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.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     static {
  88         Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
  89     }
  90
  91     public static MaskFormatter createMaskFormatter( final String s ) {
  92         MaskFormatter formatter = null;
  93         try {
  94             formatter = new MaskFormatter( s );
  95         }
  96         catch ( final ParseException e ) {
  97             throw new IllegalArgumentException( e );
  98         }
  99         return formatter;
 100     }
 101
 102     final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
 103         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 104         while ( it.hasNext() ) {
 105             if ( it.next().getNodeData().isHasEvent() ) {
 106                 return true;
 107             }
 108         }
 109         return false;
 110     }
 111
 112     /**
 113      * Returns true if at least one branch has a length larger than zero.
 114      *
 115      *
 116      * @param phy
 117      */
 118     final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
 119         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 120         while ( it.hasNext() ) {
 121             if ( it.next().getDistanceToParent() > 0.0 ) {
 122                 return true;
 123             }
 124         }
 125         return false;
 126     }
 127
 128     final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) {
 129         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 130         while ( it.hasNext() ) {
 131             if ( it.next().getBranchData().isHasConfidences() ) {
 132                 return true;
 133             }
 134         }
 135         return false;
 136     }
 137
 138     final public static void launchWebBrowser( final URI uri,
 139                                                final boolean is_applet,
 140                                                final JApplet applet,
 141                                                final String frame_name ) throws IOException {
 142         if ( is_applet ) {
 143             applet.getAppletContext().showDocument( uri.toURL(), frame_name );
 144         }
 145         else {
 146             // This requires Java 1.6:
 147             // =======================
 148             // boolean no_desktop = false;
 149             // try {
 150             // if ( Desktop.isDesktopSupported() ) {
 151             // System.out.println( "desktop supported" );
 152             // final Desktop dt = Desktop.getDesktop();
 153             // dt.browse( uri );
 154             // }
 155             // else {
 156             // no_desktop = true;
 157             // }
 158             // }
 159             // catch ( final Exception ex ) {
 160             // ex.printStackTrace();
 161             // no_desktop = true;
 162             // }
 163             // catch ( final Error er ) {
 164             // er.printStackTrace();
 165             // no_desktop = true;
 166             // }
 167             // if ( no_desktop ) {
 168             // System.out.println( "desktop not supported" );
 169             try {
 170                 openUrlInWebBrowser( uri.toString() );
 171             }
 172             catch ( final Exception e ) {
 173                 throw new IOException( e );
 174             }
 175             // }
 176         }
 177     }
 178
 179     public static Set<Taxonomy> obtainAllDistinctTaxonomies( final PhylogenyNode node ) {
 180         final List<PhylogenyNode> descs = node.getAllExternalDescendants();
 181         final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
 182         for( final PhylogenyNode n : descs ) {
 183             if ( n.getNodeData().isHasTaxonomy() && !n.getNodeData().getTaxonomy().isEmpty() ) {
 184                 tax_set.add( n.getNodeData().getTaxonomy() );
 185             }
 186         }
 187         return tax_set;
 188     }
 189
 190     public final static void printWarningMessage( final String name, final String message ) {
 191         System.out.println( "[" + name + "] > " + message );
 192     }
 193
 194     final public static void showErrorMessage( final Component parent, final String error_msg ) {
 195         printAppletMessage( Constants.PRG_NAME, error_msg );
 196         JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION
 197                 + "] Error", JOptionPane.ERROR_MESSAGE );
 198     }
 199
 200     public static void writePhylogenyToGraphicsFile( final File intree,
 201                                                      final File outfile,
 202                                                      final int width,
 203                                                      final int height,
 204                                                      final GraphicsExportType type,
 205                                                      final Configuration config ) throws IOException {
 206         final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
 207         Phylogeny[] phys = null;
 208         phys = PhylogenyMethods.readPhylogenies( parser, intree );
 209         writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config );
 210     }
 211
 212     public static void writePhylogenyToGraphicsFile( final Phylogeny phy,
 213                                                      final File outfile,
 214                                                      final int width,
 215                                                      final int height,
 216                                                      final GraphicsExportType type,
 217                                                      final Configuration config ) throws IOException {
 218         final Phylogeny[] phys = new Phylogeny[ 1 ];
