X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=37f396eb842d5d6a204ee8279559c200dba18460;hb=fc895e8dacdbb7f49df0ec5c9f475b841082e9b3;hp=0d7143dcca095f12842be7fed11f90f2ee60c07a;hpb=e6fd516209d8b5162cd155c9d500ca27a6dd8e1e;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 0d7143d..37f396e 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -70,7 +70,14 @@ 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
+ * 
+ * or on Windows: java -classpath "$PATH_TO_LIB$/*;$PATH_TO_CLASSES$" \
+ * jalview.bin.Jalview jalview.bin.Jalview
+ * 
+ * (ensure -classpath arg is quoted to avoid shell expansion of '*' and do not
+ * embellish '*' to e.g. '*.jar')
  * 
  * @author $author$
  * @version $Revision$
@@ -89,13 +96,21 @@ public class Jalview
 
   public static AlignFrame currentAlignFrame;
 
-  public static boolean isJS = /** @j2sNative true || */ // BH 2018
-          false;
+  /**
+   * Answers true if Jalview is running as Javascript, else false. The value is
+   * set at compile time.
+   * 
+   * @return
+   */
+  public static boolean isJS()
+  {
+    return /** @j2sNative true || */
+    false;
+  }
 
   static
   {
-
-    if (!isJS)
+    if (!isJS())
     { // BH 2018
     // grab all the rights we can the JVM
     Policy.setPolicy(new Policy()
@@ -160,7 +175,6 @@ public class Jalview
           af.setProgressBar(MessageManager
                   .getString("status.das_features_being_retrived"), id);
           af.featureSettings_actionPerformed(null);
-          af.featureSettings.fetchDasFeatures(dasSources, true);
           af.setProgressBar(null, id);
           synchronized (us)
           {
@@ -200,7 +214,7 @@ public class Jalview
   void doMain(String[] args)
   {
 
-    if (!isJS)
+    if (!isJS())
     {
       System.setSecurityManager(null);
     }
@@ -288,7 +302,7 @@ 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);
     }
 
@@ -531,7 +545,7 @@ public class Jalview
       }
       System.out.println("CMD [-open " + file + "] executed successfully!");
 
-      if (!isJS && !file.startsWith("http://"))
+      if (!isJS() && !file.startsWith("http://"))
       {
         if (!(new File(file)).exists())
         {
@@ -750,7 +764,8 @@ public class Jalview
             continue;
           }
 
-          if (af.saveAlignment(file, format))
+          af.saveAlignment(file, format);
+          if (af.isSaveAlignmentSuccessful())
           {
             System.out.println("Written alignment in " + format
                     + " format to " + file);