/* ---------------- score_mat_string --------------------------
* This is not a score routine, it is not an alignment routine.
* Maybe it should go in its own file.
* Here are the tricks to remember.
* Our M+N score matrix is actually (M+2)(M+2) so as to allow
* for empty places and end-gaps. You don't have to use them if
* you don't like them.
* The loops below are far more elegant if we temporarily store
* the strings with end bits at start and end.
*/
char *
score_mat_string (struct score_mat *smat, struct seq *s1, struct seq *s2)
{
char *ret = NULL;
char *str1, *str2;
size_t n_rows = smat->n_rows;
size_t n_cols = smat->n_cols;
size_t i, j;
const char *c_fmt = "%4c ";
const char *f_fmt = "%4.2f ";
const char *hat = "^";
seq_thomas2std (s1);
seq_thomas2std (s2);
str1 = save_str (hat);
str1 = save_str_append (str1, s1->seq);
str1 = save_str_append (str1, hat);
str2 = save_str (hat);
str2 = save_str_append (str2, s2->seq);
str2 = save_str_append (str2, hat);
scr_reset();
scr_printf (c_fmt, ' ');
for ( i = 0; i < n_cols; i++)
scr_printf (c_fmt, str2[i]);
scr_printf ("\n");
for ( i = 0; i < n_rows; i++) {
scr_printf (c_fmt, str1[i]);
for ( j = 0 ; j < n_cols; j++)
scr_printf (f_fmt, smat->mat[i][j]);
ret = scr_printf ("\n");
}
free (str1);
free (str2);
return (ret);
}
/* ---------------- sub_mat_string ----------------------------
*/
char *
sub_mat_string (const struct sub_mat * smat)
{
char *ret;
int i, j;
const char *cfmt = " %4c";
const char *ffmt = " %4.1f";
scr_reset();
scr_printf ("Substitution matrix from file %s\n", smat->fname);
if (smat -> comment)
scr_printf ("File began with comment:\n%s\n", smat->comment);
scr_printf (cfmt, ' ');
for (i = 0; i < MAX_AA; i++)
scr_printf (cfmt, thomas2std_char (i));
scr_printf ("\n");
for (i = 0; i < MAX_AA; i++) {
scr_printf (cfmt, thomas2std_char (i));
for ( j = 0; j < MAX_AA; j++) {
mat_t x = smat->data [i] [j];
if (x == INVALID)
scr_printf (cfmt, '?');
else
scr_printf (ffmt, x);
}
ret = scr_printf ("\n");
}
return (ret);
}
/* ---------------- pair_set_chimera --------------------------
* Given an alignment, write pairs of atoms to a file in a format
* that chimera can read.
* We return a char * to space which is allocated by the
* scr_printf() routines.
*/
char *
pair_set_chimera (struct pair_set *pair_set,
const struct coord *c1, const struct coord *c2)
{
const char *this_sub = "pair_set_chimera";
int **p;
char *s1 = NULL;
char *s2 = NULL;
char *ret;
size_t i;
if (pair_set->n == 0) {
err_printf (this_sub, "empty pair set\n");
return NULL;
}
s1 = save_str ("#0");
s2 = save_str ("#1");
p = pair_set->indices;
for ( i = 0; i < pair_set->n; i++) {
int a = p[i][0], b = p[i][1];
if (( a != GAP_INDEX) && ( b != GAP_INDEX)) {
s1 = add_res (s1, a, c1);
s2 = add_res (s2, b, c2);
}
}
scr_reset();
ret = scr_printf ("match %s %s", s1, s2);
free (s1);
free (s2);
return (ret);
}
/*
* Redraw window after exposure or size change
*/
static void
resize_window1 (unsigned int width, unsigned int height)
{
static short first_time = 1;
int new_ncol = (width - szHint.base_width) / TermWin.fwidth;
int new_nrow = (height - szHint.base_height) / TermWin.fheight;
if (first_time ||
(new_ncol != TermWin.ncol) ||
(new_nrow != TermWin.nrow))
{
int curr_screen = -1;
/* scr_reset only works on the primary screen */
if (!first_time) /* this is not the first time thru */
{
selection_clear ();
curr_screen = scr_change_screen (PRIMARY);
}
TermWin.ncol = new_ncol;
TermWin.nrow = new_nrow;
resize_subwindows (width, height);
scr_reset ();
if (curr_screen >= 0) /* this is not the first time thru */
scr_change_screen (curr_screen);
first_time = 0;
}
}
/* ---------------- funcs2_char --------------------------------
*/
char *
funcs2_char ( void )
{
static int i = 0;
const char *this_sub = "funcs2_char";
scr_reset ();
scr_printf ("This is %s. I am being called %d times.\n", this_sub, ++i);
scr_printf ("Call2 from %s", this_sub);
return (scr_printf ("-Third-%s\n", this_sub));
}
/* ---------------- funcs1_char --------------------------------
*/
char *
funcs1_char ( char *in )
{
static int i = 0;
char s[256];
const char *this_sub = "funcs1_char";
sprintf (s, "%s has been called %d times and was given %s",
this_sub, ++i, in);
scr_reset ();
return (scr_printf ("%s", s));
}
/* ---------------- prob_vec_info --------------------------
* Print information about the probability vector.
