[med-svn] r154 - in trunk/packages/seaview/trunk: . debian
Charles Plessy
charles-guest at alioth.debian.org
Sat Oct 28 11:31:41 CEST 2006
Author: charles-guest
Date: 2006-10-28 11:31:41 +0200 (Sat, 28 Oct 2006)
New Revision: 154
Added:
trunk/packages/seaview/trunk/seaview.xcf
trunk/packages/seaview/trunk/seaview.xpm
Removed:
trunk/packages/seaview/trunk/debian/seaview.xcf.uuencode
trunk/packages/seaview/trunk/debian/seaview.xpm
trunk/packages/seaview/trunk/debian/view
Modified:
trunk/packages/seaview/trunk/align.cxx
trunk/packages/seaview/trunk/comlines.cxx
trunk/packages/seaview/trunk/debian/changelog
trunk/packages/seaview/trunk/debian/install
trunk/packages/seaview/trunk/regions.cxx
trunk/packages/seaview/trunk/seaview.cxx
trunk/packages/seaview/trunk/seaview.h
trunk/packages/seaview/trunk/seaview.help
trunk/packages/seaview/trunk/xfmatpt.cxx
Log:
new upstream version
Modified: trunk/packages/seaview/trunk/align.cxx
===================================================================
--- trunk/packages/seaview/trunk/align.cxx 2006-10-28 09:28:58 UTC (rev 153)
+++ trunk/packages/seaview/trunk/align.cxx 2006-10-28 09:31:41 UTC (rev 154)
@@ -632,7 +632,9 @@
GetFrontProcess(&newpsn); // the newly started Terminal
sleep(2);
fl_cursor(FL_CURSOR_DEFAULT, FL_BLACK, FL_BLACK);
- status = fl_ask("Wait for alignment completion in Terminal window.\nIs it completed ?") ? 0 : 1 ;
+ status = ask_with_custom_yesno(
+ "Wait for alignment completion in Terminal window.",
+ "Alignment completed","Ignore of interrupt alignment") ? 0 : 1 ;
// try to kill only a newly started Terminal and not something else
if( FSCompareFSRefs(&frontproc, &myterm) == noErr) KillProcess(&newpsn);
}
Modified: trunk/packages/seaview/trunk/comlines.cxx
===================================================================
--- trunk/packages/seaview/trunk/comlines.cxx 2006-10-28 09:28:58 UTC (rev 153)
+++ trunk/packages/seaview/trunk/comlines.cxx 2006-10-28 09:31:41 UTC (rev 154)
@@ -310,7 +310,7 @@
else if(reponse == DELETE_FOOTER) {
if(view->tot_comment_lines == 0 || view->active_comment_line == 0)
return;
- if(! fl_ask("Confirm deletion?") ) return;
+ if(! ask_with_custom_yesno("Confirm deletion?", "Delete", "Cancel") ) return;
free(view->comment_line[view->active_comment_line - 1]);
free(view->comment_name[view->active_comment_line - 1]);
for(num = view->active_comment_line; num < view->tot_comment_lines;
Modified: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog 2006-10-28 09:28:58 UTC (rev 153)
+++ trunk/packages/seaview/trunk/debian/changelog 2006-10-28 09:31:41 UTC (rev 154)
@@ -1,5 +1,6 @@
-seaview (20060918-2) unstable; urgency=low
+seaview (20061005-1) unstable; urgency=low
+ * New upstream release. The xpm icon and its sources are now included in.
* New maintainer email: the previous one was not the intended mailing list.
* Removing options passed to x-terminal-emulator if they are not a MUST in
the policy chapter 11.8.3.
