--- /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*******************************/
+
+#define SEQ2 0
+#define R2 1
+#define WE 2
+#define CONS 3
+#define MISC 4
+#define SEQ1 5
+#define R1 6
+#define INDEX 7
+
+#define ICHUNK 5
+
+#define LIST_N_FIELDS 7
+#define CLIST_TYPE int
+
+/**
+ * \file util_constraints_list.h
+ * Introduces the ::Constraint_list and other important structs.
+ *
+ * Ignore the function definitions in here because they are not complete
+ * (in fact, not all functions are defined in the header file).
+ *
+ * \attention For functions, see util_constraints_list.c!
+ */
+
+/*********************************************************************************************/
+/* */
+/* FUNCTIONS Typedef */
+/* */
+/*********************************************************************************************/
+typedef int (*Profile_cost_func) (int*, int *,struct Constraint_list *);
+typedef int (*Col_cost_func)(Alignment*, int **, int, int*, int, int **, int, int*, int, struct Constraint_list *);
+typedef int (*Pair_cost_func)(struct Constraint_list *, int, int, int, int);
+typedef int (*Pwfunc) (Alignment *, int*, int **,struct Constraint_list *);
+
+/*********************************************************************************************/
+/* */
+/* STRUCTURES FOR PDB ANALYSIS */
+/* */
+/*********************************************************************************************/
+typedef struct
+ {
+ char *use_seqan;
+}
+TC_param;
+typedef struct
+ {
+ char blast_server[FILENAMELEN+1];
+ char db[FILENAMELEN+1];
+ int min_cov;
+ int min_id;
+ int max_id;
+}
+Blast_param;
+
+typedef struct
+{
+ int n_excluded_nb;
+
+ float similarity_threshold;
+ float rmsd_threshold;
+ float md_threshold;
+ int distance_on_request;
+ char *comparison_io;
+ int print_rapdb;
+ float maximum_distance;/*Diameter of the bubble used to identify the Calpha Neighborhood*/
+ int N_ca; /*Number of Calpha to be looked at on both side*/
+ float max_delta ; /*Maximum value for delta to be positive*/
+ char *local_mode;
+ int scale; /*Value substracted to the pdb score in the bubble mode*/
+ int n_extra_param;
+ char **extra_param;
+ char *evaluate_mode;
+ char *color_mode;
+ float filter;
+ int filter_aln;
+ int irmsd_graph;
+ int nirmsd_graph;
+
+
+ }
+Pdb_param;
+
+struct Atom
+{
+ int num;
+ int res_num;/*Residue number from 1 to N*/
+ char res[10];
+ char type[10];
+ float r; //Van Der Wall Radius in Angstrom
+ float x;
+ float y;
+ float z;
+ struct Atom *N;//Next Atom in a Chain of Atoms
+ struct Atom *L;//List of Atoms linked to CA or C3'
+};
+typedef struct Atom Atom;
+
+
+typedef struct
+ {
+
+ Atom*CA;
+ Atom *C;
+ Atom *N;
+ Atom *CB;
+ }
+Amino_acid;
+
+
+typedef struct
+ {
+ /*Distances used for the Neighbour mode*/
+ int **nb; /*Neighbors of each Ca ( sorted by distance) given as atoms*/
+ /*nb[x][0] contains the number of neighbor atoms*/
+ float **d_nb; /* contains the distances between atom y=nb[x][5] and Ca x*/
