--- /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
+/* 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/"
+
+#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 */
+/********************************************/
+
+
+
+
+/* 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*******************************/
git://source.jalview.org / jabaws.git / blobdiff