-/*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
-/* PROGRAM PATH */
-
-
-//ERROR MESSAGES
-
-
-#define ADDRESS_BUILT_IN "built_in"
-#define PROGRAM_BUILT_IN "t_coffee"
-#define TEST_WWWSITE_4_TCOFFEE "www.google.com"
-
-
-//TclinkdbStart
-
-#define TCOFFEE_4_TCOFFEE "t_coffee"
-#define TCOFFEE_type "sequence_multiple_aligner"
-#define TCOFFEE_ADDRESS "http://www.tcoffee.org"
-#define TCOFFEE_language "C"
-#define TCOFFEE_language2 "C"
-#define TCOFFEE_source "http://www.tcoffee.org/Packages/T-COFFEE_distribution.tar.gz"
-#define TCOFFEE_update_action "always"
-#define TCOFFEE_mode "tcoffee,mcoffee,rcoffee,expresso,3dcoffee"
-#define CLUSTALW2_4_TCOFFEE "clustalw2"
-#define CLUSTALW2_type "sequence_multiple_aligner"
-#define CLUSTALW2_ADDRESS "http://www.clustal.org"
-#define CLUSTALW2_language "C++"
-#define CLUSTALW2_language2 "CXX"
-#define CLUSTALW2_source "http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz"
-#define CLUSTALW2_mode "mcoffee,rcoffee"
-#define CLUSTALW2_version "2.0.10"
-#define CLUSTALW_4_TCOFFEE "clustalw"
-#define CLUSTALW_type "sequence_multiple_aligner"
-#define CLUSTALW_ADDRESS "http://www.clustal.org"
-#define CLUSTALW_language "C"
-#define CLUSTALW_language2 "C"
-#define CLUSTALW_source "http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz"
-#define CLUSTALW_mode "mcoffee,rcoffee"
-#define CLUSTALW_version "1.82"
-#define DIALIGNT_4_TCOFFEE "dialign-t"
-#define DIALIGNT_type "sequence_multiple_aligner"
-#define DIALIGNT_ADDRESS "http://dialign-tx.gobics.de/"
-#define DIALIGNT_DIR "/usr/share/dialign-tx/"
-#define DIALIGNT_language "C"
-#define DIALIGNT_language2 "C"
-#define DIALIGNT_source "http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz"
-#define DIALIGNT_mode "mcoffee"
-#define DIALIGNT_binary "dialign-t"
-#define DIALIGNT_version "1.0.2"
-#define DIALIGNTX_4_TCOFFEE "dialign-tx"
-#define DIALIGNTX_type "sequence_multiple_aligner"
-#define DIALIGNTX_ADDRESS "http://dialign-tx.gobics.de/"
-#define DIALIGNTX_DIR "/usr/share/dialign-tx/"
-#define DIALIGNTX_language "C"
-#define DIALIGNTX_language2 "C"
-#define DIALIGNTX_source "http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz"
-#define DIALIGNTX_mode "mcoffee"
-#define DIALIGNTX_binary "dialign-tx"
-#define DIALIGNTX_version "1.0.2"
-#define POA_4_TCOFFEE "poa"
-#define POA_type "sequence_multiple_aligner"
-#define POA_ADDRESS "http://www.bioinformatics.ucla.edu/poa/"
-#define POA_language "C"
-#define POA_language2 "C"
-#define POA_source "http://downloads.sourceforge.net/poamsa/poaV2.tar.gz"
-#define POA_DIR "/usr/share/"
-#define POA_FILE1 "blosum80.mat"
-#define POA_mode "mcoffee"
-#define POA_binary "poa"
-#define POA_version "2.0"
-#define PROBCONS_4_TCOFFEE "probcons"
-#define PROBCONS_type "sequence_multiple_aligner"
-#define PROBCONS_ADDRESS "http://probcons.stanford.edu/"
-#define PROBCONS_language2 "CXX"
-#define PROBCONS_language "C++"
-#define PROBCONS_source "http://probcons.stanford.edu/probcons_v1_12.tar.gz"
-#define PROBCONS_mode "mcoffee"
-#define PROBCONS_binary "probcons"
-#define PROBCONS_version "1.12"
-#define MAFFT_4_TCOFFEE "mafft"
-#define MAFFT_type "sequence_multiple_aligner"
-#define MAFFT_ADDRESS "http://align.bmr.kyushu-u.ac.jp/mafft/online/server/"
-#define MAFFT_language "C"
-#define MAFFT_language "C"
-#define MAFFT_source "http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz"
-#define MAFFT_windows "http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-mingw.tar"
-#define MAFFT_mode "mcoffee,rcoffee"
-#define MAFFT_binary "mafft.tar.gz"
-#define MAFFT_version "6.603"
-#define MUSCLE_4_TCOFFEE "muscle"
-#define MUSCLE_type "sequence_multiple_aligner"
-#define MUSCLE_ADDRESS "http://www.drive5.com/muscle/"
-#define MUSCLE_language "C++"
-#define MUSCLE_language2 "GPP"
-#define MUSCLE_source "http://www.drive5.com/muscle/downloads3.7/muscle3.7_src.tar.gz"
-#define MUSCLE_windows "http://www.drive5.com/muscle/downloads3.7/muscle3.7_win32.zip"
-#define MUSCLE_linux "http://www.drive5.com/muscle/downloads3.7/muscle3.7_linux_ia32.tar.gz"
-#define MUSCLE_mode "mcoffee,rcoffee"
-#define MUSCLE_version "3.7"
-#define MUS4_4_TCOFFEE "mus4"
-#define MUS4_type "sequence_multiple_aligner"
-#define MUS4_ADDRESS "http://www.drive5.com/muscle/"
-#define MUS4_language "C++"
-#define MUS4_language2 "GPP"
-#define MUS4_source "http://www.drive5.com/muscle/muscle4.0_src.tar.gz"
-#define MUS4_mode "mcoffee,rcoffee"
-#define MUS4_version "4.0"
-#define PCMA_4_TCOFFEE "pcma"
-#define PCMA_type "sequence_multiple_aligner"
-#define PCMA_ADDRESS "ftp://iole.swmed.edu/pub/PCMA/"
-#define PCMA_language "C"
-#define PCMA_language2 "C"
-#define PCMA_source "ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz"
-#define PCMA_mode "mcoffee"
-#define PCMA_version "1.0"
-#define KALIGN_4_TCOFFEE "kalign"
-#define KALIGN_type "sequence_multiple_aligner"
-#define KALIGN_ADDRESS "http://msa.cgb.ki.se"
-#define KALIGN_language "C"
-#define KALIGN_language2 "C"
-#define KALIGN_source "http://msa.cgb.ki.se/downloads/kalign/current.tar.gz"
-#define KALIGN_mode "mcoffee"
-#define KALIGN_version "1.0"
-#define AMAP_4_TCOFFEE "amap"
-#define AMAP_type "sequence_multiple_aligner"
-#define AMAP_ADDRESS "http://bio.math.berkeley.edu/amap/"
-#define AMAP_language "C++"
-#define AMAP_language2 "CXX"
-#define AMAP_source "http://amap-align.googlecode.com/files/amap.2.0.tar.gz"
-#define AMAP_mode "mcoffee"
-#define AMAP_version "2.0"
-#define PRODA_4_TCOFFEE "proda"
-#define PRODA_type "sequence_multiple_aligner"
-#define PRODA_ADDRESS "http://proda.stanford.edu"
-#define PRODA_language "C++"
-#define PRODA_language2 "CXX"
-#define PRODA_source "http://proda.stanford.edu/proda_1_0.tar.gz"
-#define PRODA_mode "mcoffee"
-#define PRODA_version "1.0"
-#define FSA_4_TCOFFEE "fsa"
-#define FSA_type "sequence_multiple_aligner"
-#define FSA_ADDRESS "http://fsa.sourceforge.net/"
-#define FSA_language "C++"
-#define FSA_language2 "CXX"
-#define FSA_source "http://sourceforge.net/projects/fsa/files/fsa-1.15.3.tar.gz/download/"
-#define FSA_mode "mcoffee"
-#define FSA_version "1.15.3"
-#define PRANK_4_TCOFFEE "prank"
-#define PRANK_type "sequence_multiple_aligner"
-#define PRANK_ADDRESS "http://www.ebi.ac.uk/goldman-srv/prank/"
-#define PRANK_language "C++"
-#define PRANK_language2 "CXX"
-#define PRANK_source "http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.100303.tgz"
-#define PRANK_mode "mcoffee"
-#define PRANK_version "100303"
-#define SAP_4_TCOFFEE "sap"
-#define SAP_type "structure_pairwise_aligner"
-#define SAP_ADDRESS "http://mathbio.nimr.mrc.ac.uk/wiki/Software"
-#define SAP_language "C"
-#define SAP_language2 "C"
-#define SAP_source "http://mathbio.nimr.mrc.ac.uk/download/sap-1.1.1.tar.gz"
-#define SAP_mode "expresso,3dcoffee"
-#define SAP_version "1.1.1"
-#define TMALIGN_4_TCOFFEE "TMalign"
-#define TMALIGN_type "structure_pairwise_aligner"
-#define TMALIGN_ADDRESS "http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f"
-#define TMALIGN_language "Fortran"
-#define TMALIGN_language2 "Fortran"
-#define TMALIGN_source "http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f"
-#define TMALIGN_linux "http://zhang.bioinformatics.ku.edu/TM-align/TMalign_32.gz"
-#define TMALIGN_mode "expresso,3dcoffee"
-#define TMALIGN_version "1.0"
-#define MUSTANG_4_TCOFFEE "mustang"
-#define MUSTANG_type "structure_pairwise_aligner"
-#define MUSTANG_ADDRESS "http://www.cs.mu.oz.au/~arun/mustang"
-#define MUSTANG_language "C++"
-#define MUSTANG_language2 "CXX"
-#define MUSTANG_source "http://ww2.cs.mu.oz.au/~arun/mustang/mustang_v3.2.1.tgz"
-#define MUSTANG_mode "expresso,3dcoffee"
-#define MUSTANG_version "3.2.1"
-#define LSQMAN_4_TCOFFEE "lsqman"
-#define LSQMAN_type "structure_pairwise_aligner"
-#define LSQMAN_ADDRESS "empty"
-#define LSQMAN_language "empty"
-#define LSQMAN_language2 "empty"
-#define LSQMAN_source "empty"
-#define LSQMAN_update_action "never"
-#define LSQMAN_mode "expresso,3dcoffee"
-#define ALIGN_PDB_4_TCOFFEE "align_pdb"
-#define ALIGN_PDB_type "structure_pairwise_aligner"
-#define ALIGN_PDB_ADDRESS "empty"
-#define ALIGN_PDB_language "empty"
-#define ALIGN_PDB_language2 "empty"
-#define ALIGN_PDB_source "empty"
-#define ALIGN_PDB_update_action "never"
-#define ALIGN_PDB_mode "expresso,3dcoffee"
-#define FUGUE_4_TCOFFEE "fugueali"
-#define FUGUE_type "structure_pairwise_aligner"
-#define FUGUE_ADDRESS "http://www-cryst.bioc.cam.ac.uk/fugue/download.html"
-#define FUGUE_language "empty"
-#define FUGUE_language2 "empty"
-#define FUGUE_source "empty"
-#define FUGUE_update_action "never"
-#define FUGUE_mode "expresso,3dcoffee"
-#define DALILITEc_4_TCOFFEE "dalilite.pl"
-#define DALILITEc_type "structure_pairwise_aligner"
-#define DALILITEc_ADDRESS "built_in"
-#define DALILITEc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/dalilite"
-#define DALILITEc_language "Perl"
-#define DALILITEc_language2 "Perl"
-#define DALILITEc_source "empty"
-#define DALILITEc_update_action "never"
-#define DALILITEc_mode "expresso,3dcoffee"
-#define PROBCONSRNA_4_TCOFFEE "probconsRNA"
-#define PROBCONSRNA_type "RNA_multiple_aligner"
-#define PROBCONSRNA_ADDRESS "http://probcons.stanford.edu/"
-#define PROBCONSRNA_language "C++"
-#define PROBCONSRNA_language2 "CXX"
-#define PROBCONSRNA_source "http://probcons.stanford.edu/probconsRNA.tar.gz"
-#define PROBCONSRNA_mode "mcoffee,rcoffee"
-#define PROBCONSRNA_version "1.0"
-#define CONSAN_4_TCOFFEE "sfold"
-#define CONSAN_type "RNA_pairwise_aligner"
-#define CONSAN_ADDRESS "http://selab.janelia.org/software/consan/"
-#define CONSAN_language "empty"
-#define CONSAN_language2 "empty"
-#define CONSAN_source "empty"
-#define CONSAN_update_action "never"
-#define CONSAN_mode "rcoffee"
-#define RNAPLFOLD_4_TCOFFEE "RNAplfold"
-#define RNAPLFOLD_type "RNA_secondarystructure_predictor"
-#define RNAPLFOLD_ADDRESS "http://www.tbi.univie.ac.at/~ivo/RNA/"
-#define RNAPLFOLD_language "C"
-#define RNAPLFOLD_language2 "C"
-#define RNAPLFOLD_source "http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.7.2.tar.gz"
-#define RNAPLFOLD_mode "rcoffee,"
-#define RNAPLFOLD_version "1.7.2"