+ /* !!!d_nb[x][0] is empty, the array starts at +1 to folow nb*/
+ int max_nb; /* Largest neigborhood*/
+}
+Struct_nb;
+
+typedef struct
+ {
+
+ int len; /*Number of Calpha Carbons*/
+ int n_atom; /*Number of atoms*/
+ char *name; /*Name of the sequence*/
+ char *seq; /*Sequence ( Complete)*/
+ Atom **structure; /*Atoms*/
+ Atom **ca; /*List of pointers to the Calpha Atoms from 0 to N-1*/
+ Amino_acid **peptide_chain;/*List of pointers to the Calpha Atoms from 0 to N-1*/
+
+
+ Struct_nb *Chain;
+ Struct_nb *Bubble;
+ Struct_nb *Transversal;
+
+ float ** ca_dist;
+ Pdb_param *pdb_param;
+}
+
+Ca_trace;
+/*********************************************************************************************/
+/* */
+/* MOCA: Data structure for domains and alignments */
+/* */
+/*********************************************************************************************/
+struct Moca
+{
+ /*Normalisation factor: value by which each constraint weight is decreased*/
+ int moca_scale;
+ /*Functions used for domain extraction:*/
+ /*Function for evaluating the score of a domain: returns 0 if not acceptable, value if OK*/
+ int (*evaluate_domain)(Alignment*,struct Constraint_list *);
+ int moca_threshold;
+
+ /*Function for hiding previously used residues*/
+ int ** (*cache_cl_with_domain)(Alignment*, struct Constraint_list *);
+ int **forbiden_residues; /*List of residues already used for domain construction*/
+
+
+ /*Function for trunkating the result into a non-overlapping alignment*/
+ Alignment* (*make_nol_aln)(Alignment*, struct Constraint_list *);
+
+ /*Parameters Coordinates of the first motif to extract*/
+ int moca_start;
+ int moca_len;
+ int moca_interactive;
+
+};
+typedef struct Moca Moca;
+/*********************************************************************************************/
+/* */
+/* CONSTRAINT LISTS */
+/* */
+/*********************************************************************************************/
+struct Distance_matrix
+{
+ char mode[100];
+ char sim_mode[100];
+ char nseq;
+ int **similarity_matrix; /*Pairwise ID levels: 1-10000*/
+ int **score_similarity_matrix; /*Pairwise ID levels: 1-10000*/
+ int **distance_matrix; /*Pairwise ID levels: 1-10000*/
+};
+typedef struct Distance_matrix Distance_matrix;
+
+
+/**
+ * The central data structure (library) containing nearly all information to produce an alignment.
+ *
+ * \todo Document this
+ *
+ */
+struct Constraint_list
+ {
+ /*In Case of Modif, synchronize with:
+ util_declare/declare_constraint_list
+ util_declare/cache_dp_value4constraint_list
+ util_declare/duplicate_constraint_list
+ util_declare/free_constraint_list
+ */
+
+ //Generic parameters
+ TC_param *TC;
+
+ int copy_mode;
+ struct Constraint_list *pCL;
+
+ /**
+ * ::Sequence object, containing several sequences and parameters.
+ */
+ Sequence *S;
+ int *master; //Sequences used as master sequences
+ int o2a_byte; // number of one to all provided in one go.
