--- /dev/null
+/*DEBUGGING*/
+/*#include "mshell.h"*/
+/*MEMORY MANAGEMENT*/
+#include <float.h>
+#define MY_EPS 1000*DBL_EPSILON
+//Maximum number of tries for interactibve things
+#define MAX_N_TRIES 3
+
+//Maximum CACHE and Temporary file size and age (Mb and days, 0: unlimited)
+#define TMP_MAX_SIZE 0
+#define TMP_MAX_KEEP 10
+#define CACHE_MAX_SIZE 2000
+#define CACHE_MAX_KEEP 180
+#define MAX_N_PID 260000
+//Importnat Values Affecting the Program Behavior
+#define O2A_BYTE 50
+#define SCORE_K 10
+#define NORM_F 1000
+#define PAVIE_MAT_FACTOR 1000
+#define MAXID 100
+#define CLEAN_FUNCTION NULL
+#define MINSIM_4_TCOFFEE 25 //The minimum similarity between a sequence and its PDB template
+#define MINCOV_4_TCOFFEE 25 //The minimum similarity between a sequence and its PDB template
+
+
+#define TRACE_TYPE int
+#define MAX_LEN_FOR_DP 600
+
+
+#define GIVE_MEMORY_BACK 0
+#define MEMSET0 1
+#define NO_MEMSET0 0
+/*OUTPUT DEFINITIONS*/
+#define NO_COLOR_RESIDUE 127
+#define NO_COLOR_GAP 126
+#define CLOSE_HTML_SPAN -1
+/*SPECIAL_CODES*/
+#define GAP_CODE 60
+/*TYPE DEFINITIONS*/
+
+//Formats
+#define BLAST_XML 100
+#define BLAST_TXT 101
+
+/*SWITCHES*/
+
+
+#define USED 1
+#define UNUSED 2
+
+
+#define TEMPLATES 1
+#define NOTEMPLATES 0
+
+#define EXTEND 1
+#define RESIZE 2
+
+#define SEN 0
+#define SPE 1
+#define REC 2
+#define SEN2 2
+
+#define ALL 1
+#define SEGMENTS 2
+#define DIAGONALS 3
+
+#define START_STATE 0
+#define END_STATE 1
+
+#define KEEP_CASE 2 /*Hard set in several places*/
+#define LOWER_CASE 0
+#define UPPER_CASE 1
+#define CHANGE_CASE 3
+#define KEEP_GAP 0
+#define RM_GAP 1
+
+#define KEEP_NAME 1
+
+#define CHECK 0
+#define NO_CHECK 1
+#define FORCE 2
+#define STORE 3
+#define FLUSH 4
+#define DUMP 5
+
+
+#define ON 8
+#define OFF 9
+#define LOCKED_ON 10
+#define LOCKED_OFF 11
+
+#define YES 12
+#define NO 13
+#define MAYBE 14
+
+#define NEVER 15
+#define ALWAYS 16
+#define SOMETIMES 17
+
+#define UPPER 18
+#define LOWER 19
+#define DELETE 20
+#define SWITCHCASE 21
+
+#define VECTOR 22
+#define NON_VECTOR 23
+#define NON_PROFILE 24
+#define BOOTSTRAP 25
+
+#define HEADER 26
+#define NO_HEADER 27
+
+#define VERY_VERBOSE 28
+#define VERBOSE 29
+#define SHORT 30
+#define VERY_SHORT 31
+
+#define OVERLAP 32
+#define NO_OVERLAP 33
+
+#define PRINT 34
+#define NO_PRINT 35
+
+#define FREE_ALN 36
+#define DECLARE_ALN 37
+#define EXTRACT_ALN 38
+#define CLEAN 39
+#define INTERACTIVE 40
+#define NON_INTERACTIVE 41
+#define PAD 42
+#define NO_PAD 43
+
+#define SET 44
