forester/java/src/org/forester/archaeopteryx/AptxUtil.java

   1 // $Id:
   2 // FORESTER -- software libraries and applications
   3 // for evolutionary biology research and applications.
   4 //
   5 // Copyright (C) 2008-2009 Christian M. Zmasek
   6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   7 // All rights reserved
   8 //
   9 // This library is free software; you can redistribute it and/or
  10 // modify it under the terms of the GNU Lesser General Public
  11 // License as published by the Free Software Foundation; either
  12 // version 2.1 of the License, or (at your option) any later version.
  13 //
  14 // This library is distributed in the hope that it will be useful,
  15 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  16 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  17 // Lesser General Public License for more details.
  18 //
  19 // You should have received a copy of the GNU Lesser General Public
  20 // License along with this library; if not, write to the Free Software
  21 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  22 //
  23 // Contact: phylosoft @ gmail . com
  24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  25
  26 package org.forester.archaeopteryx;
  27
  28 import java.awt.Color;
  29 import java.awt.Component;
  30 import java.awt.Graphics2D;
  31 import java.awt.GraphicsEnvironment;
  32 import java.awt.Rectangle;
  33 import java.awt.RenderingHints;
  34 import java.awt.image.BufferedImage;
  35 import java.io.ByteArrayOutputStream;
  36 import java.io.File;
  37 import java.io.FileNotFoundException;
  38 import java.io.IOException;
  39 import java.io.InputStream;
  40 import java.lang.reflect.InvocationTargetException;
  41 import java.lang.reflect.Method;
  42 import java.net.URI;
  43 import java.net.URL;
  44 import java.net.URLConnection;
  45 import java.text.ParseException;
  46 import java.util.Arrays;
  47 import java.util.HashSet;
  48 import java.util.Iterator;
  49 import java.util.List;
  50 import java.util.Locale;
  51 import java.util.Set;
  52 import java.util.SortedSet;
  53 import java.util.TreeSet;
  54
  55 import javax.imageio.IIOImage;
  56 import javax.imageio.ImageIO;
  57 import javax.imageio.ImageWriteParam;
  58 import javax.imageio.ImageWriter;
  59 import javax.imageio.stream.ImageOutputStream;
  60 import javax.swing.JApplet;
  61 import javax.swing.JOptionPane;
  62 import javax.swing.text.MaskFormatter;
  63
  64 import org.forester.io.parsers.PhylogenyParser;
  65 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
  66 import org.forester.io.parsers.nhx.NHXParser;
  67 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  68 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
  69 import org.forester.io.parsers.tol.TolParser;
  70 import org.forester.io.parsers.util.ParserUtils;
  71 import org.forester.phylogeny.Phylogeny;
  72 import org.forester.phylogeny.PhylogenyMethods;
  73 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  74 import org.forester.phylogeny.PhylogenyNode;
  75 import org.forester.phylogeny.data.Confidence;
  76 import org.forester.phylogeny.data.Taxonomy;
  77 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  78 import org.forester.phylogeny.factories.PhylogenyFactory;
  79 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  80 import org.forester.util.AsciiHistogram;
  81 import org.forester.util.DescriptiveStatistics;
  82 import org.forester.util.ForesterUtil;
  83
  84 public final class AptxUtil {
  85
  86     private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
  87                                                                          .getAvailableFontFamilyNames();
  88     static {
  89         Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
  90     }
  91
  92     public static MaskFormatter createMaskFormatter( final String s ) {
  93         MaskFormatter formatter = null;
  94         try {
  95             formatter = new MaskFormatter( s );
  96         }
  97         catch ( final ParseException e ) {
  98             throw new IllegalArgumentException( e );
  99         }
 100         return formatter;
 101     }
 102
 103     final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
 104         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 105         while ( it.hasNext() ) {
 106             if ( it.next().getNodeData().isHasEvent() ) {
 107                 return true;
 108             }
 109         }
 110         return false;
 111     }
 112
 113     /**
 114      * Returns true if at least one branch has a length larger than zero.
