Subject: rev 9 - trunk trunk/docs

From: [email-masked]
Date: Fri, 9 Aug 2002 19:22:35 -0500

Author: kfogel
Date: Fri, 09 Aug 2002 19:22:30 -0500
New Revision: 9

Modified:
   trunk/Makefile.in
   trunk/README
   trunk/docs/ale.texi
   trunk/docs/intro.txt
Log:
Say Emacs 21 everywhere, instead of Emacs 19.  Update email addresses.
Tweak various places in the manual for accuracy.

Modified: trunk/Makefile.in
==============================================================================
--- trunk/Makefile.in	(original)
+++ trunk/Makefile.in	Fri Aug  9 19:22:34 2002
@@ -1,8 +1,5 @@
 # Makefile for the Ale alignment editor.
 
-# Make sure this invokes a GNU Emacs 19.28 patched with the newline
-# cache and other frills, or 19.29 (which should have the newline
-# cache and frills integrated), or a later version.
 EMACS=@EMACS@
 
 # This must be an ANSI C compiler.  Sun's cc is *not* ANSI -- if

Modified: trunk/docs/intro.txt
==============================================================================
--- trunk/docs/intro.txt	(original)
+++ trunk/docs/intro.txt	Fri Aug  9 19:22:34 2002
@@ -498,13 +498,13 @@
 ------------
 
         If you don't already have a copy of ale, go and get it
-from... where?  We don't have it up for ftp yet, so just mail
[email-masked], [email-masked], or
[email-masked]. :-)
+from... where?  We don't have it up for download yet, so just mail
[email-masked] if you need a copy.  If you know how to use
+Subversion (http://subversion.tigris.org/), you can check out a
+working copy from http://svn.red-bean.com:8080/ale/trunk/.
 
-        You must also have Emacs-19.28 (or a later version) installed
-on your system.  Emacs-19.27 with some patches will also do; mail us
-for the patches.
+        You must also have GNU Emacs 21.1 (or a later version)
+installed on your system.
 
         Once you've got the ale tar file, ale-0.1.tar.gz or some
 later version, unpack it like this:

Modified: trunk/docs/ale.texi
==============================================================================
--- trunk/docs/ale.texi	(original)
+++ trunk/docs/ale.texi	Fri Aug  9 19:22:34 2002
@@ -23,9 +23,9 @@
 @titlepage
 @title Using Ale
 @c jimb: 
-@author Karl Fogel, kfogel@@cyclic.com
-@author Jim Blandy, jimb@@cyclic.com
-@author Niels Larsen, niels@@darwin.life.uiuc.edu
+@author Karl Fogel, kfogel@@red-bean.com
+@author Jim Blandy, jimb@@red-bean.com
+@author Niels Larsen, niels@@integratedgenomics.com
 @page
 @vskip 0pt plus 1filll
 Copyright @copyright{} 1994 Indiana University Foundation, Karl Franz
@@ -55,11 +55,11 @@
 @top Ale
 
         This is the on-line documentation for Ale, a genetic sequence
-alignment editor.  Ale is based on GNU Emacs 19 (if you already know
+alignment editor.  Ale is based on GNU Emacs 21 (if you already know
 Emacs, Ale may look very familiar to you).  This manual documents
 version @value{ale-version} of the editor.  We assume that you already
-know the how and why of aligning sequences.  This manual just discusses
-how to use Ale to accomplish those goals.
+know the how and why of aligning sequences.  This manual just
+discusses how to use Ale to accomplish those goals.
 
         Ale requires a computer running the Unix operating system, a
 color display managed by the X Window System, and a mouse with three
@@ -106,15 +106,13 @@
 @chapter Introduction
 
         Ale is a genetic sequence alignment editor, based on GNU Emacs
-19.  This manual documents version @value{ale-version} of the editor.
+21.  This manual documents version @value{ale-version} of the editor.
 We assume that you already know the how and why of aligning sequences.
 This manual just discusses how to use Ale to accomplish those goals.
 
         Ale requires a computer running the Unix operating system, GNU
-Emacs version 19.29 or higher@footnote{We have a specially modified GNU
-Emacs 19.28 that will work; see the @ref{Installation} for more
-details.}, a display managed by the X Window System (preferably color),
-and a mouse with three buttons.
+Emacs version 21.1 or higher, a display managed by the X Window System
+(preferably color), and a mouse with three buttons.
 
         If you have Ale installed on your system already, then
 continue reading.  If not, see @ref{Installation}.
@@ -402,14 +400,11 @@
 @cindex speed limits
 @cindex size limits on alignments
 
-        You can include as many alignment files as you like, so long as
-the sum of their sizes does not exceed eight megabytes.  Ale cannot
-align more than 8 megabytes worth of sequence data at a time
-@footnote{The current version of Emacs imposes this limitation; we're
-told it will be lifted in the next version, 19.29.}.  Furthermore, the
-larger your alignment, the less quickly certain Ale commands will run;
-Ale becomes quite slow when asked to edit more than five hundred or so
-sequences.
+        You can include as many alignment files as you like, so long
+as the sum of their sizes does not exceed 64 megabytes (this is due to
+limitations in Emacs).  Furthermore, the larger your alignment, the
+less quickly certain Ale commands will run; Ale becomes quite slow
+when asked to edit more than five hundred or so sequences.
 