+#define UNSET 45
+#define RESET 48
+#define ISSET 49
+#define GET 50
+
+#define ENV 52
+#define LLOCK 53
+#define LERROR 54
+#define LWARNING 55
+#define LSET 56
+#define LRESET 57
+#define LCHECK 58
+#define LREAD 59
+#define LRELEASE 60
+
+#define RETURN_ON_FAILURE 61
+#define EXIT_ON_FAILURE 62
+#define IGNORE_FAILURE 63
+
+#define _START 64
+#define _TERM 65
+
+#define GOP 0
+#define GCP 1
+#define GEP 2
+
+#define BOTTOM 0
+#define TOP 1
+
+#define FORWARD -1
+#define BACKWARD 1
+
+#define GO_LEFT -1
+#define GO_RIGHT 1
+
+#define LOCAL 1
+#define GLOBAL 2
+#define LALIGN 3
+#define MOCCA 4
+
+#define TRUE 1
+#define FALSE 0
+
+#define NEW 1
+#define OLD 0
+
+#define RANDOM 0
+#define DETERMINISTIC 1
+
+#define GREEDY 1
+#define NON_GREEDY 0
+
+#define IS_FATAL 1
+#define IS_NOT_FATAL 0
+#define NO_REPORT 2
+#define INSTALL 3
+#define INSTALL_OR_DIE 4
+
+#define OPTIONAL 1
+#define NON_OPTIONAL 0
+
+#define GV_MAXIMISE 1
+#define GV_MINIMISE 0
+
+#define MAXIMISE 1
+#define MINIMISE 0
+
+#define ALLOWED 0
+#define FORBIDEN -99999999
+#define END_ARRAY -99999990
+#define SOFT_COPY 1
+#define HARD_COPY 2
+
+#define VERY_SLOW 0
+#define SLOW 1
+#define FAST 2
+#define VERY_FAST 3
+#define SUPER_FAST 4
+#define ULTRA_FAST 5
+
+#define CODE 1
+#define DECODE 2
+#define CODELIST 3
+
+/*Identity measure*/
+#define UNGAPED_POSITIONS 1
+#define ALIGNED_POSITIONS 2
+#define AVERAGE_POSITIONS 3
+#define NOMATRIX NULL
+#define NOGROUP NULL
+#define NOALN NULL
+
+/*SIZE DEFINITIONS*/
+#define SIZE_OF_INT 10
+#define UNDEFINED FORBIDEN
+#define UNDEFINED_INT UNDEFINED
+#define UNDEFINED_FLOAT UNDEFINED
+#define UNDEFINED_DOUBLE UNDEFINED
+#define UNDEFINED_CHAR 125
+#define UNDEFINED_SHORT -125
+#define UNDEFINED_2 0
+#define UNDEFINED_RESIDUE '>'
+
+
+
+#define FACTOR 1
+#define MAX_N_SEQ 1
+#define MAX_N_ALN 1
+#define MAX_LEN_ALN 1
+#define MAX_N_LIST 100
+
+#define COMMENT_SIZE 1000
+#define MAXNAMES 100
+#define FILENAMELEN 500 /* Max. file name length */
+#define MAX_N_PARAM 2000
+#define MAX_PARAM_LEN 200
+#define MAX_LINE_LENGTH 10000
+#define ALN_LINE_LENGTH 50
+#define SHORT_STRING 10
+#define STRING 300
+#define LONG_STRING 1000
+#define VERY_LONG_STRING 10000
+
+#define AA_ALPHABET "acdefghiklmnpqrstvwy-ACDEFGHIKLMNPQRSTVWY"
+#define DNA_ALPHABET "AGCTUNRYMKSWHBVD-agctunrymkswhbvd"
+#define RNAONLY_ALPHABET "Uu"
+#define BLAST_AA_ALPHABET "arndcqeghilkmfpstwyvbzx*"
+#define NAMES_ALPHABET "1234567890ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz_|�-!%@&#-+=."
