X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=b1ea60bed10ab2144f2c4808af369e3c20d6235a;hb=7664ccad29d55ad2355d72feeac23d8bdd49a2a7;hp=08c12d632175938582776d2f48a603ca3ab06c0f;hpb=dc13933d1655206660d32c4e55e150dcf672ba48;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 08c12d6..b1ea60b 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -67,6 +67,7 @@ import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
+import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -93,8 +94,9 @@ public class Jalview
     Platform.getURLCommandArguments();
   }
 
-  // singleton instance of this class
-
+  /*
+   * singleton instance of this class
+   */
   private static Jalview instance;
 
   private Desktop desktop;
@@ -285,6 +287,17 @@ public class Jalview
     ArgsParser aparser = new ArgsParser(args);
     boolean headless = false;
 
+    if (aparser.contains("help") || aparser.contains("h"))
+    {
+      showUsage();
+      System.exit(0);
+    }
+    if (aparser.contains("nodisplay") || aparser.contains("nogui")
+            || aparser.contains("headless"))
+    {
+      System.setProperty("java.awt.headless", "true");
+      headless = true;
+    }
     String usrPropsFile = aparser.getValue("props");
     Cache.loadProperties(usrPropsFile); // must do this before
     if (usrPropsFile != null)
@@ -327,8 +340,8 @@ public class Jalview
                   "Invalid jabaws parameter: " + jabawsUrl + " ignored");
         }
       }
-
     }
+
     String defs = aparser.getValue("setprop");
     while (defs != null)
     {
@@ -344,6 +357,9 @@ public class Jalview
         {
           Cache.setProperty(defs.substring(0, p), defs.substring(p + 1));
         }
+        // DISABLED FOR SECURITY REASONS
+        // TODO: add a property to allow properties to be overriden by cli args
+        // Cache.setProperty(defs.substring(0,p), defs.substring(p+1));
       }
       defs = aparser.getValue("setprop");
     }
@@ -367,91 +383,7 @@ public class Jalview
 
     desktop = null;
 
-    // property laf = "crossplatform", "system", "gtk", "metal" or "mac"
-    // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
-    // try Quaqua/Vaqua.
-    String lafProp = System.getProperty("laf");
-    String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
-    String laf = "none";
-    if (lafProp != null)
-    {
-      laf = lafProp;
-    }
-    else if (lafSetting != null)
-    {
-      laf = lafSetting;
-    }
-    boolean lafSet = false;
-    switch (laf)
-    {
-    case "crossplatform":
-      lafSet = setCrossPlatformLookAndFeel();
-      if (!lafSet)
-      {
-        System.err.println("Could not set requested laf=" + laf);
-      }
-      break;
-    case "system":
-      lafSet = setSystemLookAndFeel();
-      if (!lafSet)
-      {
-        System.err.println("Could not set requested laf=" + laf);
-      }
-      break;
-    case "gtk":
-      lafSet = setGtkLookAndFeel();
-    {
-      System.err.println("Could not set requested laf=" + laf);
-    }
-      break;
-    case "metal":
-      lafSet = setMetalLookAndFeel();
-    {
-      System.err.println("Could not set requested laf=" + laf);
-    }
-      break;
-    case "nimbus":
-      lafSet = setNimbusLookAndFeel();
-    {
-      System.err.println("Could not set requested laf=" + laf);
-    }
-      break;
-    case "quaqua":
-      lafSet = setQuaquaLookAndFeel();
-    {
-      System.err.println("Could not set requested laf=" + laf);
-    }
-      break;
-    case "vaqua":
-      lafSet = setVaquaLookAndFeel();
-    {
-      System.err.println("Could not set requested laf=" + laf);
-    }
-      break;
-    case "mac":
-      lafSet = setMacLookAndFeel();
-      if (!lafSet)
-      {
-        System.err.println("Could not set requested laf=" + laf);
-      }
-      break;
-    case "none":
-      break;
-    default:
-      System.err.println("Requested laf=" + laf + " not implemented");
-    }
-    if (!lafSet)
-    {
-      setSystemLookAndFeel();
-      if (Platform.isLinux() && !Platform.isJS())
-      {
-        setMetalLookAndFeel();
-      }
-      if (Platform.isAMacAndNotJS())
-      {
-        setMacLookAndFeel();
-      }
-    }
+    setLookAndFeel();
 
