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: www.phylosoft.org/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.lang.reflect.InvocationTargetException;
  40 import java.lang.reflect.Method;
  41 import java.net.URI;
  42 import java.net.URL;
  43 import java.text.ParseException;
  44 import java.util.Arrays;
  45 import java.util.HashMap;
  46 import java.util.Iterator;
  47 import java.util.List;
  48 import java.util.Locale;
  49 import java.util.Map;
  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.analysis.AncestralTaxonomyInference;
  64 import org.forester.io.parsers.PhylogenyParser;
  65 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
  66 import org.forester.io.parsers.tol.TolParser;
  67 import org.forester.io.parsers.util.ParserUtils;
  68 import org.forester.phylogeny.Phylogeny;
  69 import org.forester.phylogeny.PhylogenyMethods;
  70 import org.forester.phylogeny.PhylogenyNode;
  71 import org.forester.phylogeny.data.BranchColor;
  72 import org.forester.phylogeny.data.Distribution;
  73 import org.forester.phylogeny.data.Sequence;
  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.phylogeny.iterators.PreorderTreeIterator;
  79 import org.forester.util.DescriptiveStatistics;
  80 import org.forester.util.ForesterUtil;
  81 import org.forester.ws.uniprot.UniProtTaxonomy;
  82
  83 public final class AptxUtil {
  84
  85     private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
  86                                                                          .getAvailableFontFamilyNames();
  87     static {
  88         Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
  89     }
  90
  91     public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) {
  92         if ( !node.getNodeData().isHasTaxonomy() ) {
  93             node.getNodeData().setTaxonomy( new Taxonomy() );
  94         }
  95     }
  96
  97     public static void ensurePresenceOfSequence( final PhylogenyNode node ) {
  98         if ( !node.getNodeData().isHasSequence() ) {
  99             node.getNodeData().setSequence( new Sequence() );
 100         }
 101     }
 102
 103     final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) {
 104         if ( !node.getNodeData().isHasDistribution() ) {
 105             node.getNodeData().setDistribution( new Distribution( "" ) );
 106         }
 107     }
 108
 109     final public static void ensurePresenceOfDate( final PhylogenyNode node ) {
 110         if ( !node.getNodeData().isHasDate() ) {
 111             node.getNodeData().setDate( new org.forester.phylogeny.data.Date() );
 112         }
 113     }
 114
 115     final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) {
 116         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 117         while ( it.hasNext() ) {
 118             if ( it.next().getBranchData().isHasConfidences() ) {
 119                 return true;
 120             }
 121         }
 122         return false;
 123     }
 124
 125     public static void writePhylogenyToGraphicsFile( final File intree,
 126                                                      final File outfile,
 127                                                      final int width,
 128                                                      final int height,
 129                                                      final GraphicsExportType type,
 130                                                      final Configuration config ) throws IOException {
 131         final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
 132         Phylogeny[] phys = null;
 133         phys = PhylogenyMethods.readPhylogenies( parser, intree );
 134         writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config );
 135     }
 136
 137     public static void writePhylogenyToGraphicsFile( final Phylogeny phy,
 138                                                      final File outfile,
 139                                                      final int width,
 140                                                      final int height,
 141                                                      final GraphicsExportType type,
 142                                                      final Configuration config ) throws IOException {
 143         final Phylogeny[] phys = new Phylogeny[ 1 ];
 144         phys[ 0 ] = phy;
 145         final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
 146         AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
 147                 .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
 148         mf.end();
 149     }
 150
 151     /**
 152      * Returns true if at least one branch has a length larger than zero.