 219         phys[ 0 ] = phy;
 220         final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
 221         AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
 222                 .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
 223         mf.end();
 224     }
 225
 226     public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile,
 227                                                                          final int width,
 228                                                                          final int height,
 229                                                                          final TreePanel tree_panel,
 230                                                                          final ControlPanel ac,
 231                                                                          final GraphicsExportType type,
 232                                                                          final Options options ) throws IOException {
 233         tree_panel.calcParametersForPainting( width, height, true );
 234         tree_panel.resetPreferredSize();
 235         tree_panel.repaint();
 236         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
 237                                                                    RenderingHints.VALUE_RENDER_QUALITY );
 238         rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
 239         if ( options.isAntialiasPrint() ) {
 240             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
 241             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
 242         }
 243         else {
 244             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
 245             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
 246         }
 247         final Phylogeny phylogeny = tree_panel.getPhylogeny();
 248         if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
 249             return;
 250         }
 251         if ( outfile.isDirectory() ) {
 252             throw new IOException( "\"" + outfile + "\" is a directory" );
 253         }
 254         final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
 255         final Graphics2D g2d = buffered_img.createGraphics();
 256         g2d.setRenderingHints( rendering_hints );
 257         tree_panel.paintPhylogeny( g2d, false, true, width, height, 0, 0 );
 258         if ( type == GraphicsExportType.TIFF ) {
 259             writeToTiff( outfile, buffered_img );
 260         }
 261         else {
 262             ImageIO.write( buffered_img, type.toString(), outfile );
 263         }
 264         g2d.dispose();
 265     }
 266
 267     final static void addPhylogeniesToTabs( final Phylogeny[] phys,
 268                                             final String default_name,
 269                                             final String full_path,
 270                                             final Configuration configuration,
 271                                             final MainPanel main_panel ) {
 272         if ( phys.length > Constants.MAX_TREES_TO_LOAD ) {
 273             JOptionPane.showMessageDialog( main_panel, "Attempt to load " + phys.length
 274                     + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME
 275                     + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE );
 276         }
 277         int i = 1;
 278         for( final Phylogeny phy : phys ) {
 279             if ( !phy.isEmpty() ) {
 280                 if ( i <= Constants.MAX_TREES_TO_LOAD ) {
 281                     String my_name = "";
 282                     String my_name_for_file = "";
 283                     if ( phys.length > 1 ) {
 284                         if ( !ForesterUtil.isEmpty( default_name ) ) {
 285                             my_name = new String( default_name );
 286                         }
 287                         if ( !ForesterUtil.isEmpty( full_path ) ) {
 288                             my_name_for_file = new String( full_path );
 289                         }
 290                         else if ( !ForesterUtil.isEmpty( default_name ) ) {
 291                             my_name_for_file = new String( default_name );
 292                         }
 293                         String suffix = "";
 294                         if ( my_name_for_file.indexOf( '.' ) > 0 ) {
 295                             suffix = my_name_for_file.substring( my_name_for_file.lastIndexOf( '.' ),
 296                                                                  my_name_for_file.length() );
 297                             my_name_for_file = my_name_for_file.substring( 0, my_name_for_file.lastIndexOf( '.' ) );
 298                         }
 299                         if ( !ForesterUtil.isEmpty( my_name_for_file ) ) {
 300                             my_name_for_file += "_";
 301                         }
 302                         if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 303                             my_name_for_file += phy.getName().replaceAll( " ", "_" );
 304                         }
 305                         else if ( phy.getIdentifier() != null ) {
 306                             final StringBuffer sb = new StringBuffer();
 307                             if ( !ForesterUtil.isEmpty( phy.getIdentifier().getProvider() ) ) {
 308                                 sb.append( phy.getIdentifier().getProvider() );
 309                                 sb.append( "_" );
 310                             }
 311                             sb.append( phy.getIdentifier().getValue() );
 312                             my_name_for_file += sb;
 313                         }
 314                         else {
 315                             my_name_for_file += i;
 316                         }