Modified: trunk/packages/seaview/trunk/debian/install
===================================================================
--- trunk/packages/seaview/trunk/debian/install 2006-10-28 09:28:58 UTC (rev 153)
+++ trunk/packages/seaview/trunk/debian/install 2006-10-28 09:31:41 UTC (rev 154)
@@ -1,5 +1,5 @@
seaview usr/bin
seaview_align.sh usr/share/seaview
seaview.help usr/share/seaview
-debian/seaview.xpm usr/share/pixmaps
+seaview.xpm usr/share/pixmaps
debian/seaview.desktop usr/share/applications
Deleted: trunk/packages/seaview/trunk/debian/seaview.xcf.uuencode
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.xcf.uuencode 2006-10-28 09:28:58 UTC (rev 153)
+++ trunk/packages/seaview/trunk/debian/seaview.xcf.uuencode 2006-10-28 09:31:41 UTC (rev 154)
@@ -1,100 +0,0 @@
-begin 644 seaview.xcf
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-`
-end
Deleted: trunk/packages/seaview/trunk/debian/seaview.xpm
===================================================================
--- trunk/packages/seaview/trunk/debian/seaview.xpm 2006-10-28 09:28:58 UTC (rev 153)
+++ trunk/packages/seaview/trunk/debian/seaview.xpm 2006-10-28 09:31:41 UTC (rev 154)
@@ -1,130 +0,0 @@
-/* XPM */
-static char * seaview_xpm[] = {
-"32 32 95 2",
-" c None",
-". c #19CC19",
-"+ c #CC4DCC",
-"@ c #129812",
-"# c #063806",
-"$ c #010D01",
-"% c #000300",
-"& c #031803",
-"* c #094C09",
-"= c #139C13",
-"- c #000000",
-"; c #118B11",
-"> c #000100",
-", c #042204",
-"' c #073D07",
-") c #14AB14",
-"! c #18C818",
-"~ c #16BB16",
-"{ c #108710",
-"] c #063206",
-"^ c #000400",
-"/ c #17BD17",
-"( c #031903",
-"_ c #0C680C",
-": c #17BC17",
-"< c #0F7E0F",
-"[ c #031C03",
-"} c #084408",
-"| c #0F800F",
-"1 c #010901",
-"2 c #042404",
-"3 c #16B916",
-"4 c #18C918",
-"5 c #14AA14",
-"6 c #0F7A0F",
-"7 c #084808",
-"8 c #15B015",
-"9 c #010E01",
-"0 c #052B05",
-"a c #0E770E",
-"b c #15AC15",
-"c c #18C618",
-"d c #18C718",
-"e c #14A414",
-"f c #042304",
-"g c #000200",
-"h c #118C11",
-"i c #0B5A0B",
-"j c #000700",
-"k c #021502",
-"l c #084308",
-"m c #139D13",
-"n c #1980E6",
-"o c #FFFFFF",
-"p c #187CDF",
-"q c #010911",
-"r c #105293",
-"s c #105294",
-"t c #051E36",
-"u c #051E37",
-"v c #146AC0",
-"w c #051C33",
-"x c #051A2E",
-"y c #146BC1",
-"z c #0A3763",
-"A c #0F4D8B",
-"B c #0F4F8E",
-"C c #0A3764",
-"D c #187BDD",
-"E c #01080E",
-"F c #000509",
-"G c #1779DA",
-"H c #01080F",
-"I c #0F4F8F",
-"J c #092F54",
-"K c #0B3865",
-"L c #0F5090",
-"M c #051B31",
-"N c #125FAC",
-"O c #156CC3",
-"P c #051C32",
-"Q c #1468BB",
-"R c #1468BC",
-"S c #0A345E",
-"T c #0A355F",
-"U c #1779DB",
-"V c #01070C",
-"W c #000101",
-"X c #1671CB",
-"Y c #177ADC",
-"Z c #0F4D8A",
-"` c #072440",
-" . c #062340",
-".. c #05192E",
-"+. c #105599",
-". . . . . . . . . . . . . . . . + + + + + + + + + + + + + + + + ",
-". . . . . . . . . . . . . . . . + + + + + + + + + + + + + + + + ",
-". . . . . @ # $ % & * = . . . . + + + + - - - - - - - - + + + + ",
-". . . . ; > - - - - - - . . . . + + + + - - - - - - - - + + + + ",
-". . . . , - ' ) ! ~ { ] . . . . + + + + - - + + + + + + + + + + ",
-". . . . ^ - / . . . . . . . . . + + + + - - + + + + + + + + + + ",
