X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2Fforester.wiki;h=3e4c70fb2dadbb99d1d5ce3d05852c6d2dc41be6;hb=511c776bd39632dc9f1004cdcdd3ce183763c3dd;hp=89469cac3292cd66a1a0c9972dbd539f8f905b89;hpb=a084495d9aab2710734db7d6146d1320822473bb;p=jalview.git diff --git a/wiki/forester.wiki b/wiki/forester.wiki index 89469ca..3e4c70f 100644 --- a/wiki/forester.wiki +++ b/wiki/forester.wiki @@ -1,18 +1,26 @@ += forester Tutorial and Examples = + + = 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(); + } + } +} + +}}} \ No newline at end of file