+ Sequence *STRUC_LIST; /*Name of the sequences with a Structure*/
+ char align_pdb_param_file[FILENAMELEN+1];
+ char align_pdb_hasch_mode[FILENAMELEN+1];
+
+
+ Weights *W; /*Sequence Weights*/
+ Distance_matrix *DM; /*Accurate Distance Matrix*/
+ Distance_matrix *ktupDM; /*Fast Distance Matrix*/
+ Fname *RunName;
+
+ int *translation;
+ char ** out_aln_format;
+ int n_out_aln_format;
+
+
+ /*Packing Sequence: To use with domain analysis*/
+ int **packed_seq_lu;
+
+ /*DATA*/
+ FILE *fp; /*File used for i/o if disk being used*/
+ //int *L; /*Array used for storing Lib if mem being used*/
+ int **M; /*substitution matrix*/
+ char rna_lib[FILENAMELEN+1]; /*name of a file containing the RNA libraries*/
+
+ /*List Information*/
+ int ne; /*Number of elements in the list*/
+ char list_name[1000]; /*Name of the list*/
+ int entry_len; /*Size of an entry in el_size*/
+ size_t el_size; /*Size of each elements in an entry in bytes*/
+
+ /*Normalisation information*/
+ int normalise;
+ int max_ext_value; /**< Maximum sum of edges going out from a single nucleotide. See ::evaluate_constraint_list_reference */
+ int max_value; /**< Overall maximum edge constraint. See ::evaluate_constraint_list_reference */
+ int overweight;
+ int filter_lib; /**< Threshold to filter the Constraint_list. Is set in ::batch_main. See ::filter_constraint_list */
+
+ /*Pair wise alignment method*/
+ int pw_parameters_set;
+ int gop;
+ int gep;
+ int f_gop;
+ int f_gep;
+ int nm_gop;
+ int nm_gep;
+
+ int nomatch;
+
+ int TG_MODE;
+ int F_TG_MODE;
+
+ char dp_mode[FILENAMELEN+1];
+ int reverse_seq;//Used for HoT
+ int extend_seq; //Used for RNA or Promoter Alignments
+ int maximise;
+ char matrix_for_aa_group[FILENAMELEN+1];
+ char method_matrix[FILENAMELEN+1];
+ float diagonal_threshold;
+ int ktup;
+ int use_fragments;
+ int fasta_step;
+ int lalign_n_top;
+ int sw_min_dist;
+ char **matrices_list;
+ int n_matrices;
+ char tree_mode[FILENAMELEN+1];
+
+ char distance_matrix_mode[FILENAMELEN+1];
+ char distance_matrix_sim_mode[FILENAMELEN+1];
+
+ Alignment *tree_aln;
+
+ /*Functions used for dynamic programming and Evaluation*/
+ int no_overaln;
+
+ Col_cost_func get_dp_cost; /**< Function for evaluating the cost of a column*/
+ Profile_cost_func profile_mode;
+ char profile_comparison [FILENAMELEN+1];
+
+ Pair_cost_func evaluate_residue_pair; /**< Function for evaluating the cost of a pair of residues */
+ Pwfunc pair_wise; /**< Function for making dynamic programming*/
+
+ /*
+ int (*get_dp_cost)(Alignment*, int **, int, int*, int, int **, int, int*, int, struct Constraint_list *);
+ int (*evaluate_residue_pair)(struct Constraint_list *, int, int, int, int);
+ int (*pair_wise)(Alignment *, int*, int **,struct Constraint_list *);
+ */
+
+ int weight_field;
+ int max_n_pair; /**< Maximum number of pairs when aligning two profiles*/
+
+ /*Extend a sequence against itself*/
+
+ /*Threading parameters*/
+ Blast_param *Prot_Blast;
+ Blast_param *Pdb_Blast;
+ Blast_param *DNA_Blast;
+ /*Split parameters*/
+ int split;
+ int split_nseq_thres;
+ int split_score_thres;
+ /*Check Structural Status*/
+ int check_pdb_status;
+ /*log*/
+ char method_log[1000];
+ char evaluate_mode[1000];
+ char method_evaluate_mode[100];
+ /*Gene Prediction Parameter*/
+ char genepred_score[100];
+
+ /*Parameters for domain extraction*/
+ Moca *moca;
+ /*Functions for hiding forbiden pairs of residues*/
+ int ****forbiden_pair_list; /* pair_list[S1][S2][L1][L2]=1 ->forbiden*/
+ /* pair_list[S1][S2][L1][L2]=0 ->allowed*/
+ /* pair_list[S1][S2][L1]=NULL ->all pairs S1L1, S2 allowed */
+ /* S-> sequences, 0..N */
+ /* L-> residues , 1..L-1 */
+
+ /*extention properties: copy*/
+ int *seq_for_quadruplet;
+ int nseq_for_quadruplet;
+
+ /*extention properties: Do Not copy*/
+ int extend_jit; /*Extend only on request*/
+ int extend_threshold; /*Do not extend pairs below the Theshold*/
+ int do_self; /*Extend a sequence against itself*/
+ char extend_clean_mode[100];
+ char extend_compact_mode[100];
+
+ /*Lookup table parameteres*/
+ /* !!!!!do not copy in duplication*/
+ /*Residue Index contains residue_index[nseq][seq_len][0]->number of links*/
+ /*[seq][res][x ]->target seq (0->N-1)*/
+ /*[seq][res][x+1]->traget res (1->len*/
+ /*[seq][res][x+2]->target weight */
+ /*It is automatically recomputed when L residue_indexed is set to 0*/
+
+ int residue_indexed;
+
+ /**
+ * Central structure containing the constraints/edges between residues.
