Merge branch 'bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows' into...

diff --git a/build.gradle b/build.gradle
index f7233f1..24f1fd9 100644 (file)
--- a/build.gradle
+++ b/build.gradle
@@ -958,6 +958,11 @@ test {
 
   workingDir = jalviewDir
   //systemProperties 'clover.jar' System.properties.clover.jar
+  def testLaf = project.findProperty("test_laf")
+  if (testLaf != null) {
+    println("Setting Test LaF to '${testLaf}'")
+    systemProperty "laf", testLaf
+  }
   sourceCompatibility = compile_source_compatibility
   targetCompatibility = compile_target_compatibility
   jvmArgs += additional_compiler_args

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index bb3ea76..dbe85fe 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -38,6 +38,10 @@ import java.util.Locale;
 import java.util.Properties;
 import java.util.StringTokenizer;
 import java.util.TreeSet;
+import java.util.regex.Pattern;
+
+import javax.swing.LookAndFeel;
+import javax.swing.UIManager;
 
 import org.apache.log4j.ConsoleAppender;
 import org.apache.log4j.Level;
@@ -1122,8 +1126,15 @@ public class Cache
             System.getProperty("installer_template_version"), "\n", null);
     appendIfNotNull(sb, "Launcher version: ",
             System.getProperty("launcher_version"), "\n", null);
-    if (jalview.bin.Cache.getDefault("VERSION", "TEST")
-            .equals("DEVELOPMENT"))
+    LookAndFeel laf = UIManager.getLookAndFeel();
+    String lafName = laf == null ? "Not obtained" : laf.getName();
+    String lafClass = laf == null ? "unknown" : laf.getClass().getName();
+    appendIfNotNull(sb, "LookAndFeel: ", lafName + " (" + lafClass + ")",
+            "\n", null);
+    // Not displayed in release version ( determined by possible version number
+    // regex 9[9.]*9[.-_a9]* )
+    if (Pattern.matches("^\\d[\\d\\.]*\\d[\\.\\-\\w]*$",
+            jalview.bin.Cache.getDefault("VERSION", "TEST")))
     {
       appendIfNotNull(sb, "Getdown appdir: ",
               System.getProperty("getdownappdir"), "\n", null);

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 8c9d391..ead9b9f 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -20,27 +20,6 @@
  */
 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.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;
@@ -61,13 +40,33 @@ import java.util.HashMap;
 import java.util.Map;
 import java.util.Vector;
 
-import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
+import javax.swing.UIManager.LookAndFeelInfo;
 
 import com.threerings.getdown.util.LaunchUtil;
 
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
+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.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;
 
 /**
  * Main class for Jalview Application <br>
@@ -183,7 +182,7 @@ public class Jalview
    * main class for Jalview application
    * 
    * @param args
-   *               open <em>filename</em>
+   *          open <em>filename</em>
    */
   public static void main(String[] args)
   {
@@ -198,22 +197,24 @@ public class Jalview
   {
     System.setSecurityManager(null);
     System.out
-            .println("Java version: "
-                    + System.getProperty("java.version"));
+            .println("Java version: " + System.getProperty("java.version"));
     System.out.println("Java Home: " + System.getProperty("java.home"));
     System.out.println(System.getProperty("os.arch") + " "
             + System.getProperty("os.name") + " "
             + System.getProperty("os.version"));
     String val = System.getProperty("sys.install4jVersion");
-    if (val != null) {
-    System.out.println("Install4j version: " + val);
+    if (val != null)
+    {
+      System.out.println("Install4j version: " + val);
     }
     val = System.getProperty("installer_template_version");
-    if (val != null) {
+    if (val != null)
+    {
       System.out.println("Install4j template version: " + val);
     }
     val = System.getProperty("launcher_version");
-    if (val != null) {
+    if (val != null)
+    {
       System.out.println("Launcher version: " + val);
     }
 
@@ -296,49 +297,90 @@ public class Jalview
 
     desktop = null;
 
