+#summary forester Tutorial and Examples
+
+= forester Tutorial and Examples =
+<wiki:toc max_depth="3" />
+
= Introduction =
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].
-Author: [http://www.cmzmasek.net/ Christian M Zmasek], Sanford-Burnham Medical Research Institute
+*All examples require jar-file "forester.jar" to be in the class-path.*
+
+Download: http://code.google.com/p/forester/downloads/list
+
+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.
+
-= Parsing of phylogenetic trees and displaying them with Archaeopteryx =
+= Reading and writing of phylogenetic trees =
+
-This needs file "forester.jar" to be in the class-path.
{{{
import java.io.File;
import java.io.IOException;
-import org.forester.archaeopteryx.Archaeopteryx;
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 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 = ParserUtils.createParserDependingOnFileType( treefile, true );
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ Phylogeny[] phys = null;
+ try {
+ phys = PhylogenyMethods.readPhylogenies( parser, treefile );
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ // Writing trees to a file.
+ final File outfile = new File( "/path/to/out_tree.xml" );
+ try {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( phys, 0, outfile, ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ }
+ }
+}
+
+}}}
+
+
+
+= Reading of phylogenetic trees and displaying them with Archaeopteryx =
+
+
+{{{
+
+package examples;
+
+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.phylogeny.PhylogenyMethods;
+
+public class Example {
public static void main( final String[] args ) {
- // Reads in (a) tree(s) from a file.
+ // 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();
}}}
+
+
= Creating a new tree and displaying it with Archaeopteryx =
-This needs file "forester.jar" to be in the class-path.
{{{
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.
}
}
+}}}
+
+
+
+
+
+
+= Using iterators to visit tree nodes in certain orders =
+
+{{{
+
+package examples;
+
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+
+public class Example {
+
+ public static void main( final String[] args ) {
+ // Creating a new rooted tree with four external nodes.
+ final Phylogeny phy = new Phylogeny();
+ final PhylogenyNode root = new PhylogenyNode();
+ final PhylogenyNode d1 = new PhylogenyNode();
+ final PhylogenyNode d2 = new PhylogenyNode();
+ final PhylogenyNode d11 = new PhylogenyNode();
+ final PhylogenyNode d12 = new PhylogenyNode();
+ root.setName( "root" );
+ d1.setName( "1" );
+ d2.setName( "2" );
+ d11.setName( "1-1" );
+ d12.setName( "1-2" );
+ root.addAsChild( d1 );
+ root.addAsChild( d2 );
+ d2.addAsChild( d11 );
+ d2.addAsChild( d12 );
+ phy.setRoot( root );
+ phy.setRooted( true );
+ // Using a variety of iterators to visit the nodes of the newly created tree.
+ System.out.println( "post-order:" );
+ for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
+ System.out.println( it.next().getName() );
+ }
+ System.out.println( "pre-order:" );
+ for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
+ System.out.println( it.next().getName() );
+ }
+ System.out.println( "level-order:" );
+ for( final PhylogenyNodeIterator it = phy.iteratorLevelOrder(); it.hasNext(); ) {
+ System.out.println( it.next().getName() );
+ }
+ System.out.println( "external nodes only:" );
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ System.out.println( it.next().getName() );
+ }
+ }
+}
+
+}}}
+
+
+
+
+
+
+
+
+
+= Creating a basic gene tree (with branch lengths) =
+
+
+{{{
+
+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 Example {
+
+ public static void main( final String[] args ) {
+ // Creating a new rooted tree with two external nodes.
+ final Phylogeny phy = new Phylogeny();
+ final PhylogenyNode root = new PhylogenyNode();
+ final PhylogenyNode d1 = new PhylogenyNode();
+ final PhylogenyNode d2 = new PhylogenyNode();
+ // Setting of distances.
+ d1.setDistanceToParent( 1.2 );
+ d2.setDistanceToParent( 2.4 );
+ // Adding species information.
+ final Taxonomy t1 = new Taxonomy();
+ t1.setScientificName( "Nematostella vectensis" );
+ d1.getNodeData().addTaxonomy( t1 );
+ final Taxonomy t2 = new Taxonomy();
+ t2.setScientificName( "Monosiga brevicollis" );
+ d2.getNodeData().addTaxonomy( t2 );
+ // Adding gene names.
+ final Sequence s1 = new Sequence();
+ s1.setName( "Bcl-2" );
+ d1.getNodeData().addSequence( s1 );
+ 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 );
+ phy.setRoot( root );
+ phy.setRooted( true );
+ // Displaying the newly created tree with Archaeopteryx.
+ Archaeopteryx.createApplication( phy );
+ }
+}
+
+}}}
+
+= 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();
+ }
+ }
+}
+
+}}}
+
+= 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<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();
+ }
+ }
+}
+
}}}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff