2 // FORESTER -- software libraries and applications
3 // for evolutionary biology research and applications.
5 // Copyright (C) 2008-2009 Christian M. Zmasek
6 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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.
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.
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
23 // Contact: phylosoft @ gmail . com
24 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
26 package org.forester.archaeopteryx;
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;
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;
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;
51 import java.util.SortedSet;
52 import java.util.TreeSet;
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;
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;
82 public final class AptxUtil {
84 private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
85 .getAvailableFontFamilyNames();
87 Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
90 public static MaskFormatter createMaskFormatter( final String s ) {
91 MaskFormatter formatter = null;
93 formatter = new MaskFormatter( s );
95 catch ( final ParseException e ) {
96 throw new IllegalArgumentException( e );
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() ) {
112 * Returns true if at least one branch has a length larger than zero.
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 ) {
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() ) {
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 {
142 applet.getAppletContext().showDocument( uri.toURL(), frame_name );
145 // This requires Java 1.6:
146 // =======================
147 // boolean no_desktop = false;
149 // if ( Desktop.isDesktopSupported() ) {
150 // System.out.println( "desktop supported" );
151 // final Desktop dt = Desktop.getDesktop();
155 // no_desktop = true;
158 // catch ( final Exception ex ) {
159 // ex.printStackTrace();
160 // no_desktop = true;
162 // catch ( final Error er ) {
163 // er.printStackTrace();
164 // no_desktop = true;
166 // if ( no_desktop ) {
167 // System.out.println( "desktop not supported" );
169 openUrlInWebBrowser( uri.toString() );
171 catch ( final Exception e ) {
172 throw new IOException( e );
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() );
189 public final static void printWarningMessage( final String name, final String message ) {
190 System.out.println( "[" + name + "] > " + message );
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 );
199 public static void writePhylogenyToGraphicsFile( final File intree,
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 );
211 public static void writePhylogenyToGraphicsFile( final Phylogeny phy,
215 final GraphicsExportType type,
216 final Configuration config ) throws IOException {
217 final Phylogeny[] phys = new Phylogeny[ 1 ];
219 final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
220 AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
221 .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
225 public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile,
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 );
243 rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
244 rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
246 final Phylogeny phylogeny = tree_panel.getPhylogeny();
247 if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
250 if ( outfile.isDirectory() ) {
251 throw new IOException( "\"" + outfile + "\" is a directory" );
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 );
261 ImageIO.write( buffered_img, type.toString(), outfile );
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 );
277 for( final Phylogeny phy : phys ) {
278 if ( !phy.isEmpty() ) {
279 if ( i <= Constants.MAX_TREES_TO_LOAD ) {
281 String my_name_for_file = "";
282 if ( phys.length > 1 ) {
283 if ( !ForesterUtil.isEmpty( default_name ) ) {
284 my_name = new String( default_name );
286 if ( !ForesterUtil.isEmpty( full_path ) ) {
287 my_name_for_file = new String( full_path );
289 else if ( !ForesterUtil.isEmpty( default_name ) ) {
290 my_name_for_file = new String( default_name );
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( '.' ) );
298 if ( !ForesterUtil.isEmpty( my_name_for_file ) ) {
299 my_name_for_file += "_";
301 if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
302 my_name_for_file += phy.getName().replaceAll( " ", "_" );
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() );
310 sb.append( phy.getIdentifier().getValue() );
311 my_name_for_file += sb;
314 my_name_for_file += i;
316 if ( !ForesterUtil.isEmpty( my_name ) && ForesterUtil.isEmpty( phy.getName() )
317 && ( phy.getIdentifier() == null ) ) {
318 my_name = my_name + " [" + i + "]";
320 if ( !ForesterUtil.isEmpty( suffix ) ) {
321 my_name_for_file += suffix;
325 if ( !ForesterUtil.isEmpty( default_name ) ) {
326 my_name = new String( default_name );
328 my_name_for_file = "";
329 if ( !ForesterUtil.isEmpty( full_path ) ) {
330 my_name_for_file = new String( full_path );
332 else if ( !ForesterUtil.isEmpty( default_name ) ) {
333 my_name_for_file = new String( default_name );
335 if ( ForesterUtil.isEmpty( my_name_for_file ) ) {
336 if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
337 my_name_for_file = new String( phy.getName() ).replaceAll( " ", "_" );
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() );
345 sb.append( phy.getIdentifier().getValue() );
346 my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
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 );
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 );
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();
373 final static String createBasicInformation( final Phylogeny phy, final File treefile ) {
374 final StringBuilder desc = new StringBuilder();
375 if ( ( phy != null ) && !phy.isEmpty() ) {
377 if ( treefile != null ) {
379 f = treefile.getCanonicalPath();
381 catch ( final IOException e ) {
382 //Not important, ignore.
384 if ( !ForesterUtil.isEmpty( f ) ) {
385 desc.append( "Path: " );
390 if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
391 desc.append( "Name: " );
392 desc.append( phy.getName() );
395 if ( phy.getIdentifier() != null ) {
396 desc.append( "Id: " );
397 desc.append( phy.getIdentifier().toString() );
400 if ( !ForesterUtil.isEmpty( phy.getDescription() ) ) {
401 desc.append( "Description: " );
402 desc.append( phy.getDescription() );
405 if ( !ForesterUtil.isEmpty( phy.getDistanceUnit() ) ) {
406 desc.append( "Distance Unit: " );
407 desc.append( phy.getDistanceUnit() );
410 if ( !ForesterUtil.isEmpty( phy.getType() ) ) {
411 desc.append( "Type: " );
412 desc.append( phy.getType() );
415 desc.append( "Rooted: " );
416 desc.append( phy.isRooted() );
418 desc.append( "Rerootable: " );
419 desc.append( phy.isRerootable() );
421 desc.append( "Nodes: " );
422 desc.append( phy.getNodeCount() );
424 desc.append( "External nodes: " );
425 desc.append( phy.getNumberOfExternalNodes() );
427 desc.append( "Internal nodes: " );
428 desc.append( phy.getNodeCount() - phy.getNumberOfExternalNodes() );
430 desc.append( "Internal nodes with polytomies: " );
431 desc.append( PhylogenyMethods.countNumberOfPolytomies( phy ) );
433 desc.append( "Branches: " );
434 desc.append( phy.getNumberOfBranches() );
436 desc.append( "Depth: " );
437 desc.append( PhylogenyMethods.calculateMaxDepth( phy ) );
439 desc.append( "Maximum distance to root: " );
440 desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) );
442 final Set<Taxonomy> taxs = obtainAllDistinctTaxonomies( phy.getRoot() );
443 if ( taxs != null ) {
444 desc.append( "Distinct external taxonomies: " );
445 desc.append( taxs.size() );
447 for( final Taxonomy t : taxs ) {
448 System.out.println( t.toString() );
451 final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy );
452 if ( bs.getN() > 3 ) {
454 desc.append( "Branch-length statistics: " );
456 desc.append( " Number of branches with non-negative branch-lengths: " + bs.getN() );
458 desc.append( " Median: " + ForesterUtil.round( bs.median(), 6 ) );
460 desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (stdev: "
461 + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) + ")" );
463 desc.append( " Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
465 desc.append( " Maximum: " + ForesterUtil.round( bs.getMax(), 6 ) );
467 if ( Math.abs( bs.getMax() - bs.getMin() ) > 0.0001 ) {
469 final AsciiHistogram histo = new AsciiHistogram( bs );
470 desc.append( histo.toStringBuffer( 12, '#', 40, 7, " " ) );
473 final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
474 if ( ds.getN() > 2 ) {
476 desc.append( "Descendants per node statistics: " );
478 desc.append( " Median: " + ForesterUtil.round( ds.median(), 6 ) );
480 desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 6 ) + " (stdev: "
481 + ForesterUtil.round( ds.sampleStandardDeviation(), 6 ) + ")" );
483 desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
485 desc.append( " Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) );
488 List<DescriptiveStatistics> css = null;
490 css = PhylogenyMethods.calculatConfidenceStatistics( phy );
492 catch ( final IllegalArgumentException e ) {
493 ForesterUtil.printWarningMessage( Constants.PRG_NAME, e.getMessage() );
495 if ( ( css != null ) && ( css.size() > 0 ) ) {
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 ) + ": " );
504 desc.append( "Support statistics: " );
506 if ( !ForesterUtil.isEmpty( cs.getDescription() ) ) {
508 desc.append( " Type: " + cs.getDescription() );
511 desc.append( " Branches with support: " + cs.getN() );
513 desc.append( " Median: " + ForesterUtil.round( cs.median(), 6 ) );
515 desc.append( " Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
516 if ( cs.getN() > 2 ) {
517 desc.append( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" );
520 desc.append( " Minimum: " + ForesterUtil.round( cs.getMin(), 6 ) );
522 desc.append( " Maximum: " + ForesterUtil.round( cs.getMax(), 6 ) );
528 return desc.toString();
536 * to message to be printed
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();
547 final static String[] getAllPossibleRanks() {
548 final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
550 for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) {
551 if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) {
552 str_array[ i++ ] = e;
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() );
566 return ForesterUtil.stringSetToArray( ranks );
569 final static String[] getAvailableFontFamiliesSorted() {
570 return AVAILABLE_FONT_FAMILIES_SORTED;
573 final static boolean isUsOrCanada() {
575 if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
579 catch ( final Exception e ) {
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 );
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 );
600 atv_control.setDrawPhylogram( false );
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 );
610 atv_control.setCheckbox( Configuration.write_confidence_values, false );
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 );
620 atv_control.setCheckbox( Configuration.write_events, false );
627 final static void openWebsite( final String url, final boolean is_applet, final JApplet applet ) throws IOException {
629 AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, Constants.PRG_NAME );
631 catch ( final Exception e ) {
632 throw new IOException( e );
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();
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 );
650 final static void printAppletMessage( final String applet_name, final String message ) {
651 System.out.println( "[" + applet_name + "] > " + message );
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();
668 parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
669 if ( parser instanceof NHXParser ) {
671 final NHXParser nhx = ( NHXParser ) parser;
672 nhx.setReplaceUnderscores( replace_underscores );
673 nhx.setIgnoreQuotes( false );
674 nhx.setTaxonomyExtraction( taxonomy_extraction );
676 else if ( parser instanceof NexusPhylogeniesParser ) {
678 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