 115      *
 116      *
 117      * @param phy
 118      */
 119     final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
 120         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 121         while ( it.hasNext() ) {
 122             if ( it.next().getDistanceToParent() > 0.0 ) {
 123                 return true;
 124             }
 125         }
 126         return false;
 127     }
 128
 129     final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) {
 130         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 131         while ( it.hasNext() ) {
 132             if ( it.next().getBranchData().isHasConfidences() ) {
 133                 return true;
 134             }
 135         }
 136         return false;
 137     }
 138
 139     final static public boolean isHasAtLeastOneBranchWithSupportSD( final Phylogeny phy ) {
 140         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 141         while ( it.hasNext() ) {
 142             final PhylogenyNode n = it.next();
 143             if ( n.getBranchData().isHasConfidences() ) {
 144                 final List<Confidence> c = n.getBranchData().getConfidences();
 145                 for( final Confidence confidence : c ) {
 146                     if ( confidence.getStandardDeviation() > 0 ) {
 147                         return true;
 148                     }
 149                 }
 150             }
 151         }
 152         return false;
 153     }
 154
 155     final static public boolean isHasAtLeastOneNodeWithScientificName( final Phylogeny phy ) {
 156         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 157         while ( it.hasNext() ) {
 158             final PhylogenyNode n = it.next();
 159             if ( n.getNodeData().isHasTaxonomy()
 160                     && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
 161                 return true;
 162             }
 163         }
 164         return false;
 165     }
 166
 167     final static public boolean isHasAtLeastOneNodeWithSequenceAnnotation( final Phylogeny phy ) {
 168         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 169         while ( it.hasNext() ) {
 170             final PhylogenyNode n = it.next();
 171             if ( n.getNodeData().isHasSequence()
 172                     && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAnnotations() ) ) {
 173                 return true;
 174             }
 175         }
 176         return false;
 177     }
 178
 179     final public static void launchWebBrowser( final URI uri,
 180                                                final boolean is_applet,
 181                                                final JApplet applet,
 182                                                final String frame_name ) throws IOException {
 183         if ( is_applet ) {
 184             applet.getAppletContext().showDocument( uri.toURL(), frame_name );
 185         }
 186         else {
 187             // This requires Java 1.6:
 188             // =======================
 189             // boolean no_desktop = false;
 190             // try {
 191             // if ( Desktop.isDesktopSupported() ) {
 192             // System.out.println( "desktop supported" );
 193             // final Desktop dt = Desktop.getDesktop();
 194             // dt.browse( uri );
 195             // }
 196             // else {
 197             // no_desktop = true;
 198             // }
 199             // }
 200             // catch ( final Exception ex ) {
 201             // ex.printStackTrace();
 202             // no_desktop = true;
 203             // }
 204             // catch ( final Error er ) {
 205             // er.printStackTrace();
 206             // no_desktop = true;
 207             // }
 208             // if ( no_desktop ) {
 209             // System.out.println( "desktop not supported" );
 210             try {
 211                 openUrlInWebBrowser( uri.toString() );
 212             }
 213             catch ( final Exception e ) {
 214                 throw new IOException( e );
 215             }
 216             // }
 217         }
 218     }
 219
 220     public static Set<Taxonomy> obtainAllDistinctTaxonomies( final PhylogenyNode node ) {
 221         final List<PhylogenyNode> descs = node.getAllExternalDescendants();
 222         final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
 223         for( final PhylogenyNode n : descs ) {
 224             if ( n.getNodeData().isHasTaxonomy() && !n.getNodeData().getTaxonomy().isEmpty() ) {
 225                 tax_set.add( n.getNodeData().getTaxonomy() );
 226             }
 227         }
 228         return tax_set;
 229     }
 230
 231     public final static void printWarningMessage( final String name, final String message ) {
 232         System.out.println( "[" + name + "] > " + message );
 233     }
 234
 235     final public static void showErrorMessage( final Component parent, final String error_msg ) {
 236         printAppletMessage( Constants.PRG_NAME, error_msg );
 237         JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION
 238                 + "] Error", JOptionPane.ERROR_MESSAGE );
 239     }
 240
 241     public static void writePhylogenyToGraphicsFile( final File intree,
 242                                                      final File outfile,
 243                                                      final int width,
 244                                                      final int height,
 245                                                      final GraphicsExportType type,
 246                                                      final Configuration config ) throws IOException {
 247         final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
 248         Phylogeny[] phys = null;
 249         phys = PhylogenyMethods.readPhylogenies( parser, intree );
 250         writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config );
 251     }
 252
 253     public static void writePhylogenyToGraphicsFile( final Phylogeny phy,
 254                                                      final File outfile,
 255                                                      final int width,
 256                                                      final int height,
 257                                                      final GraphicsExportType type,
 258                                                      final Configuration config ) throws IOException {
 259         final Phylogeny[] phys = new Phylogeny[ 1 ];
 260         phys[ 0 ] = phy;
 261         final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
 262         AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
 263                 .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
 264         mf.end();
 265     }
 266
 267     public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile,
 268                                                                          final int width,
 269                                                                          final int height,
 270                                                                          final TreePanel tree_panel,
 271                                                                          final ControlPanel ac,
 272                                                                          final GraphicsExportType type,
 273                                                                          final Options options ) throws IOException {
 274         tree_panel.calcParametersForPainting( width, height, true );
 275         tree_panel.resetPreferredSize();
 276         tree_panel.repaint();
 277         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
 278                                                                    RenderingHints.VALUE_RENDER_QUALITY );
 279         rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
 280         if ( options.isAntialiasPrint() ) {
 281             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
