Main Page | Namespace List | Class Hierarchy | Class List | Directories | File List | Class Members | File Members

param.h File Reference


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 []

Define Documentation

#define FILARG   4
 

#define FLTARG   2
 

#define INTARG   1
 

#define MAXARGS   100
 

#define NOARG   0
 

#define OPTARG   5
 

#define STRARG   3
 


Variable Documentation

sint boot_ntrials = 1000
 

unsigned sint boot_ran_seed = 111
 

char* bootlabels_arg[] [static]
 

Initial value:

 {
                "node",
                "branch",
                ""}

sint bootstrap_format = BS_BRANCH_LABELS
 

char* case_arg[] [static]
 

Initial value:

 {
                "lower",
                "upper",
                ""}

Boolean cl_seq_numbers = FALSE
 

cmd_line_data cmd_line_file[]
 

Initial value:

 {
     "infile",          &setinfile,             FILARG, NULL,
     "profile1",        &setprofile1,           FILARG, NULL,
     "profile2",        &setprofile2,           FILARG, NULL,
     "",                NULL,                   -1}

cmd_line_data cmd_line_para[]
 

cmd_line_data cmd_line_verb[]
 

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}

sint debug = 0
 

sint divergence_cutoff = 30
 

float dna_gap_extend = 6.66
 

float dna_gap_open = 15.0
 

sint dna_ktup = 2
 

float dna_pw_ge_penalty = 6.66
 

float dna_pw_go_penalty = 15.0
 

sint dna_signif = 4
 

sint dna_wind_gap = 5
 

sint dna_window = 4
 

sint dnamatnum = 1
 

char dnamtrxname[FILENAMELEN+1] = "iub"
 

char dnausermtrxname[FILENAMELEN+1]
 

Boolean endgappenalties = FALSE
 

Boolean explicit_dnaflag = FALSE
 

sint gap_dist = 4
 

sint helix_end_minus = 3
 

sint helix_end_penalty = 2
 

sint helix_end_plus = 0
 

sint helix_penalty = 4
 

char hyd_residues[] = "GPSNDQEKR"
 

Boolean kimura = FALSE
 

sint loop_penalty = 1
 

Boolean lowercase = TRUE
 

sint matnum = 3
 

char mtrxname[FILENAMELEN+1] = "gonnet"
 

Boolean neg_matrix = FALSE
 

sint new_seq
 

Boolean no_hyd_penalties = FALSE
 

Boolean no_pref_penalties = FALSE
 

Boolean no_var_penalties = TRUE
 

Boolean no_weights = FALSE
 

char* outorder_arg[] [static]
 

Initial value:

 {
                "input",
                "aligned",
                ""}

char* output_arg[] [static]
 

Initial value:

 {
                "gcg",
                "gde",
                "pir",
                "phylip",
                "nexus",
                "fasta",
                ""}

Boolean output_clustal = TRUE
 

Boolean output_fasta = FALSE
 

Boolean output_gcg = FALSE
 

Boolean output_gde = FALSE
 

Boolean output_nbrf = FALSE
 

Boolean output_nexus = FALSE
 

sint output_order = ALIGNED
 

Boolean output_phylip = FALSE
 

Boolean output_pim = FALSE
 

sint output_struct_penalties = 0
 

Boolean output_tree_clustal = FALSE
 

Boolean output_tree_distances = FALSE
 

Boolean output_tree_nexus = FALSE
 

Boolean output_tree_phylip = TRUE
 

char* outputsecstr_arg[] [static]
 

Initial value:

 {
                "structure",
                "mask",
                "both",
                "none",
                ""}

char* outputtree_arg[] [static]
 

Initial value:

 {
                "nj",
                "phylip",
                "dist",
                "nexus",
                ""}

Boolean percent = TRUE
 

sint profile_type = PROFILE
 

float prot_gap_extend = 0.2
 

float prot_gap_open = 10.0
 

sint prot_ktup = 1
 

float prot_pw_ge_penalty = 0.1
 

float prot_pw_go_penalty = 10.0
 

sint prot_signif = 5
 

sint prot_wind_gap = 3
 

sint prot_window = 5
 

sint pw_dnamatnum = 1
 

char pw_dnamtrxname[FILENAMELEN+1] = "iub"
 

char pw_dnausermtrxname[FILENAMELEN+1]
 

sint pw_matnum = 3
 

char pw_mtrxname[FILENAMELEN+1] = "gonnet"
 

char pw_usermtrxname[FILENAMELEN+1]
 

