Subject: rev 5 - trunk trunk/phylo trunk/lisp

From: [email-masked]
Date: Wed, 7 Aug 2002 12:30:37 -0500

Author: kfogel
Date: Wed, 07 Aug 2002 12:30:15 -0500
New Revision: 5

Removed:
   trunk/patches/
Modified:
   trunk/autogen.sh
   trunk/config.guess
   trunk/lisp/gene-analyze.el
   trunk/lisp/gene-ann-mode.el
   trunk/lisp/gene-clipboard.el
   trunk/lisp/gene-consensus.el
   trunk/lisp/gene-data-input.el
   trunk/lisp/gene-dialog.el
   trunk/lisp/gene-display.el
   trunk/lisp/gene-error.el
   trunk/lisp/gene-frame.el
   trunk/lisp/gene-help.el
   trunk/lisp/gene-id-mode.el
   trunk/lisp/gene-io.el
   trunk/lisp/gene-locking.el
   trunk/lisp/gene-menus.el
   trunk/lisp/gene-message.el
   trunk/lisp/gene-mode-tools.el
   trunk/lisp/gene-phylo.el
   trunk/lisp/gene-posmon.el
   trunk/lisp/gene-search.el
   trunk/lisp/gene-selection.el
   trunk/lisp/gene-seq-mode.el
   trunk/lisp/gene-sgroup.el
   trunk/lisp/gene-threats.el
   trunk/lisp/gene-translate.el
   trunk/lisp/gene-undo.el
   trunk/lisp/gene-windows.el
   trunk/lisp/gene.el
   trunk/phylo/lenstring.c
   trunk/phylo/lenstring.h
   trunk/phylo/phylo.c
Log:
Make Ale work with Emacs 21.3.50.3:

* everywhere: Remove all calls to hscroll-point-visible.  Emacs does
  horizontal scrolling automatically now, so this function was
  removed in 1999.  Also, remove all the CVS $Id$ strings.

* lisp/gene.el
  (gene-startup): Inhibit default Emacs startup screen and toolbar.

* lisp/gene-phylo.el 
  (gene-phylo-make-faces): Don't set fonts to nil, that doesn't work
  anymore.

* patches/: Remove this directory and everything in it.  Stock Emacs
  is now compatible with Ale.

Fix some build problems, unrelated to above:

* phylo/phylo.c
  (report_syserr): Constify message to avoid compiler warning.

* phylo/lenstring.h, phylo/lenstring.c: 
  (write_quoted): Constify text parameter.

* autogen.sh, config.guess: Set the `svn:executable' property.

Modified: trunk/phylo/lenstring.c
==============================================================================
--- trunk/phylo/lenstring.c	(original)
+++ trunk/phylo/lenstring.c	Wed Aug  7 12:30:25 2002
@@ -221,9 +221,9 @@
    here, as lenstrings aren't involved, but if you think about this
    module as dealing with fully-transparent strings, it's okay.  */
 void
-write_quoted (FILE *output_file, char *text, size_t len)
+write_quoted (FILE *output_file, const char *text, size_t len)
 {
-  char *text_end = text + len;
+  const char *text_end = text + len;
 
   putc ('"', output_file);

Modified: trunk/phylo/lenstring.h
==============================================================================
--- trunk/phylo/lenstring.h	(original)
+++ trunk/phylo/lenstring.h	Wed Aug  7 12:30:26 2002
@@ -50,7 +50,7 @@
    here, as lenstrings aren't involved, but if you think about this
    module as dealing with fully-transparent strings, it's okay.  */
 extern void write_quoted (FILE *OUTPUT_FILE,
-			  char *TEXT,
+			  const char *TEXT,
 			  size_t LEN);
 
 /* Like write_quoted, but for lenstrings.  */

Modified: trunk/phylo/phylo.c
==============================================================================
--- trunk/phylo/phylo.c	(original)
+++ trunk/phylo/phylo.c	Wed Aug  7 12:30:26 2002
@@ -639,7 +639,7 @@
 void
 report_syserr ()
 {
-  char *message;
+  const char *message;
 
   if (errno < 0 || errno > sys_nerr)
     message = "<unrecognized error code>";

