X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2Fforester.wiki;h=816f377f85d282c74a586b5399101cc552b1690d;hb=917fdd32a745f77a8b70d7779e44b8b36e11185f;hp=016504c4479621277bf286b6325b5ce709e52cb0;hpb=30f755e3fbee61504916f36ed537bc907695752a;p=jalview.git

diff --git a/wiki/forester.wiki b/wiki/forester.wiki
index 016504c..816f377 100644
--- a/wiki/forester.wiki
+++ b/wiki/forester.wiki
@@ -1,47 +1,111 @@
+#summary forester Tutorial and Examples
+
+= forester Tutorial and Examples =
+<wiki:toc max_depth="3" />
+
 = Introduction =
 
 Under development!
 
-Documentation, tutorial, and examples for [http://www.phylosoft.org/forester/ forester].
+This contains documentation, tutorials, and examples for [https://sites.google.com/site/cmzmasek/home/software/forester/ forester].
+
+Documentation for [https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/ Archaeopteryx] can be found [https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/documentation here].
+
+*All examples require jar-file "forester.jar" to be in the class-path.*
+
+Download: http://code.google.com/p/forester/downloads/list
 
-Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
+Author: [https://sites.google.com/site/cmzmasek/ Christian Zmasek], Sanford-Burnham Medical Research Institute
 
  
-Copyright (C) 2011 Christian M Zmasek. All rights reserved.
+Copyright (C) 2013 Christian M Zmasek. All rights reserved.
 
 
-= Parsing of Phylogenetic Trees and Displaying them with Archaeopteryx =
 
-This needs file "forester.jar" to be in the class-path.
+= Reading and writing of phylogenetic trees =
+
+
 
 {{{
 
-package my.examples;
+package examples;
 
 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.io.parsers.util.ParserUtils;
+import org.forester.io.writers.PhylogenyWriter;
 import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.util.ForesterUtil;
 
-public class Example1 {
+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 = ParserUtils.createParserDependingOnFileType( treefile, true );
+        }
+        catch ( final IOException e ) {
+            e.printStackTrace();
+        }
+        Phylogeny[] phys = null;
+        try {
+            phys = PhylogenyMethods.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 =
+
+
+{{{
+
+package examples;
+
+import java.io.File;
+import java.io.IOException;
+
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.io.parsers.util.ParserUtils;
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+
+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 );
+            parser = ParserUtils.createParserDependingOnFileType( treefile, true );
         }
         catch ( final IOException e ) {
             e.printStackTrace();
         }
         Phylogeny[] phys = null;
         try {
-            phys = Util.readPhylogenies( parser, treefile );
+            phys = PhylogenyMethods.readPhylogenies( parser, treefile );
         }
         catch ( final IOException e ) {
             e.printStackTrace();
@@ -51,4 +115,289 @@ public class Example1 {
     }
 }
 
+}}}
+
+
+
+
+= Creating a new tree and displaying it with Archaeopteryx =
+
+
+{{{
+
+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 =
+
+{{{
+
+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) =
+
+
+{{{
+
+package 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 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 );
+    }
+}
+
+}}}
+
+= Writing a phylogenetic tree to a graphics file (e.g. png, jpg) =
+
+{{{
+
+package examples;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+
+import org.forester.archaeopteryx.AptxUtil;
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
+import org.forester.archaeopteryx.Configuration;
+import org.forester.archaeopteryx.Options;
+import org.forester.archaeopteryx.TreeColorSet;
+
+public class phylo2graphics {
+
+    public static void main( final String[] args ) {
+        try {
+            final Configuration config = new Configuration();
+            // Could also read a configuration file with:
+            // Configuration config = new Configuration("my_configuration_file.txt", false, false, false);
+            config.putDisplayColors( TreeColorSet.BACKGROUND, new Color( 255, 255, 255 ) );
+            config.putDisplayColors( TreeColorSet.BRANCH, new Color( 0, 0, 0 ) );
+            config.putDisplayColors( TreeColorSet.TAXONOMY, new Color( 0, 0, 0 ) );
+            config.setPhylogenyGraphicsType( Options.PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+            AptxUtil.writePhylogenyToGraphicsFile( new File( "my_tree.xml" ),
+                                                   new File( "my_tree_graphics.png" ),
+                                                   1000,
+                                                   1000,
+                                                   GraphicsExportType.PNG,
+                                                   config );
+            // If the tree 'phy' already exists, can also use this:
+            AptxUtil.writePhylogenyToGraphicsFile( phy,
+                                                   new File( "out.png" ),
+                                                   1000,
+                                                   1000,
+                                                   GraphicsExportType.PNG,
+                                                   config );
+        }
+        catch ( final IOException e ) {
+            e.printStackTrace();
+        }
+    }
+}
+
+}}}
+
+= Setting node/branch colors of a phylogenetic tree and writing it to a graphics file =
+
+{{{
+
+package examples;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.forester.archaeopteryx.AptxUtil;
+import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
+import org.forester.archaeopteryx.Configuration;
+import org.forester.archaeopteryx.Options;
+import org.forester.archaeopteryx.TreeColorSet;
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.util.ParserUtils;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.BranchColor;
+import org.forester.phylogeny.data.BranchWidth;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+
+public class phylo2coloredgraphics {
+
+    public static void main( final String[] args ) {
+        try {
+            // Reading-in of a tree from a file.
+            final File treefile = new File( "my_tree.nh" );
+            final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( treefile, true );
+            final Phylogeny phy = PhylogenyMethods.readPhylogenies( parser, treefile )[ 0 ];
+            // Creating a node name -> color map.
+            final Map<String, Color> colors = new HashMap<String, Color>();
+            colors.put( "Primates", new Color( 255, 255, 0 ) );
+            colors.put( "PANTR", new Color( 255, 0, 255 ) );
+            colors.put( "HUMAN", new Color( 255, 0, 0 ) );
+            colors.put( "RAT", new Color( 155, 0, 0 ) );
+            colors.put( "MOUSE", new Color( 55, 155, 0 ) );
+            colors.put( "CAVPO", new Color( 155, 155, 0 ) );
+            colors.put( "LOTGI", new Color( 155, 155, 255 ) );
+            // Setting colors.
+            for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
+                final PhylogenyNode n = it.next();
+                if ( colors.containsKey( n.getName() ) ) {
+                    n.getBranchData().setBranchColor( new BranchColor( colors.get( n.getName() ) ) );
+                    // To make colored subtrees thicker:
+                    n.getBranchData().setBranchWidth( new BranchWidth( 4 ) );
+                }
+            }
+            // Setting up a configuration object.
+            final Configuration config = new Configuration();
+            config.putDisplayColors( TreeColorSet.BACKGROUND, new Color( 255, 255, 255 ) );
+            config.putDisplayColors( TreeColorSet.BRANCH, new Color( 0, 0, 0 ) );
+            config.putDisplayColors( TreeColorSet.TAXONOMY, new Color( 0, 0, 0 ) );
+            config.setPhylogenyGraphicsType( Options.PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
+            config.setTaxonomyColorize( false );
+            config.setColorizeBranches( true );
+            config.setUseBranchesWidths( true );
+            config.setDisplayTaxonomyCode( false );
+            // Writing to a graphics file.
+            AptxUtil.writePhylogenyToGraphicsFile( phy,
+                                                   new File( "out.png" ),
+                                                   1300,
+                                                   1300,
+                                                   GraphicsExportType.PNG,
+                                                   config );
+        }
+        catch ( final IOException e ) {
+            e.printStackTrace();
+        }
+    }
+}
+
 }}}
\ No newline at end of file