+ *
+ * The residue index bla bla bla
+ * \todo document the residue index!
+ */
+ int ***residue_index;
+ int ** freeze;
+ int residue_field;
+
+ /*Index of the pairs of sequences within L*/
+ int seq_indexed;
+ int **start_index;
+ int **end_index;
+ int max_L_len;
+ int chunk;
+
+
+
+ /*PDB STRUCTURE ALIGNMENTS*/
+ Ca_trace ** T; /*This structure contains the PDB trace for sequences with a known Struc T[Nseq]*/
+
+ /*MISC*/
+ int cpu;
+ FILE *local_stderr;
+ char multi_thread[100];
+ char lib_list[FILENAMELEN+1];
+ char *comment;
+};
+
+typedef struct Constraint_list Constraint_list;
+
+struct TC_method
+{
+
+ char executable[FILENAMELEN+1];
+ char executable2[FILENAMELEN+1];
+ char in_flag[FILENAMELEN+1];
+ char in_flag2[FILENAMELEN+1];
+ char out_flag[FILENAMELEN+1];
+ char aln_mode[FILENAMELEN+1];
+ char out_mode[FILENAMELEN+1];
+ char seq_type[FILENAMELEN+1];
+ char weight[FILENAMELEN+1];
+ char matrix[FILENAMELEN+1];
+ int gop;
+ int gep;
+ int minid;
+ int maxid;
+ char param[1000];
+ char param1[1000];
+ char param2[1000];
+ int extend_seq;
+ int reverse_seq;
+ Constraint_list *PW_CL;
+};
+typedef struct TC_method TC_method;
+
+
+
+
+
+/**
+ * @cond INCLUDE_WITH_DOXYGEN
+ *
+ * Doxygen:
+ *
+ * Do not document these functions in the *.h file.
+ *
+ * They will be documented in the *.c file.
+ *
+ *
+ */
+
+
+
+/*********************************************************************/
+/* */
+/* PRODUCE IN LIST */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list *produce_list ( Constraint_list *CL, Sequence *S, char * method,char *weight,char *mem_mode);
+Job_TC* method2job_list ( char *method, Sequence *S,char *weight, char *lib_list, Distance_matrix *DM, Constraint_list *CL);
+
+Job_TC *job_list2multi_thread_job_list (Job_TC* ojob, char *mt, Constraint_list *CL);
+Job_TC *retrieve_lib_job ( Job_TC *job);
+Job_TC *submit_lib_job ( Job_TC *job);
+int add_method_output2method_log (char *l, char *command,Alignment *A, Constraint_list *CL, char *iofile);
+
+int check_seq_type (TC_method *M, char *slist,Sequence *S);
+int check_profile_seq_type (Sequence *S, int i, char t);
+char **method_list2method4dna_list ( char **list, int n);
+int is_in_pre_set_method_list (char *fname);
+char *** display_method_names (char *mode, FILE *fp);
+
+char *method_name2method_file (char *method);
+char *make_aln_command(TC_method *m, char *seq, char *aln);
+struct TC_method* method_file2TC_method ( char *fname);
+char *method_file_tag2value (char *method, char *tag);
+int TC_method2method_file( struct TC_method*, char *fname );
+/*********************************************************************/
+/* */
+/* WRITE IN LIST */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list * empty_constraint_list (Constraint_list *CL);
+Constraint_list * unfreeze_constraint_list (Constraint_list *CL);
+Constraint_list * freeze_constraint_list (Constraint_list *CL);
+Constraint_list * undump_constraint_list (Constraint_list *CL, char *file);
+int dump_constraint_list (Constraint_list *CL, char *file,char *mode);
+int safe_dump_constraint_list (Constraint_list *CL, char *file,char *mode, Sequence *RS);
+FILE* display_constraint_list (Constraint_list *CL, FILE *fp, char *tag);
+
+
+Constraint_list *index_constraint_list ( Constraint_list *CL);
+Constraint_list *index_res_constraint_list ( Constraint_list *CL, int field);
+Constraint_list * progressive_index_res_constraint_list ( Alignment *A, int *ns, int **ls, Constraint_list *CL);
+char ** reindex_constraint_list (char **profile, int np,char **list, int *inL, Sequence *S);
