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.lang.reflect.InvocationTargetException;
39 import java.lang.reflect.Method;
42 import java.text.ParseException;
43 import java.util.Arrays;
44 import java.util.HashSet;
45 import java.util.Iterator;
46 import java.util.List;
47 import java.util.Locale;
49 import java.util.SortedSet;
50 import java.util.TreeSet;
51 import java.util.regex.Matcher;
52 import java.util.regex.Pattern;
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.Accession;
75 import org.forester.phylogeny.data.Taxonomy;
76 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
77 import org.forester.phylogeny.factories.PhylogenyFactory;
78 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
79 import org.forester.util.AsciiHistogram;
80 import org.forester.util.DescriptiveStatistics;
81 import org.forester.util.ForesterUtil;
83 public final class AptxUtil {
85 private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
86 .getAvailableFontFamilyNames();
87 private final static Pattern seq_identifier_pattern_1 = Pattern
88 .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})\\s*$" );
89 private final static Pattern seq_identifier_pattern_2 = Pattern
90 .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" );
92 Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED );
95 public static MaskFormatter createMaskFormatter( final String s ) {
96 MaskFormatter formatter = null;
98 formatter = new MaskFormatter( s );
100 catch ( final ParseException e ) {
101 throw new IllegalArgumentException( e );
106 final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
107 final PhylogenyNodeIterator it = phy.iteratorPostorder();
108 while ( it.hasNext() ) {
109 if ( it.next().getNodeData().isHasEvent() ) {
117 * Returns true if at least one branch has a length larger than zero.
122 final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) {
123 final PhylogenyNodeIterator it = phy.iteratorPostorder();
124 while ( it.hasNext() ) {
125 if ( it.next().getDistanceToParent() > 0.0 ) {
132 final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) {
133 final PhylogenyNodeIterator it = phy.iteratorPostorder();
134 while ( it.hasNext() ) {
135 if ( it.next().getBranchData().isHasConfidences() ) {
142 final public static void launchWebBrowser( final URI uri,
143 final boolean is_applet,
144 final JApplet applet,
145 final String frame_name ) throws IOException {
147 applet.getAppletContext().showDocument( uri.toURL(), frame_name );
150 // This requires Java 1.6:
151 // =======================
152 // boolean no_desktop = false;
154 // if ( Desktop.isDesktopSupported() ) {
155 // System.out.println( "desktop supported" );
156 // final Desktop dt = Desktop.getDesktop();
160 // no_desktop = true;
163 // catch ( final Exception ex ) {
164 // ex.printStackTrace();
165 // no_desktop = true;
167 // catch ( final Error er ) {
168 // er.printStackTrace();
169 // no_desktop = true;
171 // if ( no_desktop ) {
172 // System.out.println( "desktop not supported" );
174 openUrlInWebBrowser( uri.toString() );
176 catch ( final Exception e ) {
177 throw new IOException( e );
183 public static Set<Taxonomy> obtainAllDistinctTaxonomies( final PhylogenyNode node ) {
184 final List<PhylogenyNode> descs = node.getAllExternalDescendants();
185 final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
186 for( final PhylogenyNode n : descs ) {
187 if ( n.getNodeData().isHasTaxonomy() && !n.getNodeData().getTaxonomy().isEmpty() ) {
188 tax_set.add( n.getNodeData().getTaxonomy() );
194 public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) {
195 final String n = sequence_name.trim();
196 final Matcher matcher1 = seq_identifier_pattern_1.matcher( n );
199 if ( matcher1.matches() ) {
200 group1 = matcher1.group( 1 );
201 group2 = matcher1.group( 2 );
204 final Matcher matcher2 = seq_identifier_pattern_2.matcher( n );
205 if ( matcher2.matches() ) {
206 group1 = matcher2.group( 1 );
207 group2 = matcher2.group( 2 );
210 if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) {
213 return new Accession( group2, group1 );
216 public final static void printWarningMessage( final String name, final String message ) {
217 System.out.println( "[" + name + "] > " + message );
220 final public static void showErrorMessage( final Component parent, final String error_msg ) {
221 printAppletMessage( Constants.PRG_NAME, error_msg );
222 JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION
223 + "] Error", JOptionPane.ERROR_MESSAGE );
226 public static void writePhylogenyToGraphicsFile( final File intree,
230 final GraphicsExportType type,
231 final Configuration config ) throws IOException {
232 final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true );
233 Phylogeny[] phys = null;
234 phys = PhylogenyMethods.readPhylogenies( parser, intree );
235 writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config );
238 public static void writePhylogenyToGraphicsFile( final Phylogeny phy,
242 final GraphicsExportType type,
243 final Configuration config ) throws IOException {
244 final Phylogeny[] phys = new Phylogeny[ 1 ];
246 final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config );
247 AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel()
248 .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() );
