X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FJalview.java;h=341bcba46ba473708e03fd05178544cdec3ef8c7;hb=5c1262f120d4fca072bc8fd9800a1a856cc46843;hp=2e33474c1567645e783e3ce34dd696e73c69c372;hpb=2288325efdb30bead1f6a3ad264d5e0c6b9cc752;p=jalview.git

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 2e33474..341bcba 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,6 +20,28 @@
  */
 package jalview.bin;
 
+import jalview.ext.so.SequenceOntology;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.gui.PromptUserConfig;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.BioJsHTMLOutput;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatException;
+import jalview.io.FileFormatI;
+import jalview.io.FileFormats;
+import jalview.io.FileLoader;
+import jalview.io.HtmlSvgOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.jws2.Jws2Discoverer;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileOutputStream;
@@ -297,90 +319,7 @@ 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()) {
-        setMetalLookAndFeel();
-      }
-      if (Platform.isAMac())
-      {
-        setMacLookAndFeel();
-      }
-    }
+    setLookAndFeel();
 
     /*
      * configure 'full' SO model if preferences say to, else use the default (SO
@@ -402,11 +341,13 @@ public class Jalview
         JalviewTaskbar.setTaskbar(this);
       } catch (Exception e)
       {
-        System.out.println("Cannot set Taskbar");
+        Cache.log.info("Cannot set Taskbar");
+        Cache.log.error(e.getMessage());
         // e.printStackTrace();
       } catch (Throwable t)
       {
-        System.out.println("Cannot set Taskbar");
+        Cache.log.info("Cannot set Taskbar");
+        Cache.log.error(t.getMessage());
         // t.printStackTrace();
       }
 
@@ -707,18 +648,34 @@ public class Jalview
             af.createEPS(outputFile);
             continue;
           }
-
-          if (af.saveAlignment(file, format))
-          {
-            System.out.println("Written alignment in " + format
-                    + " format to " + file);
+          FileFormatI outFormat=null;
+          try {
+            outFormat = FileFormats.getInstance().forName(outputFormat);
+          } catch (Exception formatP) {
+            System.out.println("Couldn't parse "+outFormat+" as a valid Jalview format string.");
           }
-          else
+          if (outFormat != null)
           {
-            System.out.println("Error writing file " + file + " in "
-                    + format + " format!!");
+            if (!outFormat.isWritable())
+            {
+              System.out.println(
+                      "This version of Jalview does not support alignment export as "
+                              + outputFormat);
+            }
+            else
+            {
+              if (af.saveAlignment(file, outFormat))
+              {
+                System.out.println("Written alignment in " + format
+                        + " format to " + file);
+              }
+              else
+              {
+                System.out.println("Error writing file " + file + " in "
+                        + format + " format!!");
+              }
+            }
           }
-
         }
 
         while (aparser.getSize() > 0)
@@ -801,33 +758,125 @@ public class Jalview
     }
   }
 
-  private static boolean setCrossPlatformLookAndFeel()
+  private static void setLookAndFeel()
   {
-    boolean set = false;
-    try
+    // 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)
     {
-      UIManager.setLookAndFeel(
-              UIManager.getCrossPlatformLookAndFeelClassName());
-      set = true;
-    } catch (Exception ex)
+      laf = lafProp;
+    }
+    else if (lafSetting != null)
     {
-      System.err.println("Unexpected Look and Feel Exception");
-      ex.printStackTrace();
+      laf = lafSetting;
     }
-    return set;
+    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.isAMac())
+      {
+        setMacLookAndFeel();
+      }
+    }
+  }
+
+  private static boolean setCrossPlatformLookAndFeel()
+  {
+    return setGenericLookAndFeel(false);
   }
 
   private static boolean setSystemLookAndFeel()
   {
+    return setGenericLookAndFeel(true);
+  }
+
+  private static boolean setGenericLookAndFeel(boolean system)
+  {
     boolean set = false;
     try
     {
-      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+      UIManager.setLookAndFeel(
+              system ? UIManager.getSystemLookAndFeelClassName()
+                      : UIManager.getCrossPlatformLookAndFeelClassName());
       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;
   }
@@ -853,8 +902,9 @@ 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;
   }