+/*********************************************************************/
+/* */
+/* ENTRY MANIPULATION */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list * add_list_entry2list (Constraint_list *CL, int n_para, ...);
+Constraint_list * evaluate_constraint_list_reference ( Constraint_list *CL);
+
+int CLisCompacted (Constraint_list *CL, char *t);
+int checkCL( Constraint_list *CL, char *t);
+Constraint_list *add_entry2list ( CLIST_TYPE *entry, Constraint_list *CL);
+Constraint_list *add_entry2list2 ( CLIST_TYPE *entry, Constraint_list *CL);
+int *extract_entry (Constraint_list *CL);
+/*********************************************************************/
+/* */
+/* LIST EXTENTION */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list *extend_list_pair (Constraint_list *CLin,char *store_mode, int s1, int s2);
+Constraint_list *extend_list (Constraint_list *CLin, char *store_mode,char *clean_mode, char *compact_mode,int do_self, Sequence *SUBSET);
+void get_bounds (Constraint_list *CL, int s1, int s2, int *start, int *end);
+int ** fill_pos_matrix (Constraint_list *CL, int beg, int end, int slen, int **pos, int *len, int mirrored);
+
+/*********************************************************************/
+/* */
+/* SEARCH IN LIST (ARRAY AND FILE) */
+/* */
+/* */
+/*********************************************************************/
+FILE * compare_list (FILE *OUT, Constraint_list *CL1,Constraint_list *CL2);
+//CLIST_TYPE *search_in_list_constraint(int *key, int k_len, int **L, int ne, int ***start_index, int ***end_index);
+CLIST_TYPE *main_search_in_list_constraint ( int *key,int *p,int k_len,Constraint_list *CL);
+Constraint_list *sort_constraint_list_inv (Constraint_list *CL, int start, int len);
+Constraint_list *invert_constraint_list (Constraint_list *CL, int start,int len);
+Constraint_list * sort_constraint_list (Constraint_list *CL, int start, int len);
+Constraint_list * sort_constraint_list_on_n_fields (Constraint_list *CL, int start, int len, int first_field, int n_fields);
+
+/*********************************************************************/
+/* */
+/* INPUT/OUTPUT */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list* read_n_constraint_list(char **fname,int n_list, char *in_mode,char *mem_mode,char *weight_mode,char *type, FILE *local_stderr, Constraint_list *CL, char *seq_source); /**< See util_constraints_list.c::read_n_constraint_list */
+Constraint_list* read_constraint_list(Constraint_list *CL,char *fname,char *in_mode,char *mem_mode,char *weight_mode);
+Constraint_list * read_constraint_list_raw_file(Constraint_list *CL, char *fname);
+
+int read_cpu_in_n_list(char **fname, int n);
+Sequence *precompute_blast_db (Sequence *S, char **ml, int n);
+int read_seq_in_list ( char *fname, int *nseq, char ***sequences, char ***seq_name, Genomic_info **genome_co);
+
+Sequence * read_seq_in_n_list(char **fname, int n, char *type, char *SeqMode);
+
+int read_cpu_in_list ( char *fname);
+int ** read_list ( char *fname, int **list,int *ne, int *nseq, int *cpu, char ***sequences, char ***seq_name);
+
+char * expand_constraint_list_file ( char *file);
+Constraint_list * read_constraint_list_file(Constraint_list *CL, char *fname);
+Constraint_list * fast_read_constraint_list_file(Constraint_list *CL, char *fname);
+
+/*********************************************************************/
+/* */
+/* EXTENDED LIST OUTPUT */
+/* */
+/* */
+/*********************************************************************/
+FILE * save_extended_constraint_list ( Constraint_list *CL, char *mode, FILE *fp) ;