-#define PHYLIP_4_TCOFFEE "retree"
-#define PHYLIP_type "RNA_secondarystructure_predictor"
-#define PHYLIP_ADDRESS "http://evolution.gs.washington.edu/phylip/"
-#define PHYLIP_language "C"
-#define PHYLIP_language2 "C"
-#define PHYLIP_source "http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz"
-#define PHYLIP_mode "trmsd,"
-#define PHYLIP_version "3.69"
-#define HMMTOP_4_TCOFFEE "hmmtop"
-#define HMMTOP_type "protein_secondarystructure_predictor"
-#define HMMTOP_ADDRESS "www.enzim.hu/hmmtop/"
-#define HMMTOP_language "C"
-#define HMMTOP_language2 "C"
-#define HMMTOP_source "empty"
-#define HMMTOP_update_action "never"
-#define HMMTOP_mode "tcoffee"
-#define GOR4_4_TCOFFEE "gorIV"
-#define GOR4_type "protein_secondarystructure_predictor"
-#define GOR4_ADDRESS "http://mig.jouy.inra.fr/logiciels/gorIV/"
-#define GOR4_language "C"
-#define GOR4_language2 "C"
-#define GOR4_source "http://mig.jouy.inra.fr/logiciels/gorIV/GOR_IV.tar.gz"
-#define GOR4_update_action "never"
-#define GOR4_mode "tcoffee"
-#define EBIWUBLASTc_4_TCOFFEE "wublast.pl"
-#define EBIWUBLASTc_type "protein_homology_predictor"
-#define EBIWUBLASTc_ADDRESS "built_in"
-#define EBIWUBLASTc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/wublast"
-#define EBIWUBLASTc_language "Perl"
-#define EBIWUBLASTc_language2 "Perl"
-#define EBIWUBLASTc_source "empty"
-#define EBIWUBLASTc_update_action "never"
-#define EBIWUBLASTc_mode "psicoffee,expresso,accurate"
-#define EBIBLASTPGPc_4_TCOFFEE "blastpgp.pl"
-#define EBIBLASTPGPc_type "protein_homology_predictor"
-#define EBIBLASTPGPc_ADDRESS "built_in"
-#define EBIBLASTPGPc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/blastpgp"
-#define EBIBLASTPGPc_language "Perl"
-#define EBIBLASTPGPc_language2 "Perl"
-#define EBIBLASTPGPc_source "empty"
-#define EBIBLASTPGPc_update_action "never"
-#define EBIBLASTPGPc_mode "psicoffee,expresso,accurate"
-#define NCBIWEBBLAST_4_TCOFFEE "blastcl3"
-#define NCBIWEBBLAST_type "protein_homology_predictor"
-#define NCBIWEBBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
-#define NCBIWEBBLAST_language "C"
-#define NCBIWEBBLAST_language2 "C"
-#define NCBIWEBBLAST_source "empty"
-#define NCBIWEBBLAST_update_action "never"
-#define NCBIWEBBLAST_mode "psicoffee,expresso,3dcoffee"
-#define blastall_4_TCOFFEE "blastall"
-#define blastall_type "protein_homology_predictor"
-#define blastall_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
-#define blastall_language "C"
-#define blastall_language2 "C"
-#define blastall_source "empty"
-#define blastall_update_action "never"
-#define blastall_mode "psicoffee,expresso,3dcoffee"
-#define NCBIBLAST_4_TCOFFEE "legacy_blast.pl"
-#define NCBIBLAST_type "protein_homology_predictor"
-#define NCBIBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
-#define NCBIBLAST_language "C"
-#define NCBIBLAST_language2 "C"
-#define NCBIBLAST_source "empty"
-#define NCBIBLAST_update_action "never"
-#define NCBIBLAST_mode "psicoffee,expresso,3dcoffee"
-#define SOAPLITE_4_TCOFFEE "SOAP::Lite"
-#define SOAPLITE_type "library"
-#define SOAPLITE_ADDRESS "http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL"
-#define SOAPLITE_language "Perl"
-#define SOAPLITE_language2 "Perl"
-#define SOAPLITE_source "empty"
-#define _update_action "never"
-#define SOAPLITE_mode "none"
-#define XMLSIMPLE_4_TCOFFEE "XML::Simple"
