln_list ( Alignment **aln, Sequence *S, int l_seq, char **seq_list);
+
+Sequence * fill_sequence_struc ( int nseq, char **sequences, char **seq_name, Genomic_info *genome_co);
+
+int seq_list2in_file ( TC_method *M, Sequence *S, char *list, char *file);
+int seq_list2fasta_file( Sequence *S, char *list, char *file, char *outmode);
+Structure * seq2struc ( Sequence *S, Structure *ST);
+Alignment *strings2aln (int nseq,...);
+
+Alignment * seq2aln ( Sequence *S, Alignment *A,int rm_gap);
+Alignment *seq_coor2aln ( Sequence *S, Alignment *A, int **coor, int nseq);
+
+Alignment *stack_aln (Alignment *A, Alignment *B);
+Alignment *chseqIaln(char *name, int seq_n, int start,int len,Sequence *S, int seqIaln, Alignment *A);
+
+
+char *dna_aln2cons_seq ( Alignment *A);
+char *aln2cons_seq ( Alignment *A, int ns, int *ls, int n_groups, char **group_list);
+char *aln2cons_maj ( Alignment *A, int ns, int *ls, int n_groups, char **group_list);
+Alignment *aln2conservation ( Alignment *A, int threshold,char *seq);
+
+char *sub_aln2cons_seq_mat ( Alignment *A,int ns, int *ls, char *mat_name);
+char *aln2cons_seq_mat ( Alignment*A, char *mat_name);
+Alignment *aln2short_aln( Alignment *A, char *list, char *nnew, int spacer);
+Sequence *keep_residues_in_seq ( Sequence *S,char *list, char replacement);
+Alignment *keep_residues_in_aln ( Alignment *A,char *list, char replacement);
+Alignment *filter_keep_residues_in_aln ( Alignment *A,Alignment *ST, int use_cons, int value, char *list, char replacement);
+
+Alignment *aln_convert (Alignment *A, Alignment *ST, int use_cons, int value,int n, ...);
+Alignment *aln2number (Alignment *A);
+Alignment * filter_aln ( Alignment *A, Alignment *ST, int value);
+Alignment * filter_aln_lower_upper ( Alignment *A, Alignment *ST,int use_cons, int value);
+Alignment * filter_aln_upper_lower ( Alignment *A, Alignment *ST, int use_cons,int value);
+Alignment * filter_aln_switchcase ( Alignment *A, Alignment *ST, int use_cons, int value);
+
+Alignment * STseq2STaln ( Alignment *A, Alignment *ST);
+Alignment * merge_annotation ( Alignment *A, Alignment *ST, char *seq);
+Alignment * filter_aln_convert ( Alignment *A, Alignment *ST, int use_cons,int value, int n_symbol,char** symbol_list);
+int aln2ngap (Alignment *A);
+
+int * count_in_aln ( Alignment *A, Alignment *ST, int value, int n_symbol,char **symbol_list, int *table);
+void count_misc (Alignment*A, Alignment *B);
+
+Alignment * trim_aln_with_seq ( Alignment *S, Alignment *P);
+Alignment * add_align_seq2aln ( Alignment *A, char *seq, char *seq_name);
+Alignment * aln2X (Alignment *A, int x);
+Sequence * aln2seq ( Alignment *A);
+Sequence * aln2seq_main ( Alignment *A, int mode);
+Alignment * thread_profile_files2aln (Alignment *A, char *template_file, Fname *F);
+Alignment * expand_aln (Alignment *A);
+Alignment * aln2expanded_aln (Alignment *A);
+Alignment * expand_number_aln (Alignment *A,Alignment *EA);
+Alignment * remove_gap_column ( Alignment *A, char *mode);
+Alignment* ungap_sub_aln ( Alignment *A, int nseq, int *ls);
+Sequence * ungap_seq ( Sequence *A);
+Alignment * insert_gap_col (Alignment *A, int p, int l);
+Alignment * unalign_residues (Alignment *A, int i1, int i2);
+Alignment * unalign_aln_2 (Alignment *A, Alignment *C, int t);
+Alignment * unalign_aln (Alignment *A, Alignment *C, int t);
+Alignment * unalign_aln_pos (Alignment *A, int s, int p, int l);
+
+Alignment *degap_aln (Alignment *A);
+
