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.Component;
  29 import java.awt.Graphics2D;
  30 import java.awt.GraphicsEnvironment;
  31 import java.awt.Rectangle;
  32 import java.awt.RenderingHints;
  33 import java.awt.image.BufferedImage;
  34 import java.io.ByteArrayOutputStream;
  35 import java.io.File;
  36 import java.io.FileNotFoundException;
  37 import java.io.IOException;
  38 import java.lang.reflect.InvocationTargetException;
  39 import java.lang.reflect.Method;
  40 import java.net.URI;
  41 import java.net.URL;
  42 import java.text.ParseException;
  43 import java.util.Arrays;
  44 import java.util.HashSet;
  45 import java.util.Iterator;
  46 import java.util.List;
  47 import java.util.Locale;
  48 import java.util.Set;
  49 import java.util.SortedSet;
  50 import java.util.TreeSet;
  51 import java.util.regex.Matcher;
  52 import java.util.regex.Pattern;
  53
  54 import javax.imageio.IIOImage;
  55 import javax.imageio.ImageIO;
  56 import javax.imageio.ImageWriteParam;
  57 import javax.imageio.ImageWriter;
  58 import javax.imageio.stream.ImageOutputStream;
  59 import javax.swing.JApplet;
  60 import javax.swing.JOptionPane;
  61 import javax.swing.text.MaskFormatter;
  62
  63 import org.forester.io.parsers.PhylogenyParser;
  64 import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
  65 import org.forester.io.parsers.nhx.NHXParser;
  66 import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
  67 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
  68 import org.forester.io.parsers.tol.TolParser;
  69 import org.forester.io.parsers.util.ParserUtils;
  70 import org.forester.phylogeny.Phylogeny;
  71 import org.forester.phylogeny.PhylogenyMethods;
  72 import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
  73 import org.forester.phylogeny.PhylogenyNode;
  74 import org.forester.phylogeny.data.Accession;
  75 import org.forester.phylogeny.data.Taxonomy;
  76 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  77 import org.forester.phylogeny.factories.PhylogenyFactory;
  78 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  79 import org.forester.util.AsciiHistogram;
  80 import org.forester.util.DescriptiveStatistics;
  81 import org.forester.util.ForesterUtil;
  82
  83 public final class AptxUtil {
  84
  85     private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
  86                                                                          .getAvailableFontFamilyNames();
  87     private final static Pattern  seq_identifier_pattern_1       = Pattern
  88                                                                          .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})\\s*$" );
  89     private final static Pattern  seq_identifier_pattern_2       = Pattern
  90                                                                          .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" );
  91     static {
  92         Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
  93     }
  94
  95     public static MaskFormatter createMaskFormatter( final String s ) {
  96         MaskFormatter formatter = null;
  97         try {
  98             formatter = new MaskFormatter( s );
  99         }
 100         catch ( final ParseException e ) {
 101             throw new IllegalArgumentException( e );
 102         }
 103         return formatter;
 104     }
 105
 106     final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
 107         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 108         while ( it.hasNext() ) {
 109             if ( it.next().getNodeData().isHasEvent() ) {
 110                 return true;
 111             }
 112         }
 113         return false;
 114     }
 115
 116     /**
 117      * Returns true if at least one branch has a length larger than zero.
