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interfac.cpp File Reference

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

Classes

struct  rangeNum
 Part of the ClustalW package. More...

Defines

#define isgap(val1)   ( (val1 < 0) || (val1 > max_aa) )
#define isend(val1)   ((val1 == -3)||(val1 == 253) )

Typedefs

typedef rangeNum rangeNum

Functions

char * nameonly (char *s)
static sint check_param (char **args, char *params[], char *param_arg[])
static void set_optional_param (void)
static sint find_match (char *probe, char *list[], sint n)
static void show_aln (void)
static void create_parameter_output (void)
static void reset_align (void)
static void reset_prf1 (void)
static void reset_prf2 (void)
static void calc_gap_penalty_mask (int prf_length, char *struct_mask, char *gap_mask)
void print_sec_struct_mask (int prf_length, char *mask, char *struct_mask)
void init_interface (void)
void get_help (char help_pointer)
void parse_params (Boolean xmenus)
Boolean user_mat (char *str, short *mat, short *xref)
Boolean user_mat_series (char *str, short *mat, short *xref)
sint seq_input (Boolean append)
sint profile_input (void)
FILE * open_output_file (char *prompt, char *path, char *file_name, char *file_extension)
FILE * open_explicit_file (char *file_name)
void align (char *phylip_name)
void new_sequence_align (char *phylip_name)
void make_tree (char *phylip_name)
void get_tree (char *phylip_name)
void profile_align (char *p1_tree_name, char *p2_tree_name)
void fillrange (rangeNum *rnum, sint fres, sint len, sint fseq)
void fasta_out (FILE *fastaout, sint fres, sint len, sint fseq, sint lseq)
void clustal_out (FILE *clusout, sint fres, sint len, sint fseq, sint lseq)
void gcg_out (FILE *gcgout, sint fres, sint len, sint fseq, sint lseq)
int startFind (char *s)
void nexus_out (FILE *nxsout, sint fres, sint len, sint fseq, sint lseq)
void phylip_out (FILE *phyout, sint fres, sint len, sint fseq, sint lseq)
void nbrf_out (FILE *nbout, sint fres, sint len, sint fseq, sint lseq)
void gde_out (FILE *gdeout, sint fres, sint len, sint fseq, sint lseq)
Boolean open_alignment_output (char *path)
void create_alignment_output (sint fseq, sint lseq)
void fix_gaps (void)
void calc_percidentity (FILE *pfile)

Variables

sint max_names
Boolean interactive
double ** tmat
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
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 boot_ntrials
sint nseqs
sint new_seq
sint * seqlen_array
sint divergence_cutoff
sint debug
Boolean no_weights
Boolean neg_matrix
Boolean quick_pairalign
Boolean reset_alignments_new
Boolean reset_alignments_all
sint gap_dist
Boolean no_hyd_penalties
Boolean no_pref_penalties
sint max_aa
sint gap_pos1
sint gap_pos2
sint max_aln_length
sint * output_index
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 []
sint * seq_weight
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 explicit_dnaflag
Boolean usemenu
Boolean showaln
Boolean save_parameters
Boolean dnaflag
float transition_weight
unsigned sint boot_ran_seed
FILE * tree
FILE * clustal_outfile
FILE * gcg_outfile
FILE * nbrf_outfile
FILE * phylip_outfile
FILE * nexus_outfile
FILE * fasta_outfile
FILE * gde_outfile
char hyd_residues []
char * amino_acid_codes
char ** args
char seqname []
char ** seq_array
char ** names
char ** titles
char * gap_penalty_mask1
char * gap_penalty_mask2
char * sec_struct_mask1
char * sec_struct_mask2
sint struct_penalties
sint struct_penalties1
sint struct_penalties2
sint output_struct_penalties
Boolean use_ss1
Boolean use_ss2
char * ss_name1
char * ss_name2
char * ss_name = NULL
char * sec_struct_mask = NULL
char * gap_penalty_mask = NULL
char profile1_name [FILENAMELEN+1]
char profile2_name [FILENAMELEN+1]
Boolean empty
Boolean profile1_empty
Boolean profile2_empty
char outfile_name [FILENAMELEN+1] = ""
static char clustal_outname [FILENAMELEN+1]
static char gcg_outname [FILENAMELEN+1]
static char phylip_outname [FILENAMELEN+1]
static char nbrf_outname [FILENAMELEN+1]
static char gde_outname [FILENAMELEN+1]
static char nexus_outname [FILENAMELEN+1]
static char fasta_outname [FILENAMELEN+1]
char clustal_tree_name [FILENAMELEN+1] = ""
char dist_tree_name [FILENAMELEN+1] = ""
char phylip_tree_name [FILENAMELEN+1] = ""
char nexus_tree_name [FILENAMELEN+1] = ""
char p1_tree_name [FILENAMELEN+1] = ""
char p2_tree_name [FILENAMELEN+1] = ""
char pim_name [FILENAMELEN+1] = ""
static char * params [MAXARGS]
static char * param_arg [MAXARGS]
static char * cmd_line_type []
static sint numparams
static Boolean check_tree = TRUE
sint profile1_nseqs
Boolean use_tree_file = FALSE
Boolean new_tree_file = FALSE
Boolean use_tree1_file = FALSE
Boolean use_tree2_file = FALSE
Boolean new_tree1_file = FALSE
Boolean new_tree2_file = FALSE
static char * lin2
MatMenu dnamatrix_menu
MatMenu matrix_menu
MatMenu pw_matrix_menu

