2 /*#include "mshell.h"*/
5 #define MY_EPS 1000*DBL_EPSILON
6 //Maximum number of tries for interactibve things
9 //Maximum CACHE and Temporary file size and age (Mb and days, 0: unlimited)
10 #define TMP_MAX_SIZE 0
11 #define TMP_MAX_KEEP 10
12 #define CACHE_MAX_SIZE 2000
13 #define CACHE_MAX_KEEP 180
14 #define MAX_N_PID 260000
15 //Importnat Values Affecting the Program Behavior
19 #define PAVIE_MAT_FACTOR 1000
21 #define CLEAN_FUNCTION NULL
22 #define MINSIM_4_TCOFFEE 25 //The minimum similarity between a sequence and its PDB template
23 #define MINCOV_4_TCOFFEE 25 //The minimum similarity between a sequence and its PDB template
26 #define TRACE_TYPE int
27 #define MAX_LEN_FOR_DP 600
30 #define GIVE_MEMORY_BACK 0
33 /*OUTPUT DEFINITIONS*/
34 #define NO_COLOR_RESIDUE 127
35 #define NO_COLOR_GAP 126
36 #define CLOSE_HTML_SPAN -1
70 #define KEEP_CASE 2 /*Hard set in several places*/
103 #define SWITCHCASE 21
106 #define NON_VECTOR 23
107 #define NON_PROFILE 24
113 #define VERY_VERBOSE 28
116 #define VERY_SHORT 31
119 #define NO_OVERLAP 33
125 #define DECLARE_ALN 37
126 #define EXTRACT_ALN 38
128 #define INTERACTIVE 40
129 #define NON_INTERACTIVE 41
149 #define RETURN_ON_FAILURE 61
150 #define EXIT_ON_FAILURE 62
151 #define IGNORE_FAILURE 63
181 #define DETERMINISTIC 1
187 #define IS_NOT_FATAL 0
190 #define INSTALL_OR_DIE 4
193 #define NON_OPTIONAL 0
195 #define GV_MAXIMISE 1
196 #define GV_MINIMISE 0
202 #define FORBIDEN -99999999
203 #define END_ARRAY -99999990
219 #define UNGAPED_POSITIONS 1
220 #define ALIGNED_POSITIONS 2
221 #define AVERAGE_POSITIONS 3
222 #define NOMATRIX NULL
227 #define SIZE_OF_INT 10
228 #define UNDEFINED FORBIDEN
229 #define UNDEFINED_INT UNDEFINED
230 #define UNDEFINED_FLOAT UNDEFINED
231 #define UNDEFINED_DOUBLE UNDEFINED
232 #define UNDEFINED_CHAR 125
233 #define UNDEFINED_SHORT -125
234 #define UNDEFINED_2 0
235 #define UNDEFINED_RESIDUE '>'
242 #define MAX_LEN_ALN 1
243 #define MAX_N_LIST 100
245 #define COMMENT_SIZE 1000
247 #define FILENAMELEN 500 /* Max. file name length */
248 #define MAX_N_PARAM 2000
249 #define MAX_PARAM_LEN 200
250 #define MAX_LINE_LENGTH 10000
251 #define ALN_LINE_LENGTH 50
252 #define SHORT_STRING 10
254 #define LONG_STRING 1000
255 #define VERY_LONG_STRING 10000
257 #define AA_ALPHABET "acdefghiklmnpqrstvwy-ACDEFGHIKLMNPQRSTVWY"
258 #define DNA_ALPHABET "AGCTUNRYMKSWHBVD-agctunrymkswhbvd"
259 #define RNAONLY_ALPHABET "Uu"
260 #define BLAST_AA_ALPHABET "arndcqeghilkmfpstwyvbzx*"
261 #define NAMES_ALPHABET "1234567890ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz_|�-!%@&#-+=."