 118      *
 119      *
 120      * @param phy
 121      */
 122     final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
 123         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 124         while ( it.hasNext() ) {
 125             if ( it.next().getDistanceToParent() > 0.0 ) {
 126                 return true;
 127             }
 128         }
 129         return false;
 130     }
 131
 132     final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) {
 133         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 134         while ( it.hasNext() ) {
 135             if ( it.next().getBranchData().isHasConfidences() ) {
 136                 return true;
 137             }
 138         }
 139         return false;
 140     }
 141
 142     final public static void launchWebBrowser( final URI uri,
 143                                                final boolean is_applet,
 144                                                final JApplet applet,
 145                                                final String frame_name ) throws IOException {
 146         if ( is_applet ) {
 147             applet.getAppletContext().showDocument( uri.toURL(), frame_name );
 148         }
 149         else {
 150             // This requires Java 1.6:
 151             // =======================
 152             // boolean no_desktop = false;
 153             // try {
 154             // if ( Desktop.isDesktopSupported() ) {
 155             // System.out.println( "desktop supported" );
 156             // final Desktop dt = Desktop.getDesktop();
 157             // dt.browse( uri );
 158             // }
 159             // else {
 160             // no_desktop = true;
 161             // }
 162             // }
 163             // catch ( final Exception ex ) {
 164             // ex.printStackTrace();
 165             // no_desktop = true;
 166             // }
 167             // catch ( final Error er ) {
 168             // er.printStackTrace();
 169             // no_desktop = true;
 170             // }
 171             // if ( no_desktop ) {
 172             // System.out.println( "desktop not supported" );
 173             try {
 174                 openUrlInWebBrowser( uri.toString() );
 175             }
 176             catch ( final Exception e ) {
 177                 throw new IOException( e );
 178             }
 179             // }
 180         }
 181     }
 182
 183     public static Set<Taxonomy> obtainAllDistinctTaxonomies( final PhylogenyNode node ) {
 184         final List<PhylogenyNode> descs = node.getAllExternalDescendants();
 185         final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
 186         for( final PhylogenyNode n : descs ) {
 187             if ( n.getNodeData().isHasTaxonomy() && !n.getNodeData().getTaxonomy().isEmpty() ) {
 188                 tax_set.add( n.getNodeData().getTaxonomy() );
 189             }
 190         }
 191         return tax_set;
 192     }
 193
 194     public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) {
 195         final String n = sequence_name.trim();
 196         final Matcher matcher1 = seq_identifier_pattern_1.matcher( n );
 197         String group1 = "";
 198         String group2 = "";
 199         if ( matcher1.matches() ) {
 200             group1 = matcher1.group( 1 );
 201             group2 = matcher1.group( 2 );
 202         }
 203         else {
 204             final Matcher matcher2 = seq_identifier_pattern_2.matcher( n );
 205             if ( matcher2.matches() ) {
 206                 group1 = matcher2.group( 1 );
 207                 group2 = matcher2.group( 2 );
 208             }
 209         }
 210         if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) {
 211             return null;
 212         }
 213         return new Accession( group2, group1 );
 214     }
 215
 216     public final static void printWarningMessage( final String name, final String message ) {
 217         System.out.println( "[" + name + "] > " + message );
 218     }
 219
 220     final public static void showErrorMessage( final Component parent, final String error_msg ) {
 221         printAppletMessage( Constants.PRG_NAME, error_msg );
 222         JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION
 223                 + "] Error", JOptionPane.ERROR_MESSAGE );
 224     }
 225
 226     public static void writePhylogenyToGraphicsFile( final File intree,
 227                                                      final File outfile,
 228                                                      final int width,
 229                                                      final int height,
 230                                                      final GraphicsExportType type,
 231                                                      final Configuration config ) throws IOException {
 232         final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
 233         Phylogeny[] phys = null;
 234         phys = PhylogenyMethods.readPhylogenies( parser, intree );
 235         writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config );
 236     }
 237
 238     public static void writePhylogenyToGraphicsFile( final Phylogeny phy,
 239                                                      final File outfile,
 240                                                      final int width,
 241                                                      final int height,
 242                                                      final GraphicsExportType type,
 243                                                      final Configuration config ) throws IOException {
 244         final Phylogeny[] phys = new Phylogeny[ 1 ];
 245         phys[ 0 ] = phy;
 246         final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
 247         AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
 248                 .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
 249         mf.end();
 250     }
 251
 252     public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile,
 253                                                                          final int width,
 254                                                                          final int height,
 255                                                                          final TreePanel tree_panel,
 256                                                                          final ControlPanel ac,
 257                                                                          final GraphicsExportType type,
 258                                                                          final Options options ) throws IOException {
 259         tree_panel.calcParametersForPainting( width, height, true );
 260         tree_panel.resetPreferredSize();
 261         tree_panel.repaint();
 262         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
 263                                                                    RenderingHints.VALUE_RENDER_QUALITY );
 264         rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
 265         if ( options.isAntialiasPrint() ) {
 266             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
 267             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
 268         }
 269         else {
 270             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
 271             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
 272         }
 273         final Phylogeny phylogeny = tree_panel.getPhylogeny();
 274         if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
 275             return;
