update

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1769 ee4ac58c-ac51-4696-9907-e4b3aa274f04

docs/file_menu.sgml

@@ -5,6 +5,16 @@ Most of the items in this menu are used to read and write entries and parts of
 entries, the exceptions are Clone and Close.
   </PARA>
 
+  <SECT2 ID="FILEMENU-SHOW-FILEMANAGER">
+    <TITLE>Show File Manager ...</TITLE>
+    <PARA>
+This will open the file manager, or if it is already open will bring it
+to the foreground. Entries can be dragged from the file manager into
+the artemis main window and dropped. When dropped the entry is then read 
+in and displayed.
+    </PARA>
+  </SECT2>
+
   <SECT2 ID="FILEMENU-READ-AN-ENTRY">
     <TITLE>Read An Entry ...</TITLE>
     <PARA>

docs/getting_java.sgml

@@ -8,45 +8,36 @@ Explorer is not sufficient to run &prog;.
   <ITEMIZEDLIST>
     <LISTITEM>
       <PARA>
-UNIX users should get Java version 1.1 from the <ULINK
-URL="http://java.sun.com/products/jdk/1.1/">Sun JDK 1.1 download page</ULINK>
-or the <ULINK URL="http://java.sun.com/cgi-bin/java-ports.cgi">JDK 1.1 ports
-page</ULINK> (Newer versions will also work, but may have problems on some
-platforms.) 
+UNIX users should get the current Java version from the <ULINK
+URL="http://java.sun.com/">Sun</ULINK>.
       </PARA>
     </LISTITEM>
     <LISTITEM>
       <PARA>
-<ULINK URL="http://www.linux.org/">GNU/Linux</ULINK> users should install the
-<ULINK URL="http://www.blackdown.org/">Blackdown.org</ULINK> release of <ULINK
-URL="http://www.mirror.ac.uk/sites/ftp.blackdown.org/java-linux/JDK-1.4.1/i386/01/">JRE
-version 1.4.1</ULINK>.  The Sun versions of Java 1.3.1, 1.4.0 and 1.4.1 have
-various long-standing bugs (<ULINK
-URL="http://www.sanger.ac.uk/Users/kmr/4533641.html">4533641</ULINK>, <ULINK
-URL="http://www.sanger.ac.uk/Users/kmr/4627564.html">4627564</ULINK>) which
-make them unsuitable for Artemis.  Newer releases from Sun may fix these
-problems.
+<ULINK URL="http://www.linux.org/">GNU/Linux</ULINK> users should install the latest
+java stable Java release from
+<ULINK URL="http://www.blackdown.org/">Blackdown.org</ULINK> .
+The Sun versions of Java 1.3.1, 1.4.0 and 1.4.1 have
+various long-standing bugs which make them unsuitable for Artemis.
+Newer releases from Sun may fix these problems.
       </PARA>
     </LISTITEM>
     <LISTITEM>
       <PARA>
-Windows users should get Java <ULINK
-URL="http://java.sun.com/products/jdk/1.3/">version 1.3</ULINK> or better
-from <ULINK
-URL="http://www.sun.com">Sun Microsystems</ULINK>.
+Windows users should get latest <ULINK
+URL="http://java.sun.com/">Java version</ULINK> or better
+from Sun Microsystems.
 On some versions of Windows (such as Windows 2000) you will need be have
 administrator privileges for your machine to successfully install Java.
       </PARA>
     </LISTITEM>
     <LISTITEM>
       <PARA>
-Macintosh users with MacOS version 8 or 9 should install the <ULINK
-URL="http://developer.apple.com/java/text/download.html">Macintosh Runtime
-for Java (MRJ)</ULINK> version 2.2 or better before downloading &prog;.
 Macintosh users with MacOS X (ie MacOS version 10) or better do not need to
 install Java because it comes as a standard feature of the operating system.
-Note, however, that Java on the older versions of MacOS X has has irritating
+Note, however, that Java on the older versions of MacOS X has irritating
 bugs so we recommend using the latest version of MacOS, which runs &prog; well.
+Macintosh users with older MacOS versions cannot use this release of &prog;.
       </PARA>
     </LISTITEM>
   </ITEMIZEDLIST>

docs/intro_chapter.sgml

@@ -145,7 +145,8 @@ cwchen@ym,edu.tw
     <SECT2 ID="DOSINSTALLATION">
       <TITLE>Installation Instructions for Windows</TITLE>
       <PARA>
-On Windows systems with Java 1.2, installing &prog; is as simple as copying the
+On Windows systems with Java (version 1.3 or higher), installing &prog; 
+is as simple as copying the
 <ULINK URL="ftp://ftp.sanger.ac.uk/pub/pathogens/software/artemis/artemis.jar"
 TYPE="external">artemis.jar file</ULINK> to an appropriate place (such as the
 desktop or the Programs folder).

docs/requirements.sgml

 <SECT1 ID="REQUIREMENTS">
   <TITLE>System Requirements</TITLE>
   <PARA>
-&prog; will run on any machine that has a recent version of Java.  Most of the
-development has been done using JDK v1.1.7 and v1.1.8, but any version better
-than v1.1.1 is sufficient for running &prog; on UNIX.  (Early versions of v1.1
-have some bugs, so later is better.)  Version 1.2 or better is needed on
-Windows.  Please note that the version of Java that comes with Netscape and
+&prog; will run on any machine that has a recent version of Java.
+This version of &prog; requires Java 1.3 at least. Most of the
+development has been done using JDK v1.4, but any version better
+than v1.3 is sufficient for running &prog; on UNIX.
+Please note that the version of Java that comes with Netscape and
 Internet Explorer is not sufficient to run &prog;.  See <XREF
 LINKEND="INSTALLATION"> for details on how to get Java.
   </PARA>

docs/start_chapter.sgml

@@ -92,6 +92,17 @@ top of this window allow you to read a new sequence or embl entry.
     </PARA>
     <SECT2 ID="LAUNCH-WINDOW-FILE-MENU">
       <TITLE>The File Menu</TITLE>
+
+      <SECT3 ID="LAUNCH-WINDOW-FILEMANAGER">
+        <TITLE>Open File Manager ...</TITLE>
+        <PARA>
+Selecting this shows the files and directories that are in the directory &prog;
+is launched in. At the top are 2 shortcut buttons to go up a directory and to go 
+to your home directory. At the bottom of the file manager is a file filter.
+You can select a file and double click on it to launch artemis.
+        </PARA>
+      </SECT3>
+
       <SECT3 ID="LAUNCH-WINDOW-FILE-MENU-OPEN">
         <TITLE>Open ...</TITLE>
         <PARA>

docs/unix_args.sgml

@@ -36,5 +36,21 @@ This isn't on by default because the fast VM uses a lot more memory and it
 isn't as reliable.
       </PARA>
     </SECT2>
+
+    <SECT2 ID="UNIXARGS-MEM">
+      <TITLE><LITERAL>-Xmsn -Xmxn</LITERAL></TITLE>
+      <PARA>
+Use <LITERAL>-Xmsn</LITERAL> to specify the initial size, in bytes, of the
+memory allocation pool. This value must be a multiple of 1024 greater than
+1MB. Append the letter k or K to indicate kilobytes, or m or M to indicate
+megabytes.
+      </PARA>
+      <PARA>
+Use <LITERAL>-Xmxn</LITERAL> to specify the maximum size, in bytes, of the
+memory allocation pool. This value must a multiple of 1024 greater than
+2MB. Append the letter k or K to indicate kilobytes, or m or M to indicate
+megabytes.
+      </PARA>
+    </SECT2>
+
   </SECT1>
-  
\ No newline at end of file