Define Documentation

#define isend val1   )     ((val1 == -3)||(val1 == 253) )
 

#define isgap val1   )     ( (val1 < 0) || (val1 > max_aa) )
 


Typedef Documentation

typedef struct rangeNum rangeNum
 


Function Documentation

void align char *  phylip_name  ) 
 

static void calc_gap_penalty_mask int  prf_length,
char *  struct_mask,
char *  gap_mask
[static]
 

void calc_percidentity FILE *  pfile  ) 
 

static sint check_param char **  args,
char *  params[],
char *  param_arg[]
[static]
 

void clustal_out FILE *  clusout,
sint  fres,
sint  len,
sint  fseq,
sint  lseq
 

void create_alignment_output sint  fseq,
sint  lseq
 

static void create_parameter_output void   )  [static]
 

void fasta_out FILE *  fastaout,
sint  fres,
sint  len,
sint  fseq,
sint  lseq
 

void fillrange rangeNum rnum,
sint  fres,
sint  len,
sint  fseq
 

static sint find_match char *  probe,
char *  list[],
sint  n
[static]
 

void fix_gaps void   ) 
 

void gcg_out FILE *  gcgout,
sint  fres,
sint  len,
sint  fseq,
sint  lseq
 

void gde_out FILE *  gdeout,
sint  fres,
sint  len,
sint  fseq,
sint  lseq
 

void get_help char  help_pointer  ) 
 

void get_tree char *  phylip_name  ) 
 

void init_interface void   ) 
 

void make_tree char *  phylip_name  ) 
 

char* nameonly char *  s  ) 
 

void nbrf_out FILE *  nbout,
sint  fres,
sint  len,
sint  fseq,
sint  lseq
 

void new_sequence_align char *  phylip_name  ) 
 

void nexus_out FILE *  nxsout,
sint  fres,
sint  len,
sint  fseq,
sint  lseq
 

Boolean open_alignment_output char *  path  ) 
 

FILE* open_explicit_file char *  file_name  ) 
 

FILE* open_output_file char *  prompt,
char *  path,
char *  file_name,
char *  file_extension
 

void parse_params Boolean  xmenus  ) 
 

void phylip_out FILE *  phyout,
sint  fres,
sint  len,
sint  fseq,
sint  lseq
 

void print_sec_struct_mask int  prf_length,
char *  mask,
char *  struct_mask
 

void profile_align char *  p1_tree_name,
char *  p2_tree_name
 

sint profile_input void   ) 
 

static void reset_align void   )  [static]
 

static void reset_prf1 void   )  [static]
 

static void reset_prf2 void   )  [static]
 

sint seq_input Boolean  append  ) 
 

static void set_optional_param void   )  [static]
 

static void show_aln void   )  [static]
 

int startFind char *  s  ) 
 

Boolean user_mat char *  str,
short *  mat,
short *  xref
 

Boolean user_mat_series char *  str,
short *  mat,
short *  xref
 


Variable Documentation

short aa_xref[]
 

char* amino_acid_codes
 

char** args
 

sint boot_ntrials
 

unsigned sint boot_ran_seed
 

sint bootstrap_format
 

Boolean check_tree = TRUE [static]
 