 276         }
 277         if ( outfile.isDirectory() ) {
 278             throw new IOException( "\"" + outfile + "\" is a directory" );
 279         }
 280         final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
 281         final Graphics2D g2d = buffered_img.createGraphics();
 282         g2d.setRenderingHints( rendering_hints );
 283         tree_panel.paintPhylogeny( g2d, false, true, width, height, 0, 0 );
 284         if ( type == GraphicsExportType.TIFF ) {
 285             writeToTiff( outfile, buffered_img );
 286         }
 287         else {
 288             ImageIO.write( buffered_img, type.toString(), outfile );
 289         }
 290         g2d.dispose();
 291     }
 292
 293     final static void addPhylogeniesToTabs( final Phylogeny[] phys,
 294                                             final String default_name,
 295                                             final String full_path,
 296                                             final Configuration configuration,
 297                                             final MainPanel main_panel ) {
 298         if ( phys.length > Constants.MAX_TREES_TO_LOAD ) {
 299             JOptionPane.showMessageDialog( main_panel, "Attempt to load " + phys.length
 300                     + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME
 301                     + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE );
 302         }
 303         int i = 1;
 304         for( final Phylogeny phy : phys ) {
 305             if ( !phy.isEmpty() ) {
 306                 if ( i <= Constants.MAX_TREES_TO_LOAD ) {
 307                     String my_name = "";
 308                     String my_name_for_file = "";
 309                     if ( phys.length > 1 ) {
 310                         if ( !ForesterUtil.isEmpty( default_name ) ) {
 311                             my_name = new String( default_name );
 312                         }
 313                         if ( !ForesterUtil.isEmpty( full_path ) ) {
 314                             my_name_for_file = new String( full_path );
 315                         }
 316                         else if ( !ForesterUtil.isEmpty( default_name ) ) {
 317                             my_name_for_file = new String( default_name );
 318                         }
 319                         String suffix = "";
 320                         if ( my_name_for_file.indexOf( '.' ) > 0 ) {
 321                             suffix = my_name_for_file.substring( my_name_for_file.lastIndexOf( '.' ),
 322                                                                  my_name_for_file.length() );
 323                             my_name_for_file = my_name_for_file.substring( 0, my_name_for_file.lastIndexOf( '.' ) );
 324                         }
 325                         if ( !ForesterUtil.isEmpty( my_name_for_file ) ) {
 326                             my_name_for_file += "_";
 327                         }
 328                         if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 329                             my_name_for_file += phy.getName().replaceAll( " ", "_" );
 330                         }
 331                         else if ( phy.getIdentifier() != null ) {
 332                             final StringBuffer sb = new StringBuffer();
 333                             if ( !ForesterUtil.isEmpty( phy.getIdentifier().getProvider() ) ) {
 334                                 sb.append( phy.getIdentifier().getProvider() );
 335                                 sb.append( "_" );
 336                             }
 337                             sb.append( phy.getIdentifier().getValue() );
 338                             my_name_for_file += sb;
 339                         }
 340                         else {
 341                             my_name_for_file += i;
 342                         }
 343                         if ( !ForesterUtil.isEmpty( my_name ) && ForesterUtil.isEmpty( phy.getName() )
 344                                 && ( phy.getIdentifier() == null ) ) {
 345                             my_name = my_name + " [" + i + "]";
 346                         }
 347                         if ( !ForesterUtil.isEmpty( suffix ) ) {
 348                             my_name_for_file += suffix;
 349                         }
 350                     }
 351                     else {
 352                         if ( !ForesterUtil.isEmpty( default_name ) ) {
 353                             my_name = new String( default_name );
 354                         }
 355                         my_name_for_file = "";
 356                         if ( !ForesterUtil.isEmpty( full_path ) ) {
 357                             my_name_for_file = new String( full_path );
 358                         }
 359                         else if ( !ForesterUtil.isEmpty( default_name ) ) {
 360                             my_name_for_file = new String( default_name );
 361                         }
 362                         if ( ForesterUtil.isEmpty( my_name_for_file ) ) {
 363                             if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 364                                 my_name_for_file = new String( phy.getName() ).replaceAll( " ", "_" );
 365                             }
 366                             else if ( phy.getIdentifier() != null ) {
 367                                 final StringBuffer sb = new StringBuffer();
 368                                 if ( !ForesterUtil.isEmpty( phy.getIdentifier().getProvider() ) ) {
 369                                     sb.append( phy.getIdentifier().getProvider() );
 370                                     sb.append( "_" );
 371                                 }
 372                                 sb.append( phy.getIdentifier().getValue() );
 373                                 my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
 374                             }
 375                         }
 376                     }
 377                     main_panel.addPhylogenyInNewTab( phy, configuration, my_name, full_path );
 378                     main_panel.getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
 379                     lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
 380                     ++i;
 381                 }
 382             }
 383         }
 384     }
 385
 386     final static void addPhylogenyToPanel( final Phylogeny[] phys,
 387                                            final Configuration configuration,
 388                                            final MainPanel main_panel ) {
 389         final Phylogeny phy = phys[ 0 ];
 390         main_panel.addPhylogenyInPanel( phy, configuration );
 391         lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
 392     }
 393
 394     // Returns true if the specified format name can be written
 395     final static boolean canWriteFormat( final String format_name ) {
 396         final Iterator<ImageWriter> iter = ImageIO.getImageWritersByFormatName( format_name );
 397         return iter.hasNext();
 398     }
 399
 400     final static String createBasicInformation( final Phylogeny phy, final File treefile ) {
 401         final StringBuilder desc = new StringBuilder();
 402         if ( ( phy != null ) && !phy.isEmpty() ) {
 403             String f = null;
 404             if ( treefile != null ) {
 405                 try {
 406                     f = treefile.getCanonicalPath();
 407                 }
 408                 catch ( final IOException e ) {
 409                     //Not important, ignore.
 410                 }
 411                 if ( !ForesterUtil.isEmpty( f ) ) {
 412                     desc.append( "Path: " );
 413                     desc.append( f );
 414                     desc.append( "\n" );
 415                 }
 416             }
 417             if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 418                 desc.append( "Name: " );
 419                 desc.append( phy.getName() );
 420                 desc.append( "\n" );
 421             }
 422             if ( phy.getIdentifier() != null ) {
 423                 desc.append( "Id: " );
 424                 desc.append( phy.getIdentifier().toString() );
 425                 desc.append( "\n" );
 426             }
 427             if ( !ForesterUtil.isEmpty( phy.getDescription() ) ) {
 428                 desc.append( "Description: " );
 429                 desc.append( phy.getDescription() );
 430                 desc.append( "\n" );
 431             }
 432             if ( !ForesterUtil.isEmpty( phy.getDistanceUnit() ) ) {
 433                 desc.append( "Distance Unit: " );
 434                 desc.append( phy.getDistanceUnit() );
 435                 desc.append( "\n" );
 436             }
 437             if ( !ForesterUtil.isEmpty( phy.getType() ) ) {
 438                 desc.append( "Type: " );
 439                 desc.append( phy.getType() );
 440                 desc.append( "\n" );
 441             }
 442             desc.append( "Rooted: " );
 443             desc.append( phy.isRooted() );
 444             desc.append( "\n" );
 445             desc.append( "Rerootable: " );
 446             desc.append( phy.isRerootable() );
 447             desc.append( "\n" );
 448             desc.append( "Nodes: " );
 449             desc.append( phy.getNodeCount() );
 450             desc.append( "\n" );
 451             desc.append( "External nodes: " );
 452             desc.append( phy.getNumberOfExternalNodes() );
 453             desc.append( "\n" );
 454             desc.append( "Internal nodes: " );
 455             desc.append( phy.getNodeCount() - phy.getNumberOfExternalNodes() );
 456             desc.append( "\n" );
 457             desc.append( "Internal nodes with polytomies: " );
 458             desc.append( PhylogenyMethods.countNumberOfPolytomies( phy ) );
 459             desc.append( "\n" );
 460             desc.append( "Branches: " );
 461             desc.append( phy.getNumberOfBranches() );
 462             desc.append( "\n" );
 463             desc.append( "Depth: " );
 464             desc.append( PhylogenyMethods.calculateMaxDepth( phy ) );
 465             desc.append( "\n" );
 466             desc.append( "Maximum distance to root: " );
 467             desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) );
 468             desc.append( "\n" );
 469             final Set<Taxonomy> taxs = obtainAllDistinctTaxonomies( phy.getRoot() );
 470             if ( taxs != null ) {
 471                 desc.append( "Distinct external taxonomies: " );
 472                 desc.append( taxs.size() );
 473             }
 474             for( final Taxonomy t : taxs ) {
 475                 System.out.println( t.toString() );
 476             }
 477             desc.append( "\n" );
 478             final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy );
 479             if ( bs.getN() > 3 ) {
 480                 desc.append( "\n" );
 481                 desc.append( "Branch-length statistics: " );
 482                 desc.append( "\n" );
 483                 desc.append( "    Number of branches with non-negative branch-lengths: " + bs.getN() );
 484                 desc.append( "\n" );
 485                 desc.append( "    Median: " + ForesterUtil.round( bs.median(), 6 ) );
 486                 desc.append( "\n" );
 487                 desc.append( "    Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (stdev: "
 488                         + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) + ")" );
 489                 desc.append( "\n" );
 490                 desc.append( "    Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
 491                 desc.append( "\n" );
 492                 desc.append( "    Maximum: " + ForesterUtil.round( bs.getMax(), 6 ) );
 493                 desc.append( "\n" );
 494                 if ( Math.abs( bs.getMax() - bs.getMin() ) > 0.0001 ) {
 495                     desc.append( "\n" );
 496                     final AsciiHistogram histo = new AsciiHistogram( bs );
 497                     desc.append( histo.toStringBuffer( 12, '#', 40, 7, "    " ) );
 498                 }
 499             }
 500             final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
 501             if ( ds.getN() > 2 ) {
 502                 desc.append( "\n" );
 503                 desc.append( "Descendants per node statistics: " );
 504                 desc.append( "\n" );
 505                 desc.append( "    Median: " + ForesterUtil.round( ds.median(), 6 ) );
 506                 desc.append( "\n" );
 507                 desc.append( "    Mean: " + ForesterUtil.round( ds.arithmeticMean(), 6 ) + " (stdev: "
 508                         + ForesterUtil.round( ds.sampleStandardDeviation(), 6 ) + ")" );
 509                 desc.append( "\n" );
 510                 desc.append( "    Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
 511                 desc.append( "\n" );
 512                 desc.append( "    Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) );
 513                 desc.append( "\n" );
 514             }
 515             List<DescriptiveStatistics> css = null;
 516             try {
 517                 css = PhylogenyMethods.calculatConfidenceStatistics( phy );
 518             }
 519             catch ( final IllegalArgumentException e ) {
 520                 ForesterUtil.printWarningMessage( Constants.PRG_NAME, e.getMessage() );
