JAL-4298 Fixed initial log level to see .jalview_properties setting. Moved Java Conso...

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 1abb171..a44d474 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1663,27 +1663,36 @@ public class Cache
     }
     if (file == null || !file.exists())
     {
+      if (file != null)
+      {
+        jalview.bin.Console
+                .errPrintln("Could not load bootstrap preferences file '"
+                        + file.getPath() + "'");
+      }
       String channelPrefsFilename = ChannelProperties
               .getProperty("preferences.filename");
       String propertiesFilename = System.getProperty("user.home")
               + File.separatorChar + channelPrefsFilename;
+      jalview.bin.Console.errPrintln(
+              "Using default properties file '" + propertiesFilename + "'");
       file = new File(propertiesFilename);
     }
     if (file == null || !file.exists())
+
     {
       String releasePrefsFilename = fallbackPropertiesFile;
       String releasePropertiesFilename = System.getProperty("user.home")
               + File.separatorChar + releasePrefsFilename;
+      jalview.bin.Console.errPrintln("Falling back to properties file '"
+              + releasePropertiesFilename + "'");
       file = new File(releasePropertiesFilename);
     }
 
-    if (filename == null)
-      return null;
     if (!file.exists())
     {
       jalview.bin.Console
               .errPrintln("Could not load bootstrap preferences file '"
-                      + filename + "'");
+                      + file.getPath() + "'");
       return null;
     }
 

diff --git a/src/jalview/bin/Console.java b/src/jalview/bin/Console.java
index 1b230ec..1bb8162 100644 (file)
--- a/src/jalview/bin/Console.java
+++ b/src/jalview/bin/Console.java
@@ -21,10 +21,8 @@
 package jalview.bin;
 
 import java.io.PrintStream;
-import java.util.Locale;
 
 import jalview.log.JLogger;
-import jalview.log.JLoggerI;
 import jalview.log.JLoggerI.LogLevel;
 import jalview.log.JLoggerLog4j;
 import jalview.util.ChannelProperties;
@@ -241,7 +239,7 @@ public class Console
     {
       JLogger.LogLevel logLevel = JLogger.LogLevel.INFO;
 
-      if (JLogger.isLevel(providedLogLevel))
+      if (providedLogLevel != null && JLogger.isLevel(providedLogLevel))
       {
         logLevel = Console.getLogLevel(providedLogLevel);
       }
@@ -292,19 +290,23 @@ public class Console
 
   public static void setLogLevel(String logLevelString)
   {
-    for (LogLevel logLevel : JLoggerI.LogLevel.values())
+    LogLevel l = null;
+    try
+    {
+      l = LogLevel.valueOf(logLevelString);
+    } catch (IllegalArgumentException | NullPointerException e1)
+    {
+      Console.debug("Invalid log level '" + logLevelString + "'");
+      return;
+    }
+    if (l != null)
     {
-      if (logLevel.toString().toLowerCase(Locale.ROOT)
-              .equals(logLevelString.toLowerCase(Locale.ROOT)))
+      log.setLevel(l);
+      if (!Platform.isJS())
       {
-        log.setLevel(logLevel);
-        if (!Platform.isJS())
-        {
-          Log4j.init(logLevel);
-        }
-        JLoggerLog4j.getLogger("org.apache.axis", logLevel);
-        break;
+        Log4j.init(l);
       }
+      JLoggerLog4j.getLogger("org.apache.axis", l);
     }
   }
 

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index b7d15e5..18e73ed 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -642,14 +642,12 @@ public class Jalview
     try
     {
       Console.initLogger();
-    } catch (
-
-    NoClassDefFoundError error)
+    } catch (NoClassDefFoundError error)
     {
       error.printStackTrace();
       String message = "\nEssential logging libraries not found."
               + "\nUse: java -classpath \"$PATH_TO_LIB$/*:$PATH_TO_CLASSES$\" jalview.bin.Jalview";
-      Jalview.exit(message, ExitCode.OK);
+      Jalview.exit(message, ExitCode.NO_LOGGING);
     }
     desktop = null;
 
@@ -1633,8 +1631,7 @@ public class Jalview
     PromptUserConfig prompter = new PromptUserConfig(Desktop.desktop,
             "USAGESTATS",
             MessageManager.getString("prompt.analytics_title"),
-            MessageManager.getString("prompt.analytics"),
-            new Runnable()
+            MessageManager.getString("prompt.analytics"), new Runnable()
             {
               @Override
               public void run()
@@ -1862,7 +1859,7 @@ public class Jalview
     // only add new ones to the end of the list (to preserve ordinal values)
     OK, FILE_NOT_FOUND, FILE_NOT_READABLE, NO_FILES, INVALID_FORMAT,
     INVALID_ARGUMENT, INVALID_VALUE, MIXED_CLI_ARGUMENTS,
-    ERROR_RUNNING_COMMANDS;
+    ERROR_RUNNING_COMMANDS, NO_LOGGING;
   }
 
   /******************************

diff --git a/src/jalview/gui/Console.java b/src/jalview/gui/Console.java
index 6a6cb56..4600719 100644 (file)
--- a/src/jalview/gui/Console.java
+++ b/src/jalview/gui/Console.java
@@ -53,6 +53,7 @@ import javax.swing.JTextArea;
 import javax.swing.border.Border;
 import javax.swing.text.DefaultCaret;
 
+import jalview.bin.Cache;
 import jalview.log.JLoggerI.LogLevel;
 import jalview.log.JLoggerLog4j;
 import jalview.log.JalviewAppender;
@@ -106,7 +107,7 @@ public class Console extends WindowAdapter
 
   private JComboBox<LogLevel> logLevelCombo = new JComboBox<LogLevel>();
 