252 public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile,
255 final TreePanel tree_panel,
256 final ControlPanel ac,
257 final GraphicsExportType type,
258 final Options options ) throws IOException {
259 tree_panel.calcParametersForPainting( width, height, true );
260 tree_panel.resetPreferredSize();
261 tree_panel.repaint();
262 final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
263 RenderingHints.VALUE_RENDER_QUALITY );
264 rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
265 if ( options.isAntialiasPrint() ) {
266 rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
267 rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
270 rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
271 rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
273 final Phylogeny phylogeny = tree_panel.getPhylogeny();
274 if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
277 if ( outfile.isDirectory() ) {
278 throw new IOException( "\"" + outfile + "\" is a directory" );
280 final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
281 final Graphics2D g2d = buffered_img.createGraphics();
282 g2d.setRenderingHints( rendering_hints );
283 tree_panel.paintPhylogeny( g2d, false, true, width, height, 0, 0 );
284 if ( type == GraphicsExportType.TIFF ) {
285 writeToTiff( outfile, buffered_img );
288 ImageIO.write( buffered_img, type.toString(), outfile );
293 final static void addPhylogeniesToTabs( final Phylogeny[] phys,
294 final String default_name,
295 final String full_path,
296 final Configuration configuration,
297 final MainPanel main_panel ) {
298 if ( phys.length > Constants.MAX_TREES_TO_LOAD ) {
299 JOptionPane.showMessageDialog( main_panel, "Attempt to load " + phys.length
300 + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME
301 + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE );
304 for( final Phylogeny phy : phys ) {
305 if ( !phy.isEmpty() ) {
306 if ( i <= Constants.MAX_TREES_TO_LOAD ) {
308 String my_name_for_file = "";
309 if ( phys.length > 1 ) {
310 if ( !ForesterUtil.isEmpty( default_name ) ) {
311 my_name = new String( default_name );
313 if ( !ForesterUtil.isEmpty( full_path ) ) {
314 my_name_for_file = new String( full_path );
316 else if ( !ForesterUtil.isEmpty( default_name ) ) {
317 my_name_for_file = new String( default_name );
320 if ( my_name_for_file.indexOf( '.' ) > 0 ) {
321 suffix = my_name_for_file.substring( my_name_for_file.lastIndexOf( '.' ),
322 my_name_for_file.length() );
323 my_name_for_file = my_name_for_file.substring( 0, my_name_for_file.lastIndexOf( '.' ) );
325 if ( !ForesterUtil.isEmpty( my_name_for_file ) ) {
326 my_name_for_file += "_";
328 if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
329 my_name_for_file += phy.getName().replaceAll( " ", "_" );
331 else if ( phy.getIdentifier() != null ) {
332 final StringBuffer sb = new StringBuffer();
333 if ( !ForesterUtil.isEmpty( phy.getIdentifier().getProvider() ) ) {
334 sb.append( phy.getIdentifier().getProvider() );
337 sb.append( phy.getIdentifier().getValue() );
338 my_name_for_file += sb;
341 my_name_for_file += i;
343 if ( !ForesterUtil.isEmpty( my_name ) && ForesterUtil.isEmpty( phy.getName() )
344 && ( phy.getIdentifier() == null ) ) {
345 my_name = my_name + " [" + i + "]";
347 if ( !ForesterUtil.isEmpty( suffix ) ) {
348 my_name_for_file += suffix;
352 if ( !ForesterUtil.isEmpty( default_name ) ) {
353 my_name = new String( default_name );
355 my_name_for_file = "";
356 if ( !ForesterUtil.isEmpty( full_path ) ) {
357 my_name_for_file = new String( full_path );
359 else if ( !ForesterUtil.isEmpty( default_name ) ) {
360 my_name_for_file = new String( default_name );
362 if ( ForesterUtil.isEmpty( my_name_for_file ) ) {
363 if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
364 my_name_for_file = new String( phy.getName() ).replaceAll( " ", "_" );
366 else if ( phy.getIdentifier() != null ) {
367 final StringBuffer sb = new StringBuffer();
368 if ( !ForesterUtil.isEmpty( phy.getIdentifier().getProvider() ) ) {
369 sb.append( phy.getIdentifier().getProvider() );
372 sb.append( phy.getIdentifier().getValue() );
373 my_name_for_file = new String( sb.toString().replaceAll( " ", "_" ) );
377 main_panel.addPhylogenyInNewTab( phy, configuration, my_name, full_path );
378 main_panel.getCurrentTreePanel().setTreeFile( new File( my_name_for_file ) );
379 lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
386 final static void addPhylogenyToPanel( final Phylogeny[] phys,
387 final Configuration configuration,
388 final MainPanel main_panel ) {
389 final Phylogeny phy = phys[ 0 ];
390 main_panel.addPhylogenyInPanel( phy, configuration );
391 lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
394 // Returns true if the specified format name can be written
395 final static boolean canWriteFormat( final String format_name ) {
396 final Iterator<ImageWriter> iter = ImageIO.getImageWritersByFormatName( format_name );
397 return iter.hasNext();
400 final static String createBasicInformation( final Phylogeny phy, final File treefile ) {
401 final StringBuilder desc = new StringBuilder();
402 if ( ( phy != null ) && !phy.isEmpty() ) {
404 if ( treefile != null ) {
406 f = treefile.getCanonicalPath();
408 catch ( final IOException e ) {
409 //Not important, ignore.