 521             }
 522             if ( ( css != null ) && ( css.size() > 0 ) ) {
 523                 desc.append( "\n" );
 524                 for( int i = 0; i < css.size(); ++i ) {
 525                     final DescriptiveStatistics cs = css.get( i );
 526                     if ( ( cs != null ) && ( cs.getN() > 1 ) ) {
 527                         if ( css.size() > 1 ) {
 528                             desc.append( "Support statistics " + ( i + 1 ) + ": " );
 529                         }
 530                         else {
 531                             desc.append( "Support statistics: " );
 532                         }
 533                         if ( !ForesterUtil.isEmpty( cs.getDescription() ) ) {
 534                             desc.append( "\n" );
 535                             desc.append( "    Type: " + cs.getDescription() );
 536                         }
 537                         desc.append( "\n" );
 538                         desc.append( "    Branches with support: " + cs.getN() );
 539                         desc.append( "\n" );
 540                         desc.append( "    Median: " + ForesterUtil.round( cs.median(), 6 ) );
 541                         desc.append( "\n" );
 542                         desc.append( "    Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
 543                         if ( cs.getN() > 2 ) {
 544                             desc.append( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" );
 545                         }
 546                         desc.append( "\n" );
 547                         desc.append( "    Minimum: " + ForesterUtil.round( cs.getMin(), 6 ) );
 548                         desc.append( "\n" );
 549                         desc.append( "    Maximum: " + ForesterUtil.round( cs.getMax(), 6 ) );
 550                         desc.append( "\n" );
 551                     }
 552                 }
 553             }
 554         }
 555         return desc.toString();
 556     }
 557
 558     /**
 559      * Exits with -1.
 560      *
 561      *
 562      * @param message
 563      *            to message to be printed
 564      */
 565     final static void dieWithSystemError( final String message ) {
 566         System.out.println();
 567         System.out.println( Constants.PRG_NAME + " encountered the following system error: " + message );
 568         System.out.println( "Please contact the authors." );
 569         System.out.println( Constants.PRG_NAME + " needs to close." );
 570         System.out.println();
 571         System.exit( -1 );
 572     }
 573
 574     final static String[] getAllPossibleRanks() {
 575         final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
 576         int i = 0;
 577         for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) {
 578             if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) {
 579                 str_array[ i++ ] = e;
 580             }
 581         }
 582         return str_array;
 583     }
 584
 585     final static String[] getAllRanks( final Phylogeny tree ) {
 586         final SortedSet<String> ranks = new TreeSet<String>();
 587         for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
 588             final PhylogenyNode n = it.next();
 589             if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) {
 590                 ranks.add( n.getNodeData().getTaxonomy().getRank() );
 591             }
 592         }
 593         return ForesterUtil.stringSetToArray( ranks );
 594     }
 595
 596     final static String[] getAvailableFontFamiliesSorted() {
 597         return AVAILABLE_FONT_FAMILIES_SORTED;
 598     }
 599
 600     final static boolean isUsOrCanada() {
 601         try {
 602             if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
 603                 return true;
 604             }
 605         }
 606         catch ( final Exception e ) {
 607             return false;
 608         }
 609         return false;
 610     }
 611
 612     final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
 613                                                                       final ControlPanel atv_control,
 614                                                                       final Configuration configuration ) {
 615         if ( ( t != null ) && !t.isEmpty() ) {
 616             if ( !AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
 617                 atv_control.setDrawPhylogram( false );
 618                 atv_control.setDrawPhylogramEnabled( false );
 619             }
 620             if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) {
 621                 if ( atv_control.getDisplayAsPhylogramCb() != null ) {
 622                     if ( AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
 623                         atv_control.setDrawPhylogram( true );
 624                         atv_control.setDrawPhylogramEnabled( true );
 625                     }
 626                     else {
 627                         atv_control.setDrawPhylogram( false );
 628                     }
 629                 }
 630             }
 631             if ( configuration.doGuessCheckOption( Configuration.write_confidence_values ) ) {
 632                 if ( atv_control.getWriteConfidenceCb() != null ) {
 633                     if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( t ) ) {
 634                         atv_control.setCheckbox( Configuration.write_confidence_values, true );
 635                     }
 636                     else {
 637                         atv_control.setCheckbox( Configuration.write_confidence_values, false );
 638                     }
 639                 }
 640             }
 641             if ( configuration.doGuessCheckOption( Configuration.write_events ) ) {
