timing stuff addded

diff --git a/forester/java/src/org/forester/development/Time.java b/forester/java/src/org/forester/development/Time.java
new file mode 100644 (file)
index 0000000..9d9e8dc
--- /dev/null
+++ b/forester/java/src/org/forester/development/Time.java
@@ -0,0 +1,82 @@
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.development;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Date;
+
+import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.BasicDescriptiveStatistics;
+import org.forester.util.DescriptiveStatistics;
+
+@SuppressWarnings( "unused")
+public final class Time {
+
+    public static void main( final String[] args ) {
+        try {
+            final DescriptiveStatistics parse_stats = new BasicDescriptiveStatistics();
+            final DescriptiveStatistics post_stats = new BasicDescriptiveStatistics();
+            final DescriptiveStatistics pre_stats = new BasicDescriptiveStatistics();
+            final File f = new File( args[ 0 ] );
+            Phylogeny phy = null;
+            for( int i = 0; i < 10; i++ ) {
+                final long start_time = new Date().getTime();
+                phy = ParserBasedPhylogenyFactory.getInstance().create( f, new NHXParser() )[ 0 ];
+                System.out.println( phy.getNumberOfExternalNodes() );
+                parse_stats.addValue( new Date().getTime() - start_time );
+                //
+                PhylogenyNode n = null;
+                final long start_time_post = new Date().getTime();
+                final PhylogenyNodeIterator post = phy.iteratorPostorder();
+                while ( post.hasNext() ) {
+                    n = post.next();
+                }
+                post_stats.addValue( new Date().getTime() - start_time_post );
+                //
+                final long start_time_pre = new Date().getTime();
+                final PhylogenyNodeIterator pre = phy.iteratorPreorder();
+                while ( pre.hasNext() ) {
+                    n = pre.next();
+                }
+                pre_stats.addValue( new Date().getTime() - start_time_pre );
+            }
+            System.out.println( "Parsing [ms]:" );
+            System.out.println( parse_stats.toString() );
+            System.out.println( "Post-order [ms]:" );
+            System.out.println( post_stats.toString() );
+            System.out.println( "Pre-order [ms]:" );
+            System.out.println( pre_stats.toString() );
+        }
+        catch ( final IOException e ) {
+            e.printStackTrace();
+        }
+    }
+}