* This uses the ugly machinery to write into scratch space.
* Changed so it always writes out the total of probabilities
* and the sum of squares of probabilities.
*/
char *
prob_vec_info (struct prob_vec *p_v)
{
char *ret = NULL;
float *totals, *total2;
size_t i, j, k, m, n, tomall;
if (p_v -> mship == NULL)
prob_vec_expand (p_v);
scr_reset();
scr_printf ("# Probability vector as ");
if (p_v->norm_type == PVEC_TRUE_PROB)
scr_printf ("true probability form\n");
else if ( p_v->norm_type == PVEC_UNIT_VEC)
scr_printf ("unit vector normalised\n");
else
scr_printf ("unknown normalised form\n");
scr_printf ("# protein length: %u ", (unsigned) p_v->prot_len);
scr_printf (" num vectors: %u ", (unsigned) p_v->n_pvec);
scr_printf (" fragment length: %u ", (unsigned) p_v->frag_len);
scr_printf (" num classes: %u\n", (unsigned) p_v->n_class);
scr_printf ("# res class\n");
scr_printf ("# num");
for (i = 0; i < p_v->n_class; i++)
scr_printf ("%8d", i + 1);
scr_printf ("%8s", "total");
scr_printf ("%8s", "tot^2");
scr_printf ("\n");
tomall = p_v->n_pvec * sizeof (totals[0]);
totals = E_MALLOC (tomall);
memset (totals, 0, tomall);
total2 = E_MALLOC (tomall);
memset (total2, 0, tomall);
for (j = 0; j < p_v->n_pvec; j++) {
for (k = 0; k < p_v->n_class; k++) {
totals [j] += p_v->mship [j][k];
total2 [j] += (p_v->mship [j][k] * p_v->mship [j][k]);
}
}
for (m = 0; m < p_v->n_pvec; m++) {
scr_printf ("%5u ", m);
for (n = 0; n < p_v->n_class; n++)
scr_printf ("%7.2g ", p_v->mship[m][n]);
scr_printf ("%7.2g %7.2g", totals[m], total2[m]);
ret = scr_printf ("\n");
}
free (totals);
free (total2);
return ret;
}
/*{{{ main() */
int
main (int argc, char *argv[])
{
int i;
char *val, **cmd_argv = NULL;
/* "WINDOWID=\0" = 10 chars, UINT_MAX = 10 chars */
static char windowid_string[20], *display_string;
for (i = 0; i < argc; i++)
{
if (!strcmp (argv[i], "-e"))
{
argc = i;
argv[argc] = NULL;
if (argv[argc + 1] != NULL)
{
cmd_argv = (argv + argc + 1);
if (cmd_argv[0] != NULL)
rs_iconName = rs_title = my_basename (cmd_argv[0]);
}
break;
}
}
rs_name = my_basename (argv[0]);
/*
* Open display, get options/resources and create the window
*/
if ((display_name = getenv ("DISPLAY")) == NULL)
display_name = ":0";
get_options (argc, argv);
Xdisplay = XOpenDisplay (display_name);
if (!Xdisplay)
{
print_error ("can't open display %s", display_name);
exit (EXIT_FAILURE);
}
extract_resources (Xdisplay, rs_name);
/*
* set any defaults not already set
*/
if (!rs_title)
rs_title = rs_name;
if (!rs_iconName)
rs_iconName = rs_name;
if (!rs_saveLines || (TermWin.saveLines = atoi (rs_saveLines)) < 0)
TermWin.saveLines = SAVELINES;
/* no point having a scrollbar without having any scrollback! */
if (!TermWin.saveLines)
Options &= ~Opt_scrollBar;
#ifdef PRINTPIPE
if (!rs_print_pipe)
rs_print_pipe = PRINTPIPE;
#endif
if (!rs_cutchars)
rs_cutchars = CUTCHARS;
#ifndef NO_BOLDFONT
if (rs_font[0] == NULL && rs_boldFont != NULL)
{
rs_font[0] = rs_boldFont;
rs_boldFont = NULL;
}
#endif
for (i = 0; i < NFONTS; i++)
{
if (!rs_font[i])
rs_font[i] = def_fontName[i];
#ifdef KANJI