     /*
      * configure 'full' SO model if preferences say to, else use the default (full SO)
@@ -471,11 +403,21 @@ public class Jalview
       try
       {
         JalviewTaskbar.setTaskbar(this);
+      } catch (Exception e)
+      {
+        Cache.log.info("Cannot set Taskbar");
+        Cache.log.error(e.getMessage());
+        // e.printStackTrace();
       } catch (Throwable t)
       {
-        System.out.println("Error setting Taskbar: " + t.getMessage());
+        Cache.log.info("Cannot set Taskbar");
+        Cache.log.error(t.getMessage());
+        // t.printStackTrace();
       }
 
+      // set Proxy settings before all the internet calls
+      Cache.setProxyPropertiesFromPreferences();
+
       desktop.setVisible(true);
 
       if (!Platform.isJS())
@@ -593,8 +535,7 @@ public class Jalview
        * @j2sIgnore
        */
       {
-        if (!file.startsWith("http://") && !file.startsWith("https://"))
-        // BH 2019 added https check for Java
+        if (!HttpUtils.startsWithHttpOrHttps(file))
         {
           if (!(new File(file)).exists())
           {
@@ -891,6 +832,101 @@ public class Jalview
     }
   }
 
+  private static void setLookAndFeel()
+  {
+    // property laf = "crossplatform", "system", "gtk", "metal", "nimbus" or
+    // "mac"
+    // If not set (or chosen laf fails), use the normal SystemLaF and if on Mac,
+    // try Quaqua/Vaqua.
+    String lafProp = System.getProperty("laf");
+    String lafSetting = Cache.getDefault("PREFERRED_LAF", null);
+    String laf = "none";
+    if (lafProp != null)
+    {
+      laf = lafProp;
+    }
+    else if (lafSetting != null)
+    {
+      laf = lafSetting;
+    }
+    boolean lafSet = false;
+    switch (laf)
+    {
+    case "crossplatform":
+      lafSet = setCrossPlatformLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "system":
+      lafSet = setSystemLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "gtk":
+      lafSet = setGtkLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "metal":
+      lafSet = setMetalLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "nimbus":
+      lafSet = setNimbusLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "quaqua":
+      lafSet = setQuaquaLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "vaqua":
+      lafSet = setVaquaLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "mac":
+      lafSet = setMacLookAndFeel();
+      if (!lafSet)
+      {
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "none":
+      break;
+    default:
+      Cache.log.error("Requested laf=" + laf + " not implemented");
+    }
+    if (!lafSet)
+    {
+      setSystemLookAndFeel();
+      if (Platform.isLinux())
+      {
+        setMetalLookAndFeel();
+      }
+      if (Platform.isMac())
+      {
+        setMacLookAndFeel();
+      }
+    }
+  }
+
   private static boolean setCrossPlatformLookAndFeel()
   {
     boolean set = false;
@@ -901,8 +937,9 @@ public class Jalview
       set = true;
     } catch (Exception ex)
     {
-      System.err.println("Unexpected Look and Feel Exception");
-      ex.printStackTrace();
+      Cache.log.error("Unexpected Look and Feel Exception");
+      Cache.log.error(ex.getMessage());
+      Cache.log.debug(Cache.getStackTraceString(ex));
     }
     return set;
   }
@@ -916,8 +953,9 @@ public class Jalview
       set = true;
     } catch (Exception ex)
     {
-      System.err.println("Unexpected Look and Feel Exception");
-      ex.printStackTrace();
+      Cache.log.error("Unexpected Look and Feel Exception");
+      Cache.log.error(ex.getMessage());
+      Cache.log.debug(Cache.getStackTraceString(ex));
     }
     return set;
   }
@@ -943,8 +981,9 @@ public class Jalview
       set = true;
     } catch (Exception ex)
     {
-      System.err.println("Unexpected Look and Feel Exception");
-      ex.printStackTrace();
+      Cache.log.error("Unexpected Look and Feel Exception");
+      Cache.log.error(ex.getMessage());
+      Cache.log.debug(Cache.getStackTraceString(ex));
     }
     return set;
   }