 317                         if ( !ForesterUtil.isEmpty( my_name ) && ForesterUtil.isEmpty( phy.getName() )
 318                                 && ( phy.getIdentifier() == null ) ) {
 319                             my_name = my_name + " [" + i + "]";
 320                         }
 321                         if ( !ForesterUtil.isEmpty( suffix ) ) {
 322                             my_name_for_file += suffix;
 323                         }
 324                     }
 325                     else {
 326                         if ( !ForesterUtil.isEmpty( default_name ) ) {
 327                             my_name = new String( default_name );
 328                         }
 329                         my_name_for_file = "";
 330                         if ( !ForesterUtil.isEmpty( full_path ) ) {
 331                             my_name_for_file = new String( full_path );
 332                         }
 333                         else if ( !ForesterUtil.isEmpty( default_name ) ) {
 334                             my_name_for_file = new String( default_name );
 335                         }
 336                         if ( ForesterUtil.isEmpty( my_name_for_file ) ) {
 337                             if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 338                                 my_name_for_file = new String( phy.getName() ).replaceAll( " ", "_" );
 339                             }
 340                             else if ( phy.getIdentifier() != null ) {
 341                                 final StringBuffer sb = new StringBuffer();
 342                                 if ( !ForesterUtil.isEmpty( phy.getIdentifier().getProvider() ) ) {
 343                                     sb.append( phy.getIdentifier().getProvider() );
 344                                     sb.append( "_" );
 345                                 }
 346                                 sb.append( phy.getIdentifier().getValue() );
 347                                 my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
 348                             }
 349                         }
 350                     }
 351                     main_panel.addPhylogenyInNewTab( phy, configuration, my_name, full_path );
 352                     main_panel.getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
 353                     lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
 354                     ++i;
 355                 }
 356             }
 357         }
 358     }
 359
 360     final static void addPhylogenyToPanel( final Phylogeny[] phys,
 361                                            final Configuration configuration,
 362                                            final MainPanel main_panel ) {
 363         final Phylogeny phy = phys[ 0 ];
 364         main_panel.addPhylogenyInPanel( phy, configuration );
 365         lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
 366     }
 367
 368     // Returns true if the specified format name can be written
 369     final static boolean canWriteFormat( final String format_name ) {
 370         final Iterator<ImageWriter> iter = ImageIO.getImageWritersByFormatName( format_name );
 371         return iter.hasNext();
 372     }
 373
 374     final static String createBasicInformation( final Phylogeny phy, final File treefile ) {
 375         final StringBuilder desc = new StringBuilder();
 376         if ( ( phy != null ) && !phy.isEmpty() ) {
 377             String f = null;
 378             if ( treefile != null ) {
 379                 try {
 380                     f = treefile.getCanonicalPath();
 381                 }
 382                 catch ( final IOException e ) {
 383                     //Not important, ignore.
 384                 }
 385                 if ( !ForesterUtil.isEmpty( f ) ) {
 386                     desc.append( "Path: " );
 387                     desc.append( f );
 388                     desc.append( "\n" );
 389                 }
 390             }
 391             if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 392                 desc.append( "Name: " );
 393                 desc.append( phy.getName() );
 394                 desc.append( "\n" );
 395             }
 396             if ( phy.getIdentifier() != null ) {
 397                 desc.append( "Id: " );
 398                 desc.append( phy.getIdentifier().toString() );
 399                 desc.append( "\n" );
 400             }
 401             if ( !ForesterUtil.isEmpty( phy.getDescription() ) ) {
 402                 desc.append( "Description: " );
 403                 desc.append( phy.getDescription() );
 404                 desc.append( "\n" );
 405             }
 406             if ( !ForesterUtil.isEmpty( phy.getDistanceUnit() ) ) {
 407                 desc.append( "Distance Unit: " );
 408                 desc.append( phy.getDistanceUnit() );
 409                 desc.append( "\n" );
 410             }
 411             if ( !ForesterUtil.isEmpty( phy.getType() ) ) {
 412                 desc.append( "Type: " );
 413                 desc.append( phy.getType() );
 414                 desc.append( "\n" );
 415             }
 416             desc.append( "Rooted: " );
 417             desc.append( phy.isRooted() );
 418             desc.append( "\n" );
 419             desc.append( "Rerootable: " );
 420             desc.append( phy.isRerootable() );
 421             desc.append( "\n" );
 422             desc.append( "Nodes: " );
 423             desc.append( phy.getNodeCount() );
 424             desc.append( "\n" );
 425             desc.append( "External nodes: " );
 426             desc.append( phy.getNumberOfExternalNodes() );
 427             desc.append( "\n" );
 428             desc.append( "Internal nodes: " );
 429             desc.append( phy.getNodeCount() - phy.getNumberOfExternalNodes() );
