Defines | |
| #define | MAXARGS 100 |
| #define | NOARG 0 |
| #define | INTARG 1 |
| #define | FLTARG 2 |
| #define | STRARG 3 |
| #define | FILARG 4 |
| #define | OPTARG 5 |
Variables | |
| sint | setoptions = -1 |
| sint | sethelp = -1 |
| sint | setinteractive = -1 |
| sint | setbatch = -1 |
| sint | setgapopen = -1 |
| sint | setgapext = -1 |
| sint | setpwgapopen = -1 |
| sint | setpwgapext = -1 |
| sint | setoutorder = -1 |
| sint | setbootlabels = -1 |
| sint | setpwmatrix = -1 |
| sint | setmatrix = -1 |
| sint | setpwdnamatrix = -1 |
| sint | setdnamatrix = -1 |
| sint | setnegative = -1 |
| sint | setnoweights = -1 |
| sint | setoutput = -1 |
| sint | setoutputtree = -1 |
| sint | setquicktree = -1 |
| sint | settype = -1 |
| sint | setcase = -1 |
| sint | setseqno = -1 |
| sint | setseqno_range = -1 |
| sint | setrange = -1 |
| sint | settransweight = -1 |
| sint | setseed = -1 |
| sint | setscore = -1 |
| sint | setwindow = -1 |
| sint | setktuple = -1 |
| sint | setkimura = -1 |
| sint | settopdiags = -1 |
| sint | setpairgap = -1 |
| sint | settossgaps = -1 |
| sint | setnopgap = -1 |
| sint | setnohgap = -1 |
| sint | setnovgap = -1 |
| sint | sethgapres = -1 |
| sint | setvgapres = -1 |
| sint | setuseendgaps = -1 |
| sint | setmaxdiv = -1 |
| sint | setgapdist = -1 |
| sint | setdebug = -1 |
| sint | setoutfile = -1 |
| sint | setinfile = -1 |
| sint | setprofile1 = -1 |
| sint | setprofile2 = -1 |
| sint | setalign = -1 |
| sint | setconvert = -1 |
| sint | setnewtree = -1 |
| sint | setusetree = -1 |
| sint | setnewtree1 = -1 |
| sint | setusetree1 = -1 |
| sint | setnewtree2 = -1 |
| sint | setusetree2 = -1 |
| sint | setbootstrap = -1 |
| sint | settree = -1 |
| sint | setprofile = -1 |
| sint | setsequences = -1 |
| sint | setsecstr1 = -1 |
| sint | setsecstr2 = -1 |
| sint | setsecstroutput = -1 |
| sint | sethelixgap = -1 |
| sint | setstrandgap = -1 |
| sint | setloopgap = -1 |
| sint | setterminalgap = -1 |
| sint | sethelixendin = -1 |
| sint | sethelixendout = -1 |
| sint | setstrandendin = -1 |
| sint | setstrandendout = -1 |
| float | dna_gap_open = 15.0 |
| float | dna_gap_extend = 6.66 |
| float | prot_gap_open = 10.0 |
| float | prot_gap_extend = 0.2 |
| sint | profile_type = PROFILE |
| sint | gap_dist = 4 |
| sint | output_order = ALIGNED |
| sint | divergence_cutoff = 30 |
| sint | matnum = 3 |
| char | mtrxname [FILENAMELEN+1] = "gonnet" |
| sint | dnamatnum = 1 |
| char | dnamtrxname [FILENAMELEN+1] = "iub" |
| char | hyd_residues [] = "GPSNDQEKR" |
| Boolean | no_weights = FALSE |
| Boolean | neg_matrix = FALSE |
| Boolean | no_hyd_penalties = FALSE |
| Boolean | no_var_penalties = TRUE |
| Boolean | no_pref_penalties = FALSE |
| Boolean | use_endgaps = FALSE |
| Boolean | endgappenalties = FALSE |
| Boolean | reset_alignments_new = FALSE |
| Boolean | reset_alignments_all = FALSE |
| sint | output_struct_penalties = 0 |
| sint | struct_penalties1 = NONE |
| sint | struct_penalties2 = NONE |
| Boolean | use_ss1 = TRUE |
| Boolean | use_ss2 = TRUE |
| sint | helix_penalty = 4 |
| sint | strand_penalty = 4 |
| sint | loop_penalty = 1 |
| sint | helix_end_minus = 3 |
| sint | helix_end_plus = 0 |
| sint | strand_end_minus = 1 |
| sint | strand_end_plus = 1 |
| sint | helix_end_penalty = 2 |
| sint | strand_end_penalty = 2 |
| Boolean | use_ambiguities = FALSE |
| float | dna_pw_go_penalty = 15.0 |
| float | dna_pw_ge_penalty = 6.66 |
| float | prot_pw_go_penalty = 10.0 |
| float | prot_pw_ge_penalty = 0.1 |
| sint | pw_matnum = 3 |
| char | pw_mtrxname [FILENAMELEN+1] = "gonnet" |
| sint | pw_dnamatnum = 1 |
| char | pw_dnamtrxname [FILENAMELEN+1] = "iub" |
| char | usermtrxname [FILENAMELEN+1] |
| char | pw_usermtrxname [FILENAMELEN+1] |
| char | dnausermtrxname [FILENAMELEN+1] |
| char | pw_dnausermtrxname [FILENAMELEN+1] |
| Boolean | quick_pairalign = FALSE |