if (!rs_kfont[i])
rs_kfont[i] = def_kfontName[i];
#endif
}
#ifdef XTERM_REVERSE_VIDEO
/* this is how xterm implements reverseVideo */
if (Options & Opt_reverseVideo)
{
if (!rs_color[fgColor])
rs_color[fgColor] = def_colorName[bgColor];
if (!rs_color[bgColor])
rs_color[bgColor] = def_colorName[fgColor];
}
#endif
for (i = 0; i < NRS_COLORS; i++)
if (!rs_color[i])
rs_color[i] = def_colorName[i];
#ifndef XTERM_REVERSE_VIDEO
/* this is how we implement reverseVideo */
if (Options & Opt_reverseVideo)
{
const char *name;
/* swap foreground/background colors */
name = rs_color[fgColor];
rs_color[fgColor] = rs_color[bgColor];
rs_color[bgColor] = name;
name = def_colorName[fgColor];
def_colorName[fgColor] = def_colorName[bgColor];
def_colorName[bgColor] = name;
}
#endif
/* convenient aliases for setting fg/bg to colors */
color_aliases (fgColor);
color_aliases (bgColor);
#ifndef NO_CURSORCOLOR
color_aliases (cursorColor);
color_aliases (cursorColor2);
#endif /* NO_CURSORCOLOR */
#ifndef NO_BOLDUNDERLINE
color_aliases (colorBD);
color_aliases (colorUL);
#endif /* NO_BOLDUNDERLINE */
Create_Windows (argc, argv);
scr_reset (); /* initialize screen */
Gr_reset (); /* reset graphics */
/* add scrollBar, do it directly to avoid resize() */
scrollbar_mapping (Options & Opt_scrollBar);
#ifdef DEBUG_X
XSynchronize (Xdisplay, True);
XSetErrorHandler ((XErrorHandler) abort);
#else
XSetErrorHandler ((XErrorHandler) xerror_handler);
#endif
#ifdef DISPLAY_IS_IP
/* Fixup display_name for export over pty to any interested terminal
* clients via "ESC[7n" (e.g. shells). Note we use the pure IP number
* (for the first non-loopback interface) that we get from
* network_display(). This is more "name-resolution-portable", if you
* will, and probably allows for faster x-client startup if your name
* server is beyond a slow link or overloaded at client startup. Of
* course that only helps the shell's child processes, not us.
*
* Giving out the display_name also affords a potential security hole
*/
val = display_name = network_display (display_name);
if (val == NULL)
#endif /* DISPLAY_IS_IP */
val = XDisplayString (Xdisplay);
if (display_name == NULL)
display_name = val; /* use broken `:0' value */
i = strlen (val);
display_string = MALLOC ((i + 9) * sizeof (char), "display_string");
sprintf (display_string, "DISPLAY=%s", val);
sprintf (windowid_string, "WINDOWID=%u", (unsigned int) TermWin.parent);
/* add entries to the environment:
* @ DISPLAY: in case we started with -display
* @ WINDOWID: X window id number of the window
* @ COLORTERM: terminal sub-name and also indicates its color
* @ TERM: terminal name
*/
putenv (display_string);
putenv (windowid_string);
if (Xdepth <= 2)
{
putenv ("COLORTERM=" COLORTERMENV "-mono");
putenv ("TERM=" TERMENV);
}
else
{
#ifdef XPM_BACKGROUND
putenv ("COLORTERM=" COLORTERMENV "-xpm");
#else
putenv ("COLORTERM=" COLORTERMENV);
#endif
#ifdef DEFINE_XTERM_COLOR
putenv ("TERM=" TERMENV "-color");
#else
putenv ("TERM=" TERMENV);
#endif
}
init_command (cmd_argv);
main_loop (); /* main processing loop */
return EXIT_SUCCESS;
}
