--- /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*******************************/
+/**
+ * \file io_structures.h
+ *
+ * Defines structs like ::Seqeunce, ::Weights, ::Alignment and ::Template.
+ */
+
+#include "define_header.h"
+
+typedef struct
+ {
+ char *mode;
+ char *comments;
+ int nseq;
+ char **seq_name;
+ float **PW_SD;
+ float **PW_ID;
+ float *SEQ_W;
+ }Weights;
+
+typedef struct
+ {
+ int **list;
+ int tot_list;
+ int **stem;
+ int tot_stem;
+ int n_fields;
+ int nseq;
+ int *len;
+ int ***struc;
+ struct Sequence *S;
+ }Structure;
+
+
+typedef struct
+{
+ char *seg_name; /// Name of chromosome, contig...
+ char strand; /// The strand of the sequence: +/-
+ unsigned int start; /// Start point (always from + point of view) start at 0
+ unsigned int end; ///last nucleotide included (always from + point of view)
+ unsigned int seg_len; ///The length of the chromosome
+}
+Genomic_info;
+
+
+
+/**
+ * Container for several sequences and their attributes.
+ *
+ * \note Not all members have a documentation
+ */
+struct Sequence
+{
+ char **file; /**< \c file[\c nseq ][\c filenamelength ] Name of the file where each sequence is taken from */
+ char **seq_comment; /**< \c seq_comment[\c nseq ][\c LONG_STRING ] comment read in the fasta file */
+ char **aln_comment; /*id*/
+ char **seq; /**< \c seq[\c nseq ][\c len ] Actual sequences */
+ int *len; /**< \c len[\c nseq ] length of each sequence */
+ int max_len; /**< Lenght of the longest sequence */
+ int min_len; /**< Length of the shortest sequence */
+ int nseq; /**< Number of sequences */
+ int max_nseq; /*Maximum number of sequences in the datastruct*/
+ char **name; /**< \c name[\c nseq ][\c MAXNAMELEN ] Names of the sequences */
+ int **dc; /*coordinates on the disk. Coordinates set if seq[i]==NULL*/
+
+ struct Constraint_list *CL; /**< Points to the ::Constraint_list */
+ int contains_gap; /**< Set to 1 if gaps should be kept */
+ char *type; /**< PROTEIN, DNA, RNA */
+ Weights *W; /**< Associated ::Weight object */
+ char template_file[FILENAMELEN+1];
+ struct Template **T; /**< \c T[\c nseq ] Pointer to ::Template for each sequence */
+ char *blastdb;
+ struct Sequence *blastdbS;
+ struct Sequence *MasterS;
+ Genomic_info *genome_co; //safes genome_coordinates
+
+
+};
+typedef struct Sequence Sequence;
+
+/**
+ * Any sort of Template like PDB structure, Profile or Secondary structure.
+ *
+ * The Template structure looks a little confusing on first sight. It consists of pointers
+ * of type ::X_template to different types of templates, named after their template type (*P, *R, *R etc).
+ *
+ * The ::X_template again contains pointers to all kinds of templates, but this time with each specified type
+ * like ::P_template, ::S_template, ::R_template and so on. These specific template structures contain the
+ * actual information, like a PDB identifier, an alignment or another sequence.
+ *
+ * \attention When alternative templates are given for one sequence, the first one superseeds all the others.
+ * \todo Find out whether you can use more than one of these pointers at the same time to specify several different templates.
+ * \todo See what happens to the template files you specify in :: ... where?
+ */
+struct Template
+{
+ char seq_type[10]; /**< String containing information on which templates are used.
