From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 17 May 2023 12:19:30 +0000 (+0100)
Subject: JAL-629 Changed some old -arg to --arg in help docs, and some other mailing list... 
X-Git-Tag: Release_2_11_4_0~320
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c34fa853a3659a05e67d78b337df99b65ba6070f;p=jalview.git

JAL-629 Changed some old -arg to --arg in help docs, and some other mailing list->discussion forum changes
---

diff --git a/help/help/html/features/annotationsFormat.html b/help/help/html/features/annotationsFormat.html
index 3517929..71f3046 100755
--- a/help/help/html/features/annotationsFormat.html
+++ b/help/help/html/features/annotationsFormat.html
@@ -40,7 +40,7 @@
     annotations files are imported into Jalview in the following ways:<br />
   <ul>
     <li>from the command line<strong><pre>
- -annotations &lt;<em>Annotations filename</em>&gt;</pre></strong></li>
+ --annotations &lt;<em>Annotations filename</em>&gt;</pre></strong></li>
     <li>Dragging an annotations file onto an alignment window</li>
     <li>Via the &quot;Load Features / Annotations&quot; entry in
       the <strong>File</strong> menu of an alignment window.
diff --git a/help/help/html/features/biojsmsa.html b/help/help/html/features/biojsmsa.html
index f3b6816..fb8d624 100644
--- a/help/help/html/features/biojsmsa.html
+++ b/help/help/html/features/biojsmsa.html
@@ -50,7 +50,7 @@
     templates for HTML export from our public GitHub Repository.
     Normally, this should happen without you needing to do anything, but
     if you do encounter problems, then please get in contact via the
-    jalview-discuss mailing list, or file a bug report.</p>
+    Jalview Discussion Forum, or file a bug report.</p>
   <p>Templates are downloaded to a directory called
     '.biojs_templates' in your user's home storage space (e.g.
     ~/.biojs_templates).</p>
diff --git a/help/help/html/features/featuresFormat.html b/help/help/html/features/featuresFormat.html
index 4df0b0c..a2536e2 100755
--- a/help/help/html/features/featuresFormat.html
+++ b/help/help/html/features/featuresFormat.html
@@ -42,7 +42,7 @@
   
   <ul>
     <li>from the command line <pre>
-<strong> -features &lt;<em>Features filename</em>&gt;</strong>
+<strong> --features &lt;<em>Features filename</em>&gt;</strong>
 </pre>
     </li>
 