263 #define SIZEOF_AA_MAT 60
264 #define GAP_LIST "-.#*~"
272 #define CODE4PROTEINS 10
275 #define STOCKHOLM_CHAR 'z'
276 #define STOCKHOLM_STRING "z"
281 /*1-COMMAND LINE PROCESSING*/
282 #define GET_COMMAND_LINE_INFO ((strncmp ( argv[1], "-h",2)==0)||(strncmp ( argv[1], "-man",4)==0)||(strncmp ( argv[1], "-",1)!=0))
283 #define NEXT_ARG_IS_FLAG ((argc<=(a+1)) ||(( argv[a+1][0]=='-') && !(is_number(argv[a+1]))))
287 #define BORDER(p1,l1,p2,l2) ((p1==0 || p2==0 || p1==l1 || p2==l2)?1:0)
288 #define GET_CASE(f,c) ((f==UPPER_CASE)?toupper(c):((f==LOWER_CASE)?tolower(c):c))
290 #define SWAP(x,y) {x=x+y;y=x+y; x=y-x; y=y-2*x;}
291 #define SWAPP(x,y,tp) {tp=y;y=x;x=tp;}
293 #define MAX(x, y) (((x) >(y)) ? (x):(y))
294 #define MAX2(x, y) (((x) >(y)) ? (x):(y))
295 #define MAX3(x,y,z) (MAX(MAX(x,y),z))
296 #define MAX4(a,b,c,d) (MAX(MAX(a,b),MAX(c,d)))
297 #define MAX5(a,b,c,d,e) (MAX2((MAX3(a,b,c)),(MAX2(d,e))))
298 #define MAX6(a,b,c,d,e,f) (MAX2((MAX3(a,b,c)),(MAX3(c,d,e))))
300 #define MIN(x, y) (((x) <(y)) ? (x):(y))
301 #define FABS(x) ((x<0)?(-x):(x))
302 #define is_defined(x) ((x==UNDEFINED)?0:1)
303 #define a_better_than_b(x,y,m) ((m==1)?(((x)>(y))?1:0):(((x)<(y))?1:0))
304 #define is_in_range(x,min,max) ((x>=min && x<=max)?1:0)
305 /*#define bod_a_b(x,y,m) ((m==1)?(MAX((x),(y))):(MIN((x),(y))))
306 #define bo_a_b(x,y,m) ((x==UNEFINED)?y:((y==UNDEFINED)?x:bod_a_b(y,y,m)))
307 #define best_of_a_b(x,y,m) ((x==UNDEFINED && y==UNDEFINED)?(UNDEFINED):(bo_a_b(x,y,m)))
311 #define DIE(x) HERE(x);exit(0);
312 #define best_of_a_b(x,y,m) ((m==1)?(MAX((x),(y))):(MIN((x),(y))))
314 #define strm(x,y) ((vstrcmp((x),(y))==0)?1:0)
315 #define strnm(x,y,n) ((vstrncmp((x),(y),(n))==0)?1:0)
316 #define strm2(a,b,c) (strm(a,b) || strm(a,c))
317 #define strm3(a,b,c,d) (strm2(a,b,c) || strm(a,d))
318 #define strm4(a,b,c,d,e) (strm2(a,b,c) || strm2(a,d,e))
319 #define strm5(a,b,c,d,e,f) (strm2(a,b,c) || strm3(a,d,e,f))
320 #define strm6(a,b,c,d,e,f,g) (strm3(a,b,c,d) || strm3(a,e,f,g))
321 #define declare_name(x) (x=vcalloc (MAX(FILENAMELEN,L_tmpnam)+1, sizeof (char)))
322 #define is_parameter(x) (x[0]=='-' && !isdigit(x[1]))
325 #define free_2(a, b) free(a);free(b)
326 #define free_1(a) free(a)
327 #define free_3(a, b, c) free_2(a,b);free_1(c)
328 #define free_4(a, b, c,d) free_2(a,b);free_2(c,d)
329 #define free_5(a, b, c,d,e) free_3(a,b,e);free_2(c,d)
330 #define free_6(a, b, c,d,e,f) free_3(a,b,e);free_3(c,d,f)
331 #define free_7(a, b, c,d,e,f,g) free_3(a,b,e);free_4(c,d,f,g)
333 #define SEPARATORS "\n \t,;"
334 #define LINE_SEPARATOR "\n#TC_LINE_SEPARATOR\n"
335 #define TC_REC_SEPARATOR "#### TC REC SEPARATOR ###"
340 /*WIDOWS/UNIX DISTINCTIONS
341 #if defined(_WIN32) || defined(__WIN32__) || defined(__WINDOWS__) || defined(__MSDOS__) || defined(__DOS__) || defined(__NT__) || defined(__WIN32__)
343 #define TO_NULL_DEVICE " >nul"
344 #define NULL_DEVICE "nul"
347 #define TO_NULL_DEVICE " >/dev/null 2>&1"
348 #define NULL_DEVICE "/dev/null"
351 #if defined(_WIN32) || defined(__WIN32__) || defined(__WINDOWS__) || defined(__MSDOS__) || defined(__DOS__) || defined(__NT__) || defined(__WIN32__)
353 #define TO_NULL_DEVICE " >>t_coffee.log"
