JAL-3991 JAVA_COMPILE_VERSION put into build_properties. Check for possible JVM misma...

[jalview.git] / src / jalview / bin / Jalview.java

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index f01cbb6..9574e7e 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -44,11 +44,13 @@ import java.util.logging.ConsoleHandler;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
+import javax.swing.JOptionPane;
 import javax.swing.UIManager;
 import javax.swing.UIManager.LookAndFeelInfo;
 
 import com.threerings.getdown.util.LaunchUtil;
 
+//import edu.stanford.ejalbert.launching.IBrowserLaunching;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 import jalview.ext.so.SequenceOntology;
@@ -71,6 +73,7 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.ChannelProperties;
 import jalview.util.HttpUtils;
+import jalview.util.LaunchUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -95,6 +98,10 @@ public class Jalview
   static
   {
     Platform.getURLCommandArguments();
+    Platform.addJ2SDirectDatabaseCall("https://www.jalview.org");
+    Platform.addJ2SDirectDatabaseCall("http://www.jalview.org");
+    Platform.addJ2SDirectDatabaseCall("http://www.compbio.dundee.ac.uk");
+    Platform.addJ2SDirectDatabaseCall("https://www.compbio.dundee.ac.uk");
   }
 
   /*
@@ -368,7 +375,7 @@ public class Jalview
 
     try
     {
-      Cache.initLogger();
+      Console.initLogger();
     } catch (NoClassDefFoundError error)
     {
       error.printStackTrace();
@@ -402,13 +409,13 @@ public class Jalview
         JalviewTaskbar.setTaskbar(this);
       } catch (Exception e)
       {
-        Cache.info("Cannot set Taskbar");
-        Cache.error(e.getMessage());
+        Console.info("Cannot set Taskbar");
+        Console.error(e.getMessage());
         // e.printStackTrace();
       } catch (Throwable t)
       {
-        Cache.info("Cannot set Taskbar");
-        Cache.error(t.getMessage());
+        Console.info("Cannot set Taskbar");
+        Console.error(t.getMessage());
         // t.printStackTrace();
       }
 
@@ -424,6 +431,35 @@ public class Jalview
        * @j2sIgnore
        */
       {
+
+        /**
+         * Check to see that the JVM version being run is suitable for the Java
+         * version this Jalview was compiled for. Popup a warning if not.
+         */
+        if (!LaunchUtils.checkJavaVersion())
+        {
+          Console.warn("The Java version being used (Java "
+                  + LaunchUtils.getJavaVersion()
+                  + ") may lead to problems. This installation of Jalview should be used with Java "
+                  + LaunchUtils.getJavaCompileVersion() + ".");
+
+          if (!LaunchUtils
+                  .getBooleanUserPreference("IGNORE_JVM_WARNING_POPUP"))
+          {
+            Object[] options = {
+                MessageManager.getString("label.continue") };
+            JOptionPane.showOptionDialog(null,
+                    MessageManager.formatMessage(
+                            "warning.wrong_jvm_version_message",
+                            LaunchUtils.getJavaVersion(),
+                            LaunchUtils.getJavaCompileVersion()),
+                    MessageManager
+                            .getString("warning.wrong_jvm_version_title"),
+                    JOptionPane.DEFAULT_OPTION, JOptionPane.WARNING_MESSAGE,
+                    null, options, options[0]);
+          }
+        }
+
         if (!aparser.contains("nowebservicediscovery"))
         {
           desktop.startServiceDiscovery();
@@ -444,7 +480,7 @@ public class Jalview
           {
             // Start the desktop questionnaire prompter with the specified
             // questionnaire
-            Cache.debug("Starting questionnaire url at " + url);
+            Console.debug("Starting questionnaire url at " + url);
             desktop.checkForQuestionnaire(url);
             System.out.println("CMD questionnaire[-" + url
                     + "] executed successfully!");
@@ -459,7 +495,7 @@ public class Jalview
               // "http://anaplog.compbio.dundee.ac.uk/cgi-bin/questionnaire.pl";
               // //
               String defurl = "https://www.jalview.org/cgi-bin/questionnaire.pl";
-              Cache.debug(
+              Console.debug(
                       "Starting questionnaire with default url: " + defurl);
               desktop.checkForQuestionnaire(defurl);
             }
@@ -471,15 +507,30 @@ public class Jalview
                   .println("CMD [-noquestionnaire] executed successfully!");
         }
 