+
+#define SIZEOF_AA_MAT 60
+#define GAP_LIST "-.#*~"
+#define SSPACE " "
+
+#define MATCH 1
+#define UNALIGNED 2
+#define GAP 3
+
+#define MNE 3
+#define CODE4PROTEINS 10
+#define CODE4DNA 20
+
+#define STOCKHOLM_CHAR 'z'
+#define STOCKHOLM_STRING "z"
+
+
+/*CODE SHORT CUTS*/
+
+/*1-COMMAND LINE PROCESSING*/
+#define GET_COMMAND_LINE_INFO ((strncmp ( argv[1], "-h",2)==0)||(strncmp ( argv[1], "-man",4)==0)||(strncmp ( argv[1], "-",1)!=0))
+#define NEXT_ARG_IS_FLAG ((argc<=(a+1)) ||(( argv[a+1][0]=='-') && !(is_number(argv[a+1]))))
+
+
+/*UTIL MACROS*/
+#define BORDER(p1,l1,p2,l2) ((p1==0 || p2==0 || p1==l1 || p2==l2)?1:0)
+#define GET_CASE(f,c) ((f==UPPER_CASE)?toupper(c):((f==LOWER_CASE)?tolower(c):c))
+
+#define SWAP(x,y) {x=x+y;y=x+y; x=y-x; y=y-2*x;}
+#define SWAPP(x,y,tp) {tp=y;y=x;x=tp;}
+
+#define MAX(x, y) (((x) >(y)) ? (x):(y))
+#define MAX2(x, y) (((x) >(y)) ? (x):(y))
+#define MAX3(x,y,z) (MAX(MAX(x,y),z))
+#define MAX4(a,b,c,d) (MAX(MAX(a,b),MAX(c,d)))
+#define MAX5(a,b,c,d,e) (MAX2((MAX3(a,b,c)),(MAX2(d,e))))
+#define MAX6(a,b,c,d,e,f) (MAX2((MAX3(a,b,c)),(MAX3(c,d,e))))
+
+#define MIN(x, y) (((x) <(y)) ? (x):(y))
+#define FABS(x) ((x<0)?(-x):(x))
+#define is_defined(x) ((x==UNDEFINED)?0:1)
+#define a_better_than_b(x,y,m) ((m==1)?(((x)>(y))?1:0):(((x)<(y))?1:0))
+#define is_in_range(x,min,max) ((x>=min && x<=max)?1:0)
+/*#define bod_a_b(x,y,m) ((m==1)?(MAX((x),(y))):(MIN((x),(y))))
+#define bo_a_b(x,y,m) ((x==UNEFINED)?y:((y==UNDEFINED)?x:bod_a_b(y,y,m)))
+#define best_of_a_b(x,y,m) ((x==UNDEFINED && y==UNDEFINED)?(UNDEFINED):(bo_a_b(x,y,m)))
+*/
+
+
+#define DIE(x) HERE(x);exit(0);
+#define best_of_a_b(x,y,m) ((m==1)?(MAX((x),(y))):(MIN((x),(y))))
+
+#define strm(x,y) ((vstrcmp((x),(y))==0)?1:0)
+#define strnm(x,y,n) ((vstrncmp((x),(y),(n))==0)?1:0)
+#define strm2(a,b,c) (strm(a,b) || strm(a,c))
+#define strm3(a,b,c,d) (strm2(a,b,c) || strm(a,d))
+#define strm4(a,b,c,d,e) (strm2(a,b,c) || strm2(a,d,e))
+#define strm5(a,b,c,d,e,f) (strm2(a,b,c) || strm3(a,d,e,f))
+#define strm6(a,b,c,d,e,f,g) (strm3(a,b,c,d) || strm3(a,e,f,g))
+#define declare_name(x) (x=vcalloc (MAX(FILENAMELEN,L_tmpnam)+1, sizeof (char)))
+#define is_parameter(x) (x[0]=='-' && !isdigit(x[1]))
+
+/*Freing functions*/
+#define free_2(a, b) free(a);free(b)
+#define free_1(a) free(a)
+#define free_3(a, b, c) free_2(a,b);free_1(c)
+#define free_4(a, b, c,d) free_2(a,b);free_2(c,d)
+#define free_5(a, b, c,d,e) free_3(a,b,e);free_2(c,d)
+#define free_6(a, b, c,d,e,f) free_3(a,b,e);free_3(c,d,f)
+#define free_7(a, b, c,d,e,f,g) free_3(a,b,e);free_4(c,d,f,g)
+/*2-FILE PARSING*/
+#define SEPARATORS "\n \t,;"
+#define LINE_SEPARATOR "\n#TC_LINE_SEPARATOR\n"
+#define TC_REC_SEPARATOR "#### TC REC SEPARATOR ###"
+
+/*END 1-*/
+
+
+/*WIDOWS/UNIX DISTINCTIONS
+#if defined(_WIN32) || defined(__WIN32__) || defined(__WINDOWS__) || defined(__MSDOS__) || defined(__DOS__) || defined(__NT__) || defined(__WIN32__)
+#define WIN32
+#define TO_NULL_DEVICE " >nul"
+#define NULL_DEVICE "nul"
+#define CWF "/"
+#else
+#define TO_NULL_DEVICE " >/dev/null 2>&1"
+#define NULL_DEVICE "/dev/null"
+*/
+
+#if defined(_WIN32) || defined(__WIN32__) || defined(__WINDOWS__) || defined(__MSDOS__) || defined(__DOS__) || defined(__NT__) || defined(__WIN32__)
+#define WIN32
+#define TO_NULL_DEVICE " >>t_coffee.log"
+#define NULL_DEVICE "t_coffee.log"
+#define CWF "/" /*ClustalW Flag*/
+#else
+#define TO_NULL_DEVICE " >>/dev/null 2>&1"
+#define NULL_DEVICE "/dev/null"
+
+