 430             desc.append( "\n" );
 431             desc.append( "Internal nodes with polytomies: " );
 432             desc.append( PhylogenyMethods.countNumberOfPolytomies( phy ) );
 433             desc.append( "\n" );
 434             desc.append( "Branches: " );
 435             desc.append( phy.getNumberOfBranches() );
 436             desc.append( "\n" );
 437             desc.append( "Depth: " );
 438             desc.append( PhylogenyMethods.calculateMaxDepth( phy ) );
 439             desc.append( "\n" );
 440             desc.append( "Maximum distance to root: " );
 441             desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) );
 442             desc.append( "\n" );
 443             final Set<Taxonomy> taxs = obtainAllDistinctTaxonomies( phy.getRoot() );
 444             if ( taxs != null ) {
 445                 desc.append( "Distinct external taxonomies: " );
 446                 desc.append( taxs.size() );
 447             }
 448             for( final Taxonomy t : taxs ) {
 449                 System.out.println( t.toString() );
 450             }
 451             desc.append( "\n" );
 452             final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy );
 453             if ( bs.getN() > 3 ) {
 454                 desc.append( "\n" );
 455                 desc.append( "Branch-length statistics: " );
 456                 desc.append( "\n" );
 457                 desc.append( "    Number of branches with non-negative branch-lengths: " + bs.getN() );
 458                 desc.append( "\n" );
 459                 desc.append( "    Median: " + ForesterUtil.round( bs.median(), 6 ) );
 460                 desc.append( "\n" );
 461                 desc.append( "    Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (stdev: "
 462                         + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) + ")" );
 463                 desc.append( "\n" );
 464                 desc.append( "    Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
 465                 desc.append( "\n" );
 466                 desc.append( "    Maximum: " + ForesterUtil.round( bs.getMax(), 6 ) );
 467                 desc.append( "\n" );
 468                 if ( Math.abs( bs.getMax() - bs.getMin() ) > 0.0001 ) {
 469                     desc.append( "\n" );
 470                     final AsciiHistogram histo = new AsciiHistogram( bs );
 471                     desc.append( histo.toStringBuffer( 12, '#', 40, 7, "    " ) );
 472                 }
 473             }
 474             final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
 475             if ( ds.getN() > 2 ) {
 476                 desc.append( "\n" );
 477                 desc.append( "Descendants per node statistics: " );
 478                 desc.append( "\n" );
 479                 desc.append( "    Median: " + ForesterUtil.round( ds.median(), 6 ) );
 480                 desc.append( "\n" );
 481                 desc.append( "    Mean: " + ForesterUtil.round( ds.arithmeticMean(), 6 ) + " (stdev: "
 482                         + ForesterUtil.round( ds.sampleStandardDeviation(), 6 ) + ")" );
 483                 desc.append( "\n" );
 484                 desc.append( "    Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
 485                 desc.append( "\n" );
 486                 desc.append( "    Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) );
 487                 desc.append( "\n" );
 488             }
 489             List<DescriptiveStatistics> css = null;
 490             try {
 491                 css = PhylogenyMethods.calculatConfidenceStatistics( phy );
 492             }
 493             catch ( final IllegalArgumentException e ) {
 494                 ForesterUtil.printWarningMessage( Constants.PRG_NAME, e.getMessage() );
 495             }
 496             if ( ( css != null ) && ( css.size() > 0 ) ) {
 497                 desc.append( "\n" );
 498                 for( int i = 0; i < css.size(); ++i ) {
 499                     final DescriptiveStatistics cs = css.get( i );
 500                     if ( ( cs != null ) && ( cs.getN() > 1 ) ) {
 501                         if ( css.size() > 1 ) {
 502                             desc.append( "Support statistics " + ( i + 1 ) + ": " );
 503                         }
 504                         else {
 505                             desc.append( "Support statistics: " );
 506                         }
 507                         if ( !ForesterUtil.isEmpty( cs.getDescription() ) ) {
 508                             desc.append( "\n" );
 509                             desc.append( "    Type: " + cs.getDescription() );
 510                         }
 511                         desc.append( "\n" );
 512                         desc.append( "    Branches with support: " + cs.getN() );
 513                         desc.append( "\n" );
 514                         desc.append( "    Median: " + ForesterUtil.round( cs.median(), 6 ) );
 515                         desc.append( "\n" );
 516                         desc.append( "    Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
 517                         if ( cs.getN() > 2 ) {
 518                             desc.append( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" );
 519                         }
 520                         desc.append( "\n" );
 521                         desc.append( "    Minimum: " + ForesterUtil.round( cs.getMin(), 6 ) );
 522                         desc.append( "\n" );
 523                         desc.append( "    Maximum: " + ForesterUtil.round( cs.getMax(), 6 ) );
 524                         desc.append( "\n" );
 525                     }
 526                 }
 527             }
 528         }
 529         return desc.toString();
 530     }
 531
 532     /**
 533      * Exits with -1.