Modified: trunk/lisp/gene-undo.el
==============================================================================
--- trunk/lisp/gene-undo.el	(original)
+++ trunk/lisp/gene-undo.el	Wed Aug  7 12:30:26 2002
@@ -20,7 +20,6 @@
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 ;;
 ;; Search for instances of "todo:" to find notes about future plans.
-;;	$Id: gene-undo.el,v 1.34 1995/05/15 17:21:01 kfogel Exp $     
 
 
 ;;;; Things in ale that need special undo:
@@ -117,8 +116,8 @@
         (ding)
         (gene-message "No more undo information available.")
         ))
-    (gene-handle-vertical-motion)
-    (hscroll-point-visible)))
+    (gene-handle-vertical-motion)))
+
 
 
 (defun gene-record-unchanged-state ()

Modified: trunk/lisp/gene-display.el
==============================================================================
--- trunk/lisp/gene-display.el	(original)
+++ trunk/lisp/gene-display.el	Wed Aug  7 12:30:26 2002
@@ -20,7 +20,6 @@
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 ;;
 ;; Search for instances of "todo:" to find notes about future plans.
-;;	$Id: gene-display.el,v 1.12 1995/04/26 20:11:33 kfogel Exp $

 

Modified: trunk/lisp/gene-search.el
==============================================================================
--- trunk/lisp/gene-search.el	(original)
+++ trunk/lisp/gene-search.el	Wed Aug  7 12:30:26 2002
@@ -20,7 +20,6 @@
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 ;;
 ;; Search for instances of "todo:" to find notes about future plans.
-;;	$Id: gene-search.el,v 1.10 1995/05/15 17:10:26 kfogel Exp $  
 
 ;;; searching
 ;; two possible approaches: build a string that is the current
@@ -264,7 +263,6 @@
                       (1- s-end)
                     ;; else was forward
                     (1+ s-beg)))))
-      (hscroll-point-visible)
       ;; Set this-command for `gene-search-repeat-last-search'.
       (setq this-command 'gene-search-do-search)
       retval)))
@@ -378,8 +376,7 @@
                   (match-e (match-end 0)))
               (progn
                 (goto-char (1- match-e))
-                (move-overlay gene-search-match-overlay match-s match-e)
-                (hscroll-point-visible)))
+                (move-overlay gene-search-match-overlay match-s match-e)))
           (if gene-use-bell (ding))
           (gene-message "No match for %s." str))
       (gene-message "No current sequence group."))))
@@ -404,8 +401,7 @@
                   (match-e (match-end 0)))
               (progn
                 (goto-char match-s)     ; damn o-b-o-e
-                (move-overlay gene-search-match-overlay match-s match-e)
-                (hscroll-point-visible)))
+                (move-overlay gene-search-match-overlay match-s match-e)))
           (if gene-use-bell (ding))
           (gene-message "No match for %s." str))
       (gene-message "No current sequence group."))))
@@ -424,8 +420,7 @@
               (match-e (match-end 0)))
           (progn
             (goto-char (1- match-e))
-            (move-overlay gene-search-match-overlay match-s match-e)
-            (hscroll-point-visible)))
+            (move-overlay gene-search-match-overlay match-s match-e)))
       (if gene-use-bell (ding))
       (gene-message "No match for %s." str))))
 
@@ -443,8 +438,7 @@
               (match-e (match-end 0)))
           (progn
             (goto-char match-s)         ; damn o-b-o-e
-            (move-overlay gene-search-match-overlay match-s match-e)
-            (hscroll-point-visible)))
+            (move-overlay gene-search-match-overlay match-s match-e)))
       (if gene-use-bell (ding))
       (gene-message "No match for %s." str))))