diff --git a/help/help/html/features/groovy.html b/help/help/html/features/groovy.html
index cc91154..cb0b10c 100644
--- a/help/help/html/features/groovy.html
+++ b/help/help/html/features/groovy.html
@@ -47,7 +47,7 @@
   </p>
   <p>
     <strong>Executing groovy scripts on Jalview startup</strong><br>
-    The -groovy &lt;script&gt; option on the <a href="commandline.html">
+    The --groovy &lt;script&gt; option on the <a href="commandline.html">
       Jalview command line</a> will execute the contents of &lt;script&gt;.
     &lt;script&gt; may be a file, a URL, or alternatively if it is
     &quot;STDIN&quot; then the standard input will be used.<br> <em>Note:
@@ -76,7 +76,7 @@
           window which is currently being looked at by the user</li>
       </ul></li>
     <li><strong>currentAlFrame</strong> - this is only defined when
-      running a Groovy script via the -groovy command line argument. It
+      running a Groovy script via the --groovy command line argument. It
       returns the first alignment window created after acting on the
       other arguments passed on the command line.</li>
   </ul>
diff --git a/help/help/html/features/importvcf.html b/help/help/html/features/importvcf.html
index 7b699eb..ffc9fa7 100755
--- a/help/help/html/features/importvcf.html
+++ b/help/help/html/features/importvcf.html
@@ -109,7 +109,7 @@ VCF_ASSEMBLY=assembly19=GRCh37,hs37=GRCh37</pre><br /> <br />These allow
   </ol>
   <strong>Work in Progress!</strong>
   <p>VCF support in Jalview is under active development. Please get
-    in touch via our mailing list if you have any questions, problems or
+    in touch via our discussion forum if you have any questions, problems or
     otherwise find it useful !</p>
 </body>
 </html>
diff --git a/help/help/html/logging.html b/help/help/html/logging.html
index 4d7e2e3..a7da021 100644
--- a/help/help/html/logging.html
+++ b/help/help/html/logging.html
@@ -210,8 +210,8 @@
   <p>
     For other queries or comments about Jalview, remember you can
     contact the Jalview team using email via the
-    <a href="https://www.jalview.org/mailman/listinfo/jalview-discuss">Jalview
-      discussion list</a>, on Twitter <a
+    <a href="https://discourse.jalview.org/">Jalview
+      Discussion Forum</a>, on Twitter <a
       href="https://twitter.com/Jalview/">@Jalview</a>, or for technical
     discussions, via the Jalview developer's chatroom at
     <a href="https://gitter.im/jalview/developers">https://gitter.im/jalview/developers</a>.
diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index a326575..17dc557 100755
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -95,12 +95,12 @@
       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa</pre>
       Alternatively, you can use the standard Jalview command line
       arguments with or without the jvl file (first), e.g. <pre>
-       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl -open https://www.jalview.org/examples/jpred_msa.fasta -annotations https://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
+       /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl --open https://www.jalview.org/examples/jpred_msa.fasta --annotations https://www.jalview.org/examples/jpred_msa.seq.concise --colour Clustal</pre>
       You can use command line arguments to control memory settings in
       Windows and macOS too: <br /> In Windows you must use, e.g. <pre>
-      \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl -open %HOMEPATH%\myalignment.fa</pre>
+      \PATH_TO_JALVIEW\Jalview.exe %HOMEPATH%\mymemorysetting.jvl --open %HOMEPATH%\myalignment.fa</pre>
       In macOS you can use the macOS <em>open</em> command like this: <pre>
-      open /Applications/Jalview.app --args ~/mymemorysetting.jvl -open ~/myalignment.fa</pre><em>(put
+      open /Applications/Jalview.app --args ~/mymemorysetting.jvl --open ~/myalignment.fa</pre><em>(put
         all the Jalview arguments <em>after</em> the --args parameter)
     </em><br />
     <br /></li>
@@ -112,9 +112,9 @@
     </li>
     <li><em><font size="3"><a name="jar">Command line arguments when using the executable jar (jalview-all.jar) or jalview.bin.Launcher</a></em><br/>
       If you are using the Jalview standalone executable jar (usually named <em>jalview-all-....jar</em> with a Jalview and Java version designation) or using <em>jalview.bin.Launcher</em> to start Jalview,
-      then you can set the <em>jvmmempc</em> and <em>jvmmemmax</em> values using application command line arguments <em>-jvmmempc=PERCENT</em>
-      and <em>-jvmmemmax=MAXMEMORY</em> respectively.  <em>PERCENT</em> should be an integer between 1 and 100, and MAXMEMORY should be an amount of memory in bytes, or you can append a "k", "m", "g", or "t" to use units of kilobytes, megabytes, gigabytes or terabytes, e.g.
-      <pre>java -jar jalview-all-2.11.1.0-j1.8.jar -jvmmempc=50 -jvmmemmax=20g</pre>
+      then you can set the <em>jvmmempc</em> and <em>jvmmemmax</em> values using application command line arguments <em>--jvmmempc=PERCENT</em>
+      and <em>--jvmmemmax=MAXMEMORY</em> respectively.  <em>PERCENT</em> should be an integer between 1 and 100, and MAXMEMORY should be an amount of memory in bytes, or you can append a "k", "m", "g", or "t" to use units of kilobytes, megabytes, gigabytes or terabytes, e.g.
+      <pre>java -jar jalview-all-2.11.1.0-j1.8.jar --jvmmempc=50 --jvmmemmax=20g</pre>
       (this example will launch Jalview with a maximum heap size of the smaller of 20GB or 50% of physical memory detected).
       <br/>The default value for jvmmempc is 90, whilst the default value for jvmmemmax is 32g if Jalview can determine a total physical memory size of the host system, and a more cautious 8g if Jalview is unable to determine a total physical memory size.
       <br/><br/>