 534      *
 535      *
 536      * @param message
 537      *            to message to be printed
 538      */
 539     final static void dieWithSystemError( final String message ) {
 540         System.out.println();
 541         System.out.println( Constants.PRG_NAME + " encountered the following system error: " + message );
 542         System.out.println( "Please contact the authors." );
 543         System.out.println( Constants.PRG_NAME + " needs to close." );
 544         System.out.println();
 545         System.exit( -1 );
 546     }
 547
 548     final static String[] getAllPossibleRanks() {
 549         final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
 550         int i = 0;
 551         for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) {
 552             if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) {
 553                 str_array[ i++ ] = e;
 554             }
 555         }
 556         return str_array;
 557     }
 558
 559     final static String[] getAllRanks( final Phylogeny tree ) {
 560         final SortedSet<String> ranks = new TreeSet<String>();
 561         for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
 562             final PhylogenyNode n = it.next();
 563             if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) {
 564                 ranks.add( n.getNodeData().getTaxonomy().getRank() );
 565             }
 566         }
 567         return ForesterUtil.stringSetToArray( ranks );
 568     }
 569
 570     final static String[] getAvailableFontFamiliesSorted() {
 571         return AVAILABLE_FONT_FAMILIES_SORTED;
 572     }
 573
 574     final static boolean isUsOrCanada() {
 575         try {
 576             if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
 577                 return true;
 578             }
 579         }
 580         catch ( final Exception e ) {
 581             return false;
 582         }
 583         return false;
 584     }
 585
 586     final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
 587                                                                       final ControlPanel atv_control,
 588                                                                       final Configuration configuration ) {
 589         if ( ( t != null ) && !t.isEmpty() ) {
 590             if ( !AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
 591                 atv_control.setDrawPhylogram( false );
 592                 atv_control.setDrawPhylogramEnabled( false );
 593             }
 594             if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) {
 595                 if ( atv_control.getDisplayAsPhylogramCb() != null ) {
 596                     if ( AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
 597                         atv_control.setDrawPhylogram( true );
 598                         atv_control.setDrawPhylogramEnabled( true );
 599                     }
 600                     else {
 601                         atv_control.setDrawPhylogram( false );
 602                     }
 603                 }
 604             }
 605             if ( configuration.doGuessCheckOption( Configuration.write_confidence_values ) ) {
 606                 if ( atv_control.getWriteConfidenceCb() != null ) {
 607                     if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( t ) ) {
 608                         atv_control.setCheckbox( Configuration.write_confidence_values, true );
 609                     }
 610                     else {
 611                         atv_control.setCheckbox( Configuration.write_confidence_values, false );
 612                     }
 613                 }
 614             }
 615             if ( configuration.doGuessCheckOption( Configuration.write_events ) ) {
 616                 if ( atv_control.getShowEventsCb() != null ) {
 617                     if ( AptxUtil.isHasAtLeastNodeWithEvent( t ) ) {
 618                         atv_control.setCheckbox( Configuration.write_events, true );
 619                     }
 620                     else {
 621                         atv_control.setCheckbox( Configuration.write_events, false );
 622                     }
 623                 }
 624             }
 625         }
 626     }
 627
 628     final static void openWebsite( final String url, final boolean is_applet, final JApplet applet ) throws IOException {
 629         try {
 630             AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, Constants.PRG_NAME );
 631         }
 632         catch ( final Exception e ) {
 633             throw new IOException( e );
 634         }
 635     }
 636
 637     final static void outOfMemoryError( final OutOfMemoryError e ) {
 638         System.err.println();
 639         System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
 640         System.err.println();
 641         e.printStackTrace();
 642         System.err.println();
 643         JOptionPane.showMessageDialog( null,
 644                                        "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option"
 645                                                + "\n\nError: " + e.getLocalizedMessage(),
 646                                        "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
 647                                        JOptionPane.ERROR_MESSAGE );
 648         System.exit( -1 );
 649     }
 650
 651     final static void printAppletMessage( final String applet_name, final String message ) {
 652         System.out.println( "[" + applet_name + "] > " + message );
 653     }
 654
 655     final public static Phylogeny[] readPhylogeniesFromUrl( final URL url,
 656                                                             final boolean phyloxml_validate_against_xsd,
 657                                                             final boolean replace_underscores,
 658                                                             final boolean internal_numbers_are_confidences,
 659                                                             final TAXONOMY_EXTRACTION taxonomy_extraction,
 660                                                             final boolean midpoint_reroot )