679 nex.setReplaceUnderscores( replace_underscores );
680 nex.setIgnoreQuotes( false );
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 );
689 if ( phys != null ) {
690 if ( nhx_or_nexus && internal_numbers_are_confidences ) {
691 for( final Phylogeny phy : phys ) {
692 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" );
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 );
705 final static void removeBranchColors( final Phylogeny phy ) {
706 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
707 it.next().getBranchData().setBranchColor( null );
711 final static void removeVisualStyles( final Phylogeny phy ) {
712 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
713 it.next().getNodeData().setNodeVisualData( null );
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" );
726 .showMessageDialog( null,
727 "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
728 + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
730 "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
731 JOptionPane.ERROR_MESSAGE );
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" );
743 JOptionPane.showMessageDialog( null,
744 "An unexpected exception has occured. \nPlease contact: "
745 + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
747 "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
748 JOptionPane.ERROR_MESSAGE );
751 final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
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" );
762 tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
763 tree_panel.resetPreferredSize();
764 tree_panel.repaint();
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 );
774 rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
775 rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
777 final Phylogeny phylogeny = tree_panel.getPhylogeny();
778 if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
781 Rectangle visible = null;
782 if ( !options.isGraphicsExportUsingActualSize() ) {
783 width = options.getPrintSizeX();
784 height = options.getPrintSizeY();
786 else if ( options.isGraphicsExportVisibleOnly() ) {
787 visible = tree_panel.getVisibleRect();
788 width = visible.width;
789 height = visible.height;
791 final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
792 Graphics2D g2d = buffered_img.createGraphics();
793 g2d.setRenderingHints( rendering_hints );
796 if ( options.isGraphicsExportVisibleOnly() ) {
797 g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
802 tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
803 ImageIO.write( buffered_img, type.toString(), baos );
806 if ( !options.isGraphicsExportUsingActualSize() ) {
807 tree_panel.getMainPanel().getControlPanel().showWhole();
809 String msg = baos.toString();
810 if ( ( width > 0 ) && ( height > 0 ) ) {
811 msg += " [size: " + width + ", " + height + "]";
816 final static String writePhylogenyToGraphicsFile( final String file_name,
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" );
827 tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
828 tree_panel.resetPreferredSize();
829 tree_panel.repaint();
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 );
839 rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
840 rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
842 final Phylogeny phylogeny = tree_panel.getPhylogeny();
843 if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
846 final File file = new File( file_name );
847 if ( file.isDirectory() ) {
848 throw new IOException( "\"" + file_name + "\" is a directory" );
850 Rectangle visible = null;
851 if ( !options.isGraphicsExportUsingActualSize() ) {
852 width = options.getPrintSizeX();
853 height = options.getPrintSizeY();
855 else if ( options.isGraphicsExportVisibleOnly() ) {
856 visible = tree_panel.getVisibleRect();
857 width = visible.width;
858 height = visible.height;
860 final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
861 Graphics2D g2d = buffered_img.createGraphics();
862 g2d.setRenderingHints( rendering_hints );
865 if ( options.isGraphicsExportVisibleOnly() ) {
866 g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
871 tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
872 if ( type == GraphicsExportType.TIFF ) {
873 writeToTiff( file, buffered_img );
876 ImageIO.write( buffered_img, type.toString(), file );
880 if ( !options.isGraphicsExportUsingActualSize() ) {
881 tree_panel.getMainPanel().getControlPanel().showWhole();
883 String msg = file.toString();
884 if ( ( width > 0 ) && ( height > 0 ) ) {
885 msg += " [size: " + width + ", " + height + "]";
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() ) {
900 throw new IOException( "failed to get TIFF image 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
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 );
914 // Convert to an IIOImage:
915 final IIOImage iio_image = new IIOImage( image, null, null );
916 writer.write( null, iio_image, image_write_param );
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 );
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 } );
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 ];
940 if ( browser == null ) {
941 throw new IOException( "could not find a web browser to open [" + url + "] in" );
944 runtime.exec( new String[] { browser, url } );
949 // See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2
950 // static void openDDBJRest() throws IOException {
952 // URL url = new URL( "http://xml.nig.ac.jp/rest/Invoke" );
954 // String query = "service=GetEntry&method=getDDBJEntry&accession=AB000100";
956 // URLConnection urlc = url.openConnection();
958 // urlc.setDoOutput( true );
959 // urlc.setAllowUserInteraction( false );
961 // PrintStream ps = new PrintStream( urlc.getOutputStream() );
962 // ps.print( query );
965 // BufferedReader br = new BufferedReader( new InputStreamReader(
966 // urlc.getInputStream() ) );
968 // while ( ( l = br.readLine() ) != null ) {
969 // System.out.println( l );
973 public static enum GraphicsExportType {
974 BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
976 private final String _suffix;
978 private GraphicsExportType( final String suffix ) {
983 public String toString() {