From ea3b8b0efd5a826a590cdaa5537a104c73fa466e Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Thu, 3 Nov 2011 17:50:03 +0000 Subject: [PATCH] Edited wiki page forester through web user interface. --- wiki/forester.wiki | 68 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 68 insertions(+) diff --git a/wiki/forester.wiki b/wiki/forester.wiki index 9eaf25f..806da33 100644 --- a/wiki/forester.wiki +++ b/wiki/forester.wiki @@ -326,6 +326,74 @@ public class phylo2graphics { 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 -- 1.7.10.2