X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=a2cf3516d021c0812d33034859598e31096c614e;hb=f3d4d888187b8cbdea5d2ea2e7637a0da11afb43;hp=e95283d11de17071b15b555feb8197d97c0c5f37;hpb=7e567e18a5ba32035a8db4ca041023c9e862d25b;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index e95283d..a2cf351 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -36,18 +36,20 @@ import java.io.ByteArrayOutputStream; import java.io.File; import java.io.FileNotFