JAL-4298 Added diagnostics and minor dimension changes to Java Console. Added a...

diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html
index b2e29e9..b1588e5 100644 (file)
--- a/help/help/html/features/clarguments-reference.html
+++ b/help/help/html/features/clarguments-reference.html
@@ -92,6 +92,11 @@
     </tr>
 
     <tr valign="top">
+    <td><code>&#8209;&#8209;javaconsole / &#8209;&#8209;nojavaconsole</code></td>
+    <td>Show (/ or don't show) the Java Console.  Using one of these overrides any saved Preference.</td>
+    </tr>
+
+    <tr valign="top">
     <td><code>&#8209;&#8209;questionnaire / &#8209;&#8209;noquestionnaire</code></td>
     <td>Show (/ or don't show) the questionnaire if one is available.</td>
     </tr>

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index a44d474..483b1fc 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -54,6 +54,8 @@ import javax.swing.LookAndFeel;
 import javax.swing.UIManager;
 
 import jalview.analytics.Plausible;
+import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.ArgParser;
 import jalview.datamodel.PDBEntry;
 import jalview.gui.Preferences;
 import jalview.gui.UserDefinedColours;
@@ -1732,4 +1734,10 @@ public class Cache
   {
     return key == null ? null : sessionProperties.get(key);
   }
+
+  public static boolean getArgCacheDefault(Arg a, String pref, boolean def)
+  {
+    ArgParser ap = Jalview.getInstance().getArgParser();
+    return ap.isSet(a) ? ap.getBoolean(a) : getDefault(pref, def);
+  }
 }

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 2a3a4a1..93156ac 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -44,6 +44,8 @@ public enum Arg
   QUESTIONNAIRE(Type.CONFIG,
           "Show (or don't show) the questionnaire if one is available.",
           true, Opt.BOOLEAN, Opt.BOOTSTRAP),
+  JAVACONSOLE(Type.CONFIG, "Show (or don't show) the Java Console.", false,
+          Opt.BOOLEAN, Opt.BOOTSTRAP),
   NOUSAGESTATS(Type.CONFIG, "Don't send initial launch usage stats.",
           Opt.UNARY, Opt.BOOTSTRAP),
   NOSTARTUPFILE(Type.CONFIG, "Don't show the default startup file.",

diff --git a/src/jalview/gui/Console.java b/src/jalview/gui/Console.java
index 4600719..bf3942a 100644 (file)
--- a/src/jalview/gui/Console.java
+++ b/src/jalview/gui/Console.java
@@ -506,8 +506,16 @@ public class Console extends WindowAdapter
   {
     parent = desktop;
     // window name - get x,y,width, height possibly scaled
-    Rectangle bounds = parent.getLastKnownDimensions("JAVA_CONSOLE_");
-    if (bounds == null)
+    Rectangle bounds = parent == null ? null
+            : parent.getLastKnownDimensions("JAVA_CONSOLE_");
+    if (bounds != null)
+    {
+      frame = initFrame(
+              ChannelProperties.getProperty("app_name") + " Java Console",
+              bounds.width, bounds.height, bounds.x, bounds.y);
+    }
+    else if (parent != null && parent.getWidth() > 0
+            && parent.getHeight() > 0)
     {
       frame = initFrame(
               ChannelProperties.getProperty("app_name") + " Java Console",
@@ -518,7 +526,7 @@ public class Console extends WindowAdapter
     {
       frame = initFrame(
               ChannelProperties.getProperty("app_name") + " Java Console",
-              bounds.width, bounds.height, bounds.x, bounds.y);
+              MIN_WIDTH, MIN_HEIGHT, 10, 10);
     }
     frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
     // parent.add(frame);
@@ -554,6 +562,7 @@ public class Console extends WindowAdapter
         pin.close();
       } catch (Exception e)
       {
+        jalview.bin.Console.debug("pin.close() error", e);
       }
       try
       {
@@ -561,12 +570,14 @@ public class Console extends WindowAdapter
         pin2.close();
       } catch (Exception e)
       {
+        jalview.bin.Console.debug("pin2.close() error", e);
       }
       try
       {
         textAppender.join(10);
       } catch (Exception e)
       {
+        jalview.bin.Console.debug("textAppender.join(10) error", e);
       }
     }
     /*
@@ -633,6 +644,7 @@ public class Console extends WindowAdapter
             }
           } catch (InterruptedException ie)
           {
+            jalview.bin.Console.debug("pin.available() error", ie);
           }
         }
 
@@ -665,6 +677,7 @@ public class Console extends WindowAdapter
             }
           } catch (InterruptedException ie)
           {
+            jalview.bin.Console.debug("pin.available() error", ie);
           }
         }
         while (pin2.available() != 0)
@@ -718,6 +731,7 @@ public class Console extends WindowAdapter
               }
             } catch (InterruptedException e)
             {
+              jalview.bin.Console.debug("displayPipe.length() error", e);
             }
           }
         }
@@ -728,7 +742,7 @@ public class Console extends WindowAdapter
             this.wait(100);
           } catch (InterruptedException e)
           {
-
+            jalview.bin.Console.debug("this.wait(100) error", e);
           }
         }
         if (quit)
@@ -755,6 +769,7 @@ public class Console extends WindowAdapter
         this.wait(1000);
       } catch (InterruptedException ie)
       {
+        jalview.bin.Console.debug("this.wait(1000) error", ie);
       }
       throw new NullPointerException(
               MessageManager.getString("exception.application_test_npe"));
@@ -798,7 +813,7 @@ public class Console extends WindowAdapter
                 + "\nTruncated...\n";
       } catch (Exception e)
       {
-        e.printStackTrace();
+        jalview.bin.Console.warn("textArea Exception", e);
       }
     }
     // trim the buffer
@@ -822,7 +837,7 @@ public class Console extends WindowAdapter
           }
         } catch (Exception e)
         {
-          e.printStackTrace();
+          jalview.bin.Console.warn("textArea Exception", e);
         }
         // lines = textArea.getLineCount();
       }

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 47b8893..e0e2307 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -113,6 +113,7 @@ import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.bin.Jalview.ExitCode;
+import jalview.bin.argparser.Arg;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
@@ -498,7 +499,8 @@ public class Desktop extends jalview.jbgui.GDesktop
 
     boolean selmemusage = Cache.getDefault("SHOW_MEMUSAGE", false);
 
-    boolean showjconsole = Cache.getDefault("SHOW_JAVA_CONSOLE", false);
+    boolean showjconsole = Cache.getArgCacheDefault(Arg.JAVACONSOLE,
+            "SHOW_JAVA_CONSOLE", false);
 
     // start dialogue queue for single dialogues
     startDialogQueue();
@@ -800,17 +802,17 @@ public class Desktop extends jalview.jbgui.GDesktop
         iw = (int) (iw * sw);
         iy = (int) (iy * sh);
         ih = (int) (ih * sh);
-        while (ix >= screenSize.width)
+        if (ix >= screenSize.width)
         {
           jalview.bin.Console.debug(
                   "Window geometry location recall error: shifting horizontal to within screenbounds.");
-          ix -= screenSize.width;
+          ix = ix % screenSize.width;
         }
-        while (iy >= screenSize.height)
+        if (iy >= screenSize.height)
         {
           jalview.bin.Console.debug(
                   "Window geometry location recall error: shifting vertical to within screenbounds.");
-          iy -= screenSize.height;
+          iy = iy % screenSize.height;
         }
         jalview.bin.Console.debug(
                 "Got last known dimensions for " + windowName + ": x:" + ix