 @cindex opening files
 @cindex inserting files
@@ -2491,16 +2486,11 @@
 color display managed by the X Window System, and a mouse with three
 buttons.  
 
-        Also, you must have GNU Emacs 19.29 (or some later version)
+        Also, you must have GNU Emacs 21.1 (or some later version)
 installed on your system.  Both Emacs and GDBM are available from
-@file{ftp://prep.ai.mit.edu/pub/gnu/}, the main ftp site for the GNU
+@file{ftp://ftp.gnu.org/pub/gnu/}, the main ftp site for the GNU
 Project (more information about the GNU project can be found there).
 
-        NOTE: as of April 11, 1995, Emacs 19.29 has not yet been
-released.  We have a special patched version of Emacs 19.28 which will
-run Ale; you will need to get this version of Emacs and install it
-before trying to install the rest of Ale.
-
         It would also help to have GDBM (the GNU Project's database
 management library) installed before you compile Ale.  GDBM is a library
 of routines for building database systems; some of Ale's features use
@@ -2511,18 +2501,10 @@
 @cindex obtaining ale
 @cindex getting Ale
 @cindex Ale (obtaining)
-        Ale is currently available via anonymous ftp from
-@t{floss.cyclic.com}.  Its IP address is 128.174.228.89.  You'll want to
-get the following files:
 
-@example
-@group
-                pub/emacs-19.28.ale.tar.gz
-                pub/gdbm-1.7.3.tar.gz
-                pub/ale-0.1.XXX.tar.gz
-                pub/README.ale
-@end group
-@end example
+        We don't have Ale in a download area yet, though we hope to soon.
+However, if you use Subversion (http://subversion.tigris.org/), you
+can get a working copy from http://svn.red-bean.com:8080/ale/trunk/. 
 
         The rest of these instructions assume that Emacs and GDBM have
 already been installed correctly; see their respective @file{README} and
@@ -2531,7 +2513,10 @@
 @cindex building Ale
 @cindex making Ale
 @cindex compiling Ale
-        Once you've got the ale tar file, @file{ale-0.1.tar.gz} or
+
+@c Reinstate these instructions once we have tarballs up again.
+@ifset grobbleratchet
+        Once you've got the ale tar file, @file{ale-0.1.XXX.tar.gz} or
 some later version, unpack it like this:
 
 @example
@@ -2545,8 +2530,12 @@
 
         Ale now uses the standard GNU configuration system.  First,
 configure for compilation by typing
+@end ifset
+
+From the top level of your working copy, run
 
 @example
+        ./autogen.sh
         ./configure
 @end example
 
@@ -2577,9 +2566,7 @@
         and everything will be put in the right places.
 
         If you have any questions at all, or problems installing, please
-contact us by email: @t{ale-bug@@cyclic.com}.  There is also a mailing
-list for users of Ale: @t{ale-users@@cyclic.com}.  To join, send mail to
-@t{ale-users-request@@cyclic.com}.
+contact us by email: @t{ale@@red-bean.com}.

 @c  -*-  -*-  -*-  -*-  -*-  -*-  -*-  -*-  -*-  -*-  -*-
@@ -2592,7 +2579,7 @@
 be some, since this is a test release).  If you think you have found a
 bug, choose ``Email a Bug Report'' from the Help Menu and tell us about
 it.  If one of the bugs is that the ``Email a Bug Report'' menu item
-isn't working, just send the mail directly to @t{ale-bug@@cyclic.com}.
+isn't working, just send the mail directly to @t{ale@@red-bean.com}.
 
         If we can reproduce a bug ourselves, we can fix it; if we can't
 reproduce a bug, we probably can't fix it.  Thus, your bug report should
@@ -2636,10 +2623,10 @@
 More importantly, RDP needs to have complete control of its most
 critical software, so our ideas can be easily implemented in the future.
 
-        We decided not to make an editor from scratch, but to build upon
-the text editor Emacs 19, which is freely available with source code
-from the Free Software Foundation in Cambridge, Massachusetts.  By doing
-so, we reaped some benefits:
+        We decided not to make an editor from scratch, but to build
+upon the text editor Emacs, which is freely available with source code
+from the Free Software Foundation in Cambridge, Massachusetts.  By
+doing so, we reaped some benefits:
 
 @itemize @bullet
 @item
@@ -2662,8 +2649,8 @@
 machines.
 @end itemize
 
-        In future versions we will take advantage of Emacs's support for
-display properties, allowing us to show --- for rRNA, for example ---
+        We hope future versions can take advantage of Emacs's support
+for display properties, allowing us to show --- for rRNA, for example ---
 protein binding sites, complementarity to probes, and secondary
 structural helices.

Modified: trunk/README
==============================================================================
--- trunk/README	(original)
+++ trunk/README	Fri Aug  9 19:22:35 2002
@@ -22,7 +22,7 @@
 
 To install and run Ale, you'll need:
 - an ANSI Standard C compiler,
-- GNU Emacs 21.3.50 (it may work with earlier versions, let us know)
+- GNU Emacs 21.1 or later
 
 To build and install ale, just type