X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2Fforester.wiki;h=33be88834d8cb50c4fd2c06d3858cad7e1f6b5dd;hb=cc9d475aad3b7f53b27ee8f048c16398bdba96b5;hp=64a922e43615221887381c0b23cdc45d2bd004fe;hpb=d15565b61ab5c99e6bb08d0b8afe9f5aecec5a8f;p=jalview.git

diff --git a/wiki/forester.wiki b/wiki/forester.wiki
index 64a922e..33be888 100644
--- a/wiki/forester.wiki
+++ b/wiki/forester.wiki
@@ -1,3 +1,6 @@
+= forester Tutorial and Examples =
+<wiki:toc max_depth="3" />
+
 = Introduction =
 
 Under development!
@@ -10,7 +13,58 @@ Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical R
 Copyright (C) 2011 Christian M Zmasek. All rights reserved.
 
 
-= Parsing of Phylogenetic Trees and Displaying them with Archaeopteryx =
+= Reading and writing of phylogenetic trees =
+
+This needs file "forester.jar" to be in the class-path.
+
+{{{
+
+package 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 Example {
+
+    public static void main( final String[] args ) {
+        // Reading-in of (a) tree(s) from a file.
+        final File treefile = new File( "/path/to/tree.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( "/path/to/out_tree.xml" );
+        try {
+            final PhylogenyWriter writer = new PhylogenyWriter();
+            writer.toPhyloXML( phys, 0, outfile, ForesterUtil.LINE_SEPARATOR );
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace();
+        }
+    }
+}
+
+}}}
+
+
+
+= Reading of phylogenetic trees and displaying them with Archaeopteryx =
 
 This needs file "forester.jar" to be in the class-path.
 
@@ -22,16 +76,15 @@ import java.io.File;
 import java.io.IOException;
 
 import org.forester.archaeopteryx.Archaeopteryx;
-import org.forester.archaeopteryx.Util;
 import org.forester.io.parsers.PhylogenyParser;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.util.ForesterUtil;
 
-public class Example1 {
+public class Example {
 
     public static void main( final String[] args ) {
-        // Reads in (a) tree(s) from a file.
-        final File treefile = new File( "/home/czmasek/tol_117_TEST.xml" );
+        // Reading-in of (a) tree(s) from a file.
+        final File treefile = new File( "/path/to/tree.xml" );
         PhylogenyParser parser = null;
         try {
             parser = ForesterUtil.createParserDependingOnFileType( treefile, true );
@@ -41,7 +94,7 @@ public class Example1 {
         }
         Phylogeny[] phys = null;
         try {
-            phys = Util.readPhylogenies( parser, treefile );
+            phys = ForesterUtil.readPhylogenies( parser, treefile );
         }
         catch ( final IOException e ) {
             e.printStackTrace();
@@ -51,4 +104,165 @@ public class Example1 {
     }
 }
 
+}}}
+
+
+
+
+= Creating a new tree and displaying it with Archaeopteryx =
+
+This needs file "forester.jar" to be in the class-path.
+
+{{{
+
+package examples;
+
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+
+public class Example {
+
+    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();
+        root.setName( "root" );
+        d1.setName( "descendant 1" );
+        d2.setName( "descendant 2" );
+        root.addAsChild( d1 );
+        root.addAsChild( d2 );
+        phy.setRoot( root );
+        phy.setRooted( true );
+        // Displaying the newly created tree with Archaeopteryx.
+        Archaeopteryx.createApplication( phy );
+    }
+}
+
+}}}
+
+
+
+
+
+
+= Using iterators to visit tree nodes in certain orders =
+
+This needs file "forester.jar" to be in the class-path.
+
+{{{
+
+package examples;
+
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+
+public class Example {
+
+    public static void main( final String[] args ) {
+        // Creating a new rooted tree with four external nodes.
+        final Phylogeny phy = new Phylogeny();
+        final PhylogenyNode root = new PhylogenyNode();
+        final PhylogenyNode d1 = new PhylogenyNode();
+        final PhylogenyNode d2 = new PhylogenyNode();
+        final PhylogenyNode d11 = new PhylogenyNode();
+        final PhylogenyNode d12 = new PhylogenyNode();
+        root.setName( "root" );
+        d1.setName( "1" );
+        d2.setName( "2" );
+        d11.setName( "1-1" );
+        d12.setName( "1-2" );
+        root.addAsChild( d1 );
+        root.addAsChild( d2 );
+        d2.addAsChild( d11 );
+        d2.addAsChild( d12 );
+        phy.setRoot( root );
+        phy.setRooted( true );
+        // Using a variety of iterators to visit the nodes of the newly created tree.
+        System.out.println( "post-order:" );
+        for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
+            System.out.println( it.next().getName() );
+        }
+        System.out.println( "pre-order:" );
+        for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
+            System.out.println( it.next().getName() );
+        }
+        System.out.println( "level-order:" );
+        for( final PhylogenyNodeIterator it = phy.iteratorLevelOrder(); it.hasNext(); ) {
+            System.out.println( it.next().getName() );
+        }
+        System.out.println( "external nodes only:" );
+        for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+            System.out.println( it.next().getName() );
+        }
+    }
+}
+
+}}}
+
+
+
+
+
+
+
+
+
+= Creating a basic gene tree (with branch lengths) =
+
+This needs file "forester.jar" to be in the class-path.
+
+{{{
+
+package examples;
+
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Sequence;
+import org.forester.phylogeny.data.Taxonomy;
+
+public class Example {
+
+    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 );
+    }
+}
+
 }}}
\ No newline at end of file