JAL-3065

Change in all repo documentation advising launching Jalview with the
-Djava.ext.dirs=LIB
option to now use
-classpath="LIB/*:..."
instead. Using the -Djava.ext.dirs= option masks the JRE's own ext dir
which contains the sunjce packages.  This manifests as cipher problems
when accessing https resources (in particular https://www.ebi.ac.uk/...
when searching for PDB structures, activated when choosing Sequence->"3D
Structure Data...")

diff --git a/README b/README
index eaf226b..74f4591 100755 (executable)
--- a/README
+++ b/README
@@ -23,11 +23,11 @@ For more help, read the file doc/building.html
 
 To run application:
 
-java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar jalview.bin.Jalview
+java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
 
 Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If building from source:
 
-java -Djava.ext.dirs=JALVIEW_BUILD/dist -cp JALVIEW_BUILD/dist/jalview.jar jalview.bin.Jalview
+java -classpath "JALVIEW_BUILD/dist/*" jalview.bin.Jalview
 
 
 ##################

diff --git a/help/html/features/commandline.html b/help/html/features/commandline.html
index 9cffc51..92d9323 100644 (file)
--- a/help/html/features/commandline.html
+++ b/help/html/features/commandline.html
@@ -49,11 +49,11 @@
     provided by InstallAnywhere any output from the application will be
     sent to output.txt, not standard out.<br> The Jalview
     application also requires a number of additional libraries on the
-    class path. The command line below adds the Jalview installation's
-    'lib' directory to the list of directories that are searched for
-    jars to be added to the classpath:
+    class path. The command line below adds all the jar files in the
+    Jalview installation's 'lib' directory to the classpath, as well as
+    the Jalview application jar file:
   </p>
-  <pre>java -Djava.ext.dirs=$INSTALL_DIR$/lib -cp $INSTALL_DIR$/jalview.jar jalview.bin.Jalview -open [FILE] </pre>
+  <pre>java -classpath "$INSTALL_DIR$/lib/*:$INSTALL_DIR$/jalview.jar" jalview.bin.Jalview -open [FILE] </pre>
   <p>
     Use '-help' to get more information on the <a
       href="clarguments.html">command line arguments</a> that

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 30620a1..0b1cf60 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -70,7 +70,8 @@ import groovy.util.GroovyScriptEngine;
 /**
  * Main class for Jalview Application <br>
  * <br>
- * start with java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview
+ * start with java -classpath "$PATH_TO_LIB$/*:$PATH_TO_CLASSES$"
+ * jalview.bin.Jalview
  * 
  * @author $author$
  * @version $Revision$
@@ -265,7 +266,7 @@ public class Jalview
     {
       error.printStackTrace();
       System.out.println("\nEssential logging libraries not found."
-              + "\nUse: java -Djava.ext.dirs=$PATH_TO_LIB$ jalview.bin.Jalview");
+              + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview");
       System.exit(0);
     }
 

diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 69a3ef7..2b40a72 100644 (file)
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -55,7 +55,7 @@ public class CommandLineOperations
 
   private static final int MINFILESIZE_BIG = 4096;
 
-  private ArrayList<String> successfulCMDs = new ArrayList<String>();
+  private ArrayList<String> successfulCMDs = new ArrayList<>();
 
   /***
    * from
@@ -118,7 +118,7 @@ public class CommandLineOperations
   {
     String _cmd = "java "
             + (withAwt ? "-Djava.awt.headless=true" : "")
-            + " -Djava.ext.dirs=./lib -classpath ./classes jalview.bin.Jalview ";
+            + " -classpath \"./lib/*:./classes\" jalview.bin.Jalview ";
     System.out.println("CMD [" + cmd + "]");
     Process ls2_proc = null;
     Worker worker = null;

diff --git a/utils/InstallAnywhere/README_IA b/utils/InstallAnywhere/README_IA
index e9e5176..3ccb2a4 100755 (executable)
--- a/utils/InstallAnywhere/README_IA
+++ b/utils/InstallAnywhere/README_IA
@@ -6,7 +6,7 @@ Jalview Readme
 
 To run application:
 
-java -Djava.ext.dirs=JALVIEW_HOME/lib -jar JALVIEW_HOME/jalview.jar [-help ... ]
+java -classpath "JALVIEW_HOME/lib/*" -jar JALVIEW_HOME/jalview.jar [-help ... ]
 
 Replace JALVIEW_HOME with the full path to Jalview Installation Directory.
 Use -help to see the available command line arguments.
@@ -15,9 +15,11 @@ For best results use a Sun java run time environment (not the gcj gnu java, sorr
 
 If you want to the java runtime bundled with Jalview, then launch jalview like this:
 
-JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -Djava.ext.dirs=JALVIEW_HOME/lib -jar JALVIEW_HOME/jalview.jar 
+JAVA_HOME=JALVIEW_HOME/jre JALVIEW_HOME/jre/bin/java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+[or
+JAVA_HOME=JALVIEW_HOME/jre/Contents/Home JALVIEW_HOME/jre/Contents/Home/bin/java -classpath "JALVIEW_HOME/lib/*:JALVIEW_HOME/jalview.jar" jalview.bin.Jalview
+in macOS]
 
-Please Note: the -jar jalview.jar option launches the jalview.bin.Jalview class in the jalview.jar
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