in progress

diff --git a/forester/java/src/org/forester/test/examples/Example1.java b/forester/java/src/org/forester/test/examples/Example1.java
index 045ee6b..13b24d1 100644 (file)
--- a/forester/java/src/org/forester/test/examples/Example1.java
+++ b/forester/java/src/org/forester/test/examples/Example1.java
@@ -37,7 +37,7 @@ import org.forester.util.ForesterUtil;
 public class Example1 {
 
     public static void main( final String[] args ) {
-        // Reads in (a) tree(s) from a file.
+        // Reading-in of (a) tree(s) from a file.
         final File treefile = new File( "/home/czmasek/tol_117_TEST.xml" );
         PhylogenyParser parser = null;
         try {

diff --git a/forester/java/src/org/forester/test/examples/Example4.java b/forester/java/src/org/forester/test/examples/Example4.java
new file mode 100644 (file)
index 0000000..b363ab3
--- /dev/null
+++ b/forester/java/src/org/forester/test/examples/Example4.java
@@ -0,0 +1,66 @@
+// $Id:
+//
+// forester -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2011 Christian M. Zmasek
+// Copyright (C) 2008-2011 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.test.examples;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.util.ForesterUtil;
+
+public class Example4 {
+
+    public static void main( final String[] args ) {
+        // Reading-in of (a) tree(s) from a file.
+        final File treefile = new File( "/home/czmasek/tol_117_TEST.xml" );
+        PhylogenyParser parser = null;
+        try {
+            parser = ForesterUtil.createParserDependingOnFileType( treefile, true );
+        }
+        catch ( final IOException e ) {
+            e.printStackTrace();
+        }
+        Phylogeny[] phys = null;
+        try {
+            phys = ForesterUtil.readPhylogenies( parser, treefile );
+        }
+        catch ( final IOException e ) {
+            e.printStackTrace();
+        }
+        // Writing trees to a file.
+        final File outfile = new File( "/home/czmasek/tol_117_TEST_out.xml" );
+        try {
+            final PhylogenyWriter writer = new PhylogenyWriter();
+            writer.toPhyloXML( phys, 0, outfile, ForesterUtil.LINE_SEPARATOR );
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace();
+        }
+    }
+}

diff --git a/forester/java/src/org/forester/test/examples/Example5.java b/forester/java/src/org/forester/test/examples/Example5.java
new file mode 100644 (file)
index 0000000..facc4b9
--- /dev/null
+++ b/forester/java/src/org/forester/test/examples/Example5.java
@@ -0,0 +1,74 @@
+// $Id:
+//
+// forester -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2011 Christian M. Zmasek
+// Copyright (C) 2008-2011 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.test.examples;
+
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Event;
+import org.forester.phylogeny.data.Sequence;
+import org.forester.phylogeny.data.Taxonomy;
+
+public class Example5 {
+
+    public static void main( final String[] args ) {
+        // Creating a new rooted tree with two external nodes.
+        final Phylogeny phy = new Phylogeny();
+        final PhylogenyNode root = new PhylogenyNode();
+        final PhylogenyNode d1 = new PhylogenyNode();
+        final PhylogenyNode d2 = new PhylogenyNode();
+        // Setting of distances.
+        d1.setDistanceToParent( 1.2 );
+        d2.setDistanceToParent( 2.4 );
+        // Adding species information.
+        final Taxonomy t1 = new Taxonomy();
+        t1.setScientificName( "Nematostella vectensis" );
+        d1.getNodeData().addTaxonomy( t1 );
+        final Taxonomy t2 = new Taxonomy();
+        t2.setScientificName( "Monosiga brevicollis" );
+        d2.getNodeData().addTaxonomy( t2 );
+        // Adding gene names.
+        final Sequence s1 = new Sequence();
+        s1.setName( "Bcl-2" );
+        d1.getNodeData().addSequence( s1 );
+        final Sequence s2 = new Sequence();
+        s2.setName( "Bcl-2" );
+        d2.getNodeData().addSequence( s2 );
+        // Root is a speciation.
+        final Event ev = new Event();
+        ev.setSpeciations( 1 );
+        ev.setDuplications( 0 );
+        root.getNodeData().setEvent( ev );
+        // Putting the tree together.
+        root.addAsChild( d1 );
+        root.addAsChild( d2 );
+        phy.setRoot( root );
+        phy.setRooted( true );
+        // Displaying the newly created tree with Archaeopteryx.
+        Archaeopteryx.createApplication( phy );
+    }
+}