JAL-3348 memory.html documentation finished for 2.11.0

diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index b784451..396507b 100755 (executable)
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -67,7 +67,7 @@
     <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
+      create a text file with extension <em>.jvl</em> and with content that contains the line
       <pre>
       jalview.jvmmempc=50
       </pre>
@@ -84,51 +84,78 @@
 
       </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.
+      If you want to use a memory setting like this and open a file you can use both the jvl and alignment files as command line arguments, 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>
-
-
+      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 http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal
+      </pre>
       </p>
-    </li>
-
-
-    <li><em><font size="3"></font></em>
+      
       <p>
+      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>
+      and 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>
+      (put all the Jalview arguments <em>after</em> the --args parameter).
+      
       </p>
     </li>
 
 
-
-
-    <li><em><font size="3"></font></em>
+    <li><em><font size="3">Directly opening Jalview with a JVM</font></em>
       <p>
+      Launching Jalview directly with a JVM is entirely possible, but is not recommended as automatic updates and some other default settings will not operate.
       </p>
-    </li>
-
-
-
-
-    <li><em><font size="3"></font></em>
       <p>
+      However by launching Jalview in this way you have full access to the Java command line arguments.
+      In particular you can set the maximum allowed memory with the <em>-Xmx...</em>  JVM argument.
+      <br/>
+      <em>-Xmx</em> should be immediately followed (no space or equals) by the maximum amount of memory that you might want to launch Jalview with.  This can be specified in bytes as just a number,
+      or in kilobytes, megabytes or gigabytes by following the number with a "k", "m" or "g" respectively.  e.g.
+      <pre>
+      -Xmx8g
+      </pre> 
       </p>
-    </li>
-
-
-
-
-    <li><em><font size="3"></font></em>
       <p>
+      Jalview binaries for Windows and macOS are distributed with their own JVM which you will find in
+      <ul>
+      <li><em>Windows:</em> .../Jalview/jre/bin/java.exe</li>
+      <li><em>macOS:</em> .../Jalview.app/Contents/Resources/app/jre/Contents/Home/bin/java</li>
+      </ul>
+      For linux and other unixes you will have to install a Java 1.8 JRE (we recommend the ones found at <a href="https://adoptopenjdk.net">https://adoptopenjdk.net/</a>)
       </p>
-    </li>
-
-
-
-
-    <li><em><font size="3"></font></em>
       <p>
+      You will also need to reference the "appdir" release folder with all of the Jalview jar files.
+      <br/>
+      On Windows this will be
+      <pre>\PATH_TO_JALVIEW\release</pre>
+      whereas on macOS it will be
+      <pre>/Applications/Jalview.app/Contents/Resources/app/release</pre>
+      and on linux or unix
+      <pre>/PATH_TO_JALVIEW/release</pre>
       </p>
+      <p>
+      Assuming the <em>java</em> (or <em>java.exe</em> on Windows) commands are available to you, you can run, e.g.
+      <pre>
+      java -Xmx1500m -cp "/PATH_TO_RELEASE_DIR/*" jalview.bin.Jalview
+      </pre>
+      or on Windows
+      <pre>
+      java.exe -Xmx1500m -cp "\PATH_TO_RELEASE_DIR\*" jalview.bin.Jalview
+      </pre>
+      <em>Note</em> that the classpath argument wildcard must be simply a '*' and not '*.jar'. This is a limitation of Java.
+      </p>
+      <p>
+      You can also add other Jalview command line arguments as above after the <em>jalview.bin.Jalview</em> class name (you cannot use <em>jvl</em> files if launching Jalview in this way).     
     </li>