+Alignment * RmLowerInAln (Alignment *A, char *gap);
+Alignment * ungap_aln_n ( Alignment *A, int n);
+Alignment * ungap_aln ( Alignment *A);
+void compress_aln ( Alignment *A);
+Alignment* condense_aln (Alignment *A);
+
+Alignment * probabilistic_rm_aa ( Alignment *A, int pos, int len);
+Alignment * aln_gap2random_aa(Alignment *A);
+Alignment * make_random_aln(Alignment *A,int nseq, int len, char *alphabet);
+Alignment * add_random_sequence2aln( Alignment *A, char *alphabet);
+
+int ** trim_aln_borders ( char **seq1, char **seq2, int nseq);
+Sequence * trim_aln_seq ( Alignment *A, Alignment *B);
+Sequence * trim_aln_seq_name ( Alignment *A, Alignment *B);
+Sequence *get_defined_residues( Alignment *A);
+
+
+Alignment *thread_defined_residues_on_aln ( Alignment *A, Sequence *S1);
+Sequence *seq2number (Sequence *S);
+Sequence * merge_seq ( Sequence *IN, Sequence *OUT);
+char * seq_name2coor ( char *s, int *start, int *end, char sep);
+Alignment *seq_name2removed_seq_name(Sequence *S, Alignment *NA, float **diff);
+int seq_name2index (char *name, Sequence *S);
+
+Sequence *extract_one_seq(char *n,int start, int end, Alignment *S,int keep_name);
+Sequence * extract_sub_seq( Sequence *COOR, Sequence *S);
+
+
+Sequence * add_prf2seq (char *alnfile, Sequence *S);
+int prf_in_seq ( Sequence *S);
+Sequence * add_sequence ( Sequence *IN, Sequence *OUT, int i);
+Sequence * trim_seq ( Sequence *A, Sequence *B);
+Sequence * reorder_seq ( Sequence *A, char **name, int nseq);
+Sequence * reorder_seq_2 ( Sequence *A, int **name,int field, int nseq);
+
+char * concatenate_seq ( Sequence *S, char *conc, int *order);
+Sequence * swap_header ( Sequence *S, Sequence *H);
+
+Alignment *aln2jacknife (Alignment *A, int nseq, int len);
+char ** name2random_subset (char **in_name, int n_in, int n_out);
+Alignment * aln2random_order ( Alignment *A);
+Alignment * aln2scramble_seq ( Alignment *A);
+
+Alignment * reorder_aln ( Alignment *A, char **name, int nseq);
+
+char ** rm_name_tag (char **name, int nseq, char *tag);
+
+/******************************************************************************/
+/* TEMPLATE MANAGEMENENT */
+/******************************************************************************/
+char * string_contains_template_tag (char *string);
+Sequence * seq2template_type(Sequence *Seq);
+
+Sequence * vremove_seq_template_files (Sequence *S);
+Sequence * display_seq_template_files (Sequence *S);
+Sequence * handle_seq_template_file (Sequence *S, char *mode);
+int handle_X_template_files ( X_template *T, char *mode);
+
+
+Sequence * seq2template_seq ( Sequence *S, char *template_file, Fname *F);
+char * seq2template_file (Sequence *S, char *file);
+int seq2template_file2 (Sequence *S, char *file, char *mode);
+
+Sequence * profile_seq2template_seq ( Sequence *S, char *template_file, Fname *F);
+int seq2n_X_template ( Sequence *S, char *type);
+
+struct X_template *fill_X_template (char *name, char *p, char *type);
+FILE * display_seq_template (Sequence *S, FILE *io);
+char *template_type2type_name (char *type);
+char *template_type2short_type_name (char *type);
+
+
+FILE * display_sequence_templates ( Sequence *S, int i, FILE *io);
+FILE * display_X_template (struct X_template *X, FILE *io);
+
+struct X_template* free_X_template ( struct X_template *X);
+
+struct X_template *fill_P_template (char *name, char *p, Sequence *S);
+struct X_template *fill_F_template (char *name, char *p, Sequence *S);
