[med-svn] r447 - in trunk/packages/seaview/trunk/debian: . patches
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Sun Sep 23 01:13:17 UTC 2007
Author: charles-guest
Date: 2007-09-23 01:13:17 +0000 (Sun, 23 Sep 2007)
New Revision: 447
Added:
trunk/packages/seaview/trunk/debian/patches/xterm_to_x-terminal-emulator.patch
Removed:
trunk/packages/seaview/trunk/debian/patches/30-align.cxx.patch
Modified:
trunk/packages/seaview/trunk/debian/changelog
trunk/packages/seaview/trunk/debian/patches/series
Log:
[seaview] new upstream version
Modified: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog 2007-09-22 21:14:14 UTC (rev 446)
+++ trunk/packages/seaview/trunk/debian/changelog 2007-09-23 01:13:17 UTC (rev 447)
@@ -1,12 +1,13 @@
-seaview (1:2.0-2) UNRELEASED; urgency=low
+seaview (1:2.1-1) unstable; urgency=low
[ Nelson A. de Oliveira ]
* Updated watch file.
[ Charles Plessy ]
* Moved the Homepage: field out from the package's description.
+ * New upstream release: introduced interface to external alignment programs.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Fri, 21 Sep 2007 23:25:18 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 23 Sep 2007 10:01:09 +0900
seaview (1:2.0-1) unstable; urgency=low
Deleted: trunk/packages/seaview/trunk/debian/patches/30-align.cxx.patch
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/30-align.cxx.patch 2007-09-22 21:14:14 UTC (rev 446)
+++ trunk/packages/seaview/trunk/debian/patches/30-align.cxx.patch 2007-09-23 01:13:17 UTC (rev 447)
@@ -1,47 +0,0 @@
---- seaview/align.cxx 2006-09-25 23:41:13.000000000 +0900
-+++ seaview/align.cxx.debian 2006-09-25 23:42:26.000000000 +0900
-@@ -114,7 +114,8 @@
- static char *prog_path;
- static char algo_name[2][20] = {"clustalw", "muscle"};
-
--/* check for presence of xterm + clustalw/muscle + seaview_align.sh */
-+/* Modified in Debian to take advantage of the /etc/alternatives system */
-+/* check for presence of x-terminal-emulator + clustalw/muscle + seaview_align.sh */
- #ifdef WIN32
- p = (char *)(align_algorithm == CLUSTALW ? "clustalw.exe" : "muscle.exe" );
- status = check_path( p );
-@@ -144,11 +145,12 @@
- #else
- status = check_path((char*)(align_algorithm == CLUSTALW ? "clustalw" : "muscle"));
- if(status == 0) {
-- status = check_path("xterm");
-+ status = check_path("x-terminal-emulator");
- }
-- if(status == 0) {
-+/* if(status == 0) {
- status = check_path("seaview_align.sh");
- }
-+*/
- #endif
- if(status != 0) {
- fl_message("Alignment operation is impossible because\n"
-@@ -157,7 +159,7 @@
- #elif defined(__APPLE__)
- "program clustalw/muscle\n"
- #else
-- "one of the programs xterm, clustalw, muscle, seaview_align.sh\n"
-+ "one of the programs x-terminal-emulator, clustalw, muscle, seaview_align.sh\n"
- #endif
- "is missing");
- ((Fl_Menu_ *)view->menu_edit)->mode(ALIGN_SEQS,
-@@ -249,8 +251,8 @@
- base_fname, base_fname);
- #endif
- #else
--sprintf(commande, "xterm -T \"%s alignment\" -n %s -sb -sl 2000 "
-- "-e seaview_align.sh %s ", algo_name[align_algorithm], algo_name[align_algorithm],
-+sprintf(commande, "x-terminal-emulator -T \"%s alignment\" "
-+ "-e /usr/share/seaview/seaview_align.sh %s ", algo_name[align_algorithm], algo_name[align_algorithm],
- algo_name[align_algorithm]);
- l = strlen(commande);
- switch (align_algorithm) {
Modified: trunk/packages/seaview/trunk/debian/patches/series
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/series 2007-09-22 21:14:14 UTC (rev 446)
+++ trunk/packages/seaview/trunk/debian/patches/series 2007-09-23 01:13:17 UTC (rev 447)
@@ -1,4 +1,4 @@
20-no-PDF-in-help.patch
21-location-of-seaview.help.patch
-30-align.cxx.patch
+xterm_to_x-terminal-emulator.patch
40-seaview_align.sh-newline.patch
Added: trunk/packages/seaview/trunk/debian/patches/xterm_to_x-terminal-emulator.patch
===================================================================
--- trunk/packages/seaview/trunk/debian/patches/xterm_to_x-terminal-emulator.patch (rev 0)
+++ trunk/packages/seaview/trunk/debian/patches/xterm_to_x-terminal-emulator.patch 2007-09-23 01:13:17 UTC (rev 447)
@@ -0,0 +1,37 @@
+Index: seaview21/align.cxx
+===================================================================
+--- seaview21.orig/align.cxx 2007-09-23 09:43:47.000000000 +0900
++++ seaview21/align.cxx 2007-09-23 09:57:02.000000000 +0900
+@@ -129,14 +129,14 @@
+ static char base_fname[100], commande[300];
+
+ #if ! ( defined(WIN32) || defined(__APPLE__) )
+-/* check for presence of xterm + seaview_align.sh */
+- status = get_full_path("xterm") == NULL;
++/* check for presence of x-terminal-emulator + seaview_align.sh */
++ status = get_full_path("x-terminal-emulator") == NULL;
+ if(status == 0) {
+ status = get_full_path("seaview_align.sh") == NULL;
+ }
+ if(status != 0) {
+ fl_message("Alignment operation is impossible because\n"
+- "one of the programs xterm, seaview_align.sh\n"
++ "one of the programs x-terminal-emulator, seaview_align.sh\n"
+ "is missing");
+ ((Fl_Menu_ *)view->menu_edit)->mode(ALIGN_ALL_SEQS, FL_MENU_INACTIVE);
+ ((Fl_Menu_ *)view->menu_edit)->mode(ALIGN_SELECTION, FL_MENU_INACTIVE);
+@@ -579,12 +579,12 @@
+ #elif defined(WIN32)
+ sprintf(command, "cmd.exe /c \"%s\" %s ", w32path, local);
+ #else
+-/* if present, > must be protected by '' before sending to xterm */
++/* if present, > must be protected by '' before sending to x-terminal-emulator */
+ if((p=strchr(local, '>')) != NULL) {
+ memmove(p+3, p+1, strlen(p+1) + 1);
+ memcpy(p, "'>'", 3);
+ }
+-sprintf(command, "xterm -T \"%s alignment\" -n %s -sb -sl 2000 -e seaview_align.sh %s %s %s ",
++sprintf(command, "x-terminal-emulator -T \"%s alignment\" -n %s -sb -sl 2000 -e seaview_align.sh %s %s %s ",
+ algo_name, algo_name, algo_name, base_fname, local);
+ #endif
+ return 0;
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