 282             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
 283         }
 284         else {
 285             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
 286             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
 287         }
 288         final Phylogeny phylogeny = tree_panel.getPhylogeny();
 289         if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
 290             return;
 291         }
 292         if ( outfile.isDirectory() ) {
 293             throw new IOException( "\"" + outfile + "\" is a directory" );
 294         }
 295         final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
 296         final Graphics2D g2d = buffered_img.createGraphics();
 297         g2d.setRenderingHints( rendering_hints );
 298         tree_panel.paintPhylogeny( g2d, false, true, width, height, 0, 0 );
 299         if ( type == GraphicsExportType.TIFF ) {
 300             writeToTiff( outfile, buffered_img );
 301         }
 302         else {
 303             ImageIO.write( buffered_img, type.toString(), outfile );
 304         }
 305         g2d.dispose();
 306     }
 307
 308     final static void addPhylogeniesToTabs( final Phylogeny[] phys,
 309                                             final String default_name,
 310                                             final String full_path,
 311                                             final Configuration configuration,
 312                                             final MainPanel main_panel ) {
 313         if ( phys.length > Constants.MAX_TREES_TO_LOAD ) {
 314             JOptionPane.showMessageDialog( main_panel, "Attempt to load " + phys.length
 315                     + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME
 316                     + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE );
 317         }
 318         int i = 1;
 319         for( final Phylogeny phy : phys ) {
 320             if ( !phy.isEmpty() ) {
 321                 if ( i <= Constants.MAX_TREES_TO_LOAD ) {
 322                     String my_name = "";
 323                     String my_name_for_file = "";
 324                     if ( phys.length > 1 ) {
 325                         if ( !ForesterUtil.isEmpty( default_name ) ) {
 326                             my_name = new String( default_name );
 327                         }
 328                         if ( !ForesterUtil.isEmpty( full_path ) ) {
 329                             my_name_for_file = new String( full_path );
 330                         }
 331                         else if ( !ForesterUtil.isEmpty( default_name ) ) {
 332                             my_name_for_file = new String( default_name );
 333                         }
 334                         String suffix = "";
 335                         if ( my_name_for_file.indexOf( '.' ) > 0 ) {
 336                             suffix = my_name_for_file.substring( my_name_for_file.lastIndexOf( '.' ),
 337                                                                  my_name_for_file.length() );
 338                             my_name_for_file = my_name_for_file.substring( 0, my_name_for_file.lastIndexOf( '.' ) );
 339                         }
 340                         if ( !ForesterUtil.isEmpty( my_name_for_file ) ) {
 341                             my_name_for_file += "_";
 342                         }
 343                         if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 344                             my_name_for_file += phy.getName().replaceAll( " ", "_" );
 345                         }
 346                         else if ( phy.getIdentifier() != null ) {
 347                             final StringBuffer sb = new StringBuffer();
 348                             if ( !ForesterUtil.isEmpty( phy.getIdentifier().getProvider() ) ) {
 349                                 sb.append( phy.getIdentifier().getProvider() );
 350                                 sb.append( "_" );
 351                             }
 352                             sb.append( phy.getIdentifier().getValue() );
 353                             my_name_for_file += sb;
 354                         }
 355                         else {
 356                             my_name_for_file += i;
 357                         }
 358                         if ( !ForesterUtil.isEmpty( my_name ) && ForesterUtil.isEmpty( phy.getName() )
 359                                 && ( phy.getIdentifier() == null ) ) {
 360                             my_name = my_name + " [" + i + "]";
 361                         }
 362                         if ( !ForesterUtil.isEmpty( suffix ) ) {
 363                             my_name_for_file += suffix;
 364                         }
 365                     }
 366                     else {
 367                         if ( !ForesterUtil.isEmpty( default_name ) ) {
 368                             my_name = new String( default_name );
 369                         }
 370                         my_name_for_file = "";
 371                         if ( !ForesterUtil.isEmpty( full_path ) ) {
 372                             my_name_for_file = new String( full_path );
 373                         }
 374                         else if ( !ForesterUtil.isEmpty( default_name ) ) {
 375                             my_name_for_file = new String( default_name );
 376                         }
 377                         if ( ForesterUtil.isEmpty( my_name_for_file ) ) {
 378                             if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 379                                 my_name_for_file = new String( phy.getName() ).replaceAll( " ", "_" );
 380                             }
 381                             else if ( phy.getIdentifier() != null ) {
 382                                 final StringBuffer sb = new StringBuffer();
 383                                 if ( !ForesterUtil.isEmpty( phy.getIdentifier().getProvider() ) ) {
 384                                     sb.append( phy.getIdentifier().getProvider() );
 385                                     sb.append( "_" );
 386                                 }
 387                                 sb.append( phy.getIdentifier().getValue() );
 388                                 my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
 389                             }
 390                         }
 391                     }
 392                     main_panel.addPhylogenyInNewTab( phy, configuration, my_name, full_path );
 393                     main_panel.getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
 394                     lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
 395                     ++i;
 396                 }
 397             }
 398         }
 399     }
 400
 401     final static void addPhylogenyToPanel( final Phylogeny[] phys,
 402                                            final Configuration configuration,
 403                                            final MainPanel main_panel ) {
 404         final Phylogeny phy = phys[ 0 ];
 405         main_panel.addPhylogenyInPanel( phy, configuration );
 406         lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
 407     }
 408
 409     // Returns true if the specified format name can be written
 410     final static boolean canWriteFormat( final String format_name ) {
 411         final Iterator<ImageWriter> iter = ImageIO.getImageWritersByFormatName( format_name );
 412         return iter.hasNext();
 413     }
 414
 415     final static String createBasicInformation( final Phylogeny phy, final File treefile ) {
 416         final StringBuilder desc = new StringBuilder();
 417         if ( ( phy != null ) && !phy.isEmpty() ) {
 418             String f = null;
 419             if ( treefile != null ) {
 420                 try {
 421                     f = treefile.getCanonicalPath();
 422                 }
 423                 catch ( final IOException e ) {
 424                     //Not important, ignore.