 642                 if ( atv_control.getShowEventsCb() != null ) {
 643                     if ( AptxUtil.isHasAtLeastNodeWithEvent( t ) ) {
 644                         atv_control.setCheckbox( Configuration.write_events, true );
 645                     }
 646                     else {
 647                         atv_control.setCheckbox( Configuration.write_events, false );
 648                     }
 649                 }
 650             }
 651         }
 652     }
 653
 654     final static void openWebsite( final String url, final boolean is_applet, final JApplet applet ) throws IOException {
 655         try {
 656             AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, Constants.PRG_NAME );
 657         }
 658         catch ( final Exception e ) {
 659             throw new IOException( e );
 660         }
 661     }
 662
 663     final static void outOfMemoryError( final OutOfMemoryError e ) {
 664         System.err.println();
 665         System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
 666         System.err.println();
 667         e.printStackTrace();
 668         System.err.println();
 669         JOptionPane.showMessageDialog( null,
 670                                        "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option"
 671                                                + "\n\nError: " + e.getLocalizedMessage(),
 672                                        "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
 673                                        JOptionPane.ERROR_MESSAGE );
 674         System.exit( -1 );
 675     }
 676
 677     final static void printAppletMessage( final String applet_name, final String message ) {
 678         System.out.println( "[" + applet_name + "] > " + message );
 679     }
 680
 681     final static Phylogeny[] readPhylogeniesFromUrl( final URL url,
 682                                                      final boolean phyloxml_validate_against_xsd,
 683                                                      final boolean replace_underscores,
 684                                                      final boolean internal_numbers_are_confidences,
 685                                                      final TAXONOMY_EXTRACTION taxonomy_extraction,
 686                                                      final boolean midpoint_reroot ) throws FileNotFoundException,
 687             IOException {
 688         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 689         final PhylogenyParser parser;
 690         boolean nhx_or_nexus = false;
 691         if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
 692             parser = new TolParser();
 693         }
 694         else {
 695             parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
 696             if ( parser instanceof NHXParser ) {
 697                 nhx_or_nexus = true;
 698                 final NHXParser nhx = ( NHXParser ) parser;
 699                 nhx.setReplaceUnderscores( replace_underscores );
 700                 nhx.setIgnoreQuotes( false );
 701                 nhx.setTaxonomyExtraction( taxonomy_extraction );
 702             }
 703             else if ( parser instanceof NexusPhylogeniesParser ) {
 704                 nhx_or_nexus = true;
 705                 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
 706                 nex.setReplaceUnderscores( replace_underscores );
 707                 nex.setIgnoreQuotes( false );
 708             }
 709         }
 710         AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
 711         final Phylogeny[] phys = factory.create( url.openStream(), parser );
 712         if ( phys != null ) {
 713             if ( nhx_or_nexus && internal_numbers_are_confidences ) {
 714                 for( final Phylogeny phy : phys ) {
 715                     PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
 716                 }
 717             }
 718             if ( midpoint_reroot ) {
 719                 for( final Phylogeny phy : phys ) {
 720                     PhylogenyMethods.midpointRoot( phy );
 721                     PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
 722                 }
 723             }
 724         }
 725         return phys;
 726     }
 727
 728     final static void removeBranchColors( final Phylogeny phy ) {
 729         for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
 730             it.next().getBranchData().setBranchColor( null );
 731         }
 732     }
 733
 734     final static void unexpectedError( final Error e ) {
 735         System.err.println();
 736         e.printStackTrace( System.err );
 737         System.err.println();
 738         final StringBuffer sb = new StringBuffer();
 739         for( final StackTraceElement s : e.getStackTrace() ) {
 740             sb.append( s + "\n" );
 741         }
 742         JOptionPane
 743                 .showMessageDialog( null,
 744                                     "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
 745                                             + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
 746                                             + sb,
 747                                     "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
 748                                     JOptionPane.ERROR_MESSAGE );
 749         System.exit( -1 );
 750     }
 751
 752     final static void unexpectedException( final Exception e ) {
 753         System.err.println();
 754         e.printStackTrace( System.err );
 755         System.err.println();
 756         final StringBuffer sb = new StringBuffer();
 757         for( final StackTraceElement s : e.getStackTrace() ) {
 758             sb.append( s + "\n" );
 759         }
 760         JOptionPane.showMessageDialog( null,
