JAL-3503 2.11.2.0 release notes and docs

diff --git a/help/help/help.jhm b/help/help/help.jhm
index 449f34c..4efcd8f 100755 (executable)
--- a/help/help/help.jhm
+++ b/help/help/help.jhm
@@ -60,6 +60,7 @@
    <mapID target="varna" url="html/features/varna.html"/>
    <mapID target="xsspannotation" url="html/features/xsspannotation.html"/>
    <mapID target="preferences" url="html/features/preferences.html"/>     
+   <mapID target="startupprefs" url="html/features/preferences.html#startup"/>     
    <mapID target="strucprefs" url="html/features/preferences.html#structure"/>     
    <mapID target="commandline" url="html/features/commandline.html"/>
    <mapID target="clarguments" url="html/features/clarguments.html"/>

diff --git a/help/help/html/features/preferences.html b/help/help/html/features/preferences.html
index 5a3fe7a..d091272 100755 (executable)
--- a/help/help/html/features/preferences.html
+++ b/help/help/html/features/preferences.html
@@ -64,6 +64,10 @@
     <li>The <a href="#editing"><strong>&quot;Editing&quot;</strong>
         Preferences</a> tab contains settings affecting behaviour when editing alignments.
     </li>
+    <li>The <a href="#startup"><strong>&quot;Startup&quot;</strong>
+        Preferences</a> tab allows you to adjust how much memory is
+      allocated to Jalview when it is launched.
+    </li>
     <li>The <a href="../webServices/webServicesPrefs.html"><strong>&quot;Web
           Service&quot;</strong> Preferences</a> tab allows you to configure the <a
       href="http://www.compbio.dundee.ac.uk/jabaws">JABAWS</a>
@@ -419,6 +423,17 @@
     loaded onto the alignment will automatically sort the alignment.
   </p>
   <p>&nbsp;</p>
+  <p>
+    <a name="startup"><strong>Startup</strong></a>
+  </p>
+  <p>
+    When Jalview is launched it by default examines the available memory
+    and requests up to 90% to be allocated to the application, or 32G,
+    which ever is smaller. The <em>Startup</em> tab allows you to adjust
+    the maximum percentage and hard limits for Jalview memory allocation
+    stored in your .jalview_properties file.
+  </p>
+  <p>&nbsp;</p>
   <em>Web Services Preferences</em> - documentation for this tab is
   given in the
   <a href="../webServices/webServicesPrefs.html">Web Services

diff --git a/help/help/html/memory.html b/help/help/html/memory.html
index 7d6fb85..ec57530 100755 (executable)
--- a/help/help/html/memory.html
+++ b/help/help/html/memory.html
@@ -30,9 +30,13 @@
   </h2>
   <p>When launched as an Application, Jalview will automatically
     configure the amount of memory allocated to the program to be 90% of
-    physical memory. You may wish to change this behaviour -
-    particularly if you are working on a machine that runs other memory
-    intensive processes.
+    physical memory, or 32GB - which ever is smaller.</p>
+  <p>
+    This behaviour might not be ideal if you are working on a machine
+    that runs other memory intensive processes, and (<em>since
+      Jalview 2.11.2</em>) can be changed via the <a
+      ref="preferences.html#startup">Startup Preferences</a> panel.
+  </p>
   <p>
     <em>Signs that Jalview is Running out of Memory</em><br /> If
     Jalview has not explicitly told you that it has run out of memory,
@@ -65,28 +69,36 @@
   </p>
 
   <ul>
-    <li><em><font size="3">JVL file</font></em> <br /> 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>
+    <li><em><font size="3">Jalview's Startup
+          Preferences panel</font></em> <br /> The easiest way to launch Jalview
+      with a different percentage of physical memory available is to
+      adjust your user preferences via the <a
+      ref="preferences.html#startup">Startup Preferences</a> panel.</li>
+    <li><em><font size="3">JVL file</font></em> <br />Another way
+      to adjust launch settings is with a text file with extension <em>.jvl</em>
       and a single line to specify the percentage of memory you wish
       Jalview to request: <pre>
-      jalview.jvmmempc=50</pre> 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. <br /> <br /> 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> 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
+      jalview.jvmmempc=50</pre> 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. <br /> <br /> 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> 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 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> 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 all the Jalview arguments <em>after</em> the --args
-        parameter)
-    </em><br/><br/></li>
+       /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>
+      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
+        all the Jalview arguments <em>after</em> the --args parameter)
+    </em><br />
+    <br /></li>
     <li><em><font size="3">Maximum memory limit</em><br/>
       Since 2.11.1.0, Jalview's configuration includes a 'maximum memory limit':
       <pre>jalview.jvmmemmax = 32G</pre>

diff --git a/help/help/html/whatsNew.html b/help/help/html/whatsNew.html
index f529c56..5ecf293 100755 (executable)
--- a/help/help/html/whatsNew.html
+++ b/help/help/html/whatsNew.html
@@ -50,6 +50,7 @@
       allows predicted and observed 3D models for proteins in Uniprot
       from a range of resources, including AlphaFold DB, SWISS-MODEL and
       a growing number of other resources.</li>
+      <li><strong>Easier configuration of <a href="features/preferences.html#startup">Jalview's memory allocation</a></strong>
     <p>
       <strong>Retrieval of 3D models via 3D-Beacons</strong> <br>The
       3D-Beacons network (<a