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Defines |
#define | BADSIG (void (*)())-1 |
Functions |
static void | jumper (int) |
static void | pair_menu (void) |
static void | multi_menu (void) |
static void | gap_penalties_menu (void) |
static void | multiple_align_menu (void) |
static void | profile_align_menu (void) |
static void | phylogenetic_tree_menu (void) |
static void | format_options_menu (void) |
static void | tree_format_options_menu (void) |
static void | ss_options_menu (void) |
static sint | secstroutput_options (void) |
static sint | read_matrix (char *title, MatMenu menu, char *matnam, sint matn, short *mat, short *xref) |
void | init_amenu (void) |
void | main_menu (void) |
char | prompt_for_yes_no (char *title, char *prompt) |
void | fatal (char *msg,...) |
void | error (char *msg,...) |
void | warning (char *msg,...) |
void | info (char *msg,...) |
Variables |
static jmp_buf | jmpbuf |
float | gap_open |
float | gap_extend |
float | dna_gap_open |
float | dna_gap_extend |
float | prot_gap_open |
float | prot_gap_extend |
float | pw_go_penalty |
float | pw_ge_penalty |
float | dna_pw_go_penalty |
float | dna_pw_ge_penalty |
float | prot_pw_go_penalty |
float | prot_pw_ge_penalty |
float | transition_weight |
char | revision_level [] |
sint | wind_gap |
sint | ktup |
sint | window |
sint | signif |
sint | dna_wind_gap |
sint | dna_ktup |
sint | dna_window |
sint | dna_signif |
sint | prot_wind_gap |
sint | prot_ktup |
sint | prot_window |
sint | prot_signif |
sint | nseqs |
sint | divergence_cutoff |
sint | debug |
Boolean | neg_matrix |
Boolean | quick_pairalign |
Boolean | reset_alignments_new |
Boolean | reset_alignments_all |
sint | gap_dist |
Boolean | no_var_penalties |
Boolean | no_hyd_penalties |
Boolean | no_pref_penalties |
sint | output_order |
sint | profile_no |
short | usermat [] |
short | pw_usermat [] |
short | aa_xref [] |
short | pw_aa_xref [] |
short | userdnamat [] |
short | pw_userdnamat [] |
short | dna_xref [] |
short | pw_dna_xref [] |
Boolean | lowercase |
Boolean | cl_seq_numbers |
Boolean | seqRange |
Boolean | output_clustal |
Boolean | output_nbrf |
Boolean | output_phylip |
Boolean | output_gcg |
Boolean | output_gde |
Boolean | output_nexus |
Boolean | output_fasta |
Boolean | output_tree_clustal |
Boolean | output_tree_phylip |
Boolean | output_tree_distances |
Boolean | output_tree_nexus |
sint | bootstrap_format |
Boolean | tossgaps |
Boolean | kimura |
Boolean | percent |
Boolean | usemenu |
Boolean | showaln |
Boolean | save_parameters |
Boolean | dnaflag |
Boolean | use_ambiguities |
char | hyd_residues [] |
char | mtrxname [] |
char | pw_mtrxname [] |
char | dnamtrxname [] |
char | pw_dnamtrxname [] |
char | seqname [] |
sint | output_struct_penalties |
Boolean | use_ss1 |
Boolean | use_ss2 |
Boolean | empty |
Boolean | profile1_empty |
Boolean | profile2_empty |
char | profile1_name [FILENAMELEN+1] |
char | profile2_name [FILENAMELEN+1] |
Boolean | use_endgaps |
sint | matnum |
sint | pw_matnum |
sint | dnamatnum |
sint | pw_dnamatnum |
sint | helix_penalty |
sint | strand_penalty |
sint | loop_penalty |
sint | helix_end_minus |
sint | helix_end_plus |
sint | strand_end_minus |
sint | strand_end_plus |
sint | helix_end_penalty |
sint | strand_end_penalty |
MatMenu | matrix_menu |
MatMenu | pw_matrix_menu |
MatMenu | dnamatrix_menu |
static char | phylip_name [FILENAMELEN] = "" |
static char | clustal_name [FILENAMELEN] = "" |
static char | dist_name [FILENAMELEN] = "" |
static char | nexus_name [FILENAMELEN] = "" |
static char | fasta_name [FILENAMELEN] = "" |
static char | p1_tree_name [FILENAMELEN] = "" |
static char | p2_tree_name [FILENAMELEN] = "" |
static char * | secstroutput_txt [] |
static char * | lin1 |
static char * | lin2 |
static char * | lin3 |
static int | firstres = 0 |
static int | lastres = 0 |