From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 4 Mar 2022 14:36:11 +0000 (+0000)
Subject: Merge branch 'doc/JAL-3608+JAL-3830_added_to_help_docs' into develop
X-Git-Tag: Release_2_11_2_1~37
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=6ca73439c73bcf34362930e996f24baab3ebfb6e;hp=88394f03a1aea50f6fa9e500531f99118532458f

Merge branch 'doc/JAL-3608+JAL-3830_added_to_help_docs' into develop
---

diff --git a/help/help/html/features/commandline.html b/help/help/html/features/commandline.html
index 0ef78f9..0159a92 100644
--- a/help/help/html/features/commandline.html
+++ b/help/help/html/features/commandline.html
@@ -33,20 +33,97 @@
     automatically by the Jalview application when double-clicked in a
     file browser on Windows and OSX.
   </p>
-  The way that you launch Jalview from the command line depends on the
-  platform you are on, and how it has been installed.
 
+  <p>From version 2.11.2, Jalview includes a <strong>launching shell script</strong> which is the recommended way to
+  launch an installed Jalview application from the command line.  It supports all the <a href="clarguments.html">command line arguments</a>
+  that Jalview has previously supported, but makes it easier to launch directly from the command line.</p>
+  
+  <p>There are some important differences between the using the launching script and launching Jalview from its icon:
   <ul>
-    <li>Standard installation on Linux/Unix:<pre>
-       /PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
+  <li>The launching script will NOT look for updates or perform automatic updates.</li>
+  <li>The launching script cannot open or use JVL files.</li>
+  </ul>
+  </p>
+  
+  <p>If you installed Jalview prior to version 2.11.2 you will not have had the option to add the launching shell script to your PATH.
+  If your application has updated to 2.11.2 then the scripts will now be there, but not in your <code>PATH</code>.
+  There are instructions below to add the launching shell script to your <code>PATH</code> if you want to do so.</p>
+
+  <ul>
+  
+  <li>
+  <p><em>In <strong>Linux</strong> or <strong>Unix</strong> (<code>jalview.sh</code>)</em></p>
+  <p>The installer gives you the option of adding a symbolic link to
+  that script in your <code>$PATH</code>, if it finds a suitable place that your user can add such a
+  link (e.g. <code>~/bin</code>, <code>~/.local/bin</code>, <code>~/local/bin</code>, <code>~/opt/bin</code>).  If you chose that option then
+  you should be able to launch Jalview on the command line with the simple command
+  <pre>jalview</pre>
+  If you didn't choose that option during installation (or used an earlier version installer), or wish to make another symbolic link, you can link to the
+  launching shell script with the command
+  <pre>ln -s /PATH_TO_JALVIEW/bin/jalview.sh jalview</pre>
+  or you could add <code>/PATH_TO_JALVIEW/bin</code> to your own <code>$PATH</code> as it already contains a symbolic link <code>jalview</code>.
+  </li>
+  
+  <li>
+  <p><em>In <strong>Windows</strong> (<code>jalview.bat</code>, <code>jalview.ps1</code>)</em></p>
+  <p>The installer gives you the option of adding Jalview's script folder to your <code>%PATH%</code> allowing you to launch Jalview
+  in a Command Prompt simply with the command
+  <pre>jalview</pre>
+  If you didn't choose that option during installation (or used an earlier version installer), you can either
+  </p>
+  <ul>
+  <li>
+  add the <code>\PATH_TO_JALVIEW\bin</code> folder to your <code>%PATH%</code>, or
+  </li>
+  <li>
+  run the launcher script on the command line with its full path
+  <pre>\PATH_TO_JALVIEW\bin\jalview.bat</pre>
+  (you can leave off the <code>.bat</code> extension if you want).
+  </li>
+  </ul>
+  The <code>jalview.bat</code> file is a generic wrapper around the
+  PowerShell script <code>jalview.ps1</code> in the same folder.  This PowerShell script should work with both
+  PowerShell 5.x (which is installed by default on all modern Windows machines), and also PowerShell 6.0+
+  which might have been installed afterwards.
+  </li>
+  
+  <li>
+  <p><em>In <strong>macOS</strong> (<code>jalview</code>)</em></p>
+  <p>
+  The script you should use to launch Jalview is linked to as