411 if ( !ForesterUtil.isEmpty( f ) ) {
412 desc.append( "Path: " );
417 if ( !ForesterUtil.isEmpty( phy.getName() ) ) {
418 desc.append( "Name: " );
419 desc.append( phy.getName() );
422 if ( phy.getIdentifier() != null ) {
423 desc.append( "Id: " );
424 desc.append( phy.getIdentifier().toString() );
427 if ( !ForesterUtil.isEmpty( phy.getDescription() ) ) {
428 desc.append( "Description: " );
429 desc.append( phy.getDescription() );
432 if ( !ForesterUtil.isEmpty( phy.getDistanceUnit() ) ) {
433 desc.append( "Distance Unit: " );
434 desc.append( phy.getDistanceUnit() );
437 if ( !ForesterUtil.isEmpty( phy.getType() ) ) {
438 desc.append( "Type: " );
439 desc.append( phy.getType() );
442 desc.append( "Rooted: " );
443 desc.append( phy.isRooted() );
445 desc.append( "Rerootable: " );
446 desc.append( phy.isRerootable() );
448 desc.append( "Nodes: " );
449 desc.append( phy.getNodeCount() );
451 desc.append( "External nodes: " );
452 desc.append( phy.getNumberOfExternalNodes() );
454 desc.append( "Internal nodes: " );
455 desc.append( phy.getNodeCount() - phy.getNumberOfExternalNodes() );
457 desc.append( "Internal nodes with polytomies: " );
458 desc.append( PhylogenyMethods.countNumberOfPolytomies( phy ) );
460 desc.append( "Branches: " );
461 desc.append( phy.getNumberOfBranches() );
463 desc.append( "Depth: " );
464 desc.append( PhylogenyMethods.calculateMaxDepth( phy ) );
466 desc.append( "Maximum distance to root: " );
467 desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) );
469 final Set<Taxonomy> taxs = obtainAllDistinctTaxonomies( phy.getRoot() );
470 if ( taxs != null ) {
471 desc.append( "Distinct external taxonomies: " );
472 desc.append( taxs.size() );
474 for( final Taxonomy t : taxs ) {
475 System.out.println( t.toString() );
478 final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy );
479 if ( bs.getN() > 3 ) {
481 desc.append( "Branch-length statistics: " );
483 desc.append( " Number of branches with non-negative branch-lengths: " + bs.getN() );
485 desc.append( " Median: " + ForesterUtil.round( bs.median(), 6 ) );
487 desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (stdev: "
488 + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) + ")" );
490 desc.append( " Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
492 desc.append( " Maximum: " + ForesterUtil.round( bs.getMax(), 6 ) );
494 if ( Math.abs( bs.getMax() - bs.getMin() ) > 0.0001 ) {
496 final AsciiHistogram histo = new AsciiHistogram( bs );
497 desc.append( histo.toStringBuffer( 12, '#', 40, 7, " " ) );
500 final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy );
501 if ( ds.getN() > 2 ) {
503 desc.append( "Descendants per node statistics: " );
505 desc.append( " Median: " + ForesterUtil.round( ds.median(), 6 ) );
507 desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 6 ) + " (stdev: "
508 + ForesterUtil.round( ds.sampleStandardDeviation(), 6 ) + ")" );
510 desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
512 desc.append( " Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) );
515 List<DescriptiveStatistics> css = null;
517 css = PhylogenyMethods.calculatConfidenceStatistics( phy );
519 catch ( final IllegalArgumentException e ) {
520 ForesterUtil.printWarningMessage( Constants.PRG_NAME, e.getMessage() );
522 if ( ( css != null ) && ( css.size() > 0 ) ) {
524 for( int i = 0; i < css.size(); ++i ) {
525 final DescriptiveStatistics cs = css.get( i );
526 if ( ( cs != null ) && ( cs.getN() > 1 ) ) {
527 if ( css.size() > 1 ) {
528 desc.append( "Support statistics " + ( i + 1 ) + ": " );
531 desc.append( "Support statistics: " );
533 if ( !ForesterUtil.isEmpty( cs.getDescription() ) ) {
535 desc.append( " Type: " + cs.getDescription() );
538 desc.append( " Branches with support: " + cs.getN() );
540 desc.append( " Median: " + ForesterUtil.round( cs.median(), 6 ) );
542 desc.append( " Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) );
543 if ( cs.getN() > 2 ) {
544 desc.append( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" );
547 desc.append( " Minimum: " + ForesterUtil.round( cs.getMin(), 6 ) );
549 desc.append( " Maximum: " + ForesterUtil.round( cs.getMax(), 6 ) );
555 return desc.toString();
563 * to message to be printed
565 final static void dieWithSystemError( final String message ) {
566 System.out.println();
567 System.out.println( Constants.PRG_NAME + " encountered the following system error: " + message );
568 System.out.println( "Please contact the authors." );
