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typedef struct
    char *mode;
    char *comments;
    int nseq;
    char **seq_name;
    float **PW_SD;
    float **PW_ID;
    float *SEQ_W;

typedef struct
    int **list;
    int tot_list;
    int **stem;
    int tot_stem;
    int n_fields;
    int nseq;
    int *len;
    int ***struc;
    struct Sequence *S;  

struct Sequence
      char **file;          /* file[Nseq][FILENAMELEN] name of the file that contributed each sequence*/
      char **seq_comment;     /* seq_comment[Nseq][LONG_STRING] comment read in the file */
      char **aln_comment;  /*id*/
      char **seq;          /*seq[Nseq][sequence] sequences*/
      int *len;            /*len[Nseq] length of each sequence*/
      int max_len;         /*Lenght of the longest seq */
      int min_len;         /*Length of the shortest seq*/
      int nseq;            /*nseq*/
      int max_nseq;        /*Maximum number of sequences in the datastruct*/
      char **name;         /*name[Nseq][MAXNAMELEN]*/
/*Constraint list*/
      struct Constraint_list *CL;
      int contains_gap;   /*set to 1 if gaps are to be kept*/
      char *type;         /*PROTEIN, DNA*/
      Weights *W;         /*Associated weights*/
      char template_file[100];
      struct Template **T;
typedef struct Sequence Sequence;

struct Template
  char seq_type[10];
  struct X_template *P;
  struct X_template *S;
  struct X_template *R;
  struct X_template *G;
  struct X_template *RB;
typedef struct Template Template;

struct X_template 
  char seq_name[100];
  char template_type[100];
  char template_name[100];
  char template_file[100];
  struct P_template *VP;
  struct S_template *VS;
  struct R_template *VR;
  struct G_template *VG;
  struct R_template *VRB;
typedef struct X_template X_template;

struct P_template
  char pdb_id[100];
  char public_pdb;
typedef struct P_template P_template;

struct S_template
  Sequence *S;
typedef struct S_template S_template;

struct R_template
  struct Alignment *A;
typedef struct R_template R_template;

struct G_template
  Sequence *S;
typedef struct G_template G_template;

typedef struct
    int max_len;
    int alp_size;
    char *alphabet;
    int **count3;  
    int **count;
    int **count2;  

struct Alignment
    int max_len;
    int min_len;   
    int *  len;
    int declared_len;
    int max_n_seq;
    int nseq;
    int len_aln;

/*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
                   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 */

    int *  score_seq;
    int ** score_res;
    int score_aln;
    int score;
    int cpu;
    int finished;

/*Input/Output Options*/
    int output_res_num;
    int residue_case; /*1 for lower, 0 for Upper, 2 for keeping unchanged*/
/*Must Not be copied*/
     int used;
     int num;     
     int **pos; 
/*For linked lists*/      
    struct Alignment * A;  
    int random_tag;
typedef struct Alignment Alignment;
typedef struct
    int in_seq;   
    FILE *fp;
    int font;
    int x0;
    int y0;
    int x;
    int y;
    int n_pages;
    int max_line_ppage;
    int n_line;
    int line;
    int eop;
    int in_html_span;
    char previous_html_color[100];

typedef struct
    float r;
    float g;
    float b;
    char html_color[30];
    char html_color_class[30]; 
    int ascii_value;

Sequence * fill_sequence_struc ( int nseq, char **sequences, char **seq_name);
Sequence * cw_read_sequences ( char *seq_name);
Sequence * get_sequence_type (Sequence *S);
Alignment* get_aln_type (Alignment *A);
char     * get_string_type   (char *string);

void get_sequence (char *seq_file,int *NSEQ, char ***SEQ, char ***SN, int **sl, int *min, int *max);

int ** get_matrix   ( char *name, char *format);
int ** read_matrice (char *mat_name);
int **neg_matrix2pos_matrix ( int **matrix);   

void   print_aln ( Alignment *B);

int       output_reliability_ps     ( Alignment *B,Alignment *S, char *name);
int       output_reliability_pdf    ( Alignment *B,Alignment *S, char *name);
int       output_reliability_html   ( Alignment *B,Alignment *S, char *name);
int       output_color_ps     ( Alignment *B,Alignment *S, char *name);
int       output_color_pdf    ( Alignment *B,Alignment *S, char *name);
int       output_color_html   ( Alignment *B,Alignment *S, char *name);
void      get_rgb_values(int val, Color *C);
int       output_reliability_format ( Alignment *B,Alignment *S, char *name, \
FILE_format *(*vfopen_format)          ( char *),\
FILE_format *(*print_format_string)    ( char * ,Color *, Color *, FILE_format*),\
FILE_format *(*print_format_char)      ( int    ,Color *, Color *, FILE_format*),\
void         (*get_rgb_values_format)  ( int    ,Color *),\
FILE_format* (*vfclose_format)         ( FILE_format *));
int       output_score_format ( Alignment *B,Alignment *S, char *name, \
FILE_format *(*vfopen_format)          ( char *),\
FILE_format *(*print_format_string)    ( char * ,Color *, Color *, FILE_format*),\
FILE_format *(*print_format_char)      ( int    ,Color *, Color *, FILE_format*),\
void         (*get_rgb_values_format)  ( int    ,Color *),\
FILE_format* (*vfclose_format)         ( FILE_format *));