 425                 }
 426                 if ( !ForesterUtil.isEmpty( f ) ) {
 427                     desc.append( "Path: " );
 428                     desc.append( f );
 429                     desc.append( "\n" );
 430                 }
 431             }
 432             if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 433                 desc.append( "Name: " );
 434                 desc.append( phy.getName() );
 435                 desc.append( "\n" );
 436             }
 437             if ( phy.getIdentifier() != null ) {
 438                 desc.append( "Id: " );
 439                 desc.append( phy.getIdentifier().toString() );
 440                 desc.append( "\n" );
 441             }
 442             if ( !ForesterUtil.isEmpty( phy.getDescription() ) ) {
 443                 desc.append( "Description: " );
 444                 desc.append( phy.getDescription() );
 445                 desc.append( "\n" );
 446             }
 447             if ( !ForesterUtil.isEmpty( phy.getDistanceUnit() ) ) {
 448                 desc.append( "Distance Unit: " );
 449                 desc.append( phy.getDistanceUnit() );
 450                 desc.append( "\n" );
 451             }
 452             if ( !ForesterUtil.isEmpty( phy.getType() ) ) {
 453                 desc.append( "Type: " );
 454                 desc.append( phy.getType() );
 455                 desc.append( "\n" );
 456             }
 457             desc.append( "Rooted: " );
 458             desc.append( phy.isRooted() );
 459             desc.append( "\n" );
 460             desc.append( "Rerootable: " );
 461             desc.append( phy.isRerootable() );
 462             desc.append( "\n" );
 463             desc.append( "Nodes: " );
 464             desc.append( phy.getNodeCount() );
 465             desc.append( "\n" );
 466             desc.append( "External nodes: " );
 467             desc.append( phy.getNumberOfExternalNodes() );
 468             desc.append( "\n" );
 469             desc.append( "Internal nodes: " );
 470             desc.append( phy.getNodeCount() - phy.getNumberOfExternalNodes() );
 471             desc.append( "\n" );
 472             desc.append( "Internal nodes with polytomies: " );
 473             desc.append( PhylogenyMethods.countNumberOfPolytomies( phy ) );
 474             desc.append( "\n" );
 475             desc.append( "Branches: " );
 476             desc.append( phy.getNumberOfBranches() );
 477             desc.append( "\n" );
 478             desc.append( "Depth: " );
 479             desc.append( PhylogenyMethods.calculateMaxDepth( phy ) );
 480             desc.append( "\n" );
 481             desc.append( "Maximum distance to root: " );
 482             desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) );
 483             desc.append( "\n" );
 484             final Set<Taxonomy> taxs = obtainAllDistinctTaxonomies( phy.getRoot() );
 485             if ( taxs != null ) {
 486                 desc.append( "Distinct external taxonomies: " );
 487                 desc.append( taxs.size() );
 488             }
 489             for( final Taxonomy t : taxs ) {
 490                 System.out.println( t.toString() );
 491             }
 492             desc.append( "\n" );
 493             final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy );
 494             if ( bs.getN() > 3 ) {
 495                 desc.append( "\n" );
 496                 desc.append( "Branch-length statistics: " );
 497                 desc.append( "\n" );
 498                 desc.append( "    Number of branches with non-negative branch-lengths: " + bs.getN() );
 499                 desc.append( "\n" );
 500                 desc.append( "    Median: " + ForesterUtil.round( bs.median(), 6 ) );
 501                 desc.append( "\n" );
 502                 desc.append( "    Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (stdev: "
 503                         + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) + ")" );
 504                 desc.append( "\n" );
 505                 desc.append( "    Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
 506                 desc.append( "\n" );
 507                 desc.append( "    Maximum: " + ForesterUtil.round( bs.getMax(), 6 ) );
 508                 desc.append( "\n" );
 509                 if ( Math.abs( bs.getMax() - bs.getMin() ) > 0.0001 ) {
 510                     desc.append( "\n" );
 511                     final AsciiHistogram histo = new AsciiHistogram( bs );
 512                     desc.append( histo.toStringBuffer( 12, '#', 40, 7, "    " ) );
 513                 }
 514             }
 515             final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
 516             if ( ds.getN() > 2 ) {
 517                 desc.append( "\n" );
 518                 desc.append( "Descendants per node statistics: " );
 519                 desc.append( "\n" );
 520                 desc.append( "    Median: " + ForesterUtil.round( ds.median(), 6 ) );
 521                 desc.append( "\n" );
 522                 desc.append( "    Mean: " + ForesterUtil.round( ds.arithmeticMean(), 6 ) + " (stdev: "
 523                         + ForesterUtil.round( ds.sampleStandardDeviation(), 6 ) + ")" );
 524                 desc.append( "\n" );
 525                 desc.append( "    Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
 526                 desc.append( "\n" );
 527                 desc.append( "    Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) );
 528                 desc.append( "\n" );
 529             }
 530             List<DescriptiveStatistics> css = null;
 531             try {
 532                 css = PhylogenyMethods.calculatConfidenceStatistics( phy );
 533             }
 534             catch ( final IllegalArgumentException e ) {
 535                 ForesterUtil.printWarningMessage( Constants.PRG_NAME, e.getMessage() );
 536             }
 537             if ( ( css != null ) && ( css.size() > 0 ) ) {
 538                 desc.append( "\n" );
 539                 for( int i = 0; i < css.size(); ++i ) {
