error things

diff --git a/forester/java/src/org/forester/application/gsdi.java b/forester/java/src/org/forester/application/gsdi.java
index 0ec4958..295e542 100644 (file)
--- a/forester/java/src/org/forester/application/gsdi.java
+++ b/forester/java/src/org/forester/application/gsdi.java
@@ -267,6 +267,9 @@ public final class gsdi {
         catch ( final IOException e ) {
             fatalError( "error", e.toString(), log_writer );
         }
+        catch ( final OutOfMemoryError e ) {
+            ForesterUtil.outOfMemoryError( e );
+        }
         catch ( final Exception e ) {
             e.printStackTrace();
             fatalError( "unexpected error", e.toString(), log_writer );

diff --git a/forester/java/src/org/forester/application/rio.java b/forester/java/src/org/forester/application/rio.java
index e47e31a..01a5d6b 100644 (file)
--- a/forester/java/src/org/forester/application/rio.java
+++ b/forester/java/src/org/forester/application/rio.java
@@ -299,9 +299,15 @@ public class rio {
         catch ( final IOException e ) {
             ForesterUtil.fatalError( e.getLocalizedMessage() );
         }
+        catch ( final OutOfMemoryError e ) {
+            ForesterUtil.outOfMemoryError( e );
+        }
         catch ( final Exception e ) {
             ForesterUtil.unexpectedFatalError( e );
         }
+        catch ( final Error e ) {
+            ForesterUtil.unexpectedFatalError( e );
+        }
         time = System.currentTimeMillis() - time;
         System.out.println( "Time: " + time + "ms" );
         System.out.println( "OK" );

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index e60bc2c..1f7af11 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -947,29 +947,49 @@ public final class AptxUtil {
         }
     }
 
-    final static void unexpectedError( final Error err ) {
-        err.printStackTrace();
+    final static void unexpectedError( final Error e ) {
+        System.err.println();
+        e.printStackTrace(  System.err );
+        System.err.println();
         final StringBuffer sb = new StringBuffer();
-        for( final StackTraceElement s : err.getStackTrace() ) {
+        for( final StackTraceElement s : e.getStackTrace() ) {
             sb.append( s + "\n" );
         }
         JOptionPane
                 .showMessageDialog( null,
                                     "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
-                                            + Constants.AUTHOR_EMAIL + " \nError: " + err + "\n" + sb,
+                                            + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n" + sb,
                                     "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
                                     JOptionPane.ERROR_MESSAGE );
         System.exit( -1 );
     }
+    
+    final static void outOfMemoryError( final OutOfMemoryError e ) {
+        System.err.println();
+        System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
+        System.err.println();
+        e.printStackTrace();
+        System.err.println();
+        
+        JOptionPane
+                .showMessageDialog( null,
+                                    "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option"
+                                            + "\n\nError: " + e.getLocalizedMessage(),
+                                    "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
+                                    JOptionPane.ERROR_MESSAGE );
+        System.exit( -1 );
+    }
 
-    final static void unexpectedException( final Exception ex ) {
-        ex.printStackTrace();
+    final static void unexpectedException( final Exception e ) {
+        System.err.println();
+        e.printStackTrace(  System.err );
+        System.err.println();
         final StringBuffer sb = new StringBuffer();
-        for( final StackTraceElement s : ex.getStackTrace() ) {
+        for( final StackTraceElement s : e.getStackTrace() ) {
             sb.append( s + "\n" );
         }
         JOptionPane.showMessageDialog( null, "An unexpected exception has occured. \nPlease contact: "
-                + Constants.AUTHOR_EMAIL + " \nException: " + ex + "\n" + sb, "Unexpected Exception ["
+                + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage() + "\n" + sb, "Unexpected Exception ["
                 + Constants.PRG_NAME + Constants.VERSION + "]", JOptionPane.ERROR_MESSAGE );
     }
 

diff --git a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
index 91a8fd9..88c9588 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
+++ b/forester/java/src/org/forester/archaeopteryx/Archaeopteryx.java
@@ -128,11 +128,14 @@ public final class Archaeopteryx {
         try {
             MainFrameApplication.createInstance( phylogenies, conf, title, current_dir );
         }
-        catch ( final Exception ex ) {
-            AptxUtil.unexpectedException( ex );
+        catch ( final OutOfMemoryError e ) {
+            AptxUtil.outOfMemoryError( e );
         }
-        catch ( final Error err ) {
-            AptxUtil.unexpectedError( err );
+        catch ( final Exception e ) {
+            AptxUtil.unexpectedException( e );
+        }
+        catch ( final Error e ) {
+            AptxUtil.unexpectedError( e );
         }
     }
 }
\ No newline at end of file

diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
index d566c75..2ccf1eb 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrameApplication.java
@@ -268,9 +268,7 @@ public final class MainFrameApplication extends MainFrame {
         catch ( final IllegalAccessException e ) {
             AptxUtil.dieWithSystemError( "illegal access exception: " + e.toString() );
         }
-        catch ( final Exception e ) {
-            AptxUtil.dieWithSystemError( e.toString() );
-        }
+      
         if ( ( current_dir != null ) && current_dir.canRead() && current_dir.isDirectory() ) {
             setCurrentDir( current_dir );
         }

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index bf9dc7f..ba1af65 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -933,6 +933,14 @@ public final class ForesterUtil {
 
     final public static void unexpectedFatalError( final Exception e ) {
         System.err.println();
+        System.err.println( "unexpected exception: should not have occured! Please contact program author(s)." );
+        e.printStackTrace( System.err );
+        System.err.println();
+        System.exit( -1 );
+    }
+    
+    final public static void unexpectedFatalError( final Error e ) {
+        System.err.println();
         System.err.println( "unexpected error: should not have occured! Please contact program author(s)." );
         e.printStackTrace( System.err );
         System.err.println();
@@ -979,7 +987,7 @@ public final class ForesterUtil {
         final int width = 50;
         System.out.print( "\r[" );
         int i = 0;
-        for( ; i <= ( int ) ( progress_percentage * width ); i++ ) {
+        for( ; i <= ForesterUtil.roundToInt( progress_percentage * width ); i++ ) {
             System.out.print( "." );
         }
         for( ; i < width; i++ ) {
@@ -1054,4 +1062,13 @@ public final class ForesterUtil {
         final String regex = "[\\s;,]+";
         return str.split( regex );
     }
+
+    public final static void outOfMemoryError( final OutOfMemoryError e ) {
+        System.err.println();
+        System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
+        System.err.println();
+        e.printStackTrace( System.err );
+        System.err.println();
+        System.exit( -1 );
+    }
 }