-#define XMLSIMPLE_type "library"
-#define XMLSIMPLE_ADDRESS "http://search.cpan.org/~grantm/XML-Simple-2.18/lib/XML/Simple.pm"
-#define XMLSIMPLE_language "Perl"
-#define XMLSIMPLE_language2 "Perl"
-#define XMLSIMPLE_source "empty"
-#define XMLSIMPLE_mode "psicoffee,expresso,accurate"
-//TclinkdbEnd
-/*New Methods*/
-/********************************************/
-/* Various Methoids */
-/********************************************/
-#define METHODS_4_TCOFFEE "~/.t_coffee/methods/"
-#define METHOD_4_MSA_WEIGHTS "petra_weight"
-/********************************************/
-/* SEQAN LIBRARY */
-/********************************************/
-#define SEQAN_TCOFFEE_4_TCOFFEE "seqan_tcoffee"
-/********************************************/
-/* REFORMATING AND UTILITIES */
-/********************************************/
-#define WGET_4_TCOFFEE "wget"
-#define WGET_ADDRESS "http://www.gnu.org/software/wget/"
-
-#define CURL_4_TCOFFEE "curl"
-#define CURL_ADDRESS "http://curl.haxx.se/"
+/******************************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 DEFINE_HEADER_H
+#define DEFINE_HEADER_H
-#define SEQ_REFORMAT_4_TCOFFEE "seq_reformat"
-#define PS2PDF "ps2pdf"
-#define EXTRACT_FROM_PDB_4_TCOFFEE "extract_from_pdb"
-#define BLAST_ALN2FASTA_ALN "blast_aln2fasta_aln.pl"
-#define FASTA_ALN2FASTA_ALN_UNIQUE_NAME "fasta_aln2fasta_aln_unique_name.pl"
-#define MSF_ALN2FASTA_ALN "msf_aln2fasta_aln.pl"
-#define SEQ2MSA_WEIGHT "seq2msa_weight"
-/********************************************/
-/* DEPRECATED DEF */
-/********************************************/
-//Deprecated definitions
-#define SIB_BLAST_4_TCOFFEE "blastall.remote"
-#define LOCAL_BLAST_4_TCOFFEE "blastall"
-#define BLAST_DB_4_TCOFFEE "nr"
-#define NCBI_BLAST_4_TCOFFEE ""
-/********************************************/
-/* PARAMETER_FILE */
-/********************************************/
+#include "coffee_defines.h"
+#include "programmes_define.h"
+// the following constants are updated during the build process -- see the 'makefile' for details
+#define PROGRAM "T-COFFEE"
+#define AUTHOR "Cedric Notredame "
+#define DATE "12 Aug 2014 - 22:05"
+#define VERSION "Version_11.00.8cbe486"
+#define BUILD_INFO "2014-08-12 22:05:29 - Revision 8cbe486 - Build 477"
+#define DISTRIBUTION_ADDRESS "www.tcoffee.org/Packages"
-/* PARAMETER FILES */
-#define COLOR_FILE "seq_reformat.color"
-/*This file specifies the 10 colors available to seq_reformat.
-If the file is not on the system, hard coded defaults will be used.
-The format is as follow:
--------------------------------------------------------------------------------------------
-<Your comments (as many lines as needed >
-*
-<number in the range 0-9> <HTML code> <R value (float)> <G value (float)> <B value (float)>
--------------------------------------------------------------------------------------------
-the RGB values are used for the post-script generation, the html code is used in html documents.
-*/
-#define DATE "Fri Feb 18 08:27:45 CET 2011 - Revision 596"
-#define PROGRAM "T-COFFEE"
-#define VERSION "Version_8.99"
-#define AUTHOR "Cedric Notredame "
-#define DISTRIBUTION_ADDRESS "www.tcoffee.org/Packages/"
-/******************************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*******************************/
+#endif // DEFINE_HEADER_H
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