-". . . . ( - _ : . . . . . . . . + + + + - - + + + + + + + + + + ",
-". . . . < - - - [ } | ! . . . . + + + + - - - - - - - - + + + + ",
-". . . . . @ ' 1 - - - 2 3 . . . + + + + - - - - - - - - + + + + ",
-". . . . . . . 4 5 6 [ - 7 . . . + + + + - - + + + + + + + + + + ",
-". . . . . . . . . . 8 - 9 . . . + + + + - - + + + + + + + + + + ",
-". . . . . . . . . . : - ^ . . . + + + + - - + + + + + + + + + + ",
-". . . . 0 a b c d e # - f . . . + + + + - - + + + + + + + + + + ",
-". . . . - - - - - - - g h . . . + + + + - - - - - - - - + + + + ",
-". . . . e i 2 j ^ k l m . . . . + + + + - - - - - - - - + + + + ",
-". . . . . . . . . . . . . . . . + + + + + + + + + + + + + + + + ",
-"n n n n n n n n n n n n n n n n o o o o o o o o o o o o o o o o ",
-"n n n n n n n n n n n n n n n n o o o o o o o o o o o o o o o o ",
-"n n n n n n p q q p n n n n n n o o o o o o o o o o o o o o o o ",
-"n n n n n n r - - s n n n n n n o o o o o o o o o o o o o o o o ",
-"n n n n n n t - - u n n n n n n o o o o o o o o o o o o o o o o ",
-"n n n n n v - w x - y n n n n n o o o o o o o o o o o o o o o o ",
-"n n n n n z - A B - C n n n n n o o o o o o o o o o o o o o o o ",
-"n n n n D E F G D H H D n n n n o o o o o o - - - - - o o o o o ",
-"n n n n I - J n n K - L n n n n o o o o o o - - - - - o o o o o ",
-"n n n n M - N n n O - P n n n n o o o o o o o o o o o o o o o o ",
-"n n n Q - - - - - - - - R n n n o o o o o o o o o o o o o o o o ",
-"n n n S - - - - - - - - T n n n o o o o o o o o o o o o o o o o ",
-"n n U V W X n n n n X W V Y n n o o o o o o o o o o o o o o o o ",
-"n n Z - ` n n n n n n .- A n n o o o o o o o o o o o o o o o o ",
-"n n ..- +.n n n n n n +.- ..n n o o o o o o o o o o o o o o o o ",
-"n n n n n n n n n n n n n n n n o o o o o o o o o o o o o o o o "};
Deleted: trunk/packages/seaview/trunk/debian/view
===================================================================
Modified: trunk/packages/seaview/trunk/regions.cxx
===================================================================
--- trunk/packages/seaview/trunk/regions.cxx 2006-10-28 09:28:58 UTC (rev 153)
+++ trunk/packages/seaview/trunk/regions.cxx 2006-10-28 09:31:41 UTC (rev 154)
@@ -210,7 +210,7 @@
sprintf(question,
"Do you want to save changes\nin current sites selection?\n%s",
list->element->name);
- tmp = fl_ask(question);
+ tmp = ask_with_custom_yesno(question, "Save", "Cancel");
}
else tmp = TRUE;
if(tmp) list->element = copy_region(view->active_region, list->element);
@@ -433,7 +433,7 @@
if(tmp > 1) while( --tmp) list= list->next;
sprintf(question, "Confirm deletion of region:\n%s",
list->element->name);
- if( fl_ask(question) ) {
+ if( ask_with_custom_yesno(question, "Delete", "Cancel") ) {
delete_region(view, valeur);
view->DNA_obj->redraw();
items[0].activate();
Modified: trunk/packages/seaview/trunk/seaview.cxx
===================================================================
--- trunk/packages/seaview/trunk/seaview.cxx 2006-10-28 09:28:58 UTC (rev 153)
+++ trunk/packages/seaview/trunk/seaview.cxx 2006-10-28 09:31:41 UTC (rev 154)
@@ -640,7 +640,10 @@
int background, foreground;
static char lettre[]="A";
static char cursor_coord[100];
-
+Fl_Menu_Button *menu_props = (Fl_Menu_Button *)view->bouton_props;