Modified: trunk/lisp/gene-data-input.el
==============================================================================
--- trunk/lisp/gene-data-input.el	(original)
+++ trunk/lisp/gene-data-input.el	Wed Aug  7 12:30:27 2002
@@ -21,7 +21,6 @@
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 ;;
 ;; Search for instances of "todo:" to find notes about future plans.
-;;	$Id: gene-data-input.el,v 1.3 1995/03/21 00:16:37 kfogel Exp $
 
 (require 'gene-mode-tools)

Modified: trunk/lisp/gene-io.el
==============================================================================
--- trunk/lisp/gene-io.el	(original)
+++ trunk/lisp/gene-io.el	Wed Aug  7 12:30:27 2002
@@ -19,7 +19,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-io.el,v 1.71 1995/06/17 17:50:15 kfogel Exp $	
 
 ;; needed: 
 ;; `gene-io-revert-sequence' -- revert this sequence to the version in

Modified: trunk/lisp/gene-seq-mode.el
==============================================================================
--- trunk/lisp/gene-seq-mode.el	(original)
+++ trunk/lisp/gene-seq-mode.el	Wed Aug  7 12:30:28 2002
@@ -20,7 +20,6 @@
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 ;;
 ;; Search for instances of "todo:" to find notes about future plans.
-;;	$Id: gene-seq-mode.el,v 1.135 1995/05/05 16:34:33 kfogel Exp $
 
 
 ;;; Code:
@@ -553,10 +552,7 @@
             (if (< apparent-column half-width)
                 (scroll-right (- half-width apparent-column))
               (if (> apparent-column half-width)
-                  (scroll-left (- apparent-column half-width)))))
-          
-          ;; And make it visible.
-          (hscroll-point-visible)))))
+                  (scroll-left (- apparent-column half-width)))))))))

 (defun gene-seq-recenter ()
@@ -588,8 +584,7 @@
 
   (split-window-horizontally (gene-id-calculate-window-width nil id-width))
   (switch-to-buffer gene-id-buffer)
-  (other-window 1)
-  (hscroll-point-visible))
+  (other-window 1))

 
@@ -1327,8 +1322,7 @@
       (goto-char (gene-eol-point))
       ;; Be on, not after, the last char, and watch out for 0-length
       ;; sequences!
-      (or (bolp) (forward-char -1))
-      (hscroll-point-visible))))
+      (or (bolp) (forward-char -1)))))
 
 
 ;; Case changing a sequence:
@@ -1552,9 +1546,7 @@
 
   ;; If on a base, just move over
   (if (gene-seq-base-after-p)
-      (progn
-        (gene-seq-backward-position 1)
-        (hscroll-point-visible))
+      (gene-seq-backward-position 1)
     ;; Else do the fetch
     (gene-locking-sequence-state-p nil gene-locking-gapshift-state t)
     (let (buffer-read-only
@@ -1583,9 +1575,7 @@
   ;; that is, when there's a base at point.
 
   (if (gene-seq-base-after-p)
-      (progn
-        (gene-seq-forward-position 1)
-        (hscroll-point-visible))
+      (gene-seq-forward-position 1)
     (gene-locking-sequence-state-p nil gene-locking-gapshift-state t)
     (let (buffer-read-only
           (to-fetch
@@ -2123,8 +2113,7 @@
               nil
             (ding)
             (gene-message "Cannot move beyond end."))))
-    (forward-char parg))
-  (hscroll-point-visible))
+    (forward-char parg)))

 (defun gene-seq-backward-position (parg)
@@ -2140,8 +2129,7 @@
               nil
             (ding)
             (gene-message "Cannot move beyond beginning."))))
-    (forward-char (- parg)))
-  (hscroll-point-visible))
+    (forward-char (- parg))))

 (defun gene-seq-forward-base (parg)
@@ -2155,7 +2143,6 @@
             (re-search-forward gene-base-regexp eol t))
       (setq parg (1- parg)))
     (forward-char -1)
-    (hscroll-point-visible)
     (if (> parg 0)
         (gene-error "Cannot move past end."))))
 
