xmenu.h File Reference

Defines
#define	MAXHELPLENGTH   50000
#define	MAXHELPW   2
#define	DCOLS   60
#define	DNAMES   15
#define	DNUMBER   6
#define	SCREENMARGIN   10
#define	SCOREHEIGHT   50
#define	MAXMENU   20
#define	MAXCOLORS   16
#define	MESSLENGTH   70
#define	MESSLINES   10
#define	MAXPROMPTLEN   300
#define	MULTIPLEM   1
#define	PROFILEM   2
#define	NEW   1
#define	OLD   0
#define	HIGHLIGHT   1
#define	NORMAL   0
#define	MARGIN   1
#define	A4   0
#define	A3   1
#define	USLETTER   2
#define	PORTRAIT   1
#define	LANDSCAPE   0
#define	MAXFINDSTR   20
#define	NAMES   0
#define	SEQS   1
Typedefs
typedef aln_pos	aln_pos
	Part of the ClustalW package.
typedef menu_item	menu_item
	Part of the ClustalW package.
typedef color	color
	Part of the ClustalW package.
typedef panel_data	panel_data
	Part of the ClustalW package.
typedef spanel	spanel
	Part of the ClustalW package.
typedef range	range
	Part of the ClustalW package.
Functions
void	x_menu (void)
void	ResizeWindowProc (WindoW w)
void	shift (Handle a, int dx, int dy)
void	swap (float *scores, int s1, int s2)
void	sort_scores (float *scores, int f, int l)
void	reload_alignment (void)
void	DrawPanel (PaneL p)
void	resize_multi_window (void)
void	resize_prf_window (int numseqs1, int numseqs2)
void	position_scrollbars (spanel p)
void	color_seqs (void)
void	color_prf1 (void)
void	color_prf2 (void)
void	select_panel (spanel p)
void	deselect_panel (spanel p)
void	correct_name_bars (Boolean reset)
void	correct_seq_bars (Boolean reset)
void	load_aln_data (spanel p, int fs, int ls, Boolean reset)
void	load_aln (spanel p, int fs, int ls, Boolean reset)
void	remove_gap_pos (int fseq, int lseq, int prf_no)
GrouP	make_scroll_area (GrouP w, int prf_no, int nwidth, int swidth, int height, int firstseq, int nseqs, spanel *p)
void	draw_seq_pointer (PaneL p, int pos, int format)
void	draw_names (PaneL p)
void	draw_seqs (PaneL p)
void	draw_header (PaneL p)
void	draw_footer (PaneL p)
void	draw_colscores (PaneL p)
void	draw_allseqs (PaneL p, int fseq, int lseq)
void	draw_nameline (PaneL p, int fseq, int lseq, int format)
void	draw_seqline (panel_data data, int seq, PoinT pt, int fcol, int lcol, int format)
void	draw_seqcol (PaneL p, int col, int format)
void	highlight_seqrange (PaneL p, int fcol, int lcol, int format)
void	make_ruler (int length, char *name, char *seq)
void	make_consensus (panel_data data, char *name, char *seq)
void	make_colscores (panel_data data)
int	calc_colscore (sint matrix[NUMRES][NUMRES], int col)
void	calc_seg_exceptions (void)
int	make_struct_data (int prf_no, int length, char *name, char *seq)
int	make_gp_data (int prf_no, int length, char *name, char *seq)
void	make_colormask (panel_data data)
void	init_color_parameters (char *filename)
char *	find_file (char *filename)
void	white_on_black (void)
void	black_on_white (void)
void	text_colors (void)
void	data_colors (void)
void	switch_mode (void)
void	show_segment_exceptions (void)
void	check_menus (menu_item m, int mode)
FILE *	open_input_file (char *file_name)
void	stripspace (char *str)
void	set_scorecutoff (BaR bar, GraphiC p, Nlm_Int2 newval, Nlm_Int2 oldval)
void	set_lengthcutoff (BaR bar, GraphiC p, Nlm_Int2 newval, Nlm_Int2 oldval)
void	set_scorescale (BaR bar, GraphiC p, Nlm_Int2 newval, Nlm_Int2 oldval)
void	set_go_penalty (TexT t)
void	set_ge_penalty (TexT t)