+struct X_template *fill_S_template ( char *name,char *p, Sequence *S);
+struct X_template *fill_R_template (char *name, char *p, Sequence *S);
+struct X_template *fill_G_template (char *name, char *p, Sequence *S);
+struct X_template *fill_T_template (char *name, char *p, Sequence *S);
+struct X_template *fill_E_template (char *name, char *p, Sequence *S);
+struct X_template *fill_U_template (char *name, char *p, Sequence *S);
+
+char *seq2T_value ( Sequence *S, int i, char *param_name, char *template_type);
+char *profile2P_template_file (Sequence *S, int n);
+Alignment * seq2R_template_profile (Sequence *S, int n);
+char *seq2P_pdb_id (Sequence *S, int n);
+char * seq2P_template_file (Sequence *S, int n);
+char * seq2T_template_string (Sequence *S, int n);
+char * seq2E_template_string (Sequence *S, int n);
+int * seq2U_template (Sequence *S, int n);
+
+
+int seq2n_template (Sequence *S, char *type);
+struct X_template * seq_has_template ( Sequence *S, int n, char *type);
+
+/******************************************************************************/
+/* ALIGNMENT MANIPULATION */
+/******************************************************************************/
+
+char *aln_column2string (Alignment *A, int p);
+int **fix_seq_aln (Sequence *S, Alignment*A, int **cache);
+int **fix_seq_seq ( Sequence *S1, Sequence *S2);
+int **fix_aln_seq_new (Alignment *S1, Sequence *S2);
+
+Alignment * fix_aln_seq ( Alignment *A, Sequence *S);
+Alignment * rotate_aln ( Alignment *A, char *name);
+Alignment * invert_aln ( Alignment *A);
+Sequence * invert_seq2 ( Sequence *A);
+int invert_seq_file (char *seq);
+int invert_aln_file (char *seq);
+
+
+char * complement_string (char *s);
+Alignment * complement_aln ( Alignment *A);
+Alignment * extract_nol_local_aln( Alignment *A, int start, int max_end);
+Alignment * aln2block (Alignment *A, int start, int end, Alignment *B);
+Alignment * alnpos2block (Alignment *A, int*pos, Alignment *B);
+
+Alignment * extract_aln ( Alignment *A, int start, int end);
+Alignment * extract_aln2 ( Alignment *A, int start, int end, char *seq_name);
+Alignment * extract_aln3 ( Alignment *A, char *filename);
+Alignment * alnpos_list2block (Alignment *A, int n, char **in_list);
+
+Alignment * trunkate_local_aln ( Alignment *A);
+int get_nol_aln_border ( Alignment *A, int start, int direction);
+Alignment ** trim_local_aln ( Alignment *A, int **List, int ne, int **residue_list, Sequence *S);
+
+Alignment * aln_cat ( Alignment *A, Alignment *B);
+Alignment * concatenate_aln ( Alignment *A, Alignment *B, char *sep);
+char * extract_defined_seq ( char *in, int in_of, int in_start, int *aa_def, int dir, int *out_start, char *out_seq);
+int verify_aln ( Alignment *A, Sequence *S, char * error);
+Alignment * remove_end (Alignment *A);
+Alignment * orthologous_concatenate_aln (Alignment *A, Sequence *S, char *mode);
+Alignment * aln2N_replicate (Alignment *A, char *nn, char *name);
+FILE *aln2replicate (Alignment *A, FILE *fp);
+
+Alignment * voronoi_concatenate_aln (Alignment *A, Sequence *S);
+
+Alignment *adjust_est_aln ( Alignment *PW, Alignment *M, int s);
+Alignment * rename_seq_in_aln (Alignment *A, char ***list);
+Sequence * rename_seq_in_seq (Sequence *A, char ***list);
+/********************************************************************/
+/* */
+/* FLOAT SIMILARITIES */
+/* */
+/* */
+/* */
+/********************************************************************/