 661             throws FileNotFoundException, IOException {
 662         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 663         final PhylogenyParser parser;
 664         boolean nhx_or_nexus = false;
 665         if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
 666             parser = new TolParser();
 667         }
 668         else {
 669             parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
 670             if ( parser instanceof NHXParser ) {
 671                 nhx_or_nexus = true;
 672                 final NHXParser nhx = ( NHXParser ) parser;
 673                 nhx.setReplaceUnderscores( replace_underscores );
 674                 nhx.setIgnoreQuotes( false );
 675                 nhx.setTaxonomyExtraction( taxonomy_extraction );
 676             }
 677             else if ( parser instanceof NexusPhylogeniesParser ) {
 678                 nhx_or_nexus = true;
 679                 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
 680                 nex.setReplaceUnderscores( replace_underscores );
 681                 nex.setIgnoreQuotes( false );
 682             }
 683         }
 684         AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
 685         final URLConnection url_connection = url.openConnection();
 686         url_connection.setDefaultUseCaches( false );
 687         final InputStream i = url_connection.getInputStream();
 688         final Phylogeny[] phys = factory.create( i, parser );
 689         i.close();
 690         if ( phys != null ) {
 691             if ( nhx_or_nexus && internal_numbers_are_confidences ) {
 692                 for( final Phylogeny phy : phys ) {
 693                     PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
 694                 }
 695             }
 696             if ( midpoint_reroot ) {
 697                 for( final Phylogeny phy : phys ) {
 698                     PhylogenyMethods.midpointRoot( phy );
 699                     PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
 700                 }
 701             }
 702         }
 703         return phys;
 704     }
 705
 706     final static void removeBranchColors( final Phylogeny phy ) {
 707         for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
 708             it.next().getBranchData().setBranchColor( null );
 709         }
 710     }
 711
 712     final static void removeVisualStyles( final Phylogeny phy ) {
 713         for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
 714             it.next().getNodeData().setNodeVisualData( null );
 715         }
 716     }
 717
 718     final static void unexpectedError( final Error e ) {
 719         System.err.println();
 720         e.printStackTrace( System.err );
 721         System.err.println();
 722         final StringBuffer sb = new StringBuffer();
 723         for( final StackTraceElement s : e.getStackTrace() ) {
 724             sb.append( s + "\n" );
 725         }
 726         JOptionPane
 727                 .showMessageDialog( null,
 728                                     "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
 729                                             + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
 730                                             + sb,
 731                                     "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
 732                                     JOptionPane.ERROR_MESSAGE );
 733         System.exit( -1 );
 734     }
 735
 736     final static void unexpectedException( final Exception e ) {
 737         System.err.println();
 738         e.printStackTrace( System.err );
 739         System.err.println();
 740         final StringBuffer sb = new StringBuffer();
 741         for( final StackTraceElement s : e.getStackTrace() ) {
 742             sb.append( s + "\n" );
 743         }
 744         JOptionPane.showMessageDialog( null,
 745                                        "An unexpected exception has occured. \nPlease contact: "
 746                                                + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
 747                                                + "\n" + sb,
 748                                        "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
 749                                        JOptionPane.ERROR_MESSAGE );
 750     }
 751
 752     final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
 753                                                                        int width,
 754                                                                        int height,
 755                                                                        final TreePanel tree_panel,
 756                                                                        final ControlPanel ac,
 757                                                                        final GraphicsExportType type,
 758                                                                        final Options options ) throws IOException {
 759         if ( !options.isGraphicsExportUsingActualSize() ) {
 760             if ( options.isGraphicsExportVisibleOnly() ) {
 761                 throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
 762             }
 763             tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
 764             tree_panel.resetPreferredSize();
 765             tree_panel.repaint();
 766         }
 767         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
 768                                                                    RenderingHints.VALUE_RENDER_QUALITY );
 769         rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
 770         if ( options.isAntialiasPrint() ) {
 771             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
 772             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
 773         }
 774         else {
 775             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
 776             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
 777         }
 778         final Phylogeny phylogeny = tree_panel.getPhylogeny();
 779         if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
