*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
= Reading of phylogenetic trees and displaying them with Archaeopteryx =
-This needs file "forester.jar" to be in the class-path.
{{{
= Creating a new tree and displaying it with Archaeopteryx =
-This needs file "forester.jar" to be in the class-path.
{{{
= Using iterators to visit tree nodes in certain orders =
-This needs file "forester.jar" to be in the class-path.
-
{{{
package examples;
= Creating a basic gene tree (with branch lengths) =
-This needs file "forester.jar" to be in the class-path.
{{{
}
}
+}}}
+
+= 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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