 540                     final DescriptiveStatistics cs = css.get( i );
 541                     if ( ( cs != null ) && ( cs.getN() > 1 ) ) {
 542                         if ( css.size() > 1 ) {
 543                             desc.append( "Support statistics " + ( i + 1 ) + ": " );
 544                         }
 545                         else {
 546                             desc.append( "Support statistics: " );
 547                         }
 548                         if ( !ForesterUtil.isEmpty( cs.getDescription() ) ) {
 549                             desc.append( "\n" );
 550                             desc.append( "    Type: " + cs.getDescription() );
 551                         }
 552                         desc.append( "\n" );
 553                         desc.append( "    Branches with support: " + cs.getN() );
 554                         desc.append( "\n" );
 555                         desc.append( "    Median: " + ForesterUtil.round( cs.median(), 6 ) );
 556                         desc.append( "\n" );
 557                         desc.append( "    Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
 558                         if ( cs.getN() > 2 ) {
 559                             desc.append( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" );
 560                         }
 561                         desc.append( "\n" );
 562                         desc.append( "    Minimum: " + ForesterUtil.round( cs.getMin(), 6 ) );
 563                         desc.append( "\n" );
 564                         desc.append( "    Maximum: " + ForesterUtil.round( cs.getMax(), 6 ) );
 565                         desc.append( "\n" );
 566                     }
 567                 }
 568             }
 569         }
 570         return desc.toString();
 571     }
 572
 573     /**
 574      * Exits with -1.
 575      *
 576      *
 577      * @param message
 578      *            to message to be printed
 579      */
 580     final static void dieWithSystemError( final String message ) {
 581         System.out.println();
 582         System.out.println( Constants.PRG_NAME + " encountered the following system error: " + message );
 583         System.out.println( "Please contact the authors." );
 584         System.out.println( Constants.PRG_NAME + " needs to close." );
 585         System.out.println();
 586         System.exit( -1 );
 587     }
 588
 589     final static String[] getAllPossibleRanks() {
 590         final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
 591         int i = 0;
 592         for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) {
 593             if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) {
 594                 str_array[ i++ ] = e;
 595             }
 596         }
 597         return str_array;
 598     }
 599
 600     final static String[] getAllRanks( final Phylogeny tree ) {
 601         final SortedSet<String> ranks = new TreeSet<String>();
 602         for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
 603             final PhylogenyNode n = it.next();
 604             if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) {
 605                 ranks.add( n.getNodeData().getTaxonomy().getRank() );
 606             }
 607         }
 608         return ForesterUtil.stringSetToArray( ranks );
 609     }
 610
 611     final static String[] getAvailableFontFamiliesSorted() {
 612         return AVAILABLE_FONT_FAMILIES_SORTED;
 613     }
 614
 615     final static boolean isUsOrCanada() {
 616         try {
 617             if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
 618                 return true;
 619             }
 620         }
 621         catch ( final Exception e ) {
 622             return false;
 623         }
 624         return false;
 625     }
 626
 627     final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
 628                                                                       final ControlPanel atv_control,
 629                                                                       final Configuration configuration ) {
 630         if ( ( t != null ) && !t.isEmpty() ) {
 631             if ( !AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
 632                 atv_control.setDrawPhylogram( false );
 633                 atv_control.setDrawPhylogramEnabled( false );
 634             }
 635             if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) {
 636                 if ( atv_control.getDisplayAsPhylogramCb() != null ) {
 637                     if ( AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
 638                         atv_control.setDrawPhylogram( true );
 639                         atv_control.setDrawPhylogramEnabled( true );
 640                     }
 641                     else {
 642                         atv_control.setDrawPhylogram( false );
 643                     }
 644                 }
 645             }
 646             if ( configuration.doGuessCheckOption( Configuration.write_confidence_values ) ) {
 647                 if ( atv_control.getWriteConfidenceCb() != null ) {
 648                     if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( t ) ) {
 649                         atv_control.setCheckbox( Configuration.write_confidence_values, true );
 650                     }
 651                     else {
 652                         atv_control.setCheckbox( Configuration.write_confidence_values, false );
 653                     }
 654                 }
 655             }
 656             if ( configuration.doGuessCheckOption( Configuration.write_events ) ) {
 657                 if ( atv_control.getShowEventsCb() != null ) {
 658                     if ( AptxUtil.isHasAtLeastNodeWithEvent( t ) ) {
 659                         atv_control.setCheckbox( Configuration.write_events, true );
 660                     }
 661                     else {
 662                         atv_control.setCheckbox( Configuration.write_events, false );
 663                     }
 664                 }
 665             }
 666         }
 667     }
 668