 780             return "";
 781         }
 782         Rectangle visible = null;
 783         if ( !options.isGraphicsExportUsingActualSize() ) {
 784             width = options.getPrintSizeX();
 785             height = options.getPrintSizeY();
 786         }
 787         else if ( options.isGraphicsExportVisibleOnly() ) {
 788             visible = tree_panel.getVisibleRect();
 789             width = visible.width;
 790             height = visible.height;
 791         }
 792         final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
 793         Graphics2D g2d = buffered_img.createGraphics();
 794         g2d.setRenderingHints( rendering_hints );
 795         int x = 0;
 796         int y = 0;
 797         if ( options.isGraphicsExportVisibleOnly() ) {
 798             g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
 799             g2d.setClip( null );
 800             x = visible.x;
 801             y = visible.y;
 802         }
 803         tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
 804         ImageIO.write( buffered_img, type.toString(), baos );
 805         g2d.dispose();
 806         System.gc();
 807         if ( !options.isGraphicsExportUsingActualSize() ) {
 808             tree_panel.getMainPanel().getControlPanel().showWhole();
 809         }
 810         String msg = baos.toString();
 811         if ( ( width > 0 ) && ( height > 0 ) ) {
 812             msg += " [size: " + width + ", " + height + "]";
 813         }
 814         return msg;
 815     }
 816
 817     final static String writePhylogenyToGraphicsFile( final String file_name,
 818                                                       int width,
 819                                                       int height,
 820                                                       final TreePanel tree_panel,
 821                                                       final ControlPanel ac,
 822                                                       final GraphicsExportType type,
 823                                                       final Options options ) throws IOException {
 824         if ( !options.isGraphicsExportUsingActualSize() ) {
 825             if ( options.isGraphicsExportVisibleOnly() ) {
 826                 throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
 827             }
 828             tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
 829             tree_panel.resetPreferredSize();
 830             tree_panel.repaint();
 831         }
 832         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
 833                                                                    RenderingHints.VALUE_RENDER_QUALITY );
 834         rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
 835         if ( options.isAntialiasPrint() ) {
 836             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
 837             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
 838         }
 839         else {
 840             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
 841             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
 842         }
 843         final Phylogeny phylogeny = tree_panel.getPhylogeny();
 844         if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
 845             return "";
 846         }
 847         final File file = new File( file_name );
 848         if ( file.isDirectory() ) {
 849             throw new IOException( "\"" + file_name + "\" is a directory" );
 850         }
 851         Rectangle visible = null;
 852         if ( !options.isGraphicsExportUsingActualSize() ) {
 853             width = options.getPrintSizeX();
 854             height = options.getPrintSizeY();
 855         }
 856         else if ( options.isGraphicsExportVisibleOnly() ) {
 857             visible = tree_panel.getVisibleRect();
 858             width = visible.width;
 859             height = visible.height;
 860         }
 861         final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
 862         Graphics2D g2d = buffered_img.createGraphics();
 863         g2d.setRenderingHints( rendering_hints );
 864         int x = 0;
 865         int y = 0;
 866         if ( options.isGraphicsExportVisibleOnly() ) {
 867             g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
 868             g2d.setClip( null );
 869             x = visible.x;
 870             y = visible.y;
 871         }
 872         tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
 873         if ( type == GraphicsExportType.TIFF ) {
 874             writeToTiff( file, buffered_img );
 875         }
 876         else {
 877             ImageIO.write( buffered_img, type.toString(), file );
 878         }
 879         g2d.dispose();
 880         System.gc();
 881         if ( !options.isGraphicsExportUsingActualSize() ) {
 882             tree_panel.getMainPanel().getControlPanel().showWhole();
 883         }
 884         String msg = file.toString();
 885         if ( ( width > 0 ) && ( height > 0 ) ) {
 886             msg += " [size: " + width + ", " + height + "]";
 887         }
 888         return msg;
 889     }
 890
 891     final static void writeToTiff( final File file, final BufferedImage image ) throws IOException {
 892         // See: http://log.robmeek.com/2005/08/write-tiff-in-java.html
 893         ImageWriter writer = null;
 894         ImageOutputStream ios = null;
 895         // Find an appropriate writer:
 896         final Iterator<ImageWriter> it = ImageIO.getImageWritersByFormatName( "TIF" );
 897         if ( it.hasNext() ) {
 898             writer = it.next();
 899         }
 900         else {
 901             throw new IOException( "failed to get TIFF image writer" );
 902         }
 903         // Setup writer:
 904         ios = ImageIO.createImageOutputStream( file );
 905         writer.setOutput( ios );
 906         final ImageWriteParam image_write_param = new ImageWriteParam( Locale.getDefault() );
 907         image_write_param.setCompressionMode( ImageWriteParam.MODE_EXPLICIT );
 908         // see writeParam.getCompressionTypes() for available compression type
 909         // strings.