569 System.out.println( Constants.PRG_NAME + " needs to close." );
570 System.out.println();
574 final static String[] getAllPossibleRanks() {
575 final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ];
577 for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) {
578 if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) {
579 str_array[ i++ ] = e;
585 final static String[] getAllRanks( final Phylogeny tree ) {
586 final SortedSet<String> ranks = new TreeSet<String>();
587 for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) {
588 final PhylogenyNode n = it.next();
589 if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) {
590 ranks.add( n.getNodeData().getTaxonomy().getRank() );
593 return ForesterUtil.stringSetToArray( ranks );
596 final static String[] getAvailableFontFamiliesSorted() {
597 return AVAILABLE_FONT_FAMILIES_SORTED;
600 final static boolean isUsOrCanada() {
602 if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
606 catch ( final Exception e ) {
612 final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
613 final ControlPanel atv_control,
614 final Configuration configuration ) {
615 if ( ( t != null ) && !t.isEmpty() ) {
616 if ( !AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
617 atv_control.setDrawPhylogram( false );
618 atv_control.setDrawPhylogramEnabled( false );
620 if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) {
621 if ( atv_control.getDisplayAsPhylogramCb() != null ) {
622 if ( AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) {
623 atv_control.setDrawPhylogram( true );
624 atv_control.setDrawPhylogramEnabled( true );
627 atv_control.setDrawPhylogram( false );
631 if ( configuration.doGuessCheckOption( Configuration.write_confidence_values ) ) {
632 if ( atv_control.getWriteConfidenceCb() != null ) {
633 if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( t ) ) {
634 atv_control.setCheckbox( Configuration.write_confidence_values, true );
637 atv_control.setCheckbox( Configuration.write_confidence_values, false );
641 if ( configuration.doGuessCheckOption( Configuration.write_events ) ) {
642 if ( atv_control.getShowEventsCb() != null ) {
643 if ( AptxUtil.isHasAtLeastNodeWithEvent( t ) ) {
644 atv_control.setCheckbox( Configuration.write_events, true );
647 atv_control.setCheckbox( Configuration.write_events, false );
654 final static void openWebsite( final String url, final boolean is_applet, final JApplet applet ) throws IOException {
656 AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, Constants.PRG_NAME );
658 catch ( final Exception e ) {
659 throw new IOException( e );
663 final static void outOfMemoryError( final OutOfMemoryError e ) {
664 System.err.println();
665 System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
666 System.err.println();
668 System.err.println();
669 JOptionPane.showMessageDialog( null,
670 "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option"
671 + "\n\nError: " + e.getLocalizedMessage(),
672 "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
673 JOptionPane.ERROR_MESSAGE );
677 final static void printAppletMessage( final String applet_name, final String message ) {
678 System.out.println( "[" + applet_name + "] > " + message );
681 final static Phylogeny[] readPhylogeniesFromUrl( final URL url,
682 final boolean phyloxml_validate_against_xsd,
683 final boolean replace_underscores,
684 final boolean internal_numbers_are_confidences,
685 final TAXONOMY_EXTRACTION taxonomy_extraction,
686 final boolean midpoint_reroot ) throws FileNotFoundException,
688 final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
689 final PhylogenyParser parser;
690 boolean nhx_or_nexus = false;
691 if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
692 parser = new TolParser();
695 parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
696 if ( parser instanceof NHXParser ) {
698 final NHXParser nhx = ( NHXParser ) parser;
699 nhx.setReplaceUnderscores( replace_underscores );
700 nhx.setIgnoreQuotes( false );
701 nhx.setTaxonomyExtraction( taxonomy_extraction );
703 else if ( parser instanceof NexusPhylogeniesParser ) {
705 final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
706 nex.setReplaceUnderscores( replace_underscores );
707 nex.setIgnoreQuotes( false );
710 AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() );
711 final Phylogeny[] phys = factory.create( url.openStream(), parser );
712 if ( phys != null ) {
