-/*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
-
+/******************************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*******************************/
+#ifndef IO_LIB_HEADER_H
+#define IO_LIB_HEADER_H
-#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
+#include "io_lib/io_structures.h"
+#include "io_lib/io_func.h"
+#include "io_lib/pb_util_read_sequence.h"
+#include "io_lib/tree_util.h"
+#include "io_lib/pb_util_read_sequence2.h"
-#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*******************************/
git://source.jalview.org / jabaws.git / blobdiff