forester_applications/src/org/forester/applications/phylo2coloredgraphics.java

   1
   2 package org.forester.applications;
   3
   4 import java.awt.Color;
   5 import java.io.File;
   6 import java.io.IOException;
   7 import java.util.HashMap;
   8 import java.util.Map;
   9
  10 import org.forester.archaeopteryx.AptxUtil;
  11 import org.forester.archaeopteryx.AptxUtil.GraphicsExportType;
  12 import org.forester.archaeopteryx.Configuration;
  13 import org.forester.archaeopteryx.Options;
  14 import org.forester.archaeopteryx.TreeColorSet;
  15 import org.forester.io.parsers.PhylogenyParser;
  16 import org.forester.io.parsers.util.ParserUtils;
  17 import org.forester.phylogeny.Phylogeny;
  18 import org.forester.phylogeny.PhylogenyMethods;
  19 import org.forester.phylogeny.PhylogenyNode;
  20 import org.forester.phylogeny.data.BranchColor;
  21 import org.forester.phylogeny.data.BranchWidth;
  22 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  23
  24 public class phylo2coloredgraphics {
  25
  26     public static void main( final String[] args ) {
  27         try {
  28             // Reading-in of a tree from a file.
  29             final File treefile = new File( "/home/czmasek/tol_117_TEST.xml" );
  30             final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( treefile, true );
  31             final Phylogeny phy = PhylogenyMethods.readPhylogenies( parser, treefile )[ 0 ];
  32             // Creating a node name -> color map.
  33             final Map<String, Color> colors = new HashMap<String, Color>();
  34             colors.put( "Primates", new Color( 255, 255, 0 ) );
  35             colors.put( "PANTR", new Color( 255, 0, 255 ) );
  36             colors.put( "HUMAN", new Color( 255, 0, 0 ) );
  37             colors.put( "RAT", new Color( 155, 0, 0 ) );
  38             colors.put( "MOUSE", new Color( 55, 155, 0 ) );
  39             colors.put( "CAVPO", new Color( 155, 155, 0 ) );
  40             colors.put( "LOTGI", new Color( 155, 155, 255 ) );
  41             // Setting colors.
  42             for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
  43                 final PhylogenyNode n = it.next();
  44                 if ( colors.containsKey( n.getName() ) ) {
  45                     n.getBranchData().setBranchColor( new BranchColor( colors.get( n.getName() ) ) );
  46                     // To make colored subtrees thicker:
  47                     n.getBranchData().setBranchWidth( new BranchWidth( 4 ) );
  48                 }
  49             }
  50             // Setting up a configuration object.
  51             final Configuration config = new Configuration();
  52             config.putDisplayColors( TreeColorSet.BACKGROUND, new Color( 255, 255, 255 ) );
  53             config.putDisplayColors( TreeColorSet.BRANCH, new Color( 0, 0, 0 ) );
  54             config.putDisplayColors( TreeColorSet.TAXONOMY, new Color( 0, 0, 0 ) );
  55             config.setPhylogenyGraphicsType( Options.PHYLOGENY_GRAPHICS_TYPE.RECTANGULAR );
  56             config.setTaxonomyColorize( false );
  57             config.setColorizeBranches( true );
  58             config.setUseBranchesWidths( true );
  59             config.setDisplayTaxonomyCode( false );
  60             // Writing to a graphics file.
  61             AptxUtil.writePhylogenyToGraphicsFile( phy,
  62                                                    new File( "/home/czmasek/000.png" ),
  63                                                    1300,
  64                                                    1300,
  65                                                    GraphicsExportType.PNG,
  66                                                    config );
  67         }
  68         catch ( final IOException e ) {
  69             e.printStackTrace();
  70         }
  71     }
  72 }