X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=f84d8c4be6c8f3e0fab752b3ab3bf0d87b4d473a;hb=7aa2563168935732ea6d59a3f1c6cd8bf9a4ad61;hp=ab8bcf6b2ce08fc1b4f13c5801a4743b4b937583;hpb=8571ac663cce8aade42941742402a8fe37c27ff4;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index ab8bcf6..f84d8c4 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -21,7 +21,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.archaeopteryx; @@ -64,6 +64,9 @@ import javax.swing.text.MaskFormatter; import org.forester.analysis.TaxonomyDataManager; import org.forester.io.parsers.PhylogenyParser; +import org.forester.io.parsers.nexus.NexusPhylogeniesParser; +import org.forester.io.parsers.nhx.NHXParser; +import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION; import org.forester.io.parsers.phyloxml.PhyloXmlUtil; import org.forester.io.parsers.tol.TolParser; import org.forester.io.parsers.util.ParserUtils; @@ -72,8 +75,6 @@ import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyNode; import org.forester.phylogeny.data.Accession; import org.forester.phylogeny.data.BranchColor; -import org.forester.phylogeny.data.Distribution; -import org.forester.phylogeny.data.Sequence; import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; @@ -96,6 +97,243 @@ public final class AptxUtil { Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED ); } + public static MaskFormatter createMaskFormatter( final String s ) { + MaskFormatter formatter = null; + try { + formatter = new MaskFormatter( s ); + } + catch ( final ParseException e ) { + throw new IllegalArgumentException( e ); + } + return formatter; + } + + final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + while ( it.hasNext() ) { + if ( it.next().getNodeData().isHasEvent() ) { + return true; + } + } + return false; + } + + /** + * Returns true if at least one branch has a length larger than zero. + * + * + * @param phy + */ + final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + while ( it.hasNext() ) { + if ( it.next().getDistanceToParent() > 0.0 ) { + return true; + } + } + return false; + } + + final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + while ( it.hasNext() ) { + if ( it.next().getBranchData().isHasConfidences() ) { + return true; + } + } + return false; + } + + final public static void launchWebBrowser( final URI uri, + final boolean is_applet, + final JApplet applet, + final String frame_name ) throws IOException { + if ( is_applet ) { + applet.getAppletContext().showDocument( uri.toURL(), frame_name ); + } + else { + // This requires Java 1.6: + // ======================= + // boolean no_desktop = false; + // try { + // if ( Desktop.isDesktopSupported() ) { + // System.out.println( "desktop supported" ); + // final Desktop dt = Desktop.getDesktop(); + // dt.browse( uri ); + // } + // else { + // no_desktop = true; + // } + // } + // catch ( final Exception ex ) { + // ex.printStackTrace(); + // no_desktop = true; + // } + // catch ( final Error er ) { + // er.printStackTrace(); + // no_desktop = true; + // } + // if ( no_desktop ) { + // System.out.println( "desktop not supported" ); + try { + openUrlInWebBrowser( uri.toString() ); + } + catch ( final Exception e ) { + throw new IOException( e ); + } + // } + } + } + + public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) { + final String n = sequence_name.trim(); + final Matcher matcher1 = seq_identifier_pattern_1.matcher( n ); + String group1 = ""; + String group2 = ""; + if ( matcher1.matches() ) { + group1 = matcher1.group( 1 ); + group2 = matcher1.group( 2 ); + } + else { + final Matcher matcher2 = seq_identifier_pattern_2.matcher( n ); + if ( matcher2.matches() ) { + group1 = matcher2.group( 1 ); + group2 = matcher2.group( 2 ); + } + } + if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) { + return null; + } + return new Accession( group2, group1 ); + } + + public final static void printWarningMessage( final String name, final String message ) { + System.out.println( "[" + name + "] > " + message ); + } + + final public static void showErrorMessage( final Component parent, final String error_msg ) { + printAppletMessage( Constants.PRG_NAME, error_msg ); + JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION + + "] Error", JOptionPane.ERROR_MESSAGE ); + } + + public final static void showExtDescNodeDataUserSelectedHelper( final ControlPanel cp, + final PhylogenyNode node, + final List data ) { + final StringBuilder sb = new StringBuilder(); + if ( cp.isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getName(), sb ); + } + if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getName(), sb ); + } + if ( cp.isShowGeneSymbols() && node.