354 #define NULL_DEVICE "t_coffee.log"
355 #define CWF "/" /*ClustalW Flag*/
357 #define TO_NULL_DEVICE " >>/dev/null 2>&1"
358 #define NULL_DEVICE "/dev/null"
361 #define CWF "-" /*ClustaW Flag*/
365 #define EMAIL "cedric.notredame@europe.com"
366 #define URL "http://www.tcoffee.org"
368 #define PERL_HEADER "#!/usr/bin/env perl"
370 //Optimize the Score Computation in DP
371 #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)
372 #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))
373 #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)))
375 #define NULL_2 NULL,NULL
376 #define NULL_3 NULL_2,NULL
377 #define NULL_4 NULL_2,NULL_2
378 #define NULL_5 NULL_3,NULL_2
379 #define NULL_6 NULL_4,NULL_2
380 #define NULL_7 NULL_5,NULL_2
387 #define ADDRESS_BUILT_IN "built_in"
388 #define PROGRAM_BUILT_IN "t_coffee"
389 #define TEST_WWWSITE_4_TCOFFEE "www.google.com"
394 #define TCOFFEE_4_TCOFFEE "t_coffee"
395 #define TCOFFEE_type "sequence_multiple_aligner"
396 #define TCOFFEE_ADDRESS "http://www.tcoffee.org"
397 #define TCOFFEE_language "C"
398 #define TCOFFEE_language2 "C"
399 #define TCOFFEE_source "http://www.tcoffee.org/Packages/T-COFFEE_distribution.tar.gz"
400 #define TCOFFEE_update_action "always"
401 #define TCOFFEE_mode "tcoffee,mcoffee,rcoffee,expresso,3dcoffee"
402 #define CLUSTALW2_4_TCOFFEE "clustalw2"
403 #define CLUSTALW2_type "sequence_multiple_aligner"
404 #define CLUSTALW2_ADDRESS "http://www.clustal.org"
405 #define CLUSTALW2_language "C++"
406 #define CLUSTALW2_language2 "CXX"
407 #define CLUSTALW2_source "http://www.clustal.org/download/2.0.10/clustalw-2.0.10-src.tar.gz"
408 #define CLUSTALW2_mode "mcoffee,rcoffee"
409 #define CLUSTALW2_version "2.0.10"
410 #define CLUSTALW_4_TCOFFEE "clustalw"
411 #define CLUSTALW_type "sequence_multiple_aligner"
412 #define CLUSTALW_ADDRESS "http://www.clustal.org"
413 #define CLUSTALW_language "C"
414 #define CLUSTALW_language2 "C"
415 #define CLUSTALW_source "http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.82.UNIX.tar.gz"
416 #define CLUSTALW_mode "mcoffee,rcoffee"
417 #define CLUSTALW_version "1.82"
418 #define DIALIGNT_4_TCOFFEE "dialign-t"
419 #define DIALIGNT_type "sequence_multiple_aligner"
420 #define DIALIGNT_ADDRESS "http://dialign-tx.gobics.de/"
421 #define DIALIGNT_DIR "/usr/share/dialign-tx/"
422 #define DIALIGNT_language "C"
423 #define DIALIGNT_language2 "C"
424 #define DIALIGNT_source "http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz"
425 #define DIALIGNT_mode "mcoffee"
426 #define DIALIGNT_binary "dialign-t"
427 #define DIALIGNT_version "1.0.2"
428 #define DIALIGNTX_4_TCOFFEE "dialign-tx"
429 #define DIALIGNTX_type "sequence_multiple_aligner"
430 #define DIALIGNTX_ADDRESS "http://dialign-tx.gobics.de/"
431 #define DIALIGNTX_DIR "/usr/share/dialign-tx/"
432 #define DIALIGNTX_language "C"
433 #define DIALIGNTX_language2 "C"
434 #define DIALIGNTX_source "http://dialign-tx.gobics.de/DIALIGN-TX_1.0.2.tar.gz"
435 #define DIALIGNTX_mode "mcoffee"
436 #define DIALIGNTX_binary "dialign-tx"
437 #define DIALIGNTX_version "1.0.2"
438 #define POA_4_TCOFFEE "poa"
439 #define POA_type "sequence_multiple_aligner"