713 if ( nhx_or_nexus && internal_numbers_are_confidences ) {
714 for( final Phylogeny phy : phys ) {
715 PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
718 if ( midpoint_reroot ) {
719 for( final Phylogeny phy : phys ) {
720 PhylogenyMethods.midpointRoot( phy );
721 PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
728 final static void removeBranchColors( final Phylogeny phy ) {
729 for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
730 it.next().getBranchData().setBranchColor( null );
734 final static void unexpectedError( final Error e ) {
735 System.err.println();
736 e.printStackTrace( System.err );
737 System.err.println();
738 final StringBuffer sb = new StringBuffer();
739 for( final StackTraceElement s : e.getStackTrace() ) {
740 sb.append( s + "\n" );
743 .showMessageDialog( null,
744 "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
745 + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
747 "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
748 JOptionPane.ERROR_MESSAGE );
752 final static void unexpectedException( final Exception e ) {
753 System.err.println();
754 e.printStackTrace( System.err );
755 System.err.println();
756 final StringBuffer sb = new StringBuffer();
757 for( final StackTraceElement s : e.getStackTrace() ) {
758 sb.append( s + "\n" );
760 JOptionPane.showMessageDialog( null,
761 "An unexpected exception has occured. \nPlease contact: "
762 + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
764 "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
765 JOptionPane.ERROR_MESSAGE );
768 final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
771 final TreePanel tree_panel,
772 final ControlPanel ac,
773 final GraphicsExportType type,
774 final Options options ) throws IOException {
775 if ( !options.isGraphicsExportUsingActualSize() ) {
776 if ( options.isGraphicsExportVisibleOnly() ) {
777 throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
779 tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
780 tree_panel.resetPreferredSize();
781 tree_panel.repaint();
783 final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
784 RenderingHints.VALUE_RENDER_QUALITY );
785 rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
786 if ( options.isAntialiasPrint() ) {
787 rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
788 rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
791 rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
792 rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
794 final Phylogeny phylogeny = tree_panel.getPhylogeny();
795 if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
798 Rectangle visible = null;
799 if ( !options.isGraphicsExportUsingActualSize() ) {
800 width = options.getPrintSizeX();
801 height = options.getPrintSizeY();
803 else if ( options.isGraphicsExportVisibleOnly() ) {
804 visible = tree_panel.getVisibleRect();
805 width = visible.width;
806 height = visible.height;
808 final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
809 Graphics2D g2d = buffered_img.createGraphics();
810 g2d.setRenderingHints( rendering_hints );
813 if ( options.isGraphicsExportVisibleOnly() ) {
814 g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
819 tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
820 ImageIO.write( buffered_img, type.toString(), baos );
823 if ( !options.isGraphicsExportUsingActualSize() ) {
824 tree_panel.getMainPanel().getControlPanel().showWhole();
826 String msg = baos.toString();
827 if ( ( width > 0 ) && ( height > 0 ) ) {
828 msg += " [size: " + width + ", " + height + "]";
833 final static String writePhylogenyToGraphicsFile( final String file_name,
836 final TreePanel tree_panel,
837 final ControlPanel ac,
838 final GraphicsExportType type,
839 final Options options ) throws IOException {
840 if ( !options.isGraphicsExportUsingActualSize() ) {
841 if ( options.isGraphicsExportVisibleOnly() ) {
842 throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" );
844 tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
845 tree_panel.resetPreferredSize();
846 tree_panel.repaint();
848 final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
849 RenderingHints.VALUE_RENDER_QUALITY );
850 rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY );
851 if ( options.isAntialiasPrint() ) {
852 rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON );
853 rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON );
856 rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF );
857 rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF );
859 final Phylogeny phylogeny = tree_panel.getPhylogeny();
860 if ( ( phylogeny == null ) || phylogeny.isEmpty() ) {
863 final File file = new File( file_name );
864 if ( file.isDirectory() ) {
865 throw new IOException( "\"" + file_name + "\" is a directory" );
867 Rectangle visible = null;
868 if ( !options.isGraphicsExportUsingActualSize() ) {
869 width = options.getPrintSizeX();
870 height = options.getPrintSizeY();
872 else if ( options.isGraphicsExportVisibleOnly() ) {
873 visible = tree_panel.getVisibleRect();
874 width = visible.width;
875 height = visible.height;
877 final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB );
878 Graphics2D g2d = buffered_img.createGraphics();
879 g2d.setRenderingHints( rendering_hints );
882 if ( options.isGraphicsExportVisibleOnly() ) {
883 g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height );
888 tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y );
889 if ( type == GraphicsExportType.TIFF ) {
890 writeToTiff( file, buffered_img );
893 ImageIO.write( buffered_img, type.toString(), file );
897 if ( !options.isGraphicsExportUsingActualSize() ) {
898 tree_panel.getMainPanel().getControlPanel().showWhole();
900 String msg = file.toString();
901 if ( ( width > 0 ) && ( height > 0 ) ) {
902 msg += " [size: " + width + ", " + height + "]";
907 final static void writeToTiff( final File file, final BufferedImage image ) throws IOException {
908 // See: http://log.robmeek.com/2005/08/write-tiff-in-java.html
909 ImageWriter writer = null;
910 ImageOutputStream ios = null;
911 // Find an appropriate writer:
912 final Iterator<ImageWriter> it = ImageIO.getImageWritersByFormatName( "TIF" );
913 if ( it.hasNext() ) {
917 throw new IOException( "failed to get TIFF image writer" );
920 ios = ImageIO.createImageOutputStream( file );
921 writer.setOutput( ios );
922 final ImageWriteParam image_write_param = new ImageWriteParam( Locale.getDefault() );
923 image_write_param.setCompressionMode( ImageWriteParam.MODE_EXPLICIT );
924 // see writeParam.getCompressionTypes() for available compression type
926 image_write_param.setCompressionType( "PackBits" );
927 final String t[] = image_write_param.getCompressionTypes();
928 for( final String string : t ) {
929 System.out.println( string );
931 // Convert to an IIOImage:
932 final IIOImage iio_image = new IIOImage( image, null, null );
933 writer.write( null, iio_image, image_write_param );
936 final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException,
937 SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException,
938 InvocationTargetException, InterruptedException {
939 final String os = System.getProperty( "os.name" );
940 final Runtime runtime = Runtime.getRuntime();
941 if ( os.toLowerCase().startsWith( "win" ) ) {
942 Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
944 else if ( ForesterUtil.isMac() ) {
945 final Class<?> file_mgr = Class.forName( "com.apple.eio.FileManager" );
946 final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } );
947 open_url.invoke( null, new Object[] { url } );
950 final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" };
951 String browser = null;
952 for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) {
953 if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) {
954 browser = browsers[ i ];
957 if ( browser == null ) {
958 throw new IOException( "could not find a web browser to open [" + url + "] in" );
961 runtime.exec( new String[] { browser, url } );
966 // See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2
967 // static void openDDBJRest() throws IOException {
969 // URL url = new URL( "http://xml.nig.ac.jp/rest/Invoke" );
971 // String query = "service=GetEntry&method=getDDBJEntry&accession=AB000100";
973 // URLConnection urlc = url.openConnection();
975 // urlc.setDoOutput( true );
976 // urlc.setAllowUserInteraction( false );
978 // PrintStream ps = new PrintStream( urlc.getOutputStream() );
979 // ps.print( query );
982 // BufferedReader br = new BufferedReader( new InputStreamReader(
983 // urlc.getInputStream() ) );
985 // while ( ( l = br.readLine() ) != null ) {
986 // System.out.println( l );
990 public static enum GraphicsExportType {
991 BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
993 private final String _suffix;
995 private GraphicsExportType( final String suffix ) {
1000 public String toString() {