Edited wiki page forester through web user interface.

[jalview.git] / wiki / forester.wiki

diff --git a/wiki/forester.wiki b/wiki/forester.wiki
index 89469ca..3e4c70f 100644 (file)
--- a/wiki/forester.wiki
+++ b/wiki/forester.wiki
@@ -1,18 +1,26 @@
+= forester Tutorial and Examples =
+<wiki:toc max_depth="3" />
+
 = Introduction =
 
 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" to be in the class-path.
+
 
 {{{
 
@@ -22,25 +30,27 @@ 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 +73,6 @@ 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 +82,26 @@ 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 +118,6 @@ 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 +127,7 @@ 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.
@@ -147,8 +156,6 @@ public class Example2 {
 
 = Using iterators to visit tree nodes in certain orders =
 
-This needs file "forester.jar" to be in the class-path.
-
 {{{
 
 package examples;
@@ -157,7 +164,7 @@ 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.
@@ -210,7 +217,6 @@ public class Example3 {
 
 = Creating a basic gene tree (with branch lengths) =
 
-This needs file "forester.jar" to be in the class-path.
 
 {{{
 
@@ -219,10 +225,11 @@ 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 Example5 {
+public class Example {
 
     public static void main( final String[] args ) {
         // Creating a new rooted tree with two external nodes.
@@ -247,6 +254,11 @@ public class Example5 {
         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 );
@@ -259,3 +271,51 @@ public class Example5 {
 
 }}}
 
+= 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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