 153      *
 154      *
 155      * @param phy
 156      */
 157     final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
 158         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 159         while ( it.hasNext() ) {
 160             if ( it.next().getDistanceToParent() > 0.0 ) {
 161                 return true;
 162             }
 163         }
 164         return false;
 165     }
 166
 167     final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
 168         final PhylogenyNodeIterator it = phy.iteratorPostorder();
 169         while ( it.hasNext() ) {
 170             if ( it.next().getNodeData().isHasEvent() ) {
 171                 return true;
 172             }
 173         }
 174         return false;
 175     }
 176
 177     public static MaskFormatter createMaskFormatter( final String s ) {
 178         MaskFormatter formatter = null;
 179         try {
 180             formatter = new MaskFormatter( s );
 181         }
 182         catch ( final ParseException e ) {
 183             throw new IllegalArgumentException( e );
 184         }
 185         return formatter;
 186     }
 187
 188     final static void addPhylogeniesToTabs( final Phylogeny[] phys,
 189                                             final String default_name,
 190                                             final String full_path,
 191                                             final Configuration configuration,
 192                                             final MainPanel main_panel ) {
 193         if ( phys.length > Constants.MAX_TREES_TO_LOAD ) {
 194             JOptionPane.showMessageDialog( main_panel, "Attempt to load " + phys.length
 195                     + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME
 196                     + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE );
 197         }
 198         int i = 1;
 199         for( final Phylogeny phy : phys ) {
 200             if ( !phy.isEmpty() ) {
 201                 if ( i <= Constants.MAX_TREES_TO_LOAD ) {
 202                     String my_name = "";
 203                     String my_name_for_file = "";
 204                     if ( phys.length > 1 ) {
 205                         if ( !ForesterUtil.isEmpty( default_name ) ) {
 206                             my_name = new String( default_name );
 207                         }
 208                         if ( !ForesterUtil.isEmpty( full_path ) ) {
 209                             my_name_for_file = new String( full_path );
 210                         }
 211                         else if ( !ForesterUtil.isEmpty( default_name ) ) {
 212                             my_name_for_file = new String( default_name );
 213                         }
 214                         String suffix = "";
 215                         if ( my_name_for_file.indexOf( '.' ) > 0 ) {
 216                             suffix = my_name_for_file.substring( my_name_for_file.lastIndexOf( '.' ),
 217                                                                  my_name_for_file.length() );
 218                             my_name_for_file = my_name_for_file.substring( 0, my_name_for_file.lastIndexOf( '.' ) );
 219                         }
 220                         if ( !ForesterUtil.isEmpty( my_name_for_file ) ) {
 221                             my_name_for_file += "_";
 222                         }
 223                         if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 224                             my_name_for_file += phy.getName().replaceAll( " ", "_" );
 225                         }
 226                         else if ( phy.getIdentifier() != null ) {
 227                             final StringBuffer sb = new StringBuffer();
 228                             if ( !ForesterUtil.isEmpty( phy.getIdentifier().getProvider() ) ) {
 229                                 sb.append( phy.getIdentifier().getProvider() );
 230                                 sb.append( "_" );
 231                             }
 232                             sb.append( phy.getIdentifier().getValue() );
 233                             my_name_for_file += sb;
 234                         }
 235                         else {
 236                             my_name_for_file += i;
 237                         }
 238                         if ( !ForesterUtil.isEmpty( my_name ) && ForesterUtil.isEmpty( phy.getName() )
 239                                 && ( phy.getIdentifier() == null ) ) {
 240                             my_name = my_name + " [" + i + "]";
 241                         }
 242                         if ( !ForesterUtil.isEmpty( suffix ) ) {
 243                             my_name_for_file += suffix;
 244                         }
 245                     }
 246                     else {
 247                         if ( !ForesterUtil.isEmpty( default_name ) ) {
 248                             my_name = new String( default_name );
 249                         }
 250                         my_name_for_file = "";
 251                         if ( !ForesterUtil.isEmpty( full_path ) ) {
 252                             my_name_for_file = new String( full_path );
 253                         }
 254                         else if ( !ForesterUtil.isEmpty( default_name ) ) {
 255                             my_name_for_file = new String( default_name );
 256                         }
 257                         if ( ForesterUtil.isEmpty( my_name_for_file ) ) {
 258                             if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 259                                 my_name_for_file = new String( phy.getName() ).replaceAll( " ", "_" );
 260                             }
 261                             else if ( phy.getIdentifier() != null ) {
 262                                 final StringBuffer sb = new StringBuffer();
 263                                 if ( !ForesterUtil.isEmpty( phy.getIdentifier().getProvider() ) ) {
 264                                     sb.append( phy.getIdentifier().getProvider() );
 265                                     sb.append( "_" );
 266                                 }
 267                                 sb.append( phy.getIdentifier().getValue() );
 268                                 my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
 269                             }
 270                         }
 271                     }
 272                     main_panel.addPhylogenyInNewTab( phy, configuration, my_name, full_path );
 273                     main_panel.getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
 274                     lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
 275                     ++i;
 276                 }
 277             }
 278         }
 279     }
 280
 281     final static void addPhylogenyToPanel( final Phylogeny[] phys,
 282                                            final Configuration configuration,
 283                                            final MainPanel main_panel ) {
 284         final Phylogeny phy = phys[ 0 ];
 285         main_panel.addPhylogenyInPanel( phy, configuration );
 286         lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
 287     }
 288
 289     final static Color calculateColorFromString( final String str ) {
 290         final String species_uc = str.toUpperCase();
 291         char first = species_uc.charAt( 0 );
 292         char second = ' ';
 293         char third = ' ';
 294         if ( species_uc.length() > 1 ) {
 295             second = species_uc.charAt( 1 );
 296             if ( species_uc.length() > 2 ) {
 297                 if ( species_uc.indexOf( " " ) > 0 ) {
 298                     third = species_uc.charAt( species_uc.indexOf( " " ) + 1 );
 299                 }
 300                 else {
 301                     third = species_uc.charAt( 2 );
 302                 }
 303             }
 304         }
 305         first = AptxUtil.normalizeCharForRGB( first );
 306         second = AptxUtil.normalizeCharForRGB( second );
 307         third = AptxUtil.normalizeCharForRGB( third );
 308         if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
 309             first = 0;
 310         }
 311         else if ( ( first < 80 ) && ( second < 80 ) && ( third < 80 ) ) {
 312             second = 255;
 313         }
 314         return new Color( first, second, third );
 315     }
 316
 317     // Returns true if the specified format name can be written
 318     final static boolean canWriteFormat( final String format_name ) {
 319         final Iterator<ImageWriter> iter = ImageIO.getImageWritersByFormatName( format_name );
 320         return iter.hasNext();
 321     }
 322
 323     final public static void collapseSpeciesSpecificSubtrees( final Phylogeny phy ) {
 324         boolean inferred = false;
 325         for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
 326             final PhylogenyNode n = it.next();
 327             if ( !n.isExternal() && !n.isCollapse() && ( n.getNumberOfDescendants() > 1 ) ) {
 328                 final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( n );
 329                 if ( ( taxs != null ) && ( taxs.size() == 1 ) ) {
 330                     AptxUtil.collapseSubtree( n, true );
 331                     if ( !n.getNodeData().isHasTaxonomy() ) {
 332                         n.getNodeData().setTaxonomy( ( Taxonomy ) n.getAllExternalDescendants().get( 0 ).getNodeData()
 333                                 .getTaxonomy().copy() );
 334                     }
 335                     inferred = true;
 336                 }
 337                 else {
 338                     n.setCollapse( false );
 339                 }
 340             }
 341         }
 342         if ( inferred ) {
 343             phy.setRerootable( false );
 344         }
 345     }
 346
 347     final static void collapseSubtree( final PhylogenyNode node, final boolean collapse ) {
 348         node.setCollapse( collapse );
 349         if ( node.isExternal() ) {
 350             return;
 351         }
 352         final PhylogenyNodeIterator it = new PreorderTreeIterator( node );
 353         while ( it.hasNext() ) {
 354             it.next().setCollapse( collapse );
 355         }
 356     }
 357
 358     final static void colorPhylogenyAccordingToConfidenceValues( final Phylogeny tree, final TreePanel tree_panel ) {
 359         double max_conf = 0.0;
 360         for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
 361             final PhylogenyNode n = it.next();
 362             n.getBranchData().setBranchColor( null );
 363             if ( n.getBranchData().isHasConfidences() ) {
 364                 final double conf = PhylogenyMethods.getConfidenceValue( n );
 365                 if ( conf > max_conf ) {
 366                     max_conf = conf;
 367                 }
 368             }
 369         }
 370         if ( max_conf > 0.0 ) {
 371             final Color bg = tree_panel.getTreeColorSet().getBackgroundColor();
 372             final Color br = tree_panel.getTreeColorSet().getBranchColor();
 373             for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
 374                 final PhylogenyNode n = it.next();
 375                 if ( n.getBranchData().isHasConfidences() ) {
 376                     final double conf = PhylogenyMethods.getConfidenceValue( n );
 377                     final BranchColor c = new BranchColor( ForesterUtil.calcColor( conf, 0.0, max_conf, bg, br ) );
 378                     colorizeSubtree( n, c );
 379                 }
 380             }
 381         }
 382     }
 383
 384     final static int colorPhylogenyAccordingToRanks( final Phylogeny tree, final String rank, final TreePanel tree_panel ) {
 385         final Map<String, Color> true_lineage_to_color_map = new HashMap<String, Color>();
 386         int colorizations = 0;
 387         for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
 388             final PhylogenyNode n = it.next();
 389             if ( n.getNodeData().isHasTaxonomy()
 390                     && ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() )
 391                             || !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) || !ForesterUtil
 392                             .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) {
 393                 if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() )
 394                         && n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) ) {
 395                     final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( n.getNodeData()
 396                             .getTaxonomy() ) );
 397                     colorizeSubtree( n, c );
 398                     ++colorizations;
 399                     if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
 400                         true_lineage_to_color_map.put( n.getNodeData().getTaxonomy().getScientificName(), c.getValue() );
 401                     }
 402                 }
 403             }
 404         }
 405         for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
 406             final PhylogenyNode node = it.next();
 407             if ( ( node.getBranchData().getBranchColor() == null ) && node.getNodeData().isHasTaxonomy()
 408                     && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getLineage() ) ) {
 409                 boolean success = false;
 410                 if ( !true_lineage_to_color_map.isEmpty() ) {
 411                     for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
 412                         if ( true_lineage_to_color_map.containsKey( lin ) ) {
 413                             colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) );
 414                             ++colorizations;
 415                             success = true;
 416                             break;
 417                         }
 418                     }
 419                 }
 420                 if ( !success ) {
 421                     final Map<String, String> lineage_to_rank_map = MainPanel.getLineageToRankMap();
 422                     for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) {
 423                         final Taxonomy temp_tax = new Taxonomy();
 424                         temp_tax.setScientificName( lin );
 425                         if ( lineage_to_rank_map.containsKey( lin )
 426                                 && !ForesterUtil.isEmpty( lineage_to_rank_map.get( lin ) )
 427                                 && lineage_to_rank_map.get( lin ).equalsIgnoreCase( rank ) ) {
 428                             final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( temp_tax ) );
 429                             colorizeSubtree( node, c );
 430                             ++colorizations;
 431                             true_lineage_to_color_map.put( lin, c.getValue() );
 432                             break;
 433                         }
 434                         else {
 435                             UniProtTaxonomy up = null;
 436                             try {
 437                                 up = AncestralTaxonomyInference.obtainUniProtTaxonomy( temp_tax, null, null );
 438                             }
 439                             catch ( final Exception e ) {
 440                                 e.printStackTrace();
 441                             }
 442                             if ( ( up != null ) && !ForesterUtil.isEmpty( up.getRank() ) ) {
 443                                 lineage_to_rank_map.put( lin, up.getRank() );
 444                                 if ( up.getRank().equalsIgnoreCase( rank ) ) {
 445                                     final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( temp_tax ) );
 446                                     colorizeSubtree( node, c );
 447                                     ++colorizations;
 448                                     true_lineage_to_color_map.put( lin, c.getValue() );
 449                                     break;
 450                                 }
 451                             }
 452                         }
 453                     }
 454                 }
 455             }
 456         }
 457         return colorizations;
 458     }
 459
 460     private static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) {
 461         node.getBranchData().setBranchColor( c );
 462         final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( node );
 463         for( final PhylogenyNode desc : descs ) {
 464             desc.getBranchData().setBranchColor( c );
 465         }
 466     }
 467
 468     final static String[] getAllRanks( final Phylogeny tree ) {
 469         final SortedSet<String> ranks = new TreeSet<String>();
 470         for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
 471             final PhylogenyNode n = it.next();
 472             if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) {
 473                 ranks.add( n.getNodeData().getTaxonomy().getRank() );
 474             }
 475         }
 476         return ForesterUtil.stringSetToArray( ranks );
 477     }
 478
 479     public static String[] getAllPossibleRanks() {
 480         final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
 481         int i = 0;
 482         for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) {
 483             if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) {
 484                 str_array[ i++ ] = e;
 485             }
 486         }
 487         return str_array;
 488     }
 489
 490     final static void colorPhylogenyAccordingToExternalTaxonomy( final Phylogeny tree, final TreePanel tree_panel ) {
 491         for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
 492             it.next().getBranchData().setBranchColor( null );
 493         }
 494         for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
 495             final PhylogenyNode n = it.next();
 496             if ( !n.getBranchData().isHasBranchColor() ) {
 497                 final Taxonomy tax = PhylogenyMethods.getExternalDescendantsTaxonomy( n );
 498                 if ( tax != null ) {
 499                     n.getBranchData().setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
 500                     final List<PhylogenyNode> descs = PhylogenyMethods.getAllDescendants( n );
 501                     for( final PhylogenyNode desc : descs ) {
 502                         desc.getBranchData()
 503                                 .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) );
 504                     }
 505                 }
 506             }
 507         }
 508     }
 509
 510     final static String crateBasicInformation( final Phylogeny phy ) {
 511         final StringBuilder desc = new StringBuilder();
 512         if ( ( phy != null ) && !phy.isEmpty() ) {
 513             if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
 514                 desc.append( "Name: " );
 515                 desc.append( phy.getName() );
 516                 desc.append( "\n" );
 517             }
 518             if ( phy.getIdentifier() != null ) {
 519                 desc.append( "Id: " );
 520                 desc.append( phy.getIdentifier() );
 521                 desc.append( "\n" );
 522             }
 523             desc.append( "Rooted: " );
 524             desc.append( phy.isRooted() );
 525             desc.append( "\n" );
 526             desc.append( "Rerootable: " );
 527             desc.append( phy.isRerootable() );
 528             desc.append( "\n" );
 529             desc.append( "Node sum: " );
 530             desc.append( phy.getNodeCount() );
 531             desc.append( "\n" );
 532             desc.append( "External node sum: " );
 533             desc.append( phy.getNumberOfExternalNodes() );
 534             desc.append( "\n" );
 535             desc.append( "Internal node sum: " );
 536             desc.append( phy.getNodeCount() - phy.getNumberOfExternalNodes() );
 537             desc.append( "\n" );
 538             desc.append( "Branche sum: " );
 539             desc.append( phy.getNumberOfBranches() );
 540             desc.append( "\n" );
 541             desc.append( "Depth: " );
 542             desc.append( PhylogenyMethods.calculateMaxDepth( phy ) );
 543             desc.append( "\n" );
 544             desc.append( "Maximum distance to root: " );
 545             desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) );
 546             desc.append( "\n" );
 547             desc.append( "Descendants per node statistics: " );
 548             final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
 549             desc.append( "\n" );
 550             desc.append( "    Median: " + ForesterUtil.round( ds.median(), 2 ) );
 551             desc.append( "\n" );
 552             desc.append( "    Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) );
 553             desc.append( "\n" );
 554             desc.append( "    SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) );
 555             desc.append( "\n" );
 556             desc.append( "    Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
 557             desc.append( "\n" );
 558             desc.append( "    Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) );
 559             desc.append( "\n" );
 560             final DescriptiveStatistics cs = PhylogenyMethods.calculatConfidenceStatistics( phy );
 561             if ( cs.getN() > 1 ) {
 562                 desc.append( "Support statistics: " );
 563                 desc.append( "\n" );
 564                 desc.append( "    Branches with support: " + cs.getN() );
 565                 desc.append( "\n" );
 566                 desc.append( "    Median: " + ForesterUtil.round( cs.median(), 6 ) );
 567                 desc.append( "\n" );
 568                 desc.append( "    Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
 569                 desc.append( "\n" );
 570                 if ( cs.getN() > 2 ) {
 571                     desc.append( "    SD: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) );
 572                     desc.append( "\n" );
 573                 }
 574                 desc.append( "    Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) );
 575                 desc.append( "\n" );
 576                 desc.append( "    Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) );
 577                 desc.append( "\n" );
 578             }
 579             final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() );
 580             if ( taxs != null ) {
 581                 desc.append( "Distinct external taxonomies: " );
 582                 desc.append( taxs.size() );
 583             }
 584         }
 585         return desc.toString();
 586     }
 587
 588     /**
 589      * Exits with -1.
