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