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb ); + } + if ( cp.isShowSequenceAcc() && node.getNodeData().isHasSequence() + && ( node.getNodeData().getSequence().getAccession() != null ) + && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getAccession().toString(), sb ); + } + if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getTaxonomyCode(), sb ); + } + if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getScientificName(), sb ); + } + if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() ) + && node.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getMolecularSequence(), sb ); + } + final String s = sb.toString().trim(); + if ( !ForesterUtil.isEmpty( s ) ) { + data.add( s ); + } + } + + public final static void showExtDescNodeDataUserSelectedHelperHelper( final String s, final StringBuilder sb ) { + if ( sb.length() > 0 ) { + sb.append( "\t" ); + } + sb.append( s ); + } + + final public static void showInformationMessage( final Component parent, final String title, final String msg ) { + JOptionPane.showMessageDialog( parent, msg, title, JOptionPane.INFORMATION_MESSAGE ); + } + + public static void writePhylogenyToGraphicsFile( final File intree, + final File outfile, + final int width, + final int height, + final GraphicsExportType type, + final Configuration config ) throws IOException { + final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true ); + Phylogeny[] phys = null; + phys = PhylogenyMethods.readPhylogenies( parser, intree ); + writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config ); + } + + public static void writePhylogenyToGraphicsFile( final Phylogeny phy, + final File outfile, + final int width, + final int height, + final GraphicsExportType type, + final Configuration config ) throws IOException { + final Phylogeny[] phys = new Phylogeny[ 1 ]; + phys[ 0 ] = phy; + final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config ); + AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel() + .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() ); + mf.end(); + } + + public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile, + final int width, + final int height, + final TreePanel tree_panel, + final ControlPanel ac, + final GraphicsExportType type, + final Options options ) throws IOException { + tree_panel.calcParametersForPainting( width, height, true ); + tree_panel.resetPreferredSize(); + tree_panel.repaint(); + final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING, + RenderingHints.VALUE_RENDER_QUALITY ); + rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY ); + if ( options.isAntialiasPrint() ) { + rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON ); + rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON ); + } + else { + rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF ); + rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF ); + } + final Phylogeny phylogeny = tree_panel.getPhylogeny(); + if ( ( phylogeny == null ) || phylogeny.isEmpty() ) { + return; + } + if ( outfile.isDirectory() ) { + throw new IOException( "\"" + outfile + "\" is a directory" ); + } + final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB ); + final Graphics2D g2d = buffered_img.createGraphics(); + g2d.setRenderingHints( rendering_hints ); + tree_panel.paintPhylogeny( g2d, false, true, width, height, 0, 0 ); + if ( type == GraphicsExportType.TIFF ) { + writeToTiff( outfile, buffered_img ); + } + else { + ImageIO.write( buffered_img, type.toString(), outfile ); + } + g2d.dispose(); + } + final static void addPhylogeniesToTabs( final Phylogeny[] phys, final String default_name, final String full_path, @@ -231,7 +469,7 @@ public final class AptxUtil { return iter.hasNext(); } - final public static void collapseSpeciesSpecificSubtrees( final Phylogeny phy ) { + final static void collapseSpeciesSpecificSubtrees( final Phylogeny phy ) { boolean inferred = false; for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) { final PhylogenyNode n = it.next(); @@ -266,14 +504,6 @@ public final class AptxUtil { } } - private static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) { - node.getBranchData().setBranchColor( c ); - final List descs = PhylogenyMethods.getAllDescendants( node ); - for( final PhylogenyNode desc : descs ) { - desc.getBranchData().setBranchColor( c ); - } - } - final static void colorPhylogenyAccordingToConfidenceValues( final Phylogeny tree, final TreePanel tree_panel ) { double max_conf = 0.0; for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) { @@ -522,17 +752,6 @@ public final class AptxUtil { return desc.toString(); } - public static MaskFormatter createMaskFormatter( final String s ) { - MaskFormatter formatter = null; - try { - formatter = new MaskFormatter( s ); - } - catch ( final ParseException e ) { - throw new IllegalArgumentException( e ); - } - return formatter; - } - /** * Exits with -1. * @@ -549,31 +768,7 @@ public final class AptxUtil { System.exit( -1 ); } - final public static void ensurePresenceOfDate( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasDate() ) { - node.getNodeData().setDate( new org.forester.phylogeny.data.Date() ); - } - } - - final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasDistribution() ) { - node.getNodeData().setDistribution( new Distribution( "" ) ); - } - } - - public static void ensurePresenceOfSequence( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasSequence() ) { - node.getNodeData().setSequence( new Sequence() ); - } - } - - public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasTaxonomy() ) { - node.getNodeData().setTaxonomy( new Taxonomy() ); - } - } - - public static String[] getAllPossibleRanks() { + final static String[] getAllPossibleRanks() { final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ]; int i = 0; for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) { @@ -599,24 +794,6 @@ public final class AptxUtil { return AVAILABLE_FONT_FAMILIES_SORTED; } - final static void inferCommonPartOfScientificNames( final Phylogeny tree ) { - boolean inferred = false; - for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - if ( !n.getNodeData().isHasTaxonomy() && !n.isExternal() ) { - final String sn = PhylogenyMethods.inferCommonPartOfScientificNameOfDescendants( n ); - if ( !ForesterUtil.isEmpty( sn ) ) { - n.getNodeData().setTaxonomy( new Taxonomy() ); - n.getNodeData().getTaxonomy().setScientificName( sn ); - inferred = true; - } - } - } - if ( inferred ) { - tree.setRerootable( false ); - } - } - final static boolean isHasAssignedEvent( final PhylogenyNode node ) { if ( !node.getNodeData().isHasEvent() ) { return false; @@ -627,42 +804,6 @@ public final class AptxUtil { return true; } - final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - while ( it.hasNext() ) { - if ( it.next().getNodeData().isHasEvent() ) { - return true; - } - } - return false; - } - - /** - * Returns true if at least one branch has a length larger than zero. - * - * - * @param phy - */ - final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - while ( it.hasNext() ) { - if ( it.next().getDistanceToParent() > 0.0 ) { - return true; - } - } - return false; - } - - final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - while ( it.hasNext() ) { - if ( it.next().getBranchData().isHasConfidences() ) { - return true; - } - } - return false; - } - final static boolean isJava15() { try { final String s = ForesterUtil.JAVA_VERSION; @@ -708,47 +849,6 @@ public final class AptxUtil { } } - final public static void launchWebBrowser( final URI uri, - final boolean is_applet, - final JApplet applet, - final String frame_name ) throws IOException { - if ( is_applet ) { - applet.getAppletContext().showDocument( uri.toURL(), frame_name ); - } - else { - // This requires Java 1.6: - // ======================= - // boolean no_desktop = false; - // try { - // if ( Desktop.isDesktopSupported() ) { - // System.out.println( "desktop supported" ); - // final Desktop dt = Desktop.getDesktop(); - // dt.browse( uri ); - // } - // else { - // no_desktop = true; - // } - // } - // catch ( final Exception ex ) { - // ex.printStackTrace(); - // no_desktop = true; - // } - // catch ( final Error er ) { - // er.printStackTrace(); - // no_desktop = true; - // } - // if ( no_desktop ) { - // System.out.println( "desktop not supported" ); - try { - openUrlInWebBrowser( uri.toString() ); - } - catch ( final Exception e ) { - throw new IOException( e ); - } - // } - } - } - final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t, final ControlPanel atv_control, final Configuration configuration ) { @@ -791,66 +891,6 @@ public final class AptxUtil { } } - final private static char normalizeCharForRGB( char c ) { - c -= 65; - c *= 10.2; - c = c > 255 ? 255 : c; - c = c < 0 ? 