 669     final static void openWebsite( final String url, final boolean is_applet, final JApplet applet ) throws IOException {
 670         try {
 671             AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, Constants.PRG_NAME );
 672         }
 673         catch ( final Exception e ) {
 674             throw new IOException( e );
 675         }
 676     }
 677
 678     final static void outOfMemoryError( final OutOfMemoryError e ) {
 679         System.err.println();
 680         System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
 681         System.err.println();
 682         e.printStackTrace();
 683         System.err.println();
 684         JOptionPane.showMessageDialog( null,
 685                                        "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option"
 686                                                + "\n\nError: " + e.getLocalizedMessage(),
 687                                        "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
 688                                        JOptionPane.ERROR_MESSAGE );
 689         System.exit( -1 );
 690     }
 691
 692     final static void printAppletMessage( final String applet_name, final String message ) {
 693         System.out.println( "[" + applet_name + "] > " + message );
 694     }
 695
 696     final public static Phylogeny[] readPhylogeniesFromUrl( final URL url,
 697                                                             final boolean phyloxml_validate_against_xsd,
 698                                                             final boolean replace_underscores,
 699                                                             final boolean internal_numbers_are_confidences,
 700                                                             final TAXONOMY_EXTRACTION taxonomy_extraction,
 701                                                             final boolean midpoint_reroot )
 702             throws FileNotFoundException, IOException {
 703         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 704         final PhylogenyParser parser;
 705         boolean nhx_or_nexus = false;
 706         if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
 707             parser = new TolParser();
 708         }
 709         else {
 710             parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
 711             if ( parser instanceof NHXParser ) {
 712                 nhx_or_nexus = true;
 713                 final NHXParser nhx = ( NHXParser ) parser;
 714                 nhx.setReplaceUnderscores( replace_underscores );
 715                 nhx.setIgnoreQuotes( false );
 716                 nhx.setTaxonomyExtraction( taxonomy_extraction );
 717             }
 718             else if ( parser instanceof NexusPhylogeniesParser ) {
 719                 nhx_or_nexus = true;
 720                 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
 721                 nex.setReplaceUnderscores( replace_underscores );
 722                 nex.setIgnoreQuotes( false );
 723             }
 724         }
 725         AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
 726         final URLConnection url_connection = url.openConnection();
 727         url_connection.setDefaultUseCaches( false );
 728         final InputStream i = url_connection.getInputStream();
 729         final Phylogeny[] phys = factory.create( i, parser );
 730         i.close();
 731         if ( phys != null ) {
 732             if ( nhx_or_nexus && internal_numbers_are_confidences ) {
 733                 for( final Phylogeny phy : phys ) {
 734                     PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
 735                 }
 736             }
 737             if ( midpoint_reroot ) {
 738                 for( final Phylogeny phy : phys ) {
 739                     PhylogenyMethods.midpointRoot( phy );
 740                     PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
 741                 }
 742             }
 743         }
 744         return phys;
 745     }
 746
 747     final static void removeBranchColors( final Phylogeny phy ) {
 748         for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
 749             it.next().getBranchData().setBranchColor( null );
 750         }
 751     }
 752
 753     final static void removeVisualStyles( final Phylogeny phy ) {
 754         for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
 755             it.next().getNodeData().setNodeVisualData( null );
 756         }
 757     }
 758
 759     final static void unexpectedError( final Error e ) {
 760         System.err.println();
 761         e.printStackTrace( System.err );
 762         System.err.println();
 763         final StringBuffer sb = new StringBuffer();
 764         for( final StackTraceElement s : e.getStackTrace() ) {
 765             sb.append( s + "\n" );
 766         }
 767         JOptionPane
 768                 .showMessageDialog( null,
 769                                     "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
 770                                             + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
 771                                             + sb,
 772                                     "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
 773                                     JOptionPane.ERROR_MESSAGE );
 774         System.exit( -1 );
 775     }
 776
 777     final static void unexpectedException( final Exception e ) {
 778         System.err.println();
 779         e.printStackTrace( System.err );
 780         System.err.println();
 781         final StringBuffer sb = new StringBuffer();
 782         for( final StackTraceElement s : e.getStackTrace() ) {
 783             sb.append( s + "\n" );
 784         }
 785         JOptionPane.showMessageDialog( null,
 786                                        "An unexpected exception has occured. \nPlease contact: "
 787                                                + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
 788                                                + "\n" + sb,