 590      *
 591      *
 592      * @param message
 593      *            to message to be printed
 594      */
 595     final static void dieWithSystemError( final String message ) {
 596         System.out.println();
 597         System.out.println( Constants.PRG_NAME + " encountered the following system error: " + message );
 598         System.out.println( "Please contact the authors." );
 599         System.out.println( Constants.PRG_NAME + " needs to close." );
 600         System.out.println();
 601         System.exit( -1 );
 602     }
 603
 604     final static String[] getAvailableFontFamiliesSorted() {
 605         return AVAILABLE_FONT_FAMILIES_SORTED;
 606     }
 607
 608     final static void inferCommonPartOfScientificNames( final Phylogeny tree ) {
 609         boolean inferred = false;
 610         for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
 611             final PhylogenyNode n = it.next();
 612             if ( !n.getNodeData().isHasTaxonomy() && !n.isExternal() ) {
 613                 final String sn = PhylogenyMethods.inferCommonPartOfScientificNameOfDescendants( n );
 614                 if ( !ForesterUtil.isEmpty( sn ) ) {
 615                     n.getNodeData().setTaxonomy( new Taxonomy() );
 616                     n.getNodeData().getTaxonomy().setScientificName( sn );
 617                     inferred = true;
 618                 }
 619             }
 620         }
 621         if ( inferred ) {
 622             tree.setRerootable( false );
 623         }
 624     }
 625
 626     final static boolean isHasAssignedEvent( final PhylogenyNode node ) {
 627         if ( !node.getNodeData().isHasEvent() ) {
 628             return false;
 629         }
 630         if ( ( node.getNodeData().getEvent() ).isUnassigned() ) {
 631             return false;
 632         }
 633         return true;
 634     }
 635
 636     final static boolean isJava15() {
 637         try {
 638             final String s = ForesterUtil.JAVA_VERSION;
 639             return s.startsWith( "1.5" );
 640         }
 641         catch ( final Exception e ) {
 642             ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
 643             return false;
 644         }
 645     }
 646
 647     final static boolean isMac() {
 648         try {
 649             final String s = ForesterUtil.OS_NAME.toLowerCase();
 650             return s.startsWith( "mac" );
 651         }
 652         catch ( final Exception e ) {
 653             ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
 654             return false;
 655         }
 656     }
 657
 658     final static boolean isUsOrCanada() {
 659         try {
 660             if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
 661                 return true;
 662             }
 663         }
 664         catch ( final Exception e ) {
 665             return false;
 666         }
 667         return false;
 668     }
 669
 670     final static boolean isWindows() {
 671         try {
 672             final String s = ForesterUtil.OS_NAME.toLowerCase();
 673             return s.indexOf( "win" ) > -1;
 674         }
 675         catch ( final Exception e ) {
 676             ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
 677             return false;
 678         }
 679     }
 680
 681     final static void launchWebBrowser( final URI uri,
 682                                         final boolean is_applet,
 683                                         final JApplet applet,
 684                                         final String frame_name ) throws IOException {
 685         if ( is_applet ) {
 686             applet.getAppletContext().showDocument( uri.toURL(), frame_name );
 687         }
 688         else {
 689             // This requires Java 1.6:
 690             // =======================
 691             // boolean no_desktop = false;
 692             // try {
 693             // if ( Desktop.isDesktopSupported() ) {
 694             // System.out.println( "desktop supported" );
 695             // final Desktop dt = Desktop.getDesktop();
 696             // dt.browse( uri );
 697             // }
 698             // else {
 699             // no_desktop = true;
 700             // }
 701             // }
 702             // catch ( final Exception ex ) {
 703             // ex.printStackTrace();
 704             // no_desktop = true;
 705             // }
 706             // catch ( final Error er ) {
 707             // er.printStackTrace();
 708             // no_desktop = true;
 709             // }
 710             // if ( no_desktop ) {
 711             // System.out.println( "desktop not supported" );
 712             try {
 713                 openUrlInWebBrowser( uri.toString() );
 714             }
 715             catch ( final Exception e ) {
 716                 throw new IOException( e );
 717             }
 718             // }
 719         }
 720     }
 721
 722     final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
 723                                                                       final ControlPanel atv_control,
 724                                                                       final Configuration configuration ) {
 725         if ( ( t != null ) && !t.isEmpty() ) {
 726             if ( !AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
 727                 atv_control.setDrawPhylogram( false );
 728                 atv_control.setDrawPhylogramEnabled( false );
 729             }
 730             if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) {
 731                 if ( atv_control.getDisplayAsPhylogramCb() != null ) {
 732                     if ( AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
 733                         atv_control.setDrawPhylogram( true );
 734                         atv_control.setDrawPhylogramEnabled( true );
 735                     }
 736                     else {
 737                         atv_control.setDrawPhylogram( false );
 738                     }
 739                 }
 740             }