 761                                        "An unexpected exception has occured. \nPlease contact: "
 762                                                + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
 763                                                + "\n" + sb,
 764                                        "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
 765                                        JOptionPane.ERROR_MESSAGE );
 766     }
 767
 768     final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
 769                                                                        int width,
 770                                                                        int height,
 771                                                                        final TreePanel tree_panel,
 772                                                                        final ControlPanel ac,
 773                                                                        final GraphicsExportType type,
 774                                                                        final Options options ) throws IOException {
 775         if ( !options.isGraphicsExportUsingActualSize() ) {
 776             if ( options.isGraphicsExportVisibleOnly() ) {
 777                 throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
 778             }
 779             tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
 780             tree_panel.resetPreferredSize();
 781             tree_panel.repaint();
 782         }
 783         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
 784                                                                    RenderingHints.VALUE_RENDER_QUALITY );
 785         rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
 786         if ( options.isAntialiasPrint() ) {
 787             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
 788             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
 789         }
 790         else {
 791             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
 792             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
 793         }
 794         final Phylogeny phylogeny = tree_panel.getPhylogeny();
 795         if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
 796             return "";
 797         }
 798         Rectangle visible = null;
 799         if ( !options.isGraphicsExportUsingActualSize() ) {
 800             width = options.getPrintSizeX();
 801             height = options.getPrintSizeY();
 802         }
 803         else if ( options.isGraphicsExportVisibleOnly() ) {
 804             visible = tree_panel.getVisibleRect();
 805             width = visible.width;
 806             height = visible.height;
 807         }
 808         final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
 809         Graphics2D g2d = buffered_img.createGraphics();
 810         g2d.setRenderingHints( rendering_hints );
 811         int x = 0;
 812         int y = 0;
 813         if ( options.isGraphicsExportVisibleOnly() ) {
 814             g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
 815             g2d.setClip( null );
 816             x = visible.x;
 817             y = visible.y;
 818         }
 819         tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
 820         ImageIO.write( buffered_img, type.toString(), baos );
 821         g2d.dispose();
 822         System.gc();
 823         if ( !options.isGraphicsExportUsingActualSize() ) {
 824             tree_panel.getMainPanel().getControlPanel().showWhole();
 825         }
 826         String msg = baos.toString();
 827         if ( ( width > 0 ) && ( height > 0 ) ) {
 828             msg += " [size: " + width + ", " + height + "]";
 829         }
 830         return msg;
 831     }
 832
 833     final static String writePhylogenyToGraphicsFile( final String file_name,
 834                                                       int width,
 835                                                       int height,
 836                                                       final TreePanel tree_panel,
 837                                                       final ControlPanel ac,
 838                                                       final GraphicsExportType type,
 839                                                       final Options options ) throws IOException {
 840         if ( !options.isGraphicsExportUsingActualSize() ) {
 841             if ( options.isGraphicsExportVisibleOnly() ) {
 842                 throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
 843             }
 844             tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
 845             tree_panel.resetPreferredSize();
 846             tree_panel.repaint();
 847         }
 848         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
 849                                                                    RenderingHints.VALUE_RENDER_QUALITY );
 850         rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
 851         if ( options.isAntialiasPrint() ) {
 852             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
 853             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
 854         }
 855         else {
 856             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
 857             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
 858         }
 859         final Phylogeny phylogeny = tree_panel.getPhylogeny();
 860         if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
 861             return "";
 862         }
 863         final File file = new File( file_name );
 864         if ( file.isDirectory() ) {
 865             throw new IOException( "\"" + file_name + "\" is a directory" );
 866         }
 867         Rectangle visible = null;
 868         if ( !options.isGraphicsExportUsingActualSize() ) {
