X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=wiki%2Fforester.wiki;h=816f377f85d282c74a586b5399101cc552b1690d;hb=80ca71143800cff69681908892a19763fafc1d4a;hp=501ce08d9b98182e078e1f1125e10a4568a14f18;hpb=c8552e0b4914df5ba8f30a5b6b69f914e3850f5d;p=jalview.git
diff --git a/wiki/forester.wiki b/wiki/forester.wiki
index 501ce08..816f377 100644
--- a/wiki/forester.wiki
+++ b/wiki/forester.wiki
@@ -1,18 +1,30 @@
+#summary forester Tutorial and Examples
+
+= forester Tutorial and Examples =
+
+
= 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.
+
= Reading and writing of phylogenetic trees =
-This needs file "forester.jar" to be in the class-path.
+
{{{
@@ -22,25 +34,27 @@ 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 +77,6 @@ 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 +86,26 @@ 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 +122,6 @@ 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 +131,7 @@ 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.
@@ -145,9 +158,7 @@ public class Example2 {
-= Using iterators to visit tree nodes in certain orders=
-
-This needs file "forester.jar" to be in the class-path.
+= Using iterators to visit tree nodes in certain orders =
{{{
@@ -157,7 +168,7 @@ 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.
@@ -198,4 +209,195 @@ public class Example3 {
}
}
+}}}
+
+
+
+
+
+
+
+
+
+= 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 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();
+ }
+ }
+}
+
}}}
\ No newline at end of file