440 #define POA_ADDRESS "http://www.bioinformatics.ucla.edu/poa/"
441 #define POA_language "C"
442 #define POA_language2 "C"
443 #define POA_source "http://downloads.sourceforge.net/poamsa/poaV2.tar.gz"
444 #define POA_DIR "/usr/share/"
445 #define POA_FILE1 "blosum80.mat"
446 #define POA_mode "mcoffee"
447 #define POA_binary "poa"
448 #define POA_version "2.0"
449 #define PROBCONS_4_TCOFFEE "probcons"
450 #define PROBCONS_type "sequence_multiple_aligner"
451 #define PROBCONS_ADDRESS "http://probcons.stanford.edu/"
452 #define PROBCONS_language2 "CXX"
453 #define PROBCONS_language "C++"
454 #define PROBCONS_source "http://probcons.stanford.edu/probcons_v1_12.tar.gz"
455 #define PROBCONS_mode "mcoffee"
456 #define PROBCONS_binary "probcons"
457 #define PROBCONS_version "1.12"
458 #define MAFFT_4_TCOFFEE "mafft"
459 #define MAFFT_type "sequence_multiple_aligner"
460 #define MAFFT_ADDRESS "http://align.bmr.kyushu-u.ac.jp/mafft/online/server/"
461 #define MAFFT_language "C"
462 #define MAFFT_language "C"
463 #define MAFFT_source "http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz"
464 #define MAFFT_windows "http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-mingw.tar"
465 #define MAFFT_mode "mcoffee,rcoffee"
466 #define MAFFT_binary "mafft.tar.gz"
467 #define MAFFT_version "6.603"
468 #define MUSCLE_4_TCOFFEE "muscle"
469 #define MUSCLE_type "sequence_multiple_aligner"
470 #define MUSCLE_ADDRESS "http://www.drive5.com/muscle/"
471 #define MUSCLE_language "C++"
472 #define MUSCLE_language2 "GPP"
473 #define MUSCLE_source "http://www.drive5.com/muscle/downloads3.7/muscle3.7_src.tar.gz"
474 #define MUSCLE_windows "http://www.drive5.com/muscle/downloads3.7/muscle3.7_win32.zip"
475 #define MUSCLE_linux "http://www.drive5.com/muscle/downloads3.7/muscle3.7_linux_ia32.tar.gz"
476 #define MUSCLE_mode "mcoffee,rcoffee"
477 #define MUSCLE_version "3.7"
478 #define MUS4_4_TCOFFEE "mus4"
479 #define MUS4_type "sequence_multiple_aligner"
480 #define MUS4_ADDRESS "http://www.drive5.com/muscle/"
481 #define MUS4_language "C++"
482 #define MUS4_language2 "GPP"
483 #define MUS4_source "http://www.drive5.com/muscle/muscle4.0_src.tar.gz"
484 #define MUS4_mode "mcoffee,rcoffee"
485 #define MUS4_version "4.0"
486 #define PCMA_4_TCOFFEE "pcma"
487 #define PCMA_type "sequence_multiple_aligner"
488 #define PCMA_ADDRESS "ftp://iole.swmed.edu/pub/PCMA/"
489 #define PCMA_language "C"
490 #define PCMA_language2 "C"
491 #define PCMA_source "ftp://iole.swmed.edu/pub/PCMA/pcma.tar.gz"
492 #define PCMA_mode "mcoffee"
493 #define PCMA_version "1.0"
494 #define KALIGN_4_TCOFFEE "kalign"
495 #define KALIGN_type "sequence_multiple_aligner"
496 #define KALIGN_ADDRESS "http://msa.cgb.ki.se"
497 #define KALIGN_language "C"
498 #define KALIGN_language2 "C"
499 #define KALIGN_source "http://msa.cgb.ki.se/downloads/kalign/current.tar.gz"
500 #define KALIGN_mode "mcoffee"
501 #define KALIGN_version "1.0"
502 #define AMAP_4_TCOFFEE "amap"
503 #define AMAP_type "sequence_multiple_aligner"
504 #define AMAP_ADDRESS "http://bio.math.berkeley.edu/amap/"
505 #define AMAP_language "C++"
506 #define AMAP_language2 "CXX"