-  protected LogLevel startingLogLevel = LogLevel.INFO;
+  protected LogLevel startingLogLevel = null;
 
   public Console()
   {
@@ -147,6 +148,7 @@ public class Console extends WindowAdapter
     scrollPane.setBorder(noBorder);
     textArea.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mouseClicked(MouseEvent e)
       {
         if (e.getButton() == MouseEvent.BUTTON1)
@@ -172,6 +174,7 @@ public class Console extends WindowAdapter
             MessageManager.getString("label.copy_to_clipboard"));
     copyToClipboardButton.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         copyConsoleTextToClipboard();
@@ -183,12 +186,14 @@ public class Console extends WindowAdapter
 
       private Color fg = textArea.getForeground();
 
+      @Override
       public void mousePressed(MouseEvent e)
       {
         textArea.setBackground(textArea.getSelectionColor());
         textArea.setForeground(textArea.getSelectedTextColor());
       }
 
+      @Override
       public void mouseReleased(MouseEvent e)
       {
         textArea.setBackground(bg);
@@ -212,11 +217,35 @@ public class Console extends WindowAdapter
     // logLevelCombo.addItem(LogLevel.ERROR);
     // logLevelCombo.addItem(LogLevel.OFF);
     // set startingLogLevel
-    startingLogLevel = jalview.bin.Console.log == null ? LogLevel.INFO
-            : jalview.bin.Console.log.getLevel();
+    if (jalview.bin.Console.log == null)
+    {
+      try
+      {
+        startingLogLevel = LogLevel
+                .valueOf(Cache.getDefault(Cache.JALVIEWLOGLEVEL, null));
+      } catch (IllegalArgumentException e1)
+      {
+        jalview.bin.Console.debug(
+                "Invalid value for preference " + Cache.JALVIEWLOGLEVEL);
+      } catch (NullPointerException e2)
+      {
+        // no value in preferences
+      } finally
+      {
+        if (startingLogLevel == null)
+        {
+          startingLogLevel = LogLevel.INFO;
+        }
+      }
+    }
+    else
+    {
+      startingLogLevel = jalview.bin.Console.log.getLevel();
+    }
     setChosenLogLevelCombo();
     logLevelCombo.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         if (jalview.bin.Console.log != null)
@@ -313,7 +342,7 @@ public class Console extends WindowAdapter
         boolean added = false;
         for (int i = 0; i < logLevelCombo.getItemCount(); i++)
         {
-          LogLevel l = (LogLevel) logLevelCombo.getItemAt(i);
+          LogLevel l = logLevelCombo.getItemAt(i);
           if (l.compareTo(setLogLevel) >= 0)
           {
             logLevelCombo.insertItemAt(setLogLevel, i);
@@ -475,27 +504,15 @@ public class Console extends WindowAdapter
    */
   public Console(Desktop desktop)
   {
-    this(desktop, true);
-  }
-
-  /**
-   * attach a console to the desktop - the desktop will open it if requested.
-   * 
-   * @param desktop
-   * @param showjconsole
-   *          - if true, then redirect stdout immediately
-   */
-  public Console(Desktop desktop, boolean showjconsole)
-  {
     parent = desktop;
     // window name - get x,y,width, height possibly scaled
-    Rectangle bounds = desktop.getLastKnownDimensions("JAVA_CONSOLE_");
+    Rectangle bounds = parent.getLastKnownDimensions("JAVA_CONSOLE_");
     if (bounds == null)
     {
       frame = initFrame(
               ChannelProperties.getProperty("app_name") + " Java Console",
-              desktop.getWidth() / 2, desktop.getHeight() / 4,
-              desktop.getX(), desktop.getY());
+              parent.getWidth() / 2, parent.getHeight() / 4, parent.getX(),
+              parent.getY());
     }
     else
     {
@@ -504,7 +521,7 @@ public class Console extends WindowAdapter
               bounds.width, bounds.height, bounds.x, bounds.y);
     }
     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
-    // desktop.add(frame);
+    // parent.add(frame);
     initConsole(false);
     LogLevel level = (LogLevel) logLevelCombo.getSelectedItem();
     if (!Platform.isJS())

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index e785431..47b8893 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -499,6 +499,26 @@ public class Desktop extends jalview.jbgui.GDesktop
     boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false);
 
     boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE", false);
+
+    // start dialogue queue for single dialogues
+    startDialogQueue();
+
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      Desktop.instance.acquireDialogQueue();
+
+      jconsole = new Console(this);
+      jconsole.setHeader(Cache.getVersionDetailsForConsole());
+      showConsole(showjconsole);
+
+      Desktop.instance.releaseDialogQueue();
+    }
+
     desktop = new MyDesktopPane(selmemusage);
 
     showMemusage.setSelected(selmemusage);
@@ -545,9 +565,6 @@ public class Desktop extends jalview.jbgui.GDesktop
       setBounds(xPos, yPos, 900, 650);
     }
 
-    // start dialogue queue for single dialogues
-    startDialogQueue();
-
     if (!Platform.isJS())
     /**
      * Java only
@@ -555,10 +572,6 @@ public class Desktop extends jalview.jbgui.GDesktop
      * @j2sIgnore
      */
     {
-      jconsole = new Console(this, showjconsole);
-      jconsole.setHeader(Cache.getVersionDetailsForConsole());
-      showConsole(showjconsole);
-
       showNews.setVisible(false);
 
       experimentalFeatures.setSelected(showExperimental());