FILE_format * print_ps_string      ( char *s , Color *box, Color *ink, FILE_format *f);
FILE_format * print_ps_char        ( int   c,    Color *box, Color *ink, FILE_format *f);

void get_rgb_values_ps ( int val, Color *C);
FILE_format* vfopen_ps ( char *name);
FILE_format* vfclose_ps ( FILE_format *fps);

FILE_format *print_html_string( char *s, Color *box, Color *ink, FILE_format *fhtml);
FILE_format * print_html_char ( int c, Color *box, Color *ink, FILE_format *f);
void get_rgb_values_html ( int val, Color *C);
FILE_format* vfopen_html ( char *name);
FILE_format* vfclose_html ( FILE_format *fhtml);

int       output_reliability_ascii     ( Alignment *B,Alignment *S, char *name);
int       output_color_ascii           ( Alignment *B,Alignment *S, char *name);

FILE_format *print_ascii_string( char *s, Color *box, Color *ink, FILE_format *fascii);
FILE_format * print_ascii_char ( int c, Color *box, Color *ink, FILE_format *f);
void get_rgb_values_ascii ( int val, Color *C);

FILE_format* vfopen_ascii ( char *name);
FILE_format* vfclose_ascii ( FILE_format *fascii);
int       output_seq_reliability_ascii     ( Alignment *B,Alignment *S, char *name);

   Main header file for ClustalW.  Uncomment ONE of the following 4 lines
   depending on which compiler you wish to use.

#define VMS 1                 /*VAX or ALPHA VMS */

/*#define MAC 1                 Think_C for MacIntosh */

/*#define MSDOS 1               Turbo C for PC's */

/*#define UNIX 1                Ultrix/Decstation, Gnu C for 
                                Sun, IRIX/SGI, OSF1/ALPHA */


#define MAXTITLES       60      /* Title length */

#define UNKNOWN   0
#define EMBLSWISS 1
#define PIR         2
#define PEARSON   3
#define GDE         4
#define CLUSTAL   5     /* DES */
#define MSF       6 /* DES */
#define USER      7     /* DES */

#define PAGE_LEN       22   /* Number of lines of help sent to screen */

#ifdef VMS                                /* Defaults for VAX VMS */
#define DIRDELIM ']'          /* Last character before file name in full file 
                                             specs */
#define SEQ_MAX_LEN           10000 /* Max Sequence Length */
#define MAXN            500         /* Max Number of Sequences */
#define FSIZE       25000   /* Work space for pairwise alignments */
#define MAXTREE         5000  /* Max Nodes for phylogenetic tree */
#define LINELENGTH      60  /* Output line length */
#define GCG_LINELENGTH  50  /* Output line length for GCG output */

#elif MAC
#define DIRDELIM ':'
#define SEQ_MAX_LEN           1000
#define MAXN            30
#define FSIZE       5000
#define MAXTREE         1000
#define LINELENGTH      50
#define GCG_LINELENGTH  50

#elif MSDOS
#define DIRDELIM '\\'
#define SEQ_MAX_LEN           1300
#define MAXN            30
#define FSIZE           5000
#define MAXTREE         1000
#define LINELENGTH      50
#define GCG_LINELENGTH  50

#elif UNIX
#define DIRDELIM '/'
#define SEQ_MAX_LEN           10000
#define MAXN            500
#define FSIZE           25000
#define MAXTREE         5000
#define LINELENGTH      60
#define GCG_LINELENGTH  50

#define NUMRES 26       /* max size of comparison matrix */

#define INPUT 0
#define ALIGNED 1

#define LEFT 1
#define RIGHT 2

#define NODE 0
#define LEAF 1

#define GAPCOL 32       /* position of gap open penalty in profile */
#define LENCOL 33       /* position of gap extension penalty in profile */

typedef struct node {         /* phylogenetic tree structure */
        struct node *left;
        struct node *right;
        struct node *parent;
        float dist;
        int  leaf;
        int order;
        char name[64];
} stree, *treeptr;

typedef struct tnode *NT_node;

typedef struct tnode{
    int visited;
    char *name;
    NT_node parent;
    NT_node left;
    NT_node right;
    NT_node bot;
    int isseq;
    int seq;
    int maxnseq;
    int nseq;
    int *lseq;
    int *lseq2;
    float dist;
    float bootstrap;
    float dp;
    int order;
  int leaf;/*Number of leave below the considered node*/
  int node;/*Number of nodes below the considered node*/
    int group;
    float score;
NT_node main_prune_tree ( NT_node T, Sequence *S);
int prune_tree ( NT_node T, Sequence *S);
/*                                                                   */
/*                                   dpa_tree_manipulation           */
/*                                                                   */
/*                                                                   */
char *tree2Ngroup (Alignment *A, NT_node T, int max_n, char *fname);
int tree2group_file ( NT_node T,Sequence *S, int maxnseq, int minsim, char *name);