@@ -2169,7 +2156,6 @@
             (> parg 0)
             (re-search-backward gene-base-regexp bol t))
       (setq parg (1- parg)))
-    (hscroll-point-visible)
     (if (> parg 0)
         (gene-error "Cannot move past beginning."))))
 
@@ -2188,8 +2174,7 @@
       (progn
         (forward-char -1)
         (ding)
-        (message "No more residue groups.")))
-  (hscroll-point-visible))
+        (message "No more residue groups."))))

 (defun gene-seq-previous-base-group (parg)
@@ -2206,7 +2191,6 @@
           (ding)
           (message "No more residue groups."))
       (forward-char -1)))
-  (hscroll-point-visible)
   (if (> parg 0)
       (gene-message "Cannot move past beginning.")))
 
@@ -2215,8 +2199,7 @@
   "Go to column COL in the current sequence, or end of line if too short.
 Columns start numbering from 1, for the purposes of this function only."
   (interactive "nGo to column number: ")
-  (gene-goto-column (max 0 (1- col)))
-  (hscroll-point-visible))
+  (gene-goto-column (max 0 (1- col))))

 ;; todo: should bases start numbering from 0 instead?
@@ -2227,8 +2210,7 @@
   (beginning-of-line)
   (let ((eol (gene-eol-point)))
     (re-search-forward gene-base-regexp eol t num))
-  (forward-char -1)
-  (hscroll-point-visible))
+  (forward-char -1))

 (defun gene-read-organism-symbol (prompt)
@@ -2260,9 +2242,7 @@
       ;; Do nothing if already there.
       ;; Well, just make sure we're in the right column.
       (if col
-          (progn
-            (gene-goto-column col)
-            (or non-interactive (hscroll-point-visible))))
+          (gene-goto-column col))
     (let* ((column (or col (gene-current-column)))
            is-a-line
            (spot 
@@ -2286,7 +2266,6 @@
             (if non-interactive
                 nil
               (set-window-point (gene-seq-buffer-window t) (point))
-              (hscroll-point-visible)
               (gene-handle-vertical-motion)))
         
         ;; Else this organism isn't in the editor.
@@ -2295,16 +2274,26 @@
 
 (defun gene-seq-last-col ()
   "Move to the last residue in the sequence."
+  ;; todo: Now that we no longer call hscroll-point-visible, this
+  ;; wrapper around end-of-line may no longer be necessary.  But I'm
+  ;; leaving it in for now, because suspect that just calling
+  ;; end-of-line doesn't actually fulfill the promise made in the doc
+  ;; string (there could be a spacer at the end of this particular
+  ;; line), so we may need to do more here.
   (interactive)
-  (end-of-line)
-  (hscroll-point-visible))
+  (end-of-line))

 (defun gene-seq-first-col ()
   "Move to the first residue in the sequence."
+  ;; todo: Now that we no longer call hscroll-point-visible, this
+  ;; wrapper around beginning-of-line may no longer be necessary.  But
+  ;; I'm leaving it in for now, because suspect that just calling
+  ;; beginning-of-line doesn't actually fulfill the promise made in
+  ;; the doc  string (there could be a spacer at the start of this
+  ;; particular line), so we may need to do more here.
   (interactive)
-  (beginning-of-line)
-  (hscroll-point-visible))
+  (beginning-of-line))

 (defun gene-seq-beginning-of-alignment ()
@@ -2312,8 +2301,7 @@
   (interactive)
   (beginning-of-buffer)
   (setq this-command 'gene-seq-line-motion)
-  (gene-handle-vertical-motion t)
-  (hscroll-point-visible))
+  (gene-handle-vertical-motion t))

 (defun gene-seq-end-of-alignment ()
@@ -2324,8 +2312,7 @@
   (forward-char -2)
   (gene-seq-last-col)
   (setq this-command 'gene-seq-line-motion)
-  (gene-handle-vertical-motion t)
-  (hscroll-point-visible))
+  (gene-handle-vertical-motion t))

 

Modified: trunk/lisp/gene-threats.el
==============================================================================
--- trunk/lisp/gene-threats.el	(original)
+++ trunk/lisp/gene-threats.el	Wed Aug  7 12:30:29 2002
@@ -19,7 +19,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-threats.el,v 1.1.1.1 1995/01/20 03:06:54 jimb Exp $	
 
 ;; Let 'em know where they stand.