 869             width = options.getPrintSizeX();
 870             height = options.getPrintSizeY();
 871         }
 872         else if ( options.isGraphicsExportVisibleOnly() ) {
 873             visible = tree_panel.getVisibleRect();
 874             width = visible.width;
 875             height = visible.height;
 876         }
 877         final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
 878         Graphics2D g2d = buffered_img.createGraphics();
 879         g2d.setRenderingHints( rendering_hints );
 880         int x = 0;
 881         int y = 0;
 882         if ( options.isGraphicsExportVisibleOnly() ) {
 883             g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
 884             g2d.setClip( null );
 885             x = visible.x;
 886             y = visible.y;
 887         }
 888         tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
 889         if ( type == GraphicsExportType.TIFF ) {
 890             writeToTiff( file, buffered_img );
 891         }
 892         else {
 893             ImageIO.write( buffered_img, type.toString(), file );
 894         }
 895         g2d.dispose();
 896         System.gc();
 897         if ( !options.isGraphicsExportUsingActualSize() ) {
 898             tree_panel.getMainPanel().getControlPanel().showWhole();
 899         }
 900         String msg = file.toString();
 901         if ( ( width > 0 ) && ( height > 0 ) ) {
 902             msg += " [size: " + width + ", " + height + "]";
 903         }
 904         return msg;
 905     }
 906
 907     final static void writeToTiff( final File file, final BufferedImage image ) throws IOException {
 908         // See: http://log.robmeek.com/2005/08/write-tiff-in-java.html
 909         ImageWriter writer = null;
 910         ImageOutputStream ios = null;
 911         // Find an appropriate writer:
 912         final Iterator<ImageWriter> it = ImageIO.getImageWritersByFormatName( "TIF" );
 913         if ( it.hasNext() ) {
 914             writer = it.next();
 915         }
 916         else {
 917             throw new IOException( "failed to get TIFF image writer" );
 918         }
 919         // Setup writer:
 920         ios = ImageIO.createImageOutputStream( file );
 921         writer.setOutput( ios );
 922         final ImageWriteParam image_write_param = new ImageWriteParam( Locale.getDefault() );
 923         image_write_param.setCompressionMode( ImageWriteParam.MODE_EXPLICIT );
 924         // see writeParam.getCompressionTypes() for available compression type
 925         // strings.
 926         image_write_param.setCompressionType( "PackBits" );
 927         final String t[] = image_write_param.getCompressionTypes();
 928         for( final String string : t ) {
 929             System.out.println( string );
 930         }
 931         // Convert to an IIOImage:
 932         final IIOImage iio_image = new IIOImage( image, null, null );
 933         writer.write( null, iio_image, image_write_param );
 934     }
 935
 936     final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException,
 937             SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
 938             InvocationTargetException, InterruptedException {
 939         final String os = System.getProperty( "os.name" );
 940         final Runtime runtime = Runtime.getRuntime();
 941         if ( os.toLowerCase().startsWith( "win" ) ) {
 942             Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
 943         }
 944         else if ( ForesterUtil.isMac() ) {
 945             final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
 946             final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
 947             open_url.invoke( null, new Object[] { url } );
 948         }
 949         else {
 950             final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" };
 951             String browser = null;
 952             for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) {
 953                 if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) {
 954                     browser = browsers[ i ];
 955                 }
 956             }
 957             if ( browser == null ) {
 958                 throw new IOException( "could not find a web browser to open [" + url + "] in" );
 959             }
 960             else {
 961                 runtime.exec( new String[] { browser, url } );
 962             }
 963         }
 964     }
 965
 966     // See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2
 967     // static void openDDBJRest() throws IOException {
 968     // //set URL
 969     // URL url = new URL( "http://xml.nig.ac.jp/rest/Invoke" );
 970     // //set parameter
 971     // String query = "service=GetEntry&method=getDDBJEntry&accession=AB000100";
 972     // //make connection
 973     // URLConnection urlc = url.openConnection();
 974     // //use post mode
 975     // urlc.setDoOutput( true );
 976     // urlc.setAllowUserInteraction( false );
 977     // //send query
 978     // PrintStream ps = new PrintStream( urlc.getOutputStream() );
 979     // ps.print( query );
 980     // ps.close();
 981     // //get result
 982     // BufferedReader br = new BufferedReader( new InputStreamReader(
 983     // urlc.getInputStream() ) );
 984     // String l = null;
 985     // while ( ( l = br.readLine() ) != null ) {
 986     // System.out.println( l );
 987     // }
 988     // br.close();
 989     // }
 990     public static enum GraphicsExportType {
 991         BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
 992
 993         private final String _suffix;
 994
 995         private GraphicsExportType( final String suffix ) {
 996             _suffix = suffix;
 997         }
 998
 999         @Override
1000         public String toString() {
1001             return _suffix;
1002         }
1003     }
1004 }