 741             if ( configuration.doGuessCheckOption( Configuration.write_confidence_values ) ) {
 742                 if ( atv_control.getWriteConfidenceCb() != null ) {
 743                     if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( t ) ) {
 744                         atv_control.setCheckbox( Configuration.write_confidence_values, true );
 745                     }
 746                     else {
 747                         atv_control.setCheckbox( Configuration.write_confidence_values, false );
 748                     }
 749                 }
 750             }
 751             if ( configuration.doGuessCheckOption( Configuration.write_events ) ) {
 752                 if ( atv_control.getShowEventsCb() != null ) {
 753                     if ( AptxUtil.isHasAtLeastNodeWithEvent( t ) ) {
 754                         atv_control.setCheckbox( Configuration.write_events, true );
 755                     }
 756                     else {
 757                         atv_control.setCheckbox( Configuration.write_events, false );
 758                     }
 759                 }
 760             }
 761         }
 762     }
 763
 764     final private static char normalizeCharForRGB( char c ) {
 765         c -= 65;
 766         c *= 10.2;
 767         c = c > 255 ? 255 : c;
 768         c = c < 0 ? 0 : c;
 769         return c;
 770     }
 771
 772     final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException,
 773             SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
 774             InvocationTargetException, InterruptedException {
 775         final String os = System.getProperty( "os.name" );
 776         final Runtime runtime = Runtime.getRuntime();
 777         if ( os.toLowerCase().startsWith( "win" ) ) {
 778             Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
 779         }
 780         else if ( isMac() ) {
 781             final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
 782             final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
 783             open_url.invoke( null, new Object[] { url } );
 784         }
 785         else {
 786             final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" };
 787             String browser = null;
 788             for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) {
 789                 if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) {
 790                     browser = browsers[ i ];
 791                 }
 792             }
 793             if ( browser == null ) {
 794                 throw new IOException( "could not find a web browser to open [" + url + "] in" );
 795             }
 796             else {
 797                 runtime.exec( new String[] { browser, url } );
 798             }
 799         }
 800     }
 801
 802     final static void openWebsite( final String url, final boolean is_applet, final JApplet applet ) throws IOException {
 803         try {
 804             AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, Constants.PRG_NAME );
 805         }
 806         catch ( final Exception e ) {
 807             throw new IOException( e );
 808         }
 809     }
 810
 811     final static void printAppletMessage( final String applet_name, final String message ) {
 812         System.out.println( "[" + applet_name + "] > " + message );
 813     }
 814
 815     public final static void printWarningMessage( final String name, final String message ) {
 816         System.out.println( "[" + name + "] > " + message );
 817     }
 818
 819     final static Phylogeny[] readPhylogeniesFromUrl( final URL url, final boolean phyloxml_validate_against_xsd )
 820             throws FileNotFoundException, IOException {
 821         final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 822         PhylogenyParser parser = null;
 823         if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
 824             parser = new TolParser();
 825         }
 826         else {
 827             parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
 828         }
 829         return factory.create( url.openStream(), parser );
 830     }
 831
 832     final static void removeBranchColors( final Phylogeny phy ) {
 833         for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
 834             it.next().getBranchData().setBranchColor( null );
 835         }
 836     }
 837
 838     final static void showErrorMessage( final Component parent, final String error_msg ) {
 839         printAppletMessage( Constants.PRG_NAME, error_msg );
 840         JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION
 841                 + "] Error", JOptionPane.ERROR_MESSAGE );
 842     }
 843
 844     final static void unexpectedError( final Error err ) {
 845         err.printStackTrace();
 846         final StringBuffer sb = new StringBuffer();
 847         for( final StackTraceElement s : err.getStackTrace() ) {
 848             sb.append( s + "\n" );
 849         }
 850         JOptionPane
 851                 .showMessageDialog( null,
 852                                     "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
 853                                             + Constants.AUTHOR_EMAIL + " \nError: " + err + "\n" + sb,
 854                                     "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
 855                                     JOptionPane.ERROR_MESSAGE );
 856         System.exit( -1 );
 857     }
 858
 859     final static void unexpectedException( final Exception ex ) {
 860         ex.printStackTrace();
 861         final StringBuffer sb = new StringBuffer();
 862         for( final StackTraceElement s : ex.getStackTrace() ) {
 863             sb.append( s + "\n" );
 864         }
 865         JOptionPane.showMessageDialog( null, "An unexpected exception has occured. \nPlease contact: "
 866                 + Constants.AUTHOR_EMAIL + " \nException: " + ex + "\n" + sb, "Unexpected Exception ["
 867                 + Constants.PRG_NAME + Constants.VERSION + "]", JOptionPane.ERROR_MESSAGE );
 868     }
 869
