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amenu.cpp File Reference

#include <stdio.h>
#include <string.h>
#include <ctype.h>
#include <stdlib.h>
#include <stdarg.h>
#include <signal.h>
#include <setjmp.h>
#include "clustalw.h"

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

Define Documentation

#define BADSIG   (void (*)())-1
 


Function Documentation

void error char *  msg,
  ...
 

void fatal char *  msg,
  ...
 

static void format_options_menu void   )  [static]
 

static void gap_penalties_menu void   )  [static]
 

void info char *  msg,
  ...
 

void init_amenu void   ) 
 

static void jumper int   )  [static]
 

void main_menu void   ) 
 

static void multi_menu void   )  [static]
 

static void multiple_align_menu void   )  [static]
 

static void pair_menu void   )  [static]
 

static void phylogenetic_tree_menu void   )  [static]
 

static void profile_align_menu void   )  [static]
 

char prompt_for_yes_no char *  title,
char *  prompt
 

static sint read_matrix char *  title,
MatMenu  menu,
char *  matnam,
sint  matn,
short *  mat,
short *  xref
[static]
 

static sint secstroutput_options void   )  [static]
 

static void ss_options_menu void   )  [static]
 

static void tree_format_options_menu void   )  [static]
 

void warning char *  msg,
  ...
 


Variable Documentation

short aa_xref[]
 

sint bootstrap_format
 

Boolean cl_seq_numbers
 

char clustal_name[FILENAMELEN] = "" [static]
 

sint debug
 

char dist_name[FILENAMELEN] = "" [static]
 

sint divergence_cutoff
 

float dna_gap_extend
 

float dna_gap_open
 

sint dna_ktup
 

float dna_pw_ge_penalty
 

float dna_pw_go_penalty
 

sint dna_signif
 

sint dna_wind_gap
 

sint dna_window
 

short dna_xref[]
 

Boolean dnaflag
 

sint dnamatnum
 

MatMenu dnamatrix_menu
 

char dnamtrxname[]
 

Boolean empty
 

char fasta_name[FILENAMELEN] = "" [static]
 

int firstres = 0 [static]
 

sint gap_dist
 

float gap_extend
 

float gap_open
 

sint helix_end_minus
 

sint helix_end_penalty
 

sint helix_end_plus
 

sint helix_penalty
 

char hyd_residues[]
 

jmp_buf jmpbuf [static]
 

Boolean kimura
 

sint ktup
 

int lastres = 0 [static]
 

char* lin1 [static]
 

char * lin2 [static]
 

char * lin3 [static]
 

sint loop_penalty
 

Boolean lowercase
 

sint matnum
 

MatMenu matrix_menu
 

char mtrxname[]
 

Boolean neg_matrix
 

char nexus_name[FILENAMELEN] = "" [static]
 

Boolean no_hyd_penalties
 

Boolean no_pref_penalties
 

Boolean no_var_penalties
 

sint nseqs
 

Boolean output_clustal
 

Boolean output_fasta
 

Boolean output_gcg
 

Boolean output_gde
 

Boolean output_nbrf
 

Boolean output_nexus
 

sint output_order
 

Boolean output_phylip
 

sint output_struct_penalties
 

Boolean output_tree_clustal
 

Boolean output_tree_distances
 

Boolean output_tree_nexus
 

Boolean output_tree_phylip
 

char p1_tree_name[FILENAMELEN] = "" [static]
 

char p2_tree_name[FILENAMELEN] = "" [static]
 

Boolean percent
 

char phylip_name[FILENAMELEN] = "" [static]
 

Boolean profile1_empty
 

char profile1_name[FILENAMELEN+1]
 

Boolean profile2_empty
 

char profile2_name[FILENAMELEN+1]
 

sint profile_no
 

float prot_gap_extend
 

float prot_gap_open
 

sint prot_ktup
 

float prot_pw_ge_penalty
 

float prot_pw_go_penalty
 

sint prot_signif
 

sint prot_wind_gap
 

sint prot_window
 

short pw_aa_xref[]
 

short pw_dna_xref[]
 

sint pw_dnamatnum
 

char pw_dnamtrxname[]
 

float pw_ge_penalty
 

float pw_go_penalty
 

sint pw_matnum
 

MatMenu pw_matrix_menu
 

char pw_mtrxname[]
 

short pw_userdnamat[]
 

short pw_usermat[]
 

Boolean quick_pairalign
 

Boolean reset_alignments_all
 

Boolean reset_alignments_new
 

char revision_level[]
 

Boolean save_parameters
 

char* secstroutput_txt[] [static]
 

Initial value:

 {
                                "Secondary Structure",
                                "Gap Penalty Mask",
                                "Structure and Penalty Mask",
                                "None"  }

char seqname[]
 

Boolean seqRange
 

Boolean showaln
 

sint signif
 

sint strand_end_minus
 

sint strand_end_penalty
 

sint strand_end_plus
 

sint strand_penalty
 

Boolean tossgaps
 

float transition_weight
 

Boolean use_ambiguities
 

Boolean use_endgaps
 

Boolean use_ss1
 

Boolean use_ss2
 

Boolean usemenu
 

short userdnamat[]
 

short usermat[]
 

sint wind_gap
 

sint window
 


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