 789                                        "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
 790                                        JOptionPane.ERROR_MESSAGE );
 791     }
 792
 793     final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
 794                                                                        int width,
 795                                                                        int height,
 796                                                                        final TreePanel tree_panel,
 797                                                                        final ControlPanel ac,
 798                                                                        final GraphicsExportType type,
 799                                                                        final Options options ) throws IOException {
 800         if ( !options.isGraphicsExportUsingActualSize() ) {
 801             if ( options.isGraphicsExportVisibleOnly() ) {
 802                 throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
 803             }
 804             tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
 805             tree_panel.resetPreferredSize();
 806             tree_panel.repaint();
 807         }
 808         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
 809                                                                    RenderingHints.VALUE_RENDER_QUALITY );
 810         rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
 811         if ( options.isAntialiasPrint() ) {
 812             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
 813             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
 814         }
 815         else {
 816             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
 817             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
 818         }
 819         final Phylogeny phylogeny = tree_panel.getPhylogeny();
 820         if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
 821             return "";
 822         }
 823         Rectangle visible = null;
 824         if ( !options.isGraphicsExportUsingActualSize() ) {
 825             width = options.getPrintSizeX();
 826             height = options.getPrintSizeY();
 827         }
 828         else if ( options.isGraphicsExportVisibleOnly() ) {
 829             visible = tree_panel.getVisibleRect();
 830             width = visible.width;
 831             height = visible.height;
 832         }
 833         final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
 834         Graphics2D g2d = buffered_img.createGraphics();
 835         g2d.setRenderingHints( rendering_hints );
 836         int x = 0;
 837         int y = 0;
 838         if ( options.isGraphicsExportVisibleOnly() ) {
 839             g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
 840             g2d.setClip( null );
 841             x = visible.x;
 842             y = visible.y;
 843         }
 844         tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
 845         ImageIO.write( buffered_img, type.toString(), baos );
 846         g2d.dispose();
 847         System.gc();
 848         if ( !options.isGraphicsExportUsingActualSize() ) {
 849             tree_panel.getMainPanel().getControlPanel().showWhole();
 850         }
 851         String msg = baos.toString();
 852         if ( ( width > 0 ) && ( height > 0 ) ) {
 853             msg += " [size: " + width + ", " + height + "]";
 854         }
 855         return msg;
 856     }
 857
 858     final static String writePhylogenyToGraphicsFile( final String file_name,
 859                                                       int width,
 860                                                       int height,
 861                                                       final TreePanel tree_panel,
 862                                                       final ControlPanel ac,
 863                                                       final GraphicsExportType type,
 864                                                       final Options options ) throws IOException {
 865         if ( !options.isGraphicsExportUsingActualSize() ) {
 866             if ( options.isGraphicsExportVisibleOnly() ) {
 867                 throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
 868             }
 869             tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
 870             tree_panel.resetPreferredSize();
 871             tree_panel.repaint();
 872         }
 873         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
 874                                                                    RenderingHints.VALUE_RENDER_QUALITY );
 875         rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
 876         if ( options.isAntialiasPrint() ) {
 877             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
 878             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
 879         }
 880         else {
 881             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
 882             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
 883         }
 884         final Phylogeny phylogeny = tree_panel.getPhylogeny();
 885         if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
 886             return "";
 887         }
 888         final File file = new File( file_name );
 889         if ( file.isDirectory() ) {
 890             throw new IOException( "\"" + file_name + "\" is a directory" );
 891         }
 892         Rectangle visible = null;
 893         if ( !options.isGraphicsExportUsingActualSize() ) {
 894             width = options.getPrintSizeX();
 895             height = options.getPrintSizeY();
 896         }
 897         else if ( options.isGraphicsExportVisibleOnly() ) {
 898             visible = tree_panel.getVisibleRect();
 899             width = visible.width;
 900             height = visible.height;
 901         }
 902         final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
 903         Graphics2D g2d = buffered_img.createGraphics();
 904         g2d.setRenderingHints( rendering_hints );