 870     final static String writePhylogenyToGraphicsFile( final String file_name,
 871                                                       int width,
 872                                                       int height,
 873                                                       final TreePanel tree_panel,
 874                                                       final ControlPanel ac,
 875                                                       final GraphicsExportType type,
 876                                                       final Options options ) throws IOException {
 877         if ( !options.isGraphicsExportUsingActualSize() ) {
 878             if ( options.isGraphicsExportVisibleOnly() ) {
 879                 throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
 880             }
 881             tree_panel.setParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
 882             tree_panel.resetPreferredSize();
 883             tree_panel.repaint();
 884         }
 885         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
 886                                                                    RenderingHints.VALUE_RENDER_QUALITY );
 887         rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
 888         if ( options.isAntialiasPrint() ) {
 889             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
 890             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
 891         }
 892         else {
 893             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
 894             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
 895         }
 896         final Phylogeny phylogeny = tree_panel.getPhylogeny();
 897         if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
 898             return "";
 899         }
 900         final File file = new File( file_name );
 901         if ( file.isDirectory() ) {
 902             throw new IOException( "\"" + file_name + "\" is a directory" );
 903         }
 904         Rectangle visible = null;
 905         if ( !options.isGraphicsExportUsingActualSize() ) {
 906             width = options.getPrintSizeX();
 907             height = options.getPrintSizeY();
 908         }
 909         else if ( options.isGraphicsExportVisibleOnly() ) {
 910             visible = tree_panel.getVisibleRect();
 911             width = visible.width;
 912             height = visible.height;
 913         }
 914         final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
 915         Graphics2D g2d = buffered_img.createGraphics();
 916         g2d.setRenderingHints( rendering_hints );
 917         int x = 0;
 918         int y = 0;
 919         if ( options.isGraphicsExportVisibleOnly() ) {
 920             g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
 921             g2d.setClip( null );
 922             x = visible.x;
 923             y = visible.y;
 924         }
 925         tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
 926         if ( type == GraphicsExportType.TIFF ) {
 927             writeToTiff( file, buffered_img );
 928         }
 929         else {
 930             ImageIO.write( buffered_img, type.toString(), file );
 931         }
 932         g2d.dispose();
 933         System.gc();
 934         if ( !options.isGraphicsExportUsingActualSize() ) {
 935             tree_panel.getMainPanel().getControlPanel().showWhole();
 936         }
 937         String msg = file.toString();
 938         if ( ( width > 0 ) && ( height > 0 ) ) {
 939             msg += " [size: " + width + ", " + height + "]";
 940         }
 941         return msg;
 942     }
 943
 944     public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile,
 945                                                                          final int width,
 946                                                                          final int height,
 947                                                                          final TreePanel tree_panel,
 948                                                                          final ControlPanel ac,
 949                                                                          final GraphicsExportType type,
 950                                                                          final Options options ) throws IOException {
 951         tree_panel.setParametersForPainting( width, height, true );
 952         tree_panel.resetPreferredSize();
 953         tree_panel.repaint();
 954         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
 955                                                                    RenderingHints.VALUE_RENDER_QUALITY );
 956         rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
 957         if ( options.isAntialiasPrint() ) {
 958             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
 959             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
 960         }
 961         else {
 962             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
 963             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
 964         }
 965         final Phylogeny phylogeny = tree_panel.getPhylogeny();
 966         if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
 967             return;
 968         }
 969         if ( outfile.isDirectory() ) {
 970             throw new IOException( "\"" + outfile + "\" is a directory" );
 971         }
 972         final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
 973         final Graphics2D g2d = buffered_img.createGraphics();
 974         g2d.setRenderingHints( rendering_hints );
 975         tree_panel.paintPhylogeny( g2d, false, true, width, height, 0, 0 );
 976         if ( type == GraphicsExportType.TIFF ) {
 977             writeToTiff( outfile, buffered_img );
 978         }
 979         else {
 980             ImageIO.write( buffered_img, type.toString(), outfile );
 981         }
 982         g2d.dispose();
 983     }
 984
 985     final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
 986                                                                        int width,
