--- /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*******************************/
+#ifndef COFFEE_DEFINES_H
+#define COFFEE_DEFINES_H
+
+/*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
+#define MAX_NSEQ_4_DISPLAY 50
+//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 PROFILE 66
+#define SEQUENCE 67
+
+#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=(char*)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@gmail.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
+
+#endif // -- COFFEE_DEFINES_H
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