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

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