Modified: trunk/lisp/gene-posmon.el
==============================================================================
--- trunk/lisp/gene-posmon.el	(original)
+++ trunk/lisp/gene-posmon.el	Wed Aug  7 12:30:29 2002
@@ -20,7 +20,6 @@
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 ;;
 ;; Search for instances of "todo:" to find notes about future plans.
-;;	$Id: gene-posmon.el,v 1.26 1995/04/03 20:26:03 kfogel Exp $
 
 
 ;;;; Position monitoring in current sequence and reference sequences.

Modified: trunk/lisp/gene-id-mode.el
==============================================================================
--- trunk/lisp/gene-id-mode.el	(original)
+++ trunk/lisp/gene-id-mode.el	Wed Aug  7 12:30:29 2002
@@ -18,7 +18,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-id-mode.el,v 1.12 1995/07/26 01:28:48 kfogel Exp $	
 
 ;;; Code:
 (require 'gene-mode-tools)

Modified: trunk/lisp/gene-sgroup.el
==============================================================================
--- trunk/lisp/gene-sgroup.el	(original)
+++ trunk/lisp/gene-sgroup.el	Wed Aug  7 12:30:30 2002
@@ -18,7 +18,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-sgroup.el,v 1.29 1995/06/17 18:06:14 kfogel Exp $	
 
 ;;; Code for manipulating sequence groups.

Modified: trunk/lisp/gene-consensus.el
==============================================================================
--- trunk/lisp/gene-consensus.el	(original)
+++ trunk/lisp/gene-consensus.el	Wed Aug  7 12:30:30 2002
@@ -18,8 +18,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-consensus.el,v 1.32 1995/06/15 18:16:58 kfogel Exp $
-
 
 (require 'gene-mode-tools)

Modified: trunk/lisp/gene-mode-tools.el
==============================================================================
--- trunk/lisp/gene-mode-tools.el	(original)
+++ trunk/lisp/gene-mode-tools.el	Wed Aug  7 12:30:30 2002
@@ -20,7 +20,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-mode-tools.el,v 1.52 1995/09/06 17:37:03 kfogel Exp $
 
 (require 'cl)
 (require 'cl-19)

Modified: trunk/lisp/gene-message.el
==============================================================================
--- trunk/lisp/gene-message.el	(original)
+++ trunk/lisp/gene-message.el	Wed Aug  7 12:30:31 2002
@@ -18,7 +18,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-message.el,v 1.15 1995/06/28 23:53:43 kfogel Exp $	
 
 

Modified: trunk/lisp/gene-selection.el
==============================================================================
--- trunk/lisp/gene-selection.el	(original)
+++ trunk/lisp/gene-selection.el	Wed Aug  7 12:30:31 2002
@@ -20,7 +20,6 @@
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 ;;
 ;; Search for instances of "todo:" to find notes about future plans.
-;;	$Id: gene-selection.el,v 1.42 1995/04/27 16:01:11 kfogel Exp $	
 
 

Modified: trunk/lisp/gene-locking.el
==============================================================================
--- trunk/lisp/gene-locking.el	(original)
+++ trunk/lisp/gene-locking.el	Wed Aug  7 12:30:32 2002
@@ -19,7 +19,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-locking.el,v 1.19 1995/05/09 15:24:37 kfogel Exp $	
 
 (require 'gene-mode-tools)

Modified: trunk/lisp/gene-menus.el
==============================================================================
--- trunk/lisp/gene-menus.el	(original)
+++ trunk/lisp/gene-menus.el	Wed Aug  7 12:30:32 2002
@@ -18,7 +18,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-menus.el,v 1.62 1995/09/06 17:37:03 kfogel Exp $	
 
 ;;; gene-menus.el: menus for gene-mode.