void	set_gap_dist (TexT t)
void	set_ntrials (TexT t)
void	set_ran_seed (TexT t)
void	set_div_seq (TexT t)
void	set_pw_go_penalty (TexT t)
void	set_pw_ge_penalty (TexT t)
void	set_gp (TexT t)
void	set_ktuple (TexT t)
void	set_topdiags (TexT t)
void	set_window (TexT t)
void	set_hyd_res (TexT t)
void	set_matrix (GrouP g)
void	set_dnamatrix (GrouP g)
void	set_user_matrix (ButtoN but)
void	set_user_dnamatrix (ButtoN but)
int	get_user_matrixname (char *usermtrxname, short *usermat, short *aa_xref, int usermatnum, int *matnum, PrompT mattext)
void	set_format (GrouP g)
void	set_button (ButtoN l, Boolean *value)
void	set_toggle (PopuP l, Boolean *value)
void	set_pref_penalties (PopuP l)
void	set_hyd_penalties (PopuP l)
void	set_var_penalties (PopuP l)
void	set_endgaps (PopuP l)
void	set_align_endgappenalties (PopuP l)
void	set_realign_endgappenalties (PopuP l)
void	set_case (PopuP l)
void	set_snos (PopuP l)
void	setRange (PopuP l)
void	set_save_paras (PopuP l)
void	set_transitions (TexT t)
void	set_save_log (IteM i)
void	set_neg_matrix (PopuP l)
void	set_ambiguities (PopuP l)
void	set_aln_mode (PopuP g)
void	set_pscroll_mode (ButtoN l)
void	set_show_segments (IteM l)
void	set_font_size (PopuP g)
void	set_residue_exceptions (IteM i)
void	set_segment_exceptions (IteM i)
void	set_segment_dnascale (BaR bar, GraphiC p, Nlm_Int2 newval, Nlm_Int2 oldval)
void	set_fs_toggle (PopuP l)
void	set_score_matrix (GrouP g)
void	set_segment_matrix (GrouP g)
void	set_score_user_matrix (ButtoN but)
void	set_segment_user_matrix (ButtoN but)
void	set_score_dnamatrix (GrouP g)
void	set_segment_dnamatrix (GrouP g)
void	set_score_user_dnamatrix (ButtoN but)
void	set_segment_user_dnamatrix (ButtoN but)
void	set_pagesize (PopuP g)
void	set_orientation (PopuP g)
void	set_header (PopuP l)
void	set_ruler (PopuP l)
void	set_curve (PopuP l)
void	set_resno (PopuP l)
void	set_resize (PopuP l)
void	set_fres (TexT t)
void	set_lres (TexT t)
void	set_fpres (TexT t)
void	set_lpres (TexT t)
void	set_blocklen (TexT t)
void	set_output_clustal (ButtoN l)
void	set_output_nbrf (ButtoN l)
void	set_output_phylip (ButtoN l)
void	set_output_gcg (ButtoN l)
void	set_output_gde (ButtoN l)
void	set_output_nexus (ButtoN l)
void	set_output_pim (ButtoN l)
void	set_output_fasta (ButtoN l)
void	set_pw_matrix (GrouP g)
void	set_pw_dnamatrix (GrouP g)
void	set_pw_user_matrix (ButtoN but)
void	set_pw_user_dnamatrix (ButtoN but)
void	set_output_order (PopuP g)
void	set_output_tree_clustal (ButtoN l)
void	set_output_tree_phylip (ButtoN l)
void	set_output_tree_distances (ButtoN l)
void	set_output_tree_nexus (ButtoN l)
void	set_inverted (IteM i)
void	set_tossgaps (IteM i)
void	set_kimura (IteM i)
void	set_boot_format (PopuP g)
void	set_use_ss1 (PopuP l)
void	set_use_ss2 (PopuP l)
void	set_helix_gp (TexT t)
void	set_strand_gp (TexT t)
void	set_loop_gp (TexT t)
void	set_terminal_gp (TexT t)
void	set_helix_minus (TexT t)
void	set_helix_plus (TexT t)
void	set_strand_minus (TexT t)
void	set_strand_plus (TexT t)
void	set_ss_output (ButtoN b)
void	set_gp_output (ButtoN b)
void	calc_segment_exceptions (IteM i)
void	write_ps_file (spanel p, char *ps_file, char *par_file, int pagesize, int orientation, Boolean header, Boolean ruler, Boolean resno, Boolean resize, int first_printres, int last_printres, int blocklen, Boolean show_curve)

