X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=wiki%2Fforester.wiki;h=816f377f85d282c74a586b5399101cc552b1690d;hb=e32f4ddeda628ec89e93834f4ec00b0e0bd70e0b;hp=501ce08d9b98182e078e1f1125e10a4568a14f18;hpb=c8552e0b4914df5ba8f30a5b6b69f914e3850f5d;p=jalview.git

diff --git a/wiki/forester.wiki b/wiki/forester.wiki
index 501ce08..816f377 100644
--- a/wiki/forester.wiki
+++ b/wiki/forester.wiki
@@ -1,18 +1,30 @@
+#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].
 
-Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
+*All examples require jar-file "forester.jar" to be in the class-path.*
+
+Download: http://code.google.com/p/forester/downloads/list
+
+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.
+
 
 
 = Reading and writing of phylogenetic trees =
 
-This needs file "forester.jar" to be in the class-path.
+
 
 {{{
 
@@ -22,25 +34,27 @@ import java.io.File;
 import java.io.IOException;
 
 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 Example0 {
+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 );
+            parser = ParserUtils.createParserDependingOnFileType( treefile, true );
         }
         catch ( final IOException e ) {
             e.printStackTrace();
         }
         Phylogeny[] phys = null;
         try {
-            phys = ForesterUtil.readPhylogenies( parser, treefile );
+            phys = PhylogenyMethods.readPhylogenies( parser, treefile );
         }
         catch ( final IOException e ) {
             e.printStackTrace();
@@ -63,7 +77,6 @@ public class Example0 {
 
 = Reading of phylogenetic trees and displaying them with Archaeopteryx =
 
-This needs file "forester.jar" to be in the class-path.
 
 {{{
 
@@ -73,25 +86,26 @@ 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.util.ForesterUtil;
+import org.forester.phylogeny.PhylogenyMethods;
 
-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 = ForesterUtil.createParserDependingOnFileType( treefile, true );
+            parser = ParserUtils.createParserDependingOnFileType( treefile, true );
         }
         catch ( final IOException e ) {
             e.printStackTrace();
         }
         Phylogeny[] phys = null;
         try {
-            phys = ForesterUtil.readPhylogenies( parser, treefile );
+            phys = PhylogenyMethods.readPhylogenies( parser, treefile );
         }
         catch ( final IOException e ) {
             e.printStackTrace();
@@ -108,7 +122,6 @@ public class Example1 {
 
 = Creating a new tree and displaying it with Archaeopteryx =
 
-This needs file "forester.jar" to be in the class-path.
 
 {{{
 
@@ -118,7 +131,7 @@ import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 
-public class Example2 {
+public class Example {
 
     public static void main( final String[] args ) {
         // Creating a new rooted tree with two external nodes.
@@ -145,9 +158,7 @@ public class Example2 {
 
 
 
-= Using iterators to visit tree nodes in certain orders=
-
-This needs file "forester.jar" to be in the class-path.
+= Using iterators to visit tree nodes in certain orders =
 
 {{{
 
@@ -157,7 +168,7 @@ import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 
-public class Example3 {
+public class Example {
 
     public static void main( final String[] args ) {
         // Creating a new rooted tree with four external nodes.
@@ -198,4 +209,195 @@ public class Example3 {
     }
 }
 
+}}}
+
+
+
+
+
+
+
+
+
+= 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