X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2Fforester.wiki;h=816f377f85d282c74a586b5399101cc552b1690d;hb=03096115e1a019a975c3ced9816db8cae6808b4c;hp=4967db67082d462b992b9f51bf6d8d1fbd83c37d;hpb=237b8e1470c068cb648e55b9730e2dc8a6c20cf7;p=jalview.git
diff --git a/wiki/forester.wiki b/wiki/forester.wiki
index 4967db6..816f377 100644
--- a/wiki/forester.wiki
+++ b/wiki/forester.wiki
@@ -1,3 +1,5 @@
+#summary forester Tutorial and Examples
+
= forester Tutorial and Examples =
@@ -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.
@@ -289,27 +293,109 @@ import org.forester.archaeopteryx.TreeColorSet;
public class phylo2graphics {
- public static void main(final String[] args) {
- try {
- 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.png"),
- 800, // width
- 1000, // height
- GraphicsExportType.PNG,
- config);
+ 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();
}
- catch (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 colors = new HashMap();
+ 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();
}
}
}