507 #define AMAP_source "http://amap-align.googlecode.com/files/amap.2.0.tar.gz"
508 #define AMAP_mode "mcoffee"
509 #define AMAP_version "2.0"
510 #define PRODA_4_TCOFFEE "proda"
511 #define PRODA_type "sequence_multiple_aligner"
512 #define PRODA_ADDRESS "http://proda.stanford.edu"
513 #define PRODA_language "C++"
514 #define PRODA_language2 "CXX"
515 #define PRODA_source "http://proda.stanford.edu/proda_1_0.tar.gz"
516 #define PRODA_mode "mcoffee"
517 #define PRODA_version "1.0"
518 #define FSA_4_TCOFFEE "fsa"
519 #define FSA_type "sequence_multiple_aligner"
520 #define FSA_ADDRESS "http://fsa.sourceforge.net/"
521 #define FSA_language "C++"
522 #define FSA_language2 "CXX"
523 #define FSA_source "http://sourceforge.net/projects/fsa/files/fsa-1.15.3.tar.gz/download/"
524 #define FSA_mode "mcoffee"
525 #define FSA_version "1.15.3"
526 #define PRANK_4_TCOFFEE "prank"
527 #define PRANK_type "sequence_multiple_aligner"
528 #define PRANK_ADDRESS "http://www.ebi.ac.uk/goldman-srv/prank/"
529 #define PRANK_language "C++"
530 #define PRANK_language2 "CXX"
531 #define PRANK_source "http://www.ebi.ac.uk/goldman-srv/prank/src/prank/prank.src.100303.tgz"
532 #define PRANK_mode "mcoffee"
533 #define PRANK_version "100303"
534 #define SAP_4_TCOFFEE "sap"
535 #define SAP_type "structure_pairwise_aligner"
536 #define SAP_ADDRESS "http://mathbio.nimr.mrc.ac.uk/wiki/Software"
537 #define SAP_language "C"
538 #define SAP_language2 "C"
539 #define SAP_source "http://mathbio.nimr.mrc.ac.uk/download/sap-1.1.1.tar.gz"
540 #define SAP_mode "expresso,3dcoffee"
541 #define SAP_version "1.1.1"
542 #define TMALIGN_4_TCOFFEE "TMalign"
543 #define TMALIGN_type "structure_pairwise_aligner"
544 #define TMALIGN_ADDRESS "http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f"
545 #define TMALIGN_language "Fortran"
546 #define TMALIGN_language2 "Fortran"
547 #define TMALIGN_source "http://zhang.bioinformatics.ku.edu/TM-align/TMalign.f"
548 #define TMALIGN_linux "http://zhang.bioinformatics.ku.edu/TM-align/TMalign_32.gz"
549 #define TMALIGN_mode "expresso,3dcoffee"
550 #define TMALIGN_version "1.0"
551 #define MUSTANG_4_TCOFFEE "mustang"
552 #define MUSTANG_type "structure_pairwise_aligner"
553 #define MUSTANG_ADDRESS "http://www.cs.mu.oz.au/~arun/mustang"
554 #define MUSTANG_language "C++"
555 #define MUSTANG_language2 "CXX"
556 #define MUSTANG_source "http://ww2.cs.mu.oz.au/~arun/mustang/mustang_v3.2.1.tgz"
557 #define MUSTANG_mode "expresso,3dcoffee"
558 #define MUSTANG_version "3.2.1"
559 #define LSQMAN_4_TCOFFEE "lsqman"
560 #define LSQMAN_type "structure_pairwise_aligner"
561 #define LSQMAN_ADDRESS "empty"
562 #define LSQMAN_language "empty"
563 #define LSQMAN_language2 "empty"
564 #define LSQMAN_source "empty"
565 #define LSQMAN_update_action "never"
566 #define LSQMAN_mode "expresso,3dcoffee"
567 #define ALIGN_PDB_4_TCOFFEE "align_pdb"
568 #define ALIGN_PDB_type "structure_pairwise_aligner"
569 #define ALIGN_PDB_ADDRESS "empty"
570 #define ALIGN_PDB_language "empty"
571 #define ALIGN_PDB_language2 "empty"
572 #define ALIGN_PDB_source "empty"
573 #define ALIGN_PDB_update_action "never"
574 #define ALIGN_PDB_mode "expresso,3dcoffee"
575 #define FUGUE_4_TCOFFEE "fugueali"