 910         image_write_param.setCompressionType( "PackBits" );
 911         final String t[] = image_write_param.getCompressionTypes();
 912         for( final String string : t ) {
 913             System.out.println( string );
 914         }
 915         // Convert to an IIOImage:
 916         final IIOImage iio_image = new IIOImage( image, null, null );
 917         writer.write( null, iio_image, image_write_param );
 918     }
 919
 920     final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException,
 921             SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
 922             InvocationTargetException, InterruptedException {
 923         final String os = System.getProperty( "os.name" );
 924         final Runtime runtime = Runtime.getRuntime();
 925         if ( os.toLowerCase().startsWith( "win" ) ) {
 926             Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
 927         }
 928         else if ( ForesterUtil.isMac() ) {
 929             final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
 930             final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
 931             open_url.invoke( null, new Object[] { url } );
 932         }
 933         else {
 934             final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" };
 935             String browser = null;
 936             for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) {
 937                 if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) {
 938                     browser = browsers[ i ];
 939                 }
 940             }
 941             if ( browser == null ) {
 942                 throw new IOException( "could not find a web browser to open [" + url + "] in" );
 943             }
 944             else {
 945                 runtime.exec( new String[] { browser, url } );
 946             }
 947         }
 948     }
 949
 950     // See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2
 951     // static void openDDBJRest() throws IOException {
 952     // //set URL
 953     // URL url = new URL( "http://xml.nig.ac.jp/rest/Invoke" );
 954     // //set parameter
 955     // String query = "service=GetEntry&method=getDDBJEntry&accession=AB000100";
 956     // //make connection
 957     // URLConnection urlc = url.openConnection();
 958     // //use post mode
 959     // urlc.setDoOutput( true );
 960     // urlc.setAllowUserInteraction( false );
 961     // //send query
 962     // PrintStream ps = new PrintStream( urlc.getOutputStream() );
 963     // ps.print( query );
 964     // ps.close();
 965     // //get result
 966     // BufferedReader br = new BufferedReader( new InputStreamReader(
 967     // urlc.getInputStream() ) );
 968     // String l = null;
 969     // while ( ( l = br.readLine() ) != null ) {
 970     // System.out.println( l );
 971     // }
 972     // br.close();
 973     // }
 974     public static enum GraphicsExportType {
 975         BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
 976
 977         private final String _suffix;
 978
 979         private GraphicsExportType( final String suffix ) {
 980             _suffix = suffix;
 981         }
 982
 983         @Override
 984         public String toString() {
 985             return _suffix;
 986         }
 987     }
 988
 989     final public static Color calculateColorFromString( final String str, final boolean is_taxonomy ) {
 990         final String my_str = str.toUpperCase();
 991         char first = my_str.charAt( 0 );
 992         char second = ' ';
 993         char third = ' ';
 994         if ( my_str.length() > 1 ) {
 995             if ( is_taxonomy ) {
 996                 second = my_str.charAt( 1 );
 997             }
 998             else {
 999                 second = my_str.charAt( my_str.length() - 1 );
1000             }
1001             if ( is_taxonomy ) {
1002                 if ( my_str.length() > 2 ) {
1003                     if ( my_str.indexOf( " " ) > 0 ) {
1004                         third = my_str.charAt( my_str.indexOf( " " ) + 1 );
1005                     }
1006                     else {
1007                         third = my_str.charAt( 2 );
1008                     }
1009                 }
1010             }
1011             else if ( my_str.length() > 2 ) {
1012                 third = my_str.charAt( ( my_str.length() - 1 ) / 2 );
1013             }
1014         }
1015         first = normalizeCharForRGB( first );
1016         second = normalizeCharForRGB( second );
1017         third = normalizeCharForRGB( third );
1018         if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
1019             first = 0;
1020         }
1021         else if ( ( first < 60 ) && ( second < 60 ) && ( third < 60 ) ) {
1022             second = 255;
1023         }
1024         return new Color( first, second, third );
1025     }
1026
1027     final private static char normalizeCharForRGB( char c ) {
1028         c -= 65;
1029         c *= 10.2;
1030         c = c > 255 ? 255 : c;
1031         c = c < 0 ? 0 : c;
1032         return c;
1033     }
1034 }