+ Looks like "P..S.......", for example, where dots are actually white spaces */
+ struct X_template *P; /**< PDB structure */
+ struct X_template *F; /**< RNA secondary structure */
+ struct X_template *S; /**< sequence */
+ struct X_template *R; /**< Profile */
+ struct X_template *G; /**< Genomic structure */
+ struct X_template *T; /**< transmembrane */
+ struct X_template *E; /**< secondary structure */
+ struct X_template *U; /**< Unicode, strings */
+
+ struct X_template *RB; /**< ? */
+};
+typedef struct Template Template;
+
+
+/**
+ * See ::Template
+ */
+struct X_template
+{
+ char seq_name[FILENAMELEN+1];
+ char template_type[FILENAMELEN+1];
+ char template_format[100];
+ char template_name[FILENAMELEN+1];
+ char template_file[FILENAMELEN+1];
+
+ struct P_template *VP;
+ struct F_template *VF;
+ struct S_template *VS;
+ struct R_template *VR;
+ struct G_template *VG;
+ struct T_template *VT;
+ struct E_template *VE;
+ struct U_template *VU;
+
+
+};
+typedef struct X_template X_template;
+
+/**
+ * See ::Template
+ */
+struct P_template
+{
+ char pdb_id[100]; /**< PDB identifier */
+};
+typedef struct P_template P_template;
+
+/**
+ * RNA Secondary structure, see ::Template
+ */
+struct F_template
+{
+ int l;
+};
+typedef struct F_template F_template;
+
+/**
+ * See ::Template
+ */
+struct S_template
+{
+ Sequence *S; /**< Sequence object */
+};
+typedef struct S_template S_template;
+
+
+/**
+ * Profile associated with a sequence, see ::Template
+ */
+struct R_template
+{
+ struct Alignment *A; /**< Alignment */
+};
+typedef struct R_template R_template;
+
+
+
+/**
+ * Genomic Information, see ::Template
+ */
+struct G_template
+{
+ Sequence *S; /**< Sequence object */
+};
+typedef struct G_template G_template;
+
+/**
+ * See ::Template
+ */
+struct T_template
+{
+ Sequence *S; /**< Sequence object */
+};
+typedef struct T_template T_template;
+
+/**
+ * See ::Template
+ */
+struct E_template
+{
+ Sequence *S; /**< Sequence object */
+};
+typedef struct E_template E_template;
+
+/**
+ * See ::Template
+ */
+struct U_template
+{
+ int *list; /**< Int aray */
+};
+typedef struct U_template U_template;
+
+
+typedef struct
+ {
+ int max_len;
+ int alp_size;
+ char *alphabet;
+ int **count3;
+ int **count;
+ int **count2;
+ }Profile;
+
+
+
+struct Alignment
+ {
+/*Size*/
+ int max_len;
+ int min_len;
+ int * len;
+ //int *weight;
+ int declared_len;
+ int max_n_seq;
+ int nseq;
+ int len_aln;
+/*Generic Information*/
+ char *generic_comment;
+/*Sequence Information*/
+ char **file;
+ char **seq_comment;
+ char **aln_comment;
+ char **name;
+
+ char **expanded_order;
+ char **tree_order;
+ char **seq_al;
+
+ int **order;
+ Profile *P;
+ Sequence *S;
+ struct Dp_Result *Dp_result;
+ struct Constraint_list *CL;
+
+ int **seq_cache; /*Contains the index of the residues:
+ The sequence Numbering is relative to the sequences, and not to the alignmnent
+
+ seq_cache[0][1]=3
+ indicates that in the aln residue (0)1 corresponds to [order[0][0]][3]
+ residues: 1...N
+ Sequences 0...M
+ */
+ int **cdna_cache; /*Contains the information about wheather a nucleotide is coding or not*/
+ /*Only defined if used */
+
+
+/*Weight*/
+ float *col_weight;
+ float *seq_weight;
+ float **res_weight;
+
+/*Trees*/
+ Alignment *Tree;
+ int **RepColList;//last item set to -1
+/*Score*/
+
+ double ** dm;
+ int * score_seq;
+ int ** score_res;
+ int score_aln;
+ int score;
+ int ibit;
+ int cpu;
+ int finished;
+
+/*Input/Output Options*/
+ int output_res_num;
+ int residue_case; /*1 for lower, 0 for Upper, 2 for keeping unchanged*/
+ int expand;
+ int output_tm;
+/*Must Not be copied*/
+ int used;
+ int num;
+ int **pos;
+/*For linked lists*/
+ struct Alignment * A;
+ /*Misc*/
+ int random_tag;
+
+ };
+
+typedef struct Alignment Alignment;
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