Boolean quick_pairalign = FALSE
 

char* res_cat1[]
 

Initial value:

 {
                "STA",
                "NEQK",
                "NHQK",
                "NDEQ",
                "QHRK",
                "MILV",
                "MILF",
                "HY",
                "FYW",
                NULL }

char* res_cat2[]
 

Initial value:

 {
                "CSA",
                "ATV",
                "SAG",
                "STNK",
                "STPA",
                "SGND",
                "SNDEQK",
                "NDEQHK",
                "NEQHRK",
                "FVLIM",
                "HFY",
                NULL }

Boolean reset_alignments_all = FALSE
 

Boolean reset_alignments_new = FALSE
 

Boolean save_parameters = FALSE
 

char* score_arg[] [static]
 

Initial value:

 {
                "percent",
                "absolute",
                ""}

char* seqno_arg[] [static]
 

Initial value:

 {
                "off",
                "on",
                ""}

char* seqno_range_arg[] [static]
 

Initial value:

 {
                "off",
                "on",
                ""}

Boolean seqRange = FALSE
 

sint setalign = -1
 

sint setbatch = -1
 

sint setbootlabels = -1
 

sint setbootstrap = -1
 

sint setcase = -1
 

sint setconvert = -1
 

sint setdebug = -1
 

sint setdnamatrix = -1
 

sint setgapdist = -1
 

sint setgapext = -1
 

sint setgapopen = -1
 

sint sethelixendin = -1
 

sint sethelixendout = -1
 

sint sethelixgap = -1
 

sint sethelp = -1
 

sint sethgapres = -1
 

sint setinfile = -1
 

sint setinteractive = -1
 

sint setkimura = -1
 

sint setktuple = -1
 

sint setloopgap = -1
 

sint setmatrix = -1
 

sint setmaxdiv = -1
 

sint setnegative = -1
 

sint setnewtree = -1
 

sint setnewtree1 = -1
 

sint setnewtree2 = -1
 

sint setnohgap = -1
 

sint setnopgap = -1
 

sint setnovgap = -1
 

sint setnoweights = -1
 

sint setoptions = -1
 

sint setoutfile = -1
 

sint setoutorder = -1
 

sint setoutput = -1
 

sint setoutputtree = -1
 

sint setpairgap = -1
 

sint setprofile = -1
 

sint setprofile1 = -1
 

sint setprofile2 = -1
 

sint setpwdnamatrix = -1
 

sint setpwgapext = -1
 

sint setpwgapopen = -1
 

sint setpwmatrix = -1
 

sint setquicktree = -1
 

sint setrange = -1
 

sint setscore = -1
 

sint setsecstr1 = -1
 

sint setsecstr2 = -1
 

sint setsecstroutput = -1
 

sint setseed = -1
 

sint setseqno = -1
 

sint setseqno_range = -1
 

sint setsequences = -1
 

sint setstrandendin = -1
 

sint setstrandendout = -1
 

sint setstrandgap = -1
 

sint setterminalgap = -1
 

sint settopdiags = -1
 

sint settossgaps = -1
 

sint settransweight = -1
 

sint settree = -1
 

sint settype = -1
 

sint setuseendgaps = -1
 

sint setusetree = -1
 

sint setusetree1 = -1
 

sint setusetree2 = -1
 

sint setvgapres = -1
 

sint setwindow = -1
 

Boolean showaln = TRUE
 

sint strand_end_minus = 1
 

sint strand_end_penalty = 2
 

sint strand_end_plus = 1
 

sint strand_penalty = 4
 

sint struct_penalties1 = NONE
 

sint struct_penalties2 = NONE
 

Boolean tossgaps = FALSE
 

float transition_weight = 0.5
 

char* type_arg[] [static]
 

Initial value:

 {
                "protein",
                "dna",
                ""}

Boolean use_ambiguities = FALSE
 

Boolean use_endgaps = FALSE
 

Boolean use_ss1 = TRUE
 

Boolean use_ss2 = TRUE
 

char usermtrxname[FILENAMELEN+1]
 


Generated on Fri Aug 11 16:19:42 2006 for GENtle by  doxygen 1.4.1