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Define Documentation

#define A3   1

#define A4   0

#define DCOLS   60

#define DNAMES   15

#define DNUMBER   6

#define HIGHLIGHT   1

#define LANDSCAPE   0

#define MARGIN   1

#define MAXCOLORS   16

#define MAXFINDSTR   20

#define MAXHELPLENGTH   50000

#define MAXHELPW   2

#define MAXMENU   20

#define MAXPROMPTLEN   300

#define MESSLENGTH   70

#define MESSLINES   10

#define MULTIPLEM   1

#define NAMES   0

#define NEW   1

#define NORMAL   0

#define OLD   0

#define PORTRAIT   1

#define PROFILEM   2

#define SCOREHEIGHT   50

#define SCREENMARGIN   10

#define SEQS   1

#define USLETTER   2

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Typedef Documentation

typedef struct aln_pos aln_pos

Part of the ClustalW package.

typedef struct color color

Part of the ClustalW package.

typedef struct menu_item menu_item

Part of the ClustalW package.

typedef struct panel_data panel_data

Part of the ClustalW package.

typedef struct range range

Part of the ClustalW package.

typedef struct spanel spanel

Part of the ClustalW package.

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Function Documentation

void black_on_white (  void   )

int calc_colscore (  sint  matrix[NUMRES][NUMRES], int  col )

void calc_seg_exceptions (  void   )

void calc_segment_exceptions (  IteM  i  )

void check_menus (  menu_item  m, int  mode )

void color_prf1 (  void   )

void color_prf2 (  void   )

void color_seqs (  void   )

void correct_name_bars (  Boolean  reset  )

void correct_seq_bars (  Boolean  reset  )

void data_colors (  void   )

void deselect_panel (  spanel  p  )

void draw_allseqs (  PaneL  p, int  fseq, int  lseq )

void draw_colscores (  PaneL  p  )

void draw_footer (  PaneL  p  )

void draw_header (  PaneL  p  )

void draw_nameline (  PaneL  p, int  fseq, int  lseq, int  format )

void draw_names (  PaneL  p  )

void draw_seq_pointer (  PaneL  p, int  pos, int  format )

void draw_seqcol (  PaneL  p, int  col, int  format )

void draw_seqline (  panel_data  data, int  seq, PoinT  pt, int  fcol, int  lcol, int  format )

void draw_seqs (  PaneL  p  )

void DrawPanel (  PaneL  p  )

char* find_file (  char *  filename  )

int get_user_matrixname (  char *  usermtrxname, short *  usermat, short *  aa_xref, int  usermatnum, int *  matnum, PrompT  mattext )

void highlight_seqrange (  PaneL  p, int  fcol, int  lcol, int  format )

void init_color_parameters (  char *  filename  )

void load_aln (  spanel  p, int  fs, int  ls, Boolean  reset )

void load_aln_data (  spanel  p, int  fs, int  ls, Boolean  reset )

void make_colormask (  panel_data  data  )

void make_colscores (  panel_data  data  )

void make_consensus (  panel_data  data, char *  name, char *  seq )

int make_gp_data (  int  prf_no, int  length, char *  name, char *  seq )

void make_ruler (  int  length, char *  name, char *  seq )

GrouP make_scroll_area (  GrouP  w, int  prf_no, int  nwidth, int  swidth, int  height, int  firstseq, int  nseqs, spanel *  p )

int make_struct_data (  int  prf_no, int  length, char *  name, char *  seq )

FILE* open_input_file (  char *  file_name  )

void position_scrollbars (  spanel  p  )

void reload_alignment (  void   )

void remove_gap_pos (  int  fseq, int  lseq, int  prf_no )

void resize_multi_window (  void   )

void resize_prf_window (  int  numseqs1, int  numseqs2 )

void ResizeWindowProc (  WindoW  w  )

void select_panel (  spanel  p  )

void set_align_endgappenalties (  PopuP  l  )

void set_aln_mode (  PopuP  g  )

void set_ambiguities (  PopuP  l  )

void set_blocklen (  TexT  t  )

void set_boot_format (  PopuP  g  )

void set_button (  ButtoN  l, Boolean *  value )

void set_case (  PopuP  l  )

void set_curve (  PopuP  l  )

void set_div_seq (  TexT  t  )

void set_dnamatrix (  GrouP  g  )

void set_endgaps (  PopuP  l  )

void set_font_size (  PopuP  g  )

void set_format (  GrouP  g  )

void set_fpres (  TexT  t  )

void set_fres (  TexT  t  )

void set_fs_toggle (  PopuP  l  )

void set_gap_dist (  TexT  t  )

void set_ge_penalty (  TexT  t  )

void set_go_penalty (  TexT  t  )

void set_gp (  TexT  t  )

void set_gp_output (  ButtoN  b  )

void set_header (  PopuP  l  )

void set_helix_gp (  TexT  t  )

void set_helix_minus (  TexT  t  )

void set_helix_plus (  TexT  t  )