+FILE * save_extended_constraint_list_pair ( Constraint_list *CL, char *mode, char* seq1, char * seq2,FILE *fp);
+
+/*********************************************************************/
+/* */
+/* LIST OUTPUT */
+/* */
+/* */
+/*********************************************************************/
+int constraint_list2raw_file ( Constraint_list *CL, char *fname, char *fmode);
+FILE * save_raw_constraint_list ( FILE *fp,Constraint_list *CL, int start,int len, int *translation);
+int save_contact_constraint_list (Constraint_list *CL, char *name);
+
+FILE * save_constraint_list ( Constraint_list *CL,int start, int len, char *fname, FILE *fp,char *mode,Sequence *S);
+FILE * save_sub_list_header ( FILE *OUT, int n, char **name, Constraint_list *CL);
+FILE * save_list_header ( FILE *OUT,Constraint_list *CL);
+FILE * save_list_footer (FILE *OUT,Constraint_list *CL);
+FILE * save_constraint_list_ascii ( FILE *OUT,Constraint_list *CL, int start,int len, int *translation);
+FILE * save_constraint_list_bin ( FILE *OUT,Constraint_list *CL, int start,int len, int *translation);
+
+/*********************************************************************/
+/* */
+/* LIST CONVERTION */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list * expand_constraint_list (Constraint_list *CL, int T);
+Constraint_list * shrink_constraint_list_indexed (Constraint_list *CL, int T);
+Constraint_list * shrink_constraint_list (Constraint_list *CL);
+Constraint_list * extend_constraint_list ( Constraint_list *CL);
+Constraint_list * relax_constraint_list (Constraint_list *CL);
+Constraint_list * relax_constraint_list_4gp (Constraint_list *CL);
+
+Constraint_list * expand_constraint_list_4gp (Constraint_list *CL, int T);
+
+Constraint_list * constraint_list2sub_constraint_list (Constraint_list *CL, Sequence *SMALL);
+Constraint_list * filter_constraint_list (Constraint_list *CL, int field, int T);
+int constraint_list_is_connected ( Constraint_list *CL);
+int constraint_list2avg ( Constraint_list *CL);
+float constraint_list2connectivity ( Constraint_list *CL);
+
+int constraint_list2fraction_covered ( Constraint_list *CL);
+
+int *seqpair2weight (int s1, int s2, Alignment *A,Constraint_list *CL, char *weight_mode, int *weight);
+Constraint_list *aln_file2constraint_list (char *alname, Constraint_list *CL,char *weight_mode);
+Constraint_list *aln2constraint_list (Alignment *A, Constraint_list *CL,char *weight_mode);
+Constraint_list *aln2constraint_list_full (Alignment *A, Constraint_list *CL,char *weight_mode);
+Constraint_list *aln2constraint_list_generic (Alignment *A, Constraint_list *CL,char *weight_mode, int top);
+
+double **list2mat (Constraint_list *CL,int s1,int s2, double *min, double *max);
+Constraint_list * constraint_list2bin_file(Constraint_list *clist);
+FILE * bin_file2constraint_list ( Constraint_list *CL, FILE *fp, char *name);
+
+int **list2residue_total_weight ( Constraint_list *CL);
+int **list2residue_total_extended_weight ( Constraint_list *CL);
+int **list2residue_partial_extended_weight ( Constraint_list *CL);
+/*******************************************************************************************/
+/* */
+/* */
+/* clean functions */
+/* */
+/* */
+/* */
+/*******************************************************************************************/
+Constraint_list *clean ( char *clean_mode,Constraint_list *C,int start, int len);
+Constraint_list * clean_shadow ( Constraint_list *CL, int start, int len);
+
+/*********************************************************************/
+/* */
+/* LIST FUNCTIONS */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list *merge_constraint_list ( Constraint_list *SL, Constraint_list *ML, char *mode);
