/*DEBUGGING*/ /*#include "mshell.h"*/ /*MEMORY MANAGEMENT*/ #include #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: ------------------------------------------------------------------------------------------- * ------------------------------------------------------------------------------------------- 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*******************************/