0 : c; - return c; - } - - public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) { - final String n = sequence_name.trim(); - final Matcher matcher1 = seq_identifier_pattern_1.matcher( n ); - String group1 = ""; - String group2 = ""; - if ( matcher1.matches() ) { - group1 = matcher1.group( 1 ); - group2 = matcher1.group( 2 ); - } - else { - final Matcher matcher2 = seq_identifier_pattern_2.matcher( n ); - if ( matcher2.matches() ) { - group1 = matcher2.group( 1 ); - group2 = matcher2.group( 2 ); - } - } - if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) { - return null; - } - return new Accession( group2, group1 ); - } - - final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException, - SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException, - InvocationTargetException, InterruptedException { - final String os = System.getProperty( "os.name" ); - final Runtime runtime = Runtime.getRuntime(); - if ( os.toLowerCase().startsWith( "win" ) ) { - Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url ); - } - else if ( isMac() ) { - final Class file_mgr = Class.forName( "com.apple.eio.FileManager" ); - final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } ); - open_url.invoke( null, new Object[] { url } ); - } - else { - final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" }; - String browser = null; - for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) { - if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) { - browser = browsers[ i ]; - } - } - if ( browser == null ) { - throw new IOException( "could not find a web browser to open [" + url + "] in" ); - } - else { - runtime.exec( new String[] { browser, url } ); - } - } - } - final static void openWebsite( final String url, final boolean is_applet, final JApplet applet ) throws IOException { try { AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, Constants.PRG_NAME ); @@ -864,21 +904,41 @@ public final class AptxUtil { System.out.println( "[" + applet_name + "] > " + message ); } - public final static void printWarningMessage( final String name, final String message ) { - System.out.println( "[" + name + "] > " + message ); - } - - final static Phylogeny[] readPhylogeniesFromUrl( final URL url, final boolean phyloxml_validate_against_xsd ) + final static Phylogeny[] readPhylogeniesFromUrl( final URL url, + final boolean phyloxml_validate_against_xsd, + final boolean replace_underscores, + final boolean internal_numbers_are_confidences, + final TAXONOMY_EXTRACTION taxonomy_extraction ) throws FileNotFoundException, IOException { final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - PhylogenyParser parser = null; + final PhylogenyParser parser; + boolean nhx_or_nexus = false; if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) { parser = new TolParser(); } else { parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd ); + if ( parser instanceof NHXParser ) { + nhx_or_nexus = true; + final NHXParser nhx = ( NHXParser ) parser; + nhx.setReplaceUnderscores( replace_underscores ); + nhx.setIgnoreQuotes( false ); + nhx.setTaxonomyExtraction( taxonomy_extraction ); + } + else if ( parser instanceof NexusPhylogeniesParser ) { + nhx_or_nexus = true; + final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser; + nex.setReplaceUnderscores( replace_underscores ); + nex.setIgnoreQuotes( false ); + } + } + final Phylogeny[] phys = factory.create( url.openStream(), parser ); + if ( nhx_or_nexus && internal_numbers_are_confidences ) { + for( final Phylogeny phy : phys ) { + PhylogenyMethods.transferInternalNodeNamesToConfidence( phy ); + } } - return factory.create( url.openStream(), parser ); + return phys; } final static void removeBranchColors( final Phylogeny phy ) { @@ -887,86 +947,52 @@ public final class AptxUtil { } } - final public static void showErrorMessage( final Component parent, final String error_msg ) { - printAppletMessage( Constants.PRG_NAME, error_msg ); - JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION - + "] Error", JOptionPane.ERROR_MESSAGE ); - } - - public final static void showExtDescNodeDataUserSelectedHelper( final ControlPanel cp, - final PhylogenyNode node, - final List data ) { - final StringBuilder sb = new StringBuilder(); - if ( cp.isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) { - showExtDescNodeDataUserSelectedHelperHelper( node.getName(), sb ); - } - if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence() - && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) { - showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getName(), sb ); - } - if ( cp.isShowGeneSymbols() && node.getNodeData().isHasSequence() - && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) { - showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb ); - } - if ( cp.isShowSequenceAcc() && node.getNodeData().isHasSequence() - && ( node.getNodeData().getSequence().getAccession() != null ) - && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) { - showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getAccession().toString(), sb ); - } - if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy() - && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { - showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getTaxonomyCode(), sb ); - } - if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy() - && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) { - showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getScientificName(), sb ); - } - if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() ) - && node.getNodeData().isHasSequence() - && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) { - showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getMolecularSequence(), sb ); - } - final String s = sb.toString().trim(); - if ( !ForesterUtil.isEmpty( s ) ) { - data.add( s ); - } - } - - public final static void showExtDescNodeDataUserSelectedHelperHelper( final String s, final StringBuilder sb ) { - if ( sb.length() > 0 ) { - sb.append( "\t" ); - } - sb.append( s ); - } - - final public static void showInformationMessage( final Component parent, final String title, final String msg ) { - JOptionPane.showMessageDialog( parent, msg, title, JOptionPane.INFORMATION_MESSAGE ); - } - - final static void unexpectedError( final Error err ) { - err.printStackTrace(); + final static void unexpectedError( final Error e ) { + System.err.println(); + e.printStackTrace( System.err ); + System.err.println(); final StringBuffer sb = new StringBuffer(); - for( final StackTraceElement s : err.getStackTrace() ) { + for( final StackTraceElement s : e.getStackTrace() ) { sb.append( s + "\n" ); } JOptionPane .showMessageDialog( null, "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: " - + Constants.AUTHOR_EMAIL + " \nError: " + err + "\n" + sb, + + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n" + + sb, "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]", JOptionPane.ERROR_MESSAGE ); System.exit( -1 ); } - final static void unexpectedException( final Exception ex ) { - ex.printStackTrace(); + final static void outOfMemoryError( final OutOfMemoryError e ) { + System.err.println(); + System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" ); + System.err.println(); + e.printStackTrace(); + System.err.println(); + JOptionPane.showMessageDialog( null, + "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" + + "\n\nError: " + e.getLocalizedMessage(), + "Out of Memory Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]", + JOptionPane.ERROR_MESSAGE ); + System.exit( -1 ); + } + + final static void unexpectedException( final Exception e ) { + System.err.println(); + e.printStackTrace( System.err ); + System.err.println(); final StringBuffer sb = new StringBuffer(); - for( final StackTraceElement s : ex.getStackTrace() ) { + for( final StackTraceElement s : e.getStackTrace() ) { sb.append( s + "\n" ); } - JOptionPane.showMessageDialog( null, "An unexpected exception has occured. \nPlease contact: " - + Constants.AUTHOR_EMAIL + " \nException: " + ex + "\n" + sb, "Unexpected Exception [" - + Constants.PRG_NAME + Constants.VERSION + "]", JOptionPane.ERROR_MESSAGE ); + JOptionPane.showMessageDialog( null, + "An unexpected exception has occured. \nPlease contact: " + + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage() + + "\n" + sb, + "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]", + JOptionPane.ERROR_MESSAGE ); } final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos, @@ -980,7 +1006,7 @@ public final class AptxUtil { if ( options.isGraphicsExportVisibleOnly() ) { throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" ); } - tree_panel.setParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true ); + tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true ); tree_panel.resetPreferredSize(); tree_panel.repaint(); } @@ -1034,32 +1060,6 @@ public final class AptxUtil { return msg; } - public static void writePhylogenyToGraphicsFile( final File intree, - final File outfile, - final int width, - final int height, - final GraphicsExportType type, - final Configuration config ) throws IOException { - final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true ); - Phylogeny[] phys = null; - phys = PhylogenyMethods.readPhylogenies( parser, intree ); - writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config ); - } - - public static void writePhylogenyToGraphicsFile( final Phylogeny phy, - final File outfile, - final int width, - final int height, - final GraphicsExportType type, - final Configuration config ) throws IOException { - final Phylogeny[] phys = new Phylogeny[ 1 ]; - phys[ 0 ] = phy; - final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config ); - AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel() - .