X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2Fforester.wiki;h=3e4c70fb2dadbb99d1d5ce3d05852c6d2dc41be6;hb=511c776bd39632dc9f1004cdcdd3ce183763c3dd;hp=d307578eb4e4ee0c0c18728f2514a21a468ed7d2;hpb=b25793cdd6d95d81cf1444b240cfa06cc0ec5df4;p=jalview.git

diff --git a/wiki/forester.wiki b/wiki/forester.wiki
index d307578..3e4c70f 100644
--- a/wiki/forester.wiki
+++ b/wiki/forester.wiki
@@ -7,15 +7,20 @@ Under development!
 
 Documentation, tutorial, and examples for [http://www.phylosoft.org/forester/ forester].
 
+*All examples require jar-file "forester.jar" (_actually, as of now, it requires the development version "forester_dev.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
 
  
 Copyright (C) 2011 Christian M Zmasek. All rights reserved.
 
 
+
 = Reading and writing of phylogenetic trees =
 
-*This needs file "forester.jar" (actually, as of now, it requires the development version "forester_dev.jar") to be in the class-path.*
+
 
 {{{
 
@@ -68,7 +73,6 @@ public class Example {
 
 = Reading of phylogenetic trees and displaying them with Archaeopteryx =
 
-This needs file "forester.jar" to be in the class-path.
 
 {{{
 
@@ -114,7 +118,6 @@ public class Example {
 
 = Creating a new tree and displaying it with Archaeopteryx =
 
-This needs file "forester.jar" to be in the class-path.
 
 {{{
 
@@ -153,8 +156,6 @@ public class Example {
 
 = Using iterators to visit tree nodes in certain orders =
 
-This needs file "forester.jar" to be in the class-path.
-
 {{{
 
 package examples;
@@ -216,7 +217,6 @@ public class Example {
 
 = Creating a basic gene tree (with branch lengths) =
 
-This needs file "forester.jar" to be in the class-path.
 
 {{{
 
@@ -269,4 +269,53 @@ public class Example {
     }
 }
 
+}}}
+
+= 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();
+        }
+    }
+}
+
 }}}
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