+float get_seq_fsim ( char *string1, char *string2, char *ignore, char *similarity_groups, int **matrix, int mode);
+float get_seq_fsim2 ( char *string1, char *string2, char *ignore, char *in_mode);
+float ** get_fsim_aln_array ( Alignment *A, char *mode);
+/********************************************************************/
+/* */
+/* ALIGNMENT ANALYSES */
+/* */
+/* */
+/* */
+/********************************************************************/
+int **sim_array2dist_array ( int **p, int max);
+int **dist_array2sim_array ( int **p, int max);
+int **normalize_array (int **p, int max, int norm);
+
+int aln2most_similar_sequence ( Alignment *A, char *mode);
+int aln2coverage ( Alignment *A, int ref_seq);
+
+double aln2entropy (Alignment *A, int *in_ls, int in_ns, float gap_threshold);
+int sub_aln2sim ( Alignment *A, int *ns, int **ls, char *mode);
+int sub_aln2max_sim ( Alignment *A, int *ns, int **ls, char *mode);
+int aln2sim2 ( Alignment *A);
+int aln2sim ( Alignment *A, char *mode);
+int seq2idscore_sim ( char *seq1, char *seq2);
+
+int aln_is_aligned ( Alignment *A);
+int* get_cdna_seq_winsim ( int *cache, char *string1, char *string2, char *ignore, char *mode, int *w);
+int get_cdna_seq_sim ( int *cache, char *string1, char *string2, char *ignore, char *mode);
+
+int seq2aln2sim (char *seq1, char *seq2, char *mode_aln, char *mode_id);
+int* get_seq_winsim( char *string1, char *string2, char *ignore, char *mode, int *w);
+int get_seq_sim ( char *string1, char *string2, char *ignore, char *mode);
+int get_seq_sim_2 ( char *string1, char *string2, char *ignore, char **gr, int ng);
+int get_seq_sim_3 ( char *string1, char *string2, char *ignore, int **mat);
+
+
+int *** get_winsim_aln_array ( Alignment *A, char *mode, int ***w);
+int ** get_sim_master_aln_array ( Alignment *A,int n, char *mode);
+
+int ** seq2sim_mat (Sequence *S, char *mode);
+int ** seq2cov_mat (Sequence *S, char *mode);
+int ** seq2comp_mat (Sequence *S, char *mode, char *comp_mode);
+
+int logid_score (int sim, int len);
+int ** fast_aln2sim_mat (Alignment *A, char *mode);
+int ** fast_aln2sim_list (Alignment *A, char *mode, int *ns, int **ls);
+
+int ** aln2dist_mat(Alignment *A);
+int ** aln2dist_mat_gap (Alignment *A);
+int ** aln2sim_mat_km (Alignment *A, char *mode);
+int ** aln2sim_mat (Alignment *A, char *mode);
+int **aln2cov (Alignment *A);
+int ** get_dist_aln_array ( Alignment *A, char *mode);
+int ** get_raw_sim_aln_array ( Alignment *A, char *mode);
+int ** get_sim_aln_array ( Alignment *A, char *mode);
+int generic_get_seq_sim ( char *seq1, char *seq2, int *cache, char *mode);
+Alignment * grep_seq (Alignment *S,char *field, char *mode, char *string);
+Alignment* modify_seq (Alignment *S,char *field, char *string1, char *string2);
+
+Sequence * seq2filter (Sequence *S_in, int min, int max);
+int ** get_cov_aln_array ( Alignment *A, char *mode);
+int ** get_cov_master_aln_array ( Alignment *A,int n, char *mode);
+
+
+int * get_aln_col_weight ( Alignment *A, char *mode);
+int analyse_aln_column ( Alignment *B, int col);
+
+int sub_aln2nseq_prf ( Alignment *A, int ns, int *ls);
+int **aln2count_mat (Alignment *A);
+int **sub_aln2count_mat2 (Alignment *A, int ns, int *ls);
+int **sub_aln2count_mat3 (char **al, int n);
+int **aln2count_mat2 (Alignment *A);
+char *aln2random_seq (Alignment *A, int noise1, int noise2, int noise3, int gap_noise);
+
+int * km2centroids (Alignment *A, int k, char *mode,int *keep);