-    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.getSystemLookAndFeelClassName());
-    } catch (Exception ex)
+      laf = lafProp;
+    }
+    else if (lafSetting != null)
     {
-      System.err.println("Unexpected Look and Feel Exception");
-      ex.printStackTrace();
+      laf = lafSetting;
     }
-    if (Platform.isAMac())
+    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());
-        }
+        Cache.log.error("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());
-        }
+        Cache.log.error("Could not set requested laf=" + laf);
+      }
+      break;
+    case "gtk":
+      lafSet = setGtkLookAndFeel();
+    {
+      Cache.log.error("Could not set requested laf=" + laf);
+    }
+      break;
+    case "metal":
+      lafSet = setMetalLookAndFeel();
+    {
+      Cache.log.error("Could not set requested laf=" + laf);
+    }
+      break;
+    case "nimbus":
+      lafSet = setNimbusLookAndFeel();
+    {
+      Cache.log.error("Could not set requested laf=" + laf);
+    }
+      break;
+    case "quaqua":
+      lafSet = setQuaquaLookAndFeel();
+    {
+      Cache.log.error("Could not set requested laf=" + laf);
+    }
+      break;
+    case "vaqua":
+      lafSet = setVaquaLookAndFeel();
+    {
+      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();
       }
     }
 
@@ -361,11 +403,13 @@ 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();
       }
 
@@ -760,6 +804,111 @@ public class Jalview
     }
   }
 
+  private static boolean setCrossPlatformLookAndFeel()
+  {
+    boolean set = false;
+    try
+    {
+      UIManager.setLookAndFeel(
+              UIManager.getCrossPlatformLookAndFeelClassName());
+      set = true;
+    } catch (Exception ex)
+    {
+      System.err.println("Unexpected Look and Feel Exception");
+      ex.printStackTrace();
+    }
+    return set;
+  }
+
+  private static boolean setSystemLookAndFeel()
+  {
+    boolean set = false;
+    try
+    {
+      UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
+      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(
@@ -836,10 +985,10 @@ public class Jalview
    * Locate the given string as a file and pass it to the groovy interpreter.
    * 
    * @param groovyscript
-   *                         the script to execute
+   *          the script to execute
    * @param jalviewContext
-   *                         the Jalview Desktop object passed in to the groovy
-   *                         binding as the 'Jalview' object.
+   *          the Jalview Desktop object passed in to the groovy binding as the
+   *          'Jalview' object.
    */
   private void executeGroovyScript(String groovyscript, AlignFrame af)
   {
@@ -968,8 +1117,8 @@ public class Jalview
   }
 
   /**
-   * Quit method delegates to Desktop.quit - unless running in headless mode when
-   * it just ends the JVM
+   * Quit method delegates to Desktop.quit - unless running in headless mode
+   * when it just ends the JVM
    */
   public void quit()
   {

diff --git a/src/jalview/util/Platform.java b/src/jalview/util/Platform.java
index e8558fa..a5bee7c 100644 (file)
--- a/src/jalview/util/Platform.java
+++ b/src/jalview/util/Platform.java
@@ -29,11 +29,23 @@ import java.awt.event.MouseEvent;
  */
 public class Platform
 {
-  private static Boolean isAMac = null, isWindows = null;
+  private static Boolean isAMac = null, isWindows = null, isLinux = null;
 
   private static Boolean isHeadless = null;
 
   /**
+   * added to check LaF for Linux
+   * 
+   * @return
+   */
+  public static boolean isLinux()
+  {
+    return (isLinux == null
+            ? (isLinux = (System.getProperty("os.name").indexOf("Linux") >= 0))
+            : isLinux);
+  }
+
+  /**
    * sorry folks - Macs really are different
    * 
    * @return true if we do things in a special way.
@@ -131,7 +143,8 @@ public class Platform
       {
         return false;
       }
-      return (jalview.util.ShortcutKeyMaskExWrapper.getMenuShortcutKeyMaskEx() // .getMenuShortcutKeyMaskEx()
+      return (jalview.util.ShortcutKeyMaskExWrapper
+              .getMenuShortcutKeyMaskEx() // .getMenuShortcutKeyMaskEx()
               & jalview.util.ShortcutKeyMaskExWrapper
                       .getModifiersEx(e)) != 0; // getModifiers()) != 0;
     }
@@ -139,8 +152,8 @@ public class Platform
   }
 
   /**
-   * A (case sensitive) file path comparator that ignores the difference between /
-   * and \
+   * A (case sensitive) file path comparator that ignores the difference between
+   * / and \
    * 
    * @param path1
    * @param path2