 987                                                                        int height,
 988                                                                        final TreePanel tree_panel,
 989                                                                        final ControlPanel ac,
 990                                                                        final GraphicsExportType type,
 991                                                                        final Options options ) throws IOException {
 992         if ( !options.isGraphicsExportUsingActualSize() ) {
 993             if ( options.isGraphicsExportVisibleOnly() ) {
 994                 throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
 995             }
 996             tree_panel.setParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
 997             tree_panel.resetPreferredSize();
 998             tree_panel.repaint();
 999         }
1000         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
1001                                                                    RenderingHints.VALUE_RENDER_QUALITY );
1002         rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
1003         if ( options.isAntialiasPrint() ) {
1004             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
1005             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
1006         }
1007         else {
1008             rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
1009             rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
1010         }
1011         final Phylogeny phylogeny = tree_panel.getPhylogeny();
1012         if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
1013             return "";
1014         }
1015         Rectangle visible = null;
1016         if ( !options.isGraphicsExportUsingActualSize() ) {
1017             width = options.getPrintSizeX();
1018             height = options.getPrintSizeY();
1019         }
1020         else if ( options.isGraphicsExportVisibleOnly() ) {
1021             visible = tree_panel.getVisibleRect();
1022             width = visible.width;
1023             height = visible.height;
1024         }
1025         final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
1026         Graphics2D g2d = buffered_img.createGraphics();
1027         g2d.setRenderingHints( rendering_hints );
1028         int x = 0;
1029         int y = 0;
1030         if ( options.isGraphicsExportVisibleOnly() ) {
1031             g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
1032             g2d.setClip( null );
1033             x = visible.x;
1034             y = visible.y;
1035         }
1036         tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
1037         ImageIO.write( buffered_img, type.toString(), baos );
1038         g2d.dispose();
1039         System.gc();
1040         if ( !options.isGraphicsExportUsingActualSize() ) {
1041             tree_panel.getMainPanel().getControlPanel().showWhole();
1042         }
1043         String msg = baos.toString();
1044         if ( ( width > 0 ) && ( height > 0 ) ) {
1045             msg += " [size: " + width + ", " + height + "]";
1046         }
1047         return msg;
1048     }
1049
1050     final static void writeToTiff( final File file, final BufferedImage image ) throws IOException {
1051         // See: http://log.robmeek.com/2005/08/write-tiff-in-java.html
1052         ImageWriter writer = null;
1053         ImageOutputStream ios = null;
1054         // Find an appropriate writer:
1055         final Iterator<ImageWriter> it = ImageIO.getImageWritersByFormatName( "TIF" );
1056         if ( it.hasNext() ) {
1057             writer = it.next();
1058         }
1059         else {
1060             throw new IOException( "failed to get TIFF image writer" );
1061         }
1062         // Setup writer:
1063         ios = ImageIO.createImageOutputStream( file );
1064         writer.setOutput( ios );
1065         final ImageWriteParam image_write_param = new ImageWriteParam( Locale.getDefault() );
1066         image_write_param.setCompressionMode( ImageWriteParam.MODE_EXPLICIT );
1067         // see writeParam.getCompressionTypes() for available compression type
1068         // strings.
1069         image_write_param.setCompressionType( "PackBits" );
1070         final String t[] = image_write_param.getCompressionTypes();
1071         for( final String string : t ) {
1072             System.out.println( string );
1073         }
1074         // Convert to an IIOImage:
1075         final IIOImage iio_image = new IIOImage( image, null, null );
1076         writer.write( null, iio_image, image_write_param );
1077     }
1078
1079     // See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2
1080     // static void openDDBJRest() throws IOException {
1081     // //set URL
1082     // URL url = new URL( "http://xml.nig.ac.jp/rest/Invoke" );
1083     // //set parameter
1084     // String query = "service=GetEntry&method=getDDBJEntry&accession=AB000100";
1085     // //make connection
1086     // URLConnection urlc = url.openConnection();
1087     // //use post mode
1088     // urlc.setDoOutput( true );
1089     // urlc.setAllowUserInteraction( false );
1090     // //send query
1091     // PrintStream ps = new PrintStream( urlc.getOutputStream() );
1092     // ps.print( query );
1093     // ps.close();
1094     // //get result
1095     // BufferedReader br = new BufferedReader( new InputStreamReader(
1096     // urlc.getInputStream() ) );
1097     // String l = null;
1098     // while ( ( l = br.readLine() ) != null ) {
1099     // System.out.println( l );
1100     // }
1101     // br.close();
1102     // }
1103     public static enum GraphicsExportType {
1104         GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" ), BMP( "bmp" );
1105
1106         private final String _suffix;
1107
1108         private GraphicsExportType( final String suffix ) {
1109             _suffix = suffix;
1110         }
1111
1112         @Override
1113         public String toString() {
1114             return _suffix;
1115         }
1116     }
1117 }