in progress...

[jalview.git] / wiki / forester.wiki

diff --git a/wiki/forester.wiki b/wiki/forester.wiki
index 9eaf25f..816f377 100644 (file)
--- a/wiki/forester.wiki
+++ b/wiki/forester.wiki
@@ -1,3 +1,5 @@
+#summary forester Tutorial and Examples
+
 = forester Tutorial and Examples =
 <wiki:toc max_depth="3" />
 
@@ -5,16 +7,18 @@
 
 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" (_actually, as of now, it requires the development version "forester_dev.jar"_) to be in the class-path.*
+*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.
 
 
 
@@ -326,6 +330,74 @@ public class phylo2graphics {
 
 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();
+        }
+    }
+}
 
 }}}
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