From 9c2db0c1bb8cbfc7fac9e783f1b43e379c060dad Mon Sep 17 00:00:00 2001
From: Ben Soares <bsoares@dundee.ac.uk>
Date: Wed, 3 Jul 2019 17:24:57 +0100
Subject: [PATCH] JAL-3348 start of new memory setting text

---
 help/help/html/memory.html |   93 ++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 85 insertions(+), 8 deletions(-)

diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index e583398..b784451 100755
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -30,11 +30,15 @@
   </h2>
   <p>
     When launched as an Application, Jalview automatically tries to
-    maximise the amount of memory allocated to it, but sometimes it may
-    run out of memory. This is because of the way that Java runs on a
-    computer - what is actually run is a program called a virtual
-    machine (the JVM) which executes the java instructions. The JVM has
-    limits on the memory that can be allocated to the java program - and
+    maximise the amount of memory allocated to it (default settings are
+    to try and use up to 90% of physical memory available to it).
+    Sometimes it may require more memory, or if you are working in a
+    shared memory environment you may want to limit the maximum amount
+    of memory that it might use.
+    This has to be set at the time Jalview is launched because of the way
+    that Java runs on a computer - what is actually run is a program called
+    a Java virtual machine (a JVM) which executes the java program instructions.
+    The JVM has limits on the memory that can be allocated to the java program - and
     you might need to increase them if you are working with particularly
     large datasets.<br> If Jalview has not explicitly told you that
     it has run out of memory, then a common sign is that a function that
@@ -54,8 +58,81 @@
     window's background.
   </p>
   <p>
-    <em>Increasing the memory available to Jalview</em><br>
-    Since Jalview 2.11, the program automatically configures the JVM memory settings to set the maximum memory available to Jalview to be 90% of physical memory. 
-      <p>&nbsp;</p>
+    <em>Increasing the memory available to Jalview</em><br/>
+    Since Jalview 2.11, the program automatically configures the JVM memory settings to set the maximum memory available to Jalview to be 90% of physical memory.
+    This default setting can be altered in a number of different ways, depending on how you prefer to launch Jalview and how specific you want to be with the maximum memory setting.
+  </p>
+
+  <ul>
+    <li><em><font size="3">JVL file</font></em>
+      <p>
+      The easiest way to launch Jalview with a different percentage of physical memory available is to
+      create a text file with extension <em>.jvl</em> and with content that looks like
+      <pre>
+      jalview.jvmmempc=50
+      </pre>
+      Replace the value with the percentage of memory you wish to allocate to Jalview.
+      </p>
+      <p>
+      In Windows and in macOS you can then launch Jalview by double clicking on this file, and your memory setting will be used instead of the default value of 90.
+      </p>
+      <p>
+      In Linux or other unix variants you can launch Jalview on the command line and provide your JVL file as an argument with
+      <pre>
+      /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl
+      </pre>
+
+      </p>
+      <p>
+      If you want to use a memory setting like this and open a file you can use both files as arguments in the command line, but you must put the <em>jvl</em> file first, e.g.
+      <pre>
+      /PATH_TO_JALVIEW/Jalview /path/to/file/mymemorysetting.jvl /path/to/alignments/myalignment.fa
+      </pre>
+
+
+      </p>
+    </li>
+
+
+    <li><em><font size="3"></font></em>
+      <p>
+      </p>
+    </li>
+
+
+
+
+    <li><em><font size="3"></font></em>
+      <p>
+      </p>
+    </li>
+
+
+
+
+    <li><em><font size="3"></font></em>
+      <p>
+      </p>
+    </li>
+
+
+
+
+    <li><em><font size="3"></font></em>
+      <p>
+      </p>
+    </li>
+
+
+
+
+    <li><em><font size="3"></font></em>
+      <p>
+      </p>
+    </li>
+
+
+  </ul>
+
 </body>
 </html>
-- 
1.7.10.2