void set_hyd_penalties (  PopuP  l  )

void set_hyd_res (  TexT  t  )

void set_inverted (  IteM  i  )

void set_kimura (  IteM  i  )

void set_ktuple (  TexT  t  )

void set_lengthcutoff (  BaR  bar, GraphiC  p, Nlm_Int2  newval, Nlm_Int2  oldval )

void set_loop_gp (  TexT  t  )

void set_lpres (  TexT  t  )

void set_lres (  TexT  t  )

void set_matrix (  GrouP  g  )

void set_neg_matrix (  PopuP  l  )

void set_ntrials (  TexT  t  )

void set_orientation (  PopuP  g  )

void set_output_clustal (  ButtoN  l  )

void set_output_fasta (  ButtoN  l  )

void set_output_gcg (  ButtoN  l  )

void set_output_gde (  ButtoN  l  )

void set_output_nbrf (  ButtoN  l  )

void set_output_nexus (  ButtoN  l  )

void set_output_order (  PopuP  g  )

void set_output_phylip (  ButtoN  l  )

void set_output_pim (  ButtoN  l  )

void set_output_tree_clustal (  ButtoN  l  )

void set_output_tree_distances (  ButtoN  l  )

void set_output_tree_nexus (  ButtoN  l  )

void set_output_tree_phylip (  ButtoN  l  )

void set_pagesize (  PopuP  g  )

void set_pref_penalties (  PopuP  l  )

void set_pscroll_mode (  ButtoN  l  )

void set_pw_dnamatrix (  GrouP  g  )

void set_pw_ge_penalty (  TexT  t  )

void set_pw_go_penalty (  TexT  t  )

void set_pw_matrix (  GrouP  g  )

void set_pw_user_dnamatrix (  ButtoN  but  )

void set_pw_user_matrix (  ButtoN  but  )

void set_ran_seed (  TexT  t  )

void set_realign_endgappenalties (  PopuP  l  )

void set_residue_exceptions (  IteM  i  )

void set_resize (  PopuP  l  )

void set_resno (  PopuP  l  )

void set_ruler (  PopuP  l  )

void set_save_log (  IteM  i  )

void set_save_paras (  PopuP  l  )

void set_score_dnamatrix (  GrouP  g  )

void set_score_matrix (  GrouP  g  )

void set_score_user_dnamatrix (  ButtoN  but  )

void set_score_user_matrix (  ButtoN  but  )

void set_scorecutoff (  BaR  bar, GraphiC  p, Nlm_Int2  newval, Nlm_Int2  oldval )

void set_scorescale (  BaR  bar, GraphiC  p, Nlm_Int2  newval, Nlm_Int2  oldval )

void set_segment_dnamatrix (  GrouP  g  )

void set_segment_dnascale (  BaR  bar, GraphiC  p, Nlm_Int2  newval, Nlm_Int2  oldval )

void set_segment_exceptions (  IteM  i  )

void set_segment_matrix (  GrouP  g  )

void set_segment_user_dnamatrix (  ButtoN  but  )

void set_segment_user_matrix (  ButtoN  but  )

void set_show_segments (  IteM  l  )

void set_snos (  PopuP  l  )

void set_ss_output (  ButtoN  b  )

void set_strand_gp (  TexT  t  )

void set_strand_minus (  TexT  t  )

void set_strand_plus (  TexT  t  )

void set_terminal_gp (  TexT  t  )

void set_toggle (  PopuP  l, Boolean *  value )

void set_topdiags (  TexT  t  )

void set_tossgaps (  IteM  i  )

void set_transitions (  TexT  t  )

void set_use_ss1 (  PopuP  l  )

void set_use_ss2 (  PopuP  l  )

void set_user_dnamatrix (  ButtoN  but  )

void set_user_matrix (  ButtoN  but  )

void set_var_penalties (  PopuP  l  )

void set_window (  TexT  t  )

void setRange (  PopuP  l  )

void shift (  Handle  a, int  dx, int  dy )

void show_segment_exceptions (  void   )

void sort_scores (  float *  scores, int  f, int  l )

void stripspace (  char *  str  )

void swap (  float *  scores, int  s1, int  s2 )

void switch_mode (  void   )

void text_colors (  void   )

void white_on_black (  void   )

void write_ps_file (  spanel  p, char *  ps_file, char *  par_file, int  pagesize, int  orientation, Boolean  header, Boolean  ruler, Boolean  resno, Boolean  resize, int  first_printres, int  last_printres, int  blocklen, Boolean  show_curve )

void x_menu (  void   )

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