 905         int x = 0;
 906         int y = 0;
 907         if ( options.isGraphicsExportVisibleOnly() ) {
 908             g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
 909             g2d.setClip( null );
 910             x = visible.x;
 911             y = visible.y;
 912         }
 913         tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
 914         if ( type == GraphicsExportType.TIFF ) {
 915             writeToTiff( file, buffered_img );
 916         }
 917         else {
 918             ImageIO.write( buffered_img, type.toString(), file );
 919         }
 920         g2d.dispose();
 921         System.gc();
 922         if ( !options.isGraphicsExportUsingActualSize() ) {
 923             tree_panel.getMainPanel().getControlPanel().showWhole();
 924         }
 925         String msg = file.toString();
 926         if ( ( width > 0 ) && ( height > 0 ) ) {
 927             msg += " [size: " + width + ", " + height + "]";
 928         }
 929         return msg;
 930     }
 931
 932     final static void writeToTiff( final File file, final BufferedImage image ) throws IOException {
 933         // See: http://log.robmeek.com/2005/08/write-tiff-in-java.html
 934         ImageWriter writer = null;
 935         ImageOutputStream ios = null;
 936         // Find an appropriate writer:
 937         final Iterator<ImageWriter> it = ImageIO.getImageWritersByFormatName( "TIF" );
 938         if ( it.hasNext() ) {
 939             writer = it.next();
 940         }
 941         else {
 942             throw new IOException( "failed to get TIFF image writer" );
 943         }
 944         // Setup writer:
 945         ios = ImageIO.createImageOutputStream( file );
 946         writer.setOutput( ios );
 947         final ImageWriteParam image_write_param = new ImageWriteParam( Locale.getDefault() );
 948         image_write_param.setCompressionMode( ImageWriteParam.MODE_EXPLICIT );
 949         // see writeParam.getCompressionTypes() for available compression type
 950         // strings.
 951         image_write_param.setCompressionType( "PackBits" );
 952         final String t[] = image_write_param.getCompressionTypes();
 953         for( final String string : t ) {
 954             System.out.println( string );
 955         }
 956         // Convert to an IIOImage:
 957         final IIOImage iio_image = new IIOImage( image, null, null );
 958         writer.write( null, iio_image, image_write_param );
 959     }
 960
 961     final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException,
 962             SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
 963             InvocationTargetException, InterruptedException {
 964         final String os = System.getProperty( "os.name" );
 965         final Runtime runtime = Runtime.getRuntime();
 966         if ( os.toLowerCase().startsWith( "win" ) ) {
 967             Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
 968         }
 969         else if ( ForesterUtil.isMac() ) {
 970             final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
 971             final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
 972             open_url.invoke( null, new Object[] { url } );
 973         }
 974         else {
 975             final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" };
 976             String browser = null;
 977             for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) {
 978                 if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) {
 979                     browser = browsers[ i ];
 980                 }
 981             }
 982             if ( browser == null ) {
 983                 throw new IOException( "could not find a web browser to open [" + url + "] in" );
 984             }
 985             else {
 986                 runtime.exec( new String[] { browser, url } );
 987             }
 988         }
 989     }
 990
 991     public static enum GraphicsExportType {
 992         BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
 993
 994         private final String _suffix;
 995
 996         private GraphicsExportType( final String suffix ) {
 997             _suffix = suffix;
 998         }
 999
1000         @Override
1001         public String toString() {
1002             return _suffix;
1003         }
1004     }
1005
1006     final public static Color calculateColorFromString( final String str, final boolean is_taxonomy ) {
1007         final String my_str = str.toUpperCase();
1008         char first = my_str.charAt( 0 );
1009         char second = ' ';
1010         char third = ' ';
1011         if ( my_str.length() > 1 ) {
1012             if ( is_taxonomy ) {
1013                 second = my_str.charAt( 1 );
1014             }
1015             else {
1016                 second = my_str.charAt( my_str.length() - 1 );
1017             }
1018             if ( is_taxonomy ) {
1019                 if ( my_str.length() > 2 ) {
1020                     if ( my_str.indexOf( " " ) > 0 ) {
1021                         third = my_str.charAt( my_str.indexOf( " " ) + 1 );
1022                     }
1023                     else {
1024                         third = my_str.charAt( 2 );
1025                     }
1026                 }
1027             }
1028             else if ( my_str.length() > 2 ) {
1029                 third = my_str.charAt( ( my_str.length() - 1 ) / 2 );
1030             }
1031         }
1032         first = normalizeCharForRGB( first );
1033         second = normalizeCharForRGB( second );
1034         third = normalizeCharForRGB( third );
1035         if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
1036             first = 0;
1037         }
1038         else if ( ( first < 60 ) && ( second < 60 ) && ( third < 60 ) ) {
1039             second = 255;
1040         }
1041         return new Color( first, second, third );
1042     }
1043
1044     final private static char normalizeCharForRGB( char c ) {
1045         c -= 65;
1046         c *= 10.2;
1047         c = c > 255 ? 255 : c;
1048         c = c < 0 ? 0 : c;
1049         return c;
1050     }
1051 }