-        if (!aparser.contains("nonews"))
+        if (!aparser.contains("nonews")
+                || Cache.getProperty("NONEWS") == null)
         {
           desktop.checkForNews();
         }
 
-        BioJsHTMLOutput.updateBioJS();
+        if (!aparser.contains("nohtmltemplates")
+                || Cache.getProperty("NOHTMLTEMPLATES") == null)
+        {
+          BioJsHTMLOutput.updateBioJS();
+        }
       }
     }
 
+    // Check if JVM and compile version might cause problems and log if it
+    // might.
+    if (headless && !Platform.isJS() && !LaunchUtils.checkJavaVersion())
+    {
+      Console.warn("The Java version being used (Java "
+              + LaunchUtils.getJavaVersion()
+              + ") may lead to problems. This installation of Jalview should be used with Java "
+              + LaunchUtils.getJavaCompileVersion() + ".");
+    }
+
     // Move any new getdown-launcher-new.jar into place over old
     // getdown-launcher.jar
     String appdirString = System.getProperty("getdownappdir");
@@ -874,62 +925,62 @@ public class Jalview
       lafSet = setCrossPlatformLookAndFeel();
       if (!lafSet)
       {
-        Cache.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "system":
       lafSet = setSystemLookAndFeel();
       if (!lafSet)
       {
-        Cache.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "gtk":
       lafSet = setGtkLookAndFeel();
       if (!lafSet)
       {
-        Cache.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "metal":
       lafSet = setMetalLookAndFeel();
       if (!lafSet)
       {
-        Cache.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "nimbus":
       lafSet = setNimbusLookAndFeel();
       if (!lafSet)
       {
-        Cache.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "quaqua":
       lafSet = setQuaquaLookAndFeel();
       if (!lafSet)
       {
-        Cache.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "vaqua":
       lafSet = setVaquaLookAndFeel();
       if (!lafSet)
       {
-        Cache.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "mac":
       lafSet = setMacLookAndFeel();
       if (!lafSet)
       {
-        Cache.error("Could not set requested laf=" + laf);
+        Console.error("Could not set requested laf=" + laf);
       }
       break;
     case "none":
       break;
     default:
-      Cache.error("Requested laf=" + laf + " not implemented");
+      Console.error("Requested laf=" + laf + " not implemented");
     }
     if (!lafSet)
     {
@@ -955,9 +1006,9 @@ public class Jalview
       set = true;
     } catch (Exception ex)
     {
-      Cache.error("Unexpected Look and Feel Exception");
-      Cache.error(ex.getMessage());
-      Cache.debug(Cache.getStackTraceString(ex));
+      Console.error("Unexpected Look and Feel Exception");
+      Console.error(ex.getMessage());
+      Console.debug(Cache.getStackTraceString(ex));
     }
     return set;
   }
@@ -971,9 +1022,9 @@ public class Jalview
       set = true;
     } catch (Exception ex)
     {
-      Cache.error("Unexpected Look and Feel Exception");
-      Cache.error(ex.getMessage());
-      Cache.debug(Cache.getStackTraceString(ex));
+      Console.error("Unexpected Look and Feel Exception");
+      Console.error(ex.getMessage());
+      Console.debug(Cache.getStackTraceString(ex));
     }
     return set;
   }
@@ -1000,9 +1051,9 @@ public class Jalview
       set = true;
     } catch (Exception ex)
     {
-      Cache.error("Unexpected Look and Feel Exception");
-      Cache.error(ex.getMessage());
-      Cache.debug(Cache.getStackTraceString(ex));
+      Console.error("Unexpected Look and Feel Exception");
+      Console.error(ex.getMessage());
+      Console.debug(Cache.getStackTraceString(ex));
     }
     return set;
   }
@@ -1112,16 +1163,17 @@ public class Jalview
               @Override
               public void run()
               {
-                Cache.debug("Initialising googletracker for usage stats.");
+                Console.debug(
+                        "Initialising googletracker for usage stats.");
                 Cache.initGoogleTracker();
-                Cache.debug("Tracking enabled.");
+                Console.debug("Tracking enabled.");
               }
             }, new Runnable()
             {
               @Override
               public void run()
               {
-                Cache.debug("Not enabling Google Tracking.");
+                Console.debug("Not enabling Google Tracking.");
               }
             }, null, true);
     desktop.addDialogThread(prompter);