576 #define FUGUE_type "structure_pairwise_aligner"
577 #define FUGUE_ADDRESS "http://www-cryst.bioc.cam.ac.uk/fugue/download.html"
578 #define FUGUE_language "empty"
579 #define FUGUE_language2 "empty"
580 #define FUGUE_source "empty"
581 #define FUGUE_update_action "never"
582 #define FUGUE_mode "expresso,3dcoffee"
583 #define DALILITEc_4_TCOFFEE "dalilite.pl"
584 #define DALILITEc_type "structure_pairwise_aligner"
585 #define DALILITEc_ADDRESS "built_in"
586 #define DALILITEc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/dalilite"
587 #define DALILITEc_language "Perl"
588 #define DALILITEc_language2 "Perl"
589 #define DALILITEc_source "empty"
590 #define DALILITEc_update_action "never"
591 #define DALILITEc_mode "expresso,3dcoffee"
592 #define PROBCONSRNA_4_TCOFFEE "probconsRNA"
593 #define PROBCONSRNA_type "RNA_multiple_aligner"
594 #define PROBCONSRNA_ADDRESS "http://probcons.stanford.edu/"
595 #define PROBCONSRNA_language "C++"
596 #define PROBCONSRNA_language2 "CXX"
597 #define PROBCONSRNA_source "http://probcons.stanford.edu/probconsRNA.tar.gz"
598 #define PROBCONSRNA_mode "mcoffee,rcoffee"
599 #define PROBCONSRNA_version "1.0"
600 #define CONSAN_4_TCOFFEE "sfold"
601 #define CONSAN_type "RNA_pairwise_aligner"
602 #define CONSAN_ADDRESS "http://selab.janelia.org/software/consan/"
603 #define CONSAN_language "empty"
604 #define CONSAN_language2 "empty"
605 #define CONSAN_source "empty"
606 #define CONSAN_update_action "never"
607 #define CONSAN_mode "rcoffee"
608 #define RNAPLFOLD_4_TCOFFEE "RNAplfold"
609 #define RNAPLFOLD_type "RNA_secondarystructure_predictor"
610 #define RNAPLFOLD_ADDRESS "http://www.tbi.univie.ac.at/~ivo/RNA/"
611 #define RNAPLFOLD_language "C"
612 #define RNAPLFOLD_language2 "C"
613 #define RNAPLFOLD_source "http://www.tbi.univie.ac.at/~ivo/RNA/ViennaRNA-1.7.2.tar.gz"
614 #define RNAPLFOLD_mode "rcoffee,"
615 #define RNAPLFOLD_version "1.7.2"
616 #define PHYLIP_4_TCOFFEE "retree"
617 #define PHYLIP_type "RNA_secondarystructure_predictor"
618 #define PHYLIP_ADDRESS "http://evolution.gs.washington.edu/phylip/"
619 #define PHYLIP_language "C"
620 #define PHYLIP_language2 "C"
621 #define PHYLIP_source "http://evolution.gs.washington.edu/phylip/download/phylip-3.69.tar.gz"
622 #define PHYLIP_mode "trmsd,"
623 #define PHYLIP_version "3.69"
624 #define HMMTOP_4_TCOFFEE "hmmtop"
625 #define HMMTOP_type "protein_secondarystructure_predictor"
626 #define HMMTOP_ADDRESS "www.enzim.hu/hmmtop/"
627 #define HMMTOP_language "C"
628 #define HMMTOP_language2 "C"
629 #define HMMTOP_source "empty"
630 #define HMMTOP_update_action "never"
631 #define HMMTOP_mode "tcoffee"
632 #define GOR4_4_TCOFFEE "gorIV"
633 #define GOR4_type "protein_secondarystructure_predictor"
634 #define GOR4_ADDRESS "http://mig.jouy.inra.fr/logiciels/gorIV/"
635 #define GOR4_language "C"
636 #define GOR4_language2 "C"
637 #define GOR4_source "http://mig.jouy.inra.fr/logiciels/gorIV/GOR_IV.tar.gz"
638 #define GOR4_update_action "never"
639 #define GOR4_mode "tcoffee"
640 #define EBIWUBLASTc_4_TCOFFEE "wublast.pl"
641 #define EBIWUBLASTc_type "protein_homology_predictor"
642 #define EBIWUBLASTc_ADDRESS "built_in"