+Alignment* km_seq (Alignment *S, int k, char *mode,char*name );
+Alignment** seq2kmeans_subset (Alignment *A, int k, int *n, char *mode);
+Alignment** seq2id_subset (Alignment *A, int k, int *n, char *mode);
+
+int* seq2kmeans_class (Alignment *A, int k, char *mode);
+
+int aln2gap_trimmed (Alignment *A, int n, char *alnf, char *seqf);
+Alignment *gap_trim (Alignment *A, int f);
+Alignment * master_trimseq( Alignment *A, Sequence *S,char *mode);
+Alignment * trimseq( Alignment *A, Sequence *S, char *mode);
+Alignment *simple_trimseq (Alignment *A,Alignment*K, char *mode, char *seq, int **sim);
+Alignment *sim_filter (Alignment *A, char *in_mode, char *seq_list);
+
+Sequence * seq_weight2species_weight (Alignment *A, Sequence *S);
+Alignment * aln2voronoi_weights (Alignment *A);
+float ** get_weight ( Alignment *A, Sequence *S, char *mode);
+float **seq2pwsim ( Alignment *A, Sequence *S, char *mode);
+Alignment * trimseq( Alignment *A, Sequence *S,char *mode);
+Alignment * tc_trimseq( Alignment *A, Sequence *S,char *mode);
+Alignment* seq2subseq3( Alignment *A, Sequence *S,int use_aln, int lower_sim,int upper_sim, int min_nseq, int trim_direction, char *weight_mode, float ***sim_weight, int *seq_list);
+Alignment* seq2subseq2( Alignment *A, Sequence *S,int use_aln, int lower_sim,int upper_sim, int max_nseq, int trim_direction, char *weight_mode, float ***weight_table, int *seq_list);
+float extreme_seq (int direction, Alignment *A,float **sim_weight,int *seq_list, int *seq_index);
+
+
+Alignment* seq2subseq1( Alignment *A, Sequence *S,int use_aln, int percent,int max_nseq,int max_diff, char *weight_mode);
+/********************************************************************/
+/* */
+/* AMINO ACID FUNCTIONS */
+/* */
+/* */
+/* */
+/********************************************************************/
+char** string2alphabet (char *string, int depth, int *falp_size);
+int is_in_same_group_aa ( char r1, char r2, int n_group, char **gl, char *mode);
+int find_group_aa_distribution (char *col, int nseq,int n_group, char **gl, int *distrib, char *mode );
+char** make_group_aa (int *ngroup, char *mode);
+char** make_group_aa_upgma (char *mat, int max_size);
+
+
+char * test_gene2prot (Constraint_list *CL, int s1);
+Alignment* gene2prot (Alignment *A);
+Alignment * dna_aln2_3frame_cdna_aln(Alignment *A,int *ns,int **l_s);
+
+int ** get_sim_aln_array_normal_distribution ( Alignment *A, char *mode, int *STD, int *CENTER);
+double normal(double x, double mean, double std);
+int generic_get_seq_sim_normal_distribution ( char *seq1, char *seq2, int*cache, char *mode, int *STD, int *CENTER);
+int get_seq_sim_distribution ( char *string1, char *string2, char *ignore, char *in_mode, int *STD, int *CENTER);
+
+Alignment *aln2clean_pw_aln (Alignment *A,OveralnP *F);
+char **pw_aln2clean_pw_aln (char ** aln,OveralnP *F);
+int * pw_aln2clean_aln_weight ( char *seq1, char *seq2, int w, OveralnP *F);
+
+float* aln2pred ( Alignment *A, Alignment*B, char *mode);
+float* analyze_overaln ( Alignment *A, Alignment *B, char *mode, int f,int p1,int p2, int p3,int filter);
+
+
+Alignment * mark_exon_boundaries (Alignment *A, Alignment *E);
+//simple_trimseq2
+//Creates Clusters
+//In each cluser there is a path between every pair of sequence
+//A path is made of edges connecting tow nodes with w>min_sim
+int ** simple_trimseq2 (int n, int **sim, int min_sim);
git://source.jalview.org / jabaws.git / blobdiff