Modified: trunk/lisp/gene-help.el
==============================================================================
--- trunk/lisp/gene-help.el	(original)
+++ trunk/lisp/gene-help.el	Wed Aug  7 12:30:33 2002
@@ -20,7 +20,6 @@
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 ;;
 ;; Search for instances of "todo:" to find notes about future plans.
-;;	$Id: gene-help.el,v 1.9 1995/03/06 17:28:24 kfogel Exp $	

 

Modified: trunk/lisp/gene-error.el
==============================================================================
--- trunk/lisp/gene-error.el	(original)
+++ trunk/lisp/gene-error.el	Wed Aug  7 12:30:33 2002
@@ -18,7 +18,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-error.el,v 1.2 1995/04/26 21:56:48 kfogel Exp $

 (require 'gene-mode-tools)

Modified: trunk/lisp/gene-windows.el
==============================================================================
--- trunk/lisp/gene-windows.el	(original)
+++ trunk/lisp/gene-windows.el	Wed Aug  7 12:30:33 2002
@@ -18,7 +18,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-windows.el,v 1.4 1995/05/09 20:41:00 kfogel Exp $	
 
 (require 'gene-mode-tools)
 
@@ -119,17 +118,12 @@
               (while bufwidth-list
                 ;; windowize the first buffer
                 (switch-to-buffer (aref (car bufwidth-list) 0))
-                (if (null (cdr bufwidth-list))
-                    (hscroll-point-visible)
-                  (hscroll-point-visible)
+                (unless (null (cdr bufwidth-list))
                   (split-window-horizontally (or (aref (car bufwidth-list) 1)
                                                  default-width))
                   (other-window 1))
-                (setq bufwidth-list (cdr bufwidth-list)))
-              (hscroll-point-visible)
-              )))
-      (select-frame o-frame)
-      )))
+                (setq bufwidth-list (cdr bufwidth-list))))))
+      (select-frame o-frame))))

 (defun gene-id-calculate-window-width (&optional max-width min-width)

Modified: trunk/lisp/gene-frame.el
==============================================================================
--- trunk/lisp/gene-frame.el	(original)
+++ trunk/lisp/gene-frame.el	Wed Aug  7 12:30:34 2002
@@ -18,7 +18,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-frame.el,v 1.38 1995/05/03 15:44:53 kfogel Exp $	
 
 
 ;;;; Displaying the watch pointer within a certain dynamic scope.

Modified: trunk/lisp/gene-phylo.el
==============================================================================
--- trunk/lisp/gene-phylo.el	(original)
+++ trunk/lisp/gene-phylo.el	Wed Aug  7 12:30:34 2002
@@ -24,7 +24,6 @@
 ;;;; Created: Apr 22 1994
 ;;;; Version: 0.0 (prototype)
 ;;;; Keywords: genes, ribosomes, sequences, molecular biology, milkshakes
-;;	$Id: gene-phylo.el,v 1.25 1995/04/07 17:43:17 kfogel Exp $	
 
 ;;; This code is supposed to help people choose the organisms whose
 ;;; genes they'd like to bring into the sequence buffer.  Given a file
@@ -148,11 +147,9 @@
    'phylo-selected (gene-check-color-allowable "medium orchid"))
 
   (copy-face 'default 'phylo-mouse-unselected)
-  (set-face-font 'phylo-mouse-unselected nil) ; for reloading
   (make-face-bold 'phylo-mouse-unselected nil t)
 
