From 2288325efdb30bead1f6a3ad264d5e0c6b9cc752 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Tue, 4 Aug 2020 18:13:02 +0100
Subject: [PATCH] JAL-3477 Added -help text for jvmmempc and jvmmemmax. Fixed
 typo and slight rewording in help/memory.html

---
 help/help/html/features/clarguments.html |    6 +++---
 src/jalview/bin/Jalview.java             |    2 ++
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index 89560e9..1eecfb9 100644
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -236,7 +236,7 @@
     </tr>
     <tr>
       <td><div align="center">-jvmmempc=PERCENT</div></td>
-      <td><div align="left"><em>Standalone executable jar only.</em>
+      <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
           Limit maximum heap size (memory) to PERCENT% of total physical memory detected.
 	  This defaults to 90 if total physical memory can be detected.
 	  See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
@@ -245,10 +245,10 @@
     </tr>
     <tr>
       <td><div align="center">-jvmmemmax=MAXMEMORY</div></td>
-      <td><div align="left"><em>Standalone executable jar only.</em>
+      <td><div align="left"><em>Only available with standalone executable jar or jalview.bin.Launcher.</em>
           Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m),
 	  gigabytes(g) or if you're lucky enough, terabytes(t).
-	  This defaults to 32g if total physcial memory can be detected, or to 8g if total physical memory cannot be detected.
+	  This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.
 	  See <a href="../memory.html">Memory usage settings for Jalview</a> for more details.
           </div>
       </td>
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 021aad6..2e33474 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -944,6 +944,8 @@ public class Jalview
                     + "-jabaws URL\tSpecify URL for Jabaws services (e.g. for a local installation).\n"
                     + "-fetchfrom nickname\tQuery nickname for features for the alignments and display them.\n"
                     + "-groovy FILE\tExecute groovy script in FILE, after all other arguments have been processed (if FILE is the text 'STDIN' then the file will be read from STDIN)\n"
+                    + "-jvmmempc=PERCENT\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
+                    + "-jvmmemmax=MAXMEMORY\tOnly available with standalone executable jar or jalview.bin.Launcher. Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. See https://www.jalview.org/help/html/memory.html for more details.\n"
                     + "\n~Read documentation in Application or visit http://www.jalview.org for description of Features and Annotations file~\n\n");
   }
 
-- 
1.7.10.2