NT_node tree2dpa_tree (NT_node T, Alignment *A);
FILE * tree2group ( NT_node T,Sequence *S,int maxnseq, int mindist,char *name, FILE *fp);
NT_node  tree2collapsed_tree (NT_node T, int n, char **string);

/*                                                                   */
/*                                   tree comparison                 */
/*                                                                   */
/*                                                                   */
NT_node main_compare_trees ( NT_node T1, NT_node T2, FILE *fp);
float compare_trees ( NT_node T1, NT_node T2, int nseq, int mode);
float search_node ( NT_node B, NT_node T, int nseq, int mode);
float evaluate_node_similarity ( NT_node B, NT_node T, int nseq, int mode);

int compare_node ( int *b1, int *b2, int n);
void display_node (NT_node N, char *string,int nseq);
NT_node recode_tree ( NT_node T, Sequence *S);
int compare_branch2 ( int *b1, int *b2, int n);

/*                                                                   */
/*                                   FJ_tree Computation             */
/*                                                                   */
/*                                                                   */
NT_node tree_compute ( Alignment *A, int n, char ** arg_list);
NT_node aln2fj_tree(NT_node T, Alignment *A, int limit,char* mode);
Alignment * filter_aln4tree (Alignment *A, int n,char* mode);

/*                                                                   */
/*                                   Tree Filters and MAnipulation   */
/*                                                                   */
/*                                                                   */
NT_node aln2tree (Alignment *A);
NT_node reset_boot_tree ( NT_node R, int n);
NT_node reset_dist_tree ( NT_node R, float n);
NT_node free_tree  ( NT_node R);
NT_node realloc_tree( NT_node R, int n);
NT_node free_tree_node ( NT_node R);

Sequence * tree2seq    (NT_node R, Sequence *S);
NT_node  rename_seq_in_tree ( NT_node R, char ***list);

NT_node balance_tree (NT_node);
int tree2nseq ( NT_node R);
int tree_file2nseq ( char *file);

int tree2nleaf ( NT_node R);
int tree2nnode ( NT_node R);

FILE* display_tree ( NT_node R, int n, FILE *fp);
void clear_tree (NT_node T);
void display_leaf ( NT_node T);

NT_node reroot_tree ( NT_node TREE, NT_node T);
NT_node straighten_tree ( NT_node P, NT_node C, float new_dist);
NT_node unroot_tree ( NT_node T);
FILE* print_tree ( NT_node T,char *format, FILE *fp);
FILE * rec_print_tree ( NT_node T, FILE *fp);

NT_node find_longest_branch ( NT_node T, NT_node L);
NT_node shift_root ( NT_node R);

int ** tree2cluster (NT_node T, float thres);
int ** make_sub_tree_list ( NT_node **T, int nseq, int n_node);
void make_all_sub_tree_list ( NT_node N, int **list, int *n);
void make_one_sub_tree_list ( NT_node T, int *list);
NT_node main_read_tree(char *treefile);
NT_node** read_tree(char *treefile, int *nnodes,int nseq, char **seq_names);
FILE * create_tree(NT_node ptree, NT_node parent,int *numseq,int  *ntotal,int  *nnodes,NT_node **lu, FILE *fp);
NT_node declare_tree_node (int nseq);
void set_info(NT_node p, NT_node parent, int pleaf, char *pname, float pdist, float bootstrap);
NT_node insert_tree_node(NT_node pptr);
FILE * skip_space(FILE *fd);
void create_tree_node(NT_node pptr, NT_node parent);
float calc_mean(NT_node nptr, float *maxdist, int nseq,NT_node **lu);
NT_node insert_root(NT_node p, float diff);
float calc_root_mean(NT_node root, float *maxdist, int neq, NT_node **lu);
NT_node reroot(NT_node ptree, int nseq, int ntotal, int nnodes, NT_node **lu);
/* General purpose header file - rf 12/90 */

#ifndef _H_general
#define _H_general

#define pint int              /* cast ints in printf statements as pint */
typedef int Boolean;                /* Is already defined in THINK_C */

#undef TRUE                               
#undef FALSE
#define TRUE 1
#define FALSE 0

#define EOS '\0'                    /* End-Of-String */
#define MAXLINE 512                 /* Max. line length */

#endif /* ifndef _H_general */
/*********************************COPYRIGHT NOTICE**********************************/
/* Centre National de la Recherche Scientifique (CNRS) */
/*and */
/*Cedric Notredame */
/*Tue May 10 12:08:44     2005. */
/*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*/
/*    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**********************************/

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