+#define CWF "-" /*ClustaW Flag*/
+#endif
+
+/*Generic Data*/
+#define EMAIL "cedric.notredame@europe.com"
+#define URL "http://www.tcoffee.org"
+
+#define PERL_HEADER "#!/usr/bin/env perl"
+
+//Optimize the Score Computation in DP
+#define TC_SCORE_2(x,y) (SCORE_K*CL->M[Aln->seq_al[l_s[0][0]][x]-'A'][Aln->seq_al[l_s[1][0]][y]-'A']-SCORE_K*CL->nomatch)
+#define TC_SCORE_N(x,y) ((CL->get_dp_cost)(Aln, pos, ns[0], l_s[0], x, pos, ns[1], l_s[1], y, CL))
+#define TC_SCORE(x,y) ((CL->get_dp_cost==slow_get_dp_cost && CL->evaluate_residue_pair==evaluate_matrix_score && ns[0]+ns[1]==2 && x>=0 && j>=0)? (TC_SCORE_2(x,y)):(TC_SCORE_N(x,y)))
+
+#define NULL_2 NULL,NULL
+#define NULL_3 NULL_2,NULL
+#define NULL_4 NULL_2,NULL_2
+#define NULL_5 NULL_3,NULL_2
+#define NULL_6 NULL_4,NULL_2
+#define NULL_7 NULL_5,NULL_2
+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;
+
+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]*/
+ int **dc; /*coordinates on the disk. Coordinates set if seq[i]==NULL*/
+/*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[FILENAMELEN+1];
+ struct Template **T;
+
+
+};
+typedef struct Sequence Sequence;
+
+//_E_
+struct Template
+{
+ char seq_type[10];
+ 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;
+//_E_
+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;
+
+//
+struct P_template
+{
+ char pdb_id[100];
+};
+typedef struct P_template P_template;
+
+//RNA secondary Structure
+struct F_template
+{
+ int l;
+};
+typedef struct F_template F_template;
+
+
+struct S_template
+{
+ Sequence *S;
+};
+typedef struct S_template S_template;
+
+//Prile associated with a sequence
+struct R_template
+{
+ struct Alignment *A;
+};
+typedef struct R_template R_template;
+
+//Genomic Information
+struct G_template
+{
+ Sequence *S;
+};
+typedef struct G_template G_template;
+
+
+struct T_template
+{
+ Sequence *S;
+};
+typedef struct T_template T_template;
+
+//_E_
+struct E_template
+{
+ Sequence *S;
+};
+typedef struct E_template E_template;
+
+struct U_template
+{
+ int *list;
+};
+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;
+/*Score*/
+ 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;
+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];
+
+ }
+FILE_format;
+
+typedef struct
+ {
+ float r;
+ float g;
+ float b;
+ char html_color[30];
+ char html_color_class[30];
+ int ascii_value;
+ }
+Color;
+
+
+Sequence * fill_sequence_struc ( int nseq, char **sequences, char **seq_name);
+Sequence * cw_read_sequences ( char *seq_name);
+Sequence * get_sequence_type (Sequence *S);
+char * get_array_type (int n, char **s);
+Alignment* get_aln_type (Alignment *A);
+
+char * get_string_type (char *string);
+
+char *store_mode (char *val);
+char *retrieve_mode ();
+char *unset_mode ();
+char *set_mode (int mode, char *val);
+
+char *store_seq_type (char *val);
+char *retrieve_seq_type ();
+char *unset_seq_type ();
+char *set_seq_type (int mode, char *val);
+
+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);
+int output_hit_color_html (Alignment *B, float **ffPScoreTable, int nl, char *name); //JM_ADD
+void output_hit_matrix(char *fileName, float **ffpHitScoreMatrix, int nl); //JM_ADD
+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);
+/*********************CLUSTALW.H*********************************************/
+/****************************************************************************/
+
+ /*
+ 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
+#endif
+
+#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;