   (copy-face 'default 'phylo-mouse-selected)
-  (set-face-font 'phylo-mouse-selected nil) ; for reloading
   (make-face-bold 'phylo-mouse-selected nil t)
   (set-face-background
    'phylo-mouse-selected
@@ -170,10 +167,12 @@
      'phylo-cover-region (gene-check-color-allowable foreground))
     (set-face-background
      'phylo-cover-region (gene-check-color-allowable background))
-    (set-face-font       'phylo-cover-region nil)
-    ;; Why does this make some machines barf?
-    ;; (set-face-font       'phylo-cover-region font)
+    ;; This apparently got an error on some machines, sometimes, so it
+    ;; was commented out.  But that was a long time ago; let's put it
+    ;; back and see what happens:
+    (set-face-font 'phylo-cover-region font)
     ))
+
 
 ;;;; Running and talking to the phylo server subprocess --- low-level stuff.

Modified: trunk/lisp/gene-translate.el
==============================================================================
--- trunk/lisp/gene-translate.el	(original)
+++ trunk/lisp/gene-translate.el	Wed Aug  7 12:30:34 2002
@@ -22,7 +22,6 @@
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 ;;
 ;; Search for instances of "todo:" to find notes about future plans.
-;;	$Id: gene-translate.el,v 1.7 1995/04/12 20:16:27 kfogel Exp $	
 
 
 (require 'gene-mode-tools)

Modified: trunk/lisp/gene-ann-mode.el
==============================================================================
--- trunk/lisp/gene-ann-mode.el	(original)
+++ trunk/lisp/gene-ann-mode.el	Wed Aug  7 12:30:35 2002
@@ -18,7 +18,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-ann-mode.el,v 1.15 1995/04/18 16:50:14 kfogel Exp $
 
 (require 'cl)
 (require 'cl-19)

Modified: trunk/lisp/gene-clipboard.el
==============================================================================
--- trunk/lisp/gene-clipboard.el	(original)
+++ trunk/lisp/gene-clipboard.el	Wed Aug  7 12:30:35 2002
@@ -20,7 +20,6 @@
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 ;;
 ;; Search for instances of "todo:" to find notes about future plans.
-;;	$Id: gene-clipboard.el,v 1.40 1995/04/19 21:16:39 kfogel Exp $	
 
 (require 'gene-mode-tools)

Modified: trunk/lisp/gene-dialog.el
==============================================================================
--- trunk/lisp/gene-dialog.el	(original)
+++ trunk/lisp/gene-dialog.el	Wed Aug  7 12:30:36 2002
@@ -18,8 +18,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene-dialog.el,v 1.45 1995/05/11 19:02:06 kfogel Exp $
-
 
 (require 'gene-mode-tools)

Modified: trunk/lisp/gene.el
==============================================================================
--- trunk/lisp/gene.el	(original)
+++ trunk/lisp/gene.el	Wed Aug  7 12:30:36 2002
@@ -18,7 +18,6 @@
 ;;      You should have received a copy of the GNU General Public License
 ;;      along with this program; if not, write to the Free Software
 ;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
-;;	$Id: gene.el,v 1.18 1995/05/08 17:13:29 kfogel Exp $	
 
 ;;; gene-mode.el: Major mode(s) for editing gene sequences.
 
@@ -140,6 +139,9 @@
   ;; Figure out which fonts to use.
   (gene-frame-init-fonts)
 
+  ;; We don't want the default GNU Emacs startup screen nor toolbar.
+  (setq inhibit-startup-message t)
+  (tool-bar-mode -1)
   )
 
 

Modified: trunk/lisp/gene-analyze.el
==============================================================================
--- trunk/lisp/gene-analyze.el	(original)
+++ trunk/lisp/gene-analyze.el	Wed Aug  7 12:30:36 2002
@@ -19,7 +19,6 @@
 ;;;;      along with this program; if not, write to the Free Software
 ;;;;      Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 ;;;;
-;;;; $Id: gene-analyze.el,v 1.6 1995/03/11 21:19:29 kfogel Exp $	
 
 (require 'cl)
 (require 'cl-19)