643 #define EBIWUBLASTc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/wublast"
644 #define EBIWUBLASTc_language "Perl"
645 #define EBIWUBLASTc_language2 "Perl"
646 #define EBIWUBLASTc_source "empty"
647 #define EBIWUBLASTc_update_action "never"
648 #define EBIWUBLASTc_mode "psicoffee,expresso,accurate"
649 #define EBIBLASTPGPc_4_TCOFFEE "blastpgp.pl"
650 #define EBIBLASTPGPc_type "protein_homology_predictor"
651 #define EBIBLASTPGPc_ADDRESS "built_in"
652 #define EBIBLASTPGPc_ADDRESS2 "http://www.ebi.ac.uk/Tools/webservices/services/blastpgp"
653 #define EBIBLASTPGPc_language "Perl"
654 #define EBIBLASTPGPc_language2 "Perl"
655 #define EBIBLASTPGPc_source "empty"
656 #define EBIBLASTPGPc_update_action "never"
657 #define EBIBLASTPGPc_mode "psicoffee,expresso,accurate"
658 #define NCBIWEBBLAST_4_TCOFFEE "blastcl3"
659 #define NCBIWEBBLAST_type "protein_homology_predictor"
660 #define NCBIWEBBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
661 #define NCBIWEBBLAST_language "C"
662 #define NCBIWEBBLAST_language2 "C"
663 #define NCBIWEBBLAST_source "empty"
664 #define NCBIWEBBLAST_update_action "never"
665 #define NCBIWEBBLAST_mode "psicoffee,expresso,3dcoffee"
666 #define blastall_4_TCOFFEE "blastall"
667 #define blastall_type "protein_homology_predictor"
668 #define blastall_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
669 #define blastall_language "C"
670 #define blastall_language2 "C"
671 #define blastall_source "empty"
672 #define blastall_update_action "never"
673 #define blastall_mode "psicoffee,expresso,3dcoffee"
674 #define NCBIBLAST_4_TCOFFEE "legacy_blast.pl"
675 #define NCBIBLAST_type "protein_homology_predictor"
676 #define NCBIBLAST_ADDRESS "ftp://ftp.ncbi.nih.gov/blast/executables/LATEST"
677 #define NCBIBLAST_language "C"
678 #define NCBIBLAST_language2 "C"
679 #define NCBIBLAST_source "empty"
680 #define NCBIBLAST_update_action "never"
681 #define NCBIBLAST_mode "psicoffee,expresso,3dcoffee"
682 #define SOAPLITE_4_TCOFFEE "SOAP::Lite"
683 #define SOAPLITE_type "library"
684 #define SOAPLITE_ADDRESS "http://cpansearch.perl.org/src/MKUTTER/SOAP-Lite-0.710.08/Makefile.PL"
685 #define SOAPLITE_language "Perl"
686 #define SOAPLITE_language2 "Perl"
687 #define SOAPLITE_source "empty"
688 #define _update_action "never"
689 #define SOAPLITE_mode "none"
690 #define XMLSIMPLE_4_TCOFFEE "XML::Simple"
691 #define XMLSIMPLE_type "library"
692 #define XMLSIMPLE_ADDRESS "http://search.cpan.org/~grantm/XML-Simple-2.18/lib/XML/Simple.pm"
693 #define XMLSIMPLE_language "Perl"
694 #define XMLSIMPLE_language2 "Perl"
695 #define XMLSIMPLE_source "empty"
696 #define XMLSIMPLE_mode "psicoffee,expresso,accurate"
699 /********************************************/
700 /* Various Methoids */
701 /********************************************/
702 #define METHODS_4_TCOFFEE "~/.t_coffee/methods/"
703 #define METHOD_4_MSA_WEIGHTS "petra_weight"
704 /********************************************/
706 /********************************************/
707 #define SEQAN_TCOFFEE_4_TCOFFEE "seqan_tcoffee"
708 /********************************************/
709 /* REFORMATING AND UTILITIES */