+
+void *ckalloc(size_t);
+void * ckvrealloc(void *,size_t);
+void ckfree(void *);
+
+int readseqs(char *saga_file,char ***SAGA_SEQ, char*** SAGA_NAMES, int ***SAGA_LEN) ;/*first_seq is the #no. of the first seq. to read */
+
+
+typedef struct treesim{
+ float w;
+ float uw;
+ float d;
+
+ float max_w;
+ float max_uw;
+ float max_d;
+
+ int rf;
+ int n;//n nodes;
+ int nseq;// nseq in the common subset
+ }Tree_sim;
+
+
+typedef struct tnode *NT_node;
+
+/**
+* Node of a tree
+*/
+typedef struct tnode{
+ int visited;
+ char *name;
+ char *file;
+
+ ///The parent node
+ NT_node parent;
+ ///Left child node
+ NT_node left;
+ ///Right child node
+ NT_node right;
+ NT_node bot;
+ /// is leaf?
+ int isseq;
+ int seq;
+ int maxnseq;
+ int nseq;
+
+ ///contains a list of the sequences
+ int *lseq;
+ ///contains a coded version of the node: 10010101
+ int *lseq2;
+ ///contains distances to the root, in nodes
+ int *idist;
+ ///contains real distances *1000
+ int *ldist;
+ float dist;
+ float bootstrap;
+ float dp;
+ int order;
+ int aligned;
+ ///Number of leave below the considered node
+ int leaf;
+ ///Number of nodes below the considered node
+ int node;
+ int group;
+ float score;
+ int align;
+ char *seqal;
+ int index;
+ int fork;
+ }Treenode;
+
+typedef struct split_struc Split;
+
+typedef struct split_struc{
+ char *split;
+ int n;
+ int tot;
+ float score;
+ char **tlist;//Not used yet
+ Sequence *S;
+ NT_node *L;
+}Split_struc;
+
+NT_node main_prune_tree ( NT_node T, Sequence *S);
+NT_node prune_tree ( NT_node T, Sequence *S);
+/*********************************************************************/
+/* */
+/* dpa_tree_manipulation */
+/* */
+/* */
+/*********************************************************************/
+char *tree2Ngroup (Alignment *A, NT_node T, int max_n, char *fname, char *mat4dist);
+int tree2group_file ( NT_node T,Sequence *S, int maxnseq, int minsim, char *name);
+
+NT_node seq2dpa_tree (Sequence *S, char *align_mode);
+NT_node tree2dpa_tree (NT_node T, Alignment *A, char *matrix4distance);
+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 */
+/* */
+/* */
+/*********************************************************************/
+int main_compare_cog_tree (NT_node T1, char *cogfile);
+int main_compare_aln_tree (NT_node T1, Alignment *A, FILE *fp);
+int compare_aln_tree (NT_node T, Alignment *A, int *n, FILE *fp);
+
+int main_compare_splits (NT_node T1, NT_node T2, char *mode, FILE *fp);
+Tree_sim * tree_cmp( NT_node T1, NT_node T2);
+NT_node tree_scan (Alignment *A,NT_node RT, char *pscan, char *ptree);
+
+int print_node_list (NT_node T, Sequence *S);
+NT_node main_compare_trees ( NT_node T1, NT_node T2, FILE *fp);
+NT_node main_compare_trees_list ( NT_node T1, Sequence *S, 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 index_tree_node (NT_node T);
+NT_node simple_recode_tree (NT_node T, 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 similarities_file2tree (char *mat);
+NT_node tree_compute ( Alignment *A, int n, char ** arg_list);
+static NT_node compute_std_tree (Alignment *A, int n, char **arg_list);
+NT_node compute_std_tree_2 (Alignment *A, int **s, char *arg_list);
+NT_node aln2fj_tree(NT_node T, Alignment *A, int limit,char* mode);
+Alignment * filter_aln4tree (Alignment *A, int n,int fg,char* mode);
+
+/*********************************************************************/
+/* */
+/* Tree Filters and MAnipulation */
+/* */
+/* */
