JAL-3660 Fix for specified output format when using command line arg to convert a...
[jalview.git] / src / jalview / bin / Jalview.java
index c8e453d..08cbcb2 100755 (executable)
@@ -43,8 +43,8 @@ import java.util.logging.ConsoleHandler;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 
-import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
+import javax.swing.UIManager.LookAndFeelInfo;
 
 import com.threerings.getdown.util.LaunchUtil;
 
@@ -60,6 +60,7 @@ 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;
@@ -367,49 +368,89 @@ public class Jalview
 
     desktop = null;
 
-    try
+    // 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)
     {
-      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
-    } catch (Exception ex)
+      laf = lafProp;
+    }
+    else if (lafSetting != null)
     {
-      System.err.println("Unexpected Look and Feel Exception");
-      ex.printStackTrace();
+      laf = lafSetting;
     }
-    if (Platform.isAMacAndNotJS())
+    boolean lafSet = false;
+    switch (laf)
     {
-
-      LookAndFeel lookAndFeel = ch.randelshofer.quaqua.QuaquaManager
-              .getLookAndFeel();
-      System.setProperty("com.apple.mrj.application.apple.menu.about.name",
-              "Jalview");
-      System.setProperty("apple.laf.useScreenMenuBar", "true");
-      if (lookAndFeel != null)
+    case "crossplatform":
+      lafSet = setCrossPlatformLookAndFeel();
+      if (!lafSet)
       {
-        try
-        {
-          UIManager.setLookAndFeel(lookAndFeel);
-        } catch (Throwable e)
-        {
-          System.err.println(
-                  "Failed to set QuaQua look and feel: " + e.toString());
-        }
+        System.err.println("Could not set requested laf=" + laf);
       }
-      if (lookAndFeel == null
-              || !(lookAndFeel.getClass().isAssignableFrom(
-                      UIManager.getLookAndFeel().getClass()))
-              || !UIManager.getLookAndFeel().getClass().toString()
-                      .toLowerCase().contains("quaqua"))
+      break;
+    case "system":
+      lafSet = setSystemLookAndFeel();
+      if (!lafSet)
       {
-        try
-        {
-          System.err.println(
-                  "Quaqua LaF not available on this plaform. Using VAqua(4).\nSee https://issues.jalview.org/browse/JAL-2976");
-          UIManager.setLookAndFeel("org.violetlib.aqua.AquaLookAndFeel");
-        } catch (Throwable e)
-        {
-          System.err.println(
-                  "Failed to reset look and feel: " + e.toString());
-        }
+        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();
       }
     }
 
@@ -425,6 +466,7 @@ public class Jalview
 
     if (!headless)
     {
+
       desktop = new Desktop();
       desktop.setInBatchMode(true); // indicate we are starting up
 
@@ -752,17 +794,37 @@ public class Jalview
             af.createEPS(outputFile);
             continue;
           }
-
-          af.saveAlignment(file, format);
-          if (af.isSaveAlignmentSuccessful())
+          FileFormatI outFormat = null;
+          try
+          {
+            outFormat = FileFormats.getInstance().forName(outputFormat);
+          } catch (Exception formatP)
           {
-            System.out.println("Written alignment in " + format
-                    + " format to " + file);
+            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
+            {
+              af.saveAlignment(file, outFormat);
+              if (af.isSaveAlignmentSuccessful())
+              {
+                System.out.println("Written alignment in "
+                        + outFormat.getName() + " format to " + file);
+              }
+              else
+              {
+                System.out.println("Error writing file " + file + " in "
+                        + outFormat.getName() + " format!!");
+              }
+            }
           }
 
         }
@@ -851,6 +913,107 @@ public class Jalview
     }
   }
 
+  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(
+              system ? UIManager.getSystemLookAndFeelClassName()
+                      : UIManager.getCrossPlatformLookAndFeelClassName());
+      set = true;
+    } catch (Exception ex)
+    {
+      System.err.println("Unexpected Look and Feel Exception");
+      ex.printStackTrace();
+    }
+    return set;
+  }
+
+  private static boolean setSpecificLookAndFeel(String name,
+          String className, boolean nameStartsWith)
+  {
+    boolean set = false;
+    try
+    {
+      for (LookAndFeelInfo info : UIManager.getInstalledLookAndFeels())
+      {
+        if (info.getName() != null && nameStartsWith
+                ? info.getName().toLowerCase()
+                        .startsWith(name.toLowerCase())
+                : info.getName().toLowerCase().equals(name.toLowerCase()))
+        {
+          className = info.getClassName();
+          break;
+        }
+      }
+      UIManager.setLookAndFeel(className);
+      set = true;
+    } catch (Exception ex)
+    {
+      System.err.println("Unexpected Look and Feel Exception");
+      ex.printStackTrace();
+    }
+    return set;
+  }
+
+  private static boolean setGtkLookAndFeel()
+  {
+    return setSpecificLookAndFeel("gtk",
+            "com.sun.java.swing.plaf.gtk.GTKLookAndFeel", true);
+  }
+
+  private static boolean setMetalLookAndFeel()
+  {
+    return setSpecificLookAndFeel("metal",
+            "javax.swing.plaf.metal.MetalLookAndFeel", false);
+  }
+
+  private static boolean setNimbusLookAndFeel()
+  {
+    return setSpecificLookAndFeel("nimbus",
+            "javax.swing.plaf.nimbus.NimbusLookAndFeel", false);
+  }
+
+  private static boolean setQuaquaLookAndFeel()
+  {
+    return setSpecificLookAndFeel("quaqua",
+            ch.randelshofer.quaqua.QuaquaManager.getLookAndFeel().getClass()
+                    .getName(),
+            false);
+  }
+
+  private static boolean setVaquaLookAndFeel()
+  {
+    return setSpecificLookAndFeel("vaqua",
+            "org.violetlib.aqua.AquaLookAndFeel", false);
+  }
+
+  private static boolean setMacLookAndFeel()
+  {
+    boolean set = false;
+    System.setProperty("com.apple.mrj.application.apple.menu.about.name",
+            "Jalview");
+    System.setProperty("apple.laf.useScreenMenuBar", "true");
+    set = setQuaquaLookAndFeel();
+    if ((!set) || !UIManager.getLookAndFeel().getClass().toString()
+            .toLowerCase().contains("quaqua"))
+    {
+      set = setVaquaLookAndFeel();
+    }
+    return set;
+  }
+
   private static void showUsage()
   {
     System.out.println(