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