710 /********************************************/
711 #define WGET_4_TCOFFEE "wget"
712 #define WGET_ADDRESS "http://www.gnu.org/software/wget/"
714 #define CURL_4_TCOFFEE "curl"
715 #define CURL_ADDRESS "http://curl.haxx.se/"
717 #define SEQ_REFORMAT_4_TCOFFEE "seq_reformat"
718 #define PS2PDF "ps2pdf"
719 #define EXTRACT_FROM_PDB_4_TCOFFEE "extract_from_pdb"
720 #define BLAST_ALN2FASTA_ALN "blast_aln2fasta_aln.pl"
721 #define FASTA_ALN2FASTA_ALN_UNIQUE_NAME "fasta_aln2fasta_aln_unique_name.pl"
722 #define MSF_ALN2FASTA_ALN "msf_aln2fasta_aln.pl"
723 #define SEQ2MSA_WEIGHT "seq2msa_weight"
724 /********************************************/
726 /********************************************/
727 //Deprecated definitions
728 #define SIB_BLAST_4_TCOFFEE "blastall.remote"
729 #define LOCAL_BLAST_4_TCOFFEE "blastall"
730 #define BLAST_DB_4_TCOFFEE "nr"
731 #define NCBI_BLAST_4_TCOFFEE ""
732 /********************************************/
734 /********************************************/
739 /* PARAMETER FILES */
740 #define COLOR_FILE "seq_reformat.color"
741 /*This file specifies the 10 colors available to seq_reformat.
742 If the file is not on the system, hard coded defaults will be used.
743 The format is as follow:
745 -------------------------------------------------------------------------------------------
746 <Your comments (as many lines as needed >
748 <number in the range 0-9> <HTML code> <R value (float)> <G value (float)> <B value (float)>
749 -------------------------------------------------------------------------------------------
750 the RGB values are used for the post-script generation, the html code is used in html documents.
752 #define DATE "Fri Feb 18 08:27:45 CET 2011 - Revision 596"
753 #define PROGRAM "T-COFFEE"
754 #define VERSION "Version_8.99"
755 #define AUTHOR "Cedric Notredame "
756 #define DISTRIBUTION_ADDRESS "www.tcoffee.org/Packages/"
757 /******************************COPYRIGHT NOTICE*******************************/
758 /*© Centro de Regulacio Genomica */
760 /*Cedric Notredame */
761 /*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
762 /*All rights reserved.*/
763 /*This file is part of T-COFFEE.*/
765 /* T-COFFEE is free software; you can redistribute it and/or modify*/
766 /* it under the terms of the GNU General Public License as published by*/
767 /* the Free Software Foundation; either version 2 of the License, or*/
768 /* (at your option) any later version.*/
770 /* T-COFFEE is distributed in the hope that it will be useful,*/
771 /* but WITHOUT ANY WARRANTY; without even the implied warranty of*/
772 /* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the*/
773 /* GNU General Public License for more details.*/
775 /* You should have received a copy of the GNU General Public License*/
776 /* along with Foobar; if not, write to the Free Software*/
777 /* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
778 /*............................................... |*/
779 /* If you need some more information*/
780 /* cedric.notredame@europe.com*/
781 /*............................................... |*/
785 /******************************COPYRIGHT NOTICE*******************************/