+Constraint_list *modify_weight( Constraint_list *CL,int start, int end, char *modify_mode);
+Constraint_list *compact_list (Constraint_list *CL, char *compact_mode);
+Constraint_list *rescale_list_simple (Constraint_list *CL,int start, int len,int new_min, int new_max);
+Constraint_list *rescale_list (Constraint_list *CL,int start, int len,int max1, int max2);
+Constraint_list* filter_list (Constraint_list *CL, int start, int len,int T);
+Constraint_list *undefine_list (Constraint_list *CL);
+int ** seq2defined_residues ( Sequence *S, Constraint_list *CL);
+int ** aln2defined_residues ( Alignment *A, Constraint_list *CL);
+/*********************************************************************/
+/* DEBUG */
+/* */
+/*********************************************************************/
+void print_CL_mem(Constraint_list *CL, char *function);
+int constraint_list_is_sorted ( Constraint_list *CL);
+void check_seq_pair_in_list(Constraint_list *CL,int seq1, int seq2);
+/******************************************************************/
+/* NEW METHODS */
+/* */
+/* */
+/******************************************************************/
+
+Constraint_list * align_coding_nucleotides (char *seq, char *method, char *weight, char *mem_mode, Constraint_list *CL);
+/*********************************************************************************************/
+/* */
+/* FUNCTION FOR PRUNING THE LIST */
+/* */
+/*********************************************************************************************/
+char * list2prune_list (Sequence *S, int **sm);
+/*********************************************************************************************/
+/* */
+/* FUNCTION FOR WEIGHTING THE LIST */
+/* */
+/*********************************************************************************************/
+Constraint_list *weight_constraint_list(Constraint_list * CL, char *seq_weight);
+Weights* compute_t_coffee_weight(Constraint_list * CL);
+Constraint_list *re_weight_constraint_list(Constraint_list * CL,Weights *W);
+Constraint_list *set_weight4constraint_list(Constraint_list * CL,int w);
+
+Distance_matrix *cl2distance_matrix (Constraint_list *CL, Alignment *A, char *mode, char *sim_mode, int print);
+Distance_matrix *seq2distance_matrix (Constraint_list *CL, Alignment *A, char *mode, char *sim_mode, int print);
+
+/*********************************************************************************************/
+/* */
+/* MULTI_THREAD */
+/* */
+/*********************************************************************************************/
+int run_multi_thread_file (char *fname, char *config);
+/*********************************************************************/
+/* */
+/* RNA FUNCTIONS */
+/* */
+/* */
+/*********************************************************************/
+char * seq2rna_lib ( Sequence *S, char *name);
+Constraint_list *read_contact_lib ( Sequence *S, char *fname, Constraint_list *R);
+Constraint_list *rna_lib_extension ( Constraint_list *CL, Constraint_list *R);
+char *** produce_method_file ( char *method);
+/*********************************************************************/
+/* */
+/* SCALED CONSISTENCY */
+/* */
+/* */
+/*********************************************************************/
+Constraint_list * plib_msa (Constraint_list *CL);
+int cl2worst_seq (Constraint_list *CL, int *list, int n);
+Constraint_list *add_seq2cl(int s, Constraint_list *CL);
+
+
+
+
+/**
+ * Doxygen
+ *
+ * @endcond
+ *
+ */
+
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