inprogress

[jalview.git] / forester / java / src / org / forester / util / ForesterUtil.java

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index bf9dc7f..03c2e69 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.util;
 
@@ -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++ ) {
@@ -988,6 +996,10 @@ public final class ForesterUtil {
         System.out.print( "]" );
     }
 
+    public final static void updateProgress( final int i, final DecimalFormat f ) {
+        System.out.print( "\r[" + f.format( i ) + "]" );
+    }
+
     public final static String wordWrap( final String str, final int width ) {
         final StringBuilder sb = new StringBuilder( str );
         int start = 0;
@@ -1054,4 +1066,13 @@ 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 );
+    }
 }