+props_menu_parts *props_parts = (props_menu_parts *)menu_props->user_data();
+int byreference = ((Fl_Menu_Item *)menu_props->menu() + props_parts->reference)->value();
+
if( (!cursor_in_comment) && (seq == 0 || site > view->each_length[seq-1] + 1) )
return;
cursor_x = site - view->first_site;
@@ -661,6 +664,10 @@
y = view->y_seq + cursor_y * view->line_height;
x = view->x_seq + cursor_x * view->char_width;
lettre[0] = view->sequence[seq-1][site-1];
+ if(!view->allow_lower) lettre[0] = toupper(lettre[0]);
+ if(byreference && view->inverted_colors && (!on_off) && seq >= 2) {
+ if(toupper(lettre[0]) == toupper(view->sequence[0][site-1])) lettre[0] = '.';
+ }
}
if(view->numb_gc == 1) { /* cas noir et blanc */
if(on_off) {
@@ -960,7 +967,10 @@
char *lastpos, *pos;
list_segments *segment, *first_segment;
int save_col0;
-static char up_line[1000]; char *p, *q; int i;
+static char up_line[1000]; char *p, *q, *r; int i;
+Fl_Menu_Button *menu_props = (Fl_Menu_Button *)view->bouton_props;
+props_menu_parts *props_parts = (props_menu_parts *)menu_props->user_data();
+int byreference = ((Fl_Menu_Item *)menu_props->menu() + props_parts->reference)->value();
if(view->tot_seqs == 0) {
return;
@@ -1019,12 +1029,20 @@
view->line_height);
}
if(l_line == 0) continue;
+
/*ecriture des seqs: regions en noir et autres en col2 */
fl_color( use_region ? ob->selection_color() : FL_BLACK );
p = view->sequence[nline] + offset;
- if(!view->allow_lower) {
+ memcpy(up_line, p, l_line); up_line[l_line] = 0;
+ p = up_line;
+ if(!view->allow_lower) majuscules(up_line);
+ if(byreference && nline != 0) {
q = p + l_line; i = 0;
- while( p < q) up_line[i++] = toupper(*(p++));
+ r= view->sequence[0] + offset;
+ while( p < q) {
+ up_line[i++] = (toupper(*p) == toupper(*r) ? '.' : *p);
+ p++; r++;
+ }
p = up_line;
}
fl_draw(p, l_line, x, y);
@@ -1036,9 +1054,7 @@
if(segment->debut > der_site) break;
debut = FL_max(segment->debut, view->first_site);
fin = FL_min(segment->fin, der_site);
- if(view->allow_lower)
- p = view->sequence[nline] + debut - 1;
- else p = up_line + debut - offset - 1;
+ p = up_line + debut - offset - 1;
fl_draw(p,
fin - debut + 1,
x + (debut - offset - 1)*view->char_width, y);
@@ -2590,11 +2606,7 @@
int ask_with_custom_yesno(const char *text, const char *yes, const char *no)
{
-const char *oldyes = fl_yes; const char *oldno = fl_no;
-fl_yes = yes; fl_no = no;
-int rep = fl_ask(text);
-fl_yes = oldyes; fl_no = oldno;
-return rep;
+return fl_choice(text, no, yes, NULL);
}
@@ -3053,8 +3065,7 @@
Fl_Menu_Button *menu_props = (Fl_Menu_Button *)view->bouton_props;
props_menu_parts *props_parts = (props_menu_parts *)menu_props->user_data();
if(on) { /* tenter de passer en mode par reference */
- if(view ->inverted_colors || view->tot_sel_seqs != 1 ||
- view->numb_gc == 1) {
+ if( view->tot_sel_seqs != 1 || view->numb_gc == 1) {
((Fl_Menu_Item *)menu_props->menu() + props_parts->reference)->clear();
return;
}
@@ -3062,6 +3073,7 @@
for(old_pos = 0; old_pos < view->tot_seqs; old_pos++)
if(view->sel_seqs[old_pos]) break;
deplacer_grp_seqs(view, 1);
+ view->modif_but_not_saved = FALSE;
view->first_seq = 1;
view->vertsli->Fl_Slider::value(1);