+  <pre>/Applications/Jalview.app/Contents/MacOS/jalview</pre>
+  so you can run that command with its full path, or make your own symbolic link to there, or add that folder to your <code>$PATH</code>.
+  </p>
+  <p>
+  <em>If Jalview automatically updated from a version before 2.11.2</em> you will have to make a symbolic link to <code>/Applications/Jalview.app/Content/Resources/app/bin/jalview.sh</code> with the command
+  <pre>ln -s /Applications/Jalview.app/Content/Resources/app/bin/jalview.sh jalview</pre>
+  </p>
+  </li>
+ 
+  <li>
+  <p><em>Future</em></p>
+  A future version of Jalview will include a tool to allow adding these "<code>jalview</code>" links to your <code>PATH</code> automatically.
+  </li>
+  
+  </ul>
+
+  <p><strong>Older versions of Jalview</strong></p>
+  
+  <p>
+  If you are using a version of Jalview prior to 2.11.2, you can still launch from the command line, but you will have to
+  use a more platform specific way to launch and use command line arguments.
+
+  <ul>
+    <li>Standard installation on Linux/Unix:
+    <pre>/PATH_TO_JALVIEW/Jalview -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
     </li>
-    <li>Standard installation on Windows:<pre>
-      \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
+    <li>Standard installation on Windows:
+    <pre>\PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
     </li>
-    <li>OSX Application:<pre>
-open /Applications/Jalview.app --args -open ~/myalignment.fa</pre><em>(put
-        all the Jalview arguments <em>after</em> the --args parameter)
-    </em><br />
+    <li>OSX Application:
+    <pre>open /Applications/Jalview.app --args -open /FULL/PATH/TO/myalignment.fa</pre>
+    <em>(put all the Jalview arguments <em>after</em> the --args parameter, and note that paths to files should be full paths from <code>/</code>)</em>
+    <br />
     <br /></li>
     <li>Jalview standalone executable Jar<pre>
         &lt;Path to Java home&gt;/bin/java -jar &lt;Path to Jalview Jar&gt;/jalview-all-1.8.jar -open myalignment.fa</pre></li>
@@ -85,10 +162,13 @@ open /Applications/Jalview.app --args -open ~/myalignment.fa</pre><em>(put
     <li>-Dlaf=nimbus (Java's alternative Nimbus Look and Feel)</li>
     <li>-Dlaf=mac (only has an effect on OSX)</li>
     <li>-Dlaf=gtk (only has an effect on Linux)</li>
+    <li>-Dlaf=metal (force Java's Metal Look and Feel, default on linux)</li>
+    <li>-Dlaf=quaqua (macOS only. Force attempt at old macOS theme)</li>
+    <li>-Dlaf=vaqua (macOS only. Force attempt at modern macOS theme)</li>
   </ul>
   The currently configured look and feel is logged to Jalview's console.
   Once the look and feel has been changed, it will be stored in
-  Jalview's .jalview_properties file for future Jalview sessions.
+  Jalview's .jalview_properties file for future Jalview sessions.  This property is <strong>PREFERRED_LAF</strong> and can also be used to set the Look and feel by editing your .jalview_properties file.
 
   <p>&nbsp;</p>
   <p>&nbsp;</p>
diff --git a/help/help/html/releases.html b/help/help/html/releases.html
index 9f44951..8177708 100755
--- a/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@ -138,6 +138,15 @@ li:before {
             Console and other window widgets in taskbar and dock rather
             than anonymous 'Java' icons
           </li>
+          <li>
+            <!-- JAL-3608 -->Options to allow user to choose the (Swing) Look and Feel used by Jalview
+          </li>
+          <li>
+            <!-- JAL-3830 -->New command line launcher scripts (.sh, .ps1, .bat) usable on
+            macOS, Linux/Unix, Windows and documentation in Help.  Installer wizard has option
+            to add this to PATH, or link to it in your PATH.
+          </li>
+
         </ul> <em>JalviewJS</em>
         <ul>
           <li>
diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index 4865615..d849aa2 100755
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -74,6 +74,9 @@
           allocation</a></strong></li>
     <li>Import of annotated DNA and RNA loci via GenBank and EMBL
       style flatfile</li>
+    <li>New <strong>command line launcher scripts</strong> (.sh, .ps1, .bat) usable on
+            macOS, Linux/Unix, Windows and documentation in Help
+    </li>