| float | transition_weight = 0.5 |
| sint | new_seq |
| sint | dna_ktup = 2 |
| sint | dna_wind_gap = 5 |
| sint | dna_signif = 4 |
| sint | dna_window = 4 |
| sint | prot_ktup = 1 |
| sint | prot_wind_gap = 3 |
| sint | prot_signif = 5 |
| sint | prot_window = 5 |
| Boolean | percent = TRUE |
| Boolean | tossgaps = FALSE |
| Boolean | kimura = FALSE |
| sint | boot_ntrials = 1000 |
| unsigned sint | boot_ran_seed = 111 |
| sint | debug = 0 |
| Boolean | explicit_dnaflag = FALSE |
| Boolean | lowercase = TRUE |
| Boolean | cl_seq_numbers = FALSE |
| Boolean | seqRange = FALSE |
| Boolean | output_clustal = TRUE |
| Boolean | output_gcg = FALSE |
| Boolean | output_phylip = FALSE |
| Boolean | output_nbrf = FALSE |
| Boolean | output_gde = FALSE |
| Boolean | output_nexus = FALSE |
| Boolean | output_fasta = FALSE |
| Boolean | showaln = TRUE |
| Boolean | save_parameters = FALSE |
| Boolean | output_tree_clustal = FALSE |
| Boolean | output_tree_phylip = TRUE |
| Boolean | output_tree_distances = FALSE |
| Boolean | output_tree_nexus = FALSE |
| Boolean | output_pim = FALSE |
| sint | bootstrap_format = BS_BRANCH_LABELS |
| char * | res_cat1 [] |
| char * | res_cat2 [] |
| static char * | type_arg [] |
| static char * | bootlabels_arg [] |
| static char * | outorder_arg [] |
| static char * | case_arg [] |
| static char * | seqno_arg [] |
| static char * | seqno_range_arg [] |
| static char * | score_arg [] |
| static char * | output_arg [] |
| static char * | outputtree_arg [] |
| static char * | outputsecstr_arg [] |
| cmd_line_data | cmd_line_file [] |
| cmd_line_data | cmd_line_verb [] |
| cmd_line_data | cmd_line_para [] |
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Initial value: {
"node",
"branch",
""}
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Initial value: {
"lower",
"upper",
""}
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Initial value: {
"infile", &setinfile, FILARG, NULL,
"profile1", &setprofile1, FILARG, NULL,
"profile2", &setprofile2, FILARG, NULL,
"", NULL, -1}
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Initial value: {
"help", &sethelp, NOARG, NULL,
"check", &sethelp, NOARG, NULL,
"options", &setoptions, NOARG, NULL,
"align", &setalign, NOARG, NULL,
"newtree", &setnewtree, FILARG, NULL,
"usetree", &setusetree, FILARG, NULL,
"newtree1", &setnewtree1, FILARG, NULL,
"usetree1", &setusetree1, FILARG, NULL,
"newtree2", &setnewtree2, FILARG, NULL,
"usetree2", &setusetree2, FILARG, NULL,
"bootstrap", &setbootstrap, NOARG, NULL,
"tree", &settree, NOARG, NULL,
"quicktree", &setquicktree, NOARG, NULL,
"convert", &setconvert, NOARG, NULL,
"interactive", &setinteractive, NOARG, NULL,
"batch", &setbatch, NOARG, NULL,
"", NULL, -1}
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Initial value: {
"input",
"aligned",
""}
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Initial value: {
"gcg",
"gde",
"pir",
"phylip",
"nexus",
"fasta",
""}
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Initial value: {
"structure",
"mask",
"both",
"none",
""}
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Initial value: {
"nj",
"phylip",
"dist",
"nexus",
""}
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Initial value: {
"STA",
"NEQK",
"NHQK",
"NDEQ",
"QHRK",
"MILV",
"MILF",
"HY",
"FYW",
NULL }
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Initial value: {
"CSA",
"ATV",
"SAG",
"STNK",
"STPA",
"SGND",
"SNDEQK",
"NDEQHK",
"NEQHRK",
"FVLIM",
"HFY",
NULL }
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Initial value: {
"percent",
"absolute",
""}
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Initial value: {
"off",
"on",
""}
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Initial value: {
"off",
"on",
""}
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Initial value: {
"protein",
"dna",
""}
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1.4.1