Boolean cl_seq_numbers
 

FILE* clustal_outfile
 

char clustal_outname[FILENAMELEN+1] [static]
 

char clustal_tree_name[FILENAMELEN+1] = ""
 

char* cmd_line_type[] [static]
 

Initial value:

 {
                " ",
                "=n ",
                "=f ",
                "=string ",
                "=filename ",
                ""}

sint debug
 

char dist_tree_name[FILENAMELEN+1] = ""
 

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
 

MatMenu dnamatrix_menu
 

Initial value:

 {3,
                "IUB","iub",
                "CLUSTALW(1.6)","clustalw",
                "User defined",""
                }

Boolean empty
 

Boolean explicit_dnaflag
 

FILE* fasta_outfile
 

char fasta_outname[FILENAMELEN+1] [static]
 

sint gap_dist
 

float gap_extend
 

float gap_open
 

char* gap_penalty_mask = NULL
 

char* gap_penalty_mask1
 

char * gap_penalty_mask2
 

sint gap_pos1
 

sint gap_pos2
 

FILE * gcg_outfile
 

char gcg_outname[FILENAMELEN+1] [static]
 

FILE* gde_outfile
 

char gde_outname[FILENAMELEN+1] [static]
 

char hyd_residues[]
 

Boolean interactive
 

Boolean kimura
 

sint ktup
 

char* lin2 [static]
 

Boolean lowercase
 

MatMenu matrix_menu
 

Initial value:

 {5,
                "BLOSUM series","blosum",
                "PAM series","pam",
                "Gonnet series","gonnet",
                "Identity matrix","id",
                "User defined",""
                }

sint max_aa
 

sint max_aln_length
 

sint max_names
 

char** names
 

FILE * nbrf_outfile
 

char nbrf_outname[FILENAMELEN+1] [static]
 

Boolean neg_matrix
 

sint new_seq
 

Boolean new_tree1_file = FALSE
 

Boolean new_tree2_file = FALSE
 

Boolean new_tree_file = FALSE
 

FILE * nexus_outfile
 

char nexus_outname[FILENAMELEN+1] [static]
 

char nexus_tree_name[FILENAMELEN+1] = ""
 

Boolean no_hyd_penalties
 

Boolean no_pref_penalties
 

Boolean no_weights
 

sint nseqs
 

sint numparams [static]
 

char outfile_name[FILENAMELEN+1] = ""
 

Boolean output_clustal
 

Boolean output_fasta
 

Boolean output_gcg
 

Boolean output_gde
 

sint* output_index
 

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+1] = ""
 

char p2_tree_name[FILENAMELEN+1] = ""
 

char* param_arg[MAXARGS] [static]
 

char* params[MAXARGS] [static]
 

Boolean percent
 

FILE * phylip_outfile
 

char phylip_outname[FILENAMELEN+1] [static]
 

char phylip_tree_name[FILENAMELEN+1] = ""
 

char pim_name[FILENAMELEN+1] = ""
 

Boolean profile1_empty
 

char profile1_name[FILENAMELEN+1]
 

sint profile1_nseqs
 

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[]
 

float pw_ge_penalty
 

float pw_go_penalty
 

MatMenu pw_matrix_menu
 

Initial value:

 {5,
                "BLOSUM 30","blosum",
                "PAM 350","pam",
                "Gonnet 250","gonnet",
                "Identity matrix","id",
                "User defined",""
                }

short pw_userdnamat[]
 

short pw_usermat[]
 

Boolean quick_pairalign
 

Boolean reset_alignments_all
 

Boolean reset_alignments_new
 

char revision_level[]
 

Boolean save_parameters
 

char* sec_struct_mask = NULL
 

char* sec_struct_mask1
 

char * sec_struct_mask2
 

char** seq_array
 

sint* seq_weight
 

sint* seqlen_array
 

char seqname[]
 

Boolean seqRange
 

Boolean showaln
 

sint signif
 

char* ss_name = NULL
 

char* ss_name1
 

char * ss_name2
 

sint struct_penalties
 

sint struct_penalties1
 

sint struct_penalties2
 

char ** titles
 

double** tmat
 

Boolean tossgaps
 

float transition_weight
 

FILE* tree
 

Boolean use_ss1
 

Boolean use_ss2
 

Boolean use_tree1_file = FALSE
 

Boolean use_tree2_file = FALSE
 

Boolean use_tree_file = FALSE
 

Boolean usemenu
 

short userdnamat[]
 

short usermat[]
 

sint wind_gap
 

sint window
 


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