view->alt_col_seq = prepcolseqs_by_difference(view->sequence,
@@ -3096,6 +3108,7 @@
view->numb_gc);
view->alt_col_seq = NULL;
deplacer_grp_seqs(view, old_pos + 1);
+ view->modif_but_not_saved = FALSE;
view->DNA_obj->redraw();
((Fl_Menu_Item *)menu_props->menu() + props_parts->colors - 1)->activate();
((Fl_Menu_Item *)menu_props->menu() + props_parts->reference)->clear();
@@ -3272,7 +3285,7 @@
props_menu_parts *props_parts = (props_menu_parts *)menu_props->user_data();
Fl_Menu_Item *byref = (Fl_Menu_Item *)menu_props->menu() + props_parts->reference;
if(view->tot_sel_seqs == 1) {
- if(!view->inverted_colors) byref->activate();
+ byref->activate();
items[RENAME_SEQ].activate();
items[DUPLICATE_SEQ].activate();
items[EDIT_COMMENTS].activate();
Modified: trunk/packages/seaview/trunk/seaview.h
===================================================================
--- trunk/packages/seaview/trunk/seaview.h 2006-10-28 09:28:58 UTC (rev 153)
+++ trunk/packages/seaview/trunk/seaview.h 2006-10-28 09:31:41 UTC (rev 154)
@@ -295,6 +295,7 @@
extern int insert_gap_all_comments(int numgaps, int pos, SEA_VIEW *view);
extern int delete_in_all_comments(int numdels, int pos, SEA_VIEW *view);
extern char* fl_file_chooser(const char* message, const char* pat, const char* fname);
+extern int ask_with_custom_yesno(const char *text, const char *yes, const char *no);
#ifdef __APPLE__
extern char *mac_fname_to_roman(char *in);
#endif
Modified: trunk/packages/seaview/trunk/seaview.help
===================================================================
--- trunk/packages/seaview/trunk/seaview.help 2006-10-28 09:28:58 UTC (rev 153)
+++ trunk/packages/seaview/trunk/seaview.help 2006-10-28 09:31:41 UTC (rev 154)
@@ -137,8 +137,7 @@
by Reference To display the alignment by reference to a particular sequence:
residues identical to that of the ref. seq. are displayed as dots.
- Possible only when one sequence, the reference, is selected and
- if not in inverted color mode.
+ Possible only when one sequence, the reference, is selected.
Alignment edition is impossible while in the reference mode.
When used, File:Prepare pdf produces an output by reference.
Combination ctrl/cmd+R is a shortcut for calling/exiting this mode.
Copied: trunk/packages/seaview/trunk/seaview.xcf (from rev 152, trunk/packages/seaview/branches/upstream/current/seaview.xcf)
Copied: trunk/packages/seaview/trunk/seaview.xpm (from rev 152, trunk/packages/seaview/branches/upstream/current/seaview.xpm)
Modified: trunk/packages/seaview/trunk/xfmatpt.cxx
===================================================================
--- trunk/packages/seaview/trunk/xfmatpt.cxx 2006-10-28 09:28:58 UTC (rev 153)
+++ trunk/packages/seaview/trunk/xfmatpt.cxx 2006-10-28 09:31:41 UTC (rev 154)
@@ -844,8 +844,8 @@
{
int rep;
if(matpt->modif_but_not_saved) {
- rep = fl_ask("Changes in dot plot were not saved in alignment\n"
- "Do you really want to close the dot plot?");
+ rep = ask_with_custom_yesno("Changes in dot plot were not saved in alignment\n"
+ "Do you really want to close the dot plot?", "Close", "Cancel");
if(!rep) return FALSE;
}
free(matpt->seq1 + 1);
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