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() ); - mf.end(); - } - final static String writePhylogenyToGraphicsFile( final String file_name, int width, int height, @@ -1071,7 +1071,7 @@ public final class AptxUtil { if ( options.isGraphicsExportVisibleOnly() ) { throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" ); } - tree_panel.setParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true ); + tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true ); tree_panel.resetPreferredSize(); tree_panel.repaint(); } @@ -1134,47 +1134,6 @@ public final class AptxUtil { return msg; } - public final static void writePhylogenyToGraphicsFileNonInteractive( final File outfile, - final int width, - final int height, - final TreePanel tree_panel, - final ControlPanel ac, - final GraphicsExportType type, - final Options options ) throws IOException { - tree_panel.setParametersForPainting( width, height, true ); - tree_panel.resetPreferredSize(); - tree_panel.repaint(); - final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING, - RenderingHints.VALUE_RENDER_QUALITY ); - rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY ); - if ( options.isAntialiasPrint() ) { - rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_ON ); - rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON ); - } - else { - rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF ); - rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF ); - } - final Phylogeny phylogeny = tree_panel.getPhylogeny(); - if ( ( phylogeny == null ) || phylogeny.isEmpty() ) { - return; - } - if ( outfile.isDirectory() ) { - throw new IOException( "\"" + outfile + "\" is a directory" ); - } - final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB ); - final Graphics2D g2d = buffered_img.createGraphics(); - g2d.setRenderingHints( rendering_hints ); - tree_panel.paintPhylogeny( g2d, false, true, width, height, 0, 0 ); - if ( type == GraphicsExportType.TIFF ) { - writeToTiff( outfile, buffered_img ); - } - else { - ImageIO.write( buffered_img, type.toString(), outfile ); - } - g2d.dispose(); - } - final static void writeToTiff( final File file, final BufferedImage image ) throws IOException { // See: http://log.robmeek.com/2005/08/write-tiff-in-java.html ImageWriter writer = null; @@ -1204,6 +1163,52 @@ public final class AptxUtil { writer.write( null, iio_image, image_write_param ); } + private static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) { + node.getBranchData().setBranchColor( c ); + final List descs = PhylogenyMethods.getAllDescendants( node ); + for( final PhylogenyNode desc : descs ) { + desc.getBranchData().setBranchColor( c ); + } + } + + final private static char normalizeCharForRGB( char c ) { + c -= 65; + c *= 10.2; + c = c > 255 ? 255 : c; + c = c < 0 ? 0 : c; + return c; + } + + final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException, + SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException, + InvocationTargetException, InterruptedException { + final String os = System.getProperty( "os.name" ); + final Runtime runtime = Runtime.getRuntime(); + if ( os.toLowerCase().startsWith( "win" ) ) { + Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url ); + } + else if ( isMac() ) { + final Class file_mgr = Class.forName( "com.apple.eio.FileManager" ); + final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } ); + open_url.invoke( null, new Object[] { url } ); + } + else { + final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" }; + String browser = null; + for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) { + if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) { + browser = browsers[ i ]; + } + } + if ( browser == null ) { + throw new IOException( "could not find a web browser to open [" + url + "] in" ); + } + else { + runtime.exec( new String[] { browser, url } ); + } + } + } + // See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2 // static void openDDBJRest() throws IOException { // //set URL