+/*********************************************************************/
+int tree2star_nodes (NT_node R, int n_max);
+NT_node aln2tree (Alignment *A);
+NT_node reset_boot_tree ( NT_node R, int n);
+NT_node tree_dist2normalized_tree_dist ( NT_node R, float max);
+NT_node reset_dist_tree ( NT_node R, float n);
+NT_node* free_treelist ( NT_node *R);
+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);
+int tree2_nnode_unresolved (NT_node R, int *l);
+
+FILE* display_tree ( NT_node R, int n, FILE *fp);
+void clear_tree (NT_node T);
+int display_leaf ( NT_node T, FILE *fp);
+int display_leaf_below_node ( NT_node T, FILE *fp);
+NT_node display_leaf_nb (NT_node T, int n, FILE *fp, char *name);
+NT_node display_splits (NT_node T,Sequence *S, FILE *fp);
+int tree2split_list (NT_node T, int nseq, int **split_list, int *n);
+
+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_list ( NT_node *T,char *format, FILE *fp);
+FILE* print_tree ( NT_node T,char *format, FILE *fp);
+char *tree2string (NT_node T);
+char *tree2file (NT_node T, char *name, char *mode);
+
+int print_newick_tree ( NT_node T, char *name);
+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 new_read_tree ( char *teefile);
+NT_node new_get_node (NT_node T, FILE *fp);
+
+
+NT_node** simple_read_tree(char *treefile);
+void free_read_tree (NT_node **BT);
+NT_node** read_tree(char *treefile, int *nnodes,int nseq, char **seq_names);
+FILE * create_linear_tree ( char **name, int n, FILE *fp);
+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);
+
+
+Alignment *seq2seq_chain (Alignment *A,Alignment *B, char *arg);
+
+float display_avg_bootstrap ( NT_node T);
+float tree2tot_dist ( NT_node T, int mode);
+int tree2n_branches(NT_node T, int mode);
+int **display_tree_from_node (NT_node T, int up, int down, int **array);
+NT_node tree2node ( char *name, NT_node T);
+NT_node * tree2node_list (NT_node T, NT_node *L);
+NT_node tree2root ( NT_node T);
+int new_tree_sort ( char *name, NT_node T);
+
+
+NT_node split2tree ( NT_node RT,Sequence *LIST, char *param);
+NT_node * read_tree_list (Sequence *S);
+
+int count_groups( Sequence *S, char *s);
+
+Split ** count_splits( NT_node RT, Sequence *S, char *s);
+NT_node *treelist2prune_treelist (Sequence *S, Sequence *TS, FILE *out);
+int** treelist2groups (Sequence *S, Sequence *ST, char *depth, FILE *out);
+int treelist2splits (Sequence *S, Sequence *ST);
+int treelist2leafgroup ( Sequence *S, Sequence *TS, char *taxon);
+int ***tree2dist ( NT_node T, Sequence *S, int ***d);
+int treelist2frame (Sequence *S, Sequence *TS);
+int** treelist2lti ( Sequence *S, Sequence *TS, int nb, FILE *out);
+
+float simple_tree_cmp (NT_node T1, NT_node T2,Sequence *S, int mode);
+
+int treelist2dmat ( Sequence *S);
+NT_node new_declare_tree_node ();
+int count_tree_groups( Sequence *LIST, char *group_file);
+int node_sort ( char *name, NT_node T);
+int treelist2n (NT_node *L);
+int ** treelist2avg_treecmp (NT_node *L, char *file);
+NT_node treelist2bootstrap ( NT_node *L, char *file);
+NT_node treelist2filtered_bootstrap ( NT_node *L, char *file, int **score,float f);
+
+Sequence * treelist2seq ( Sequence *S);
+Sequence * treelist2sub_seq ( Sequence *S, int f);
+
+int treelist_file2consense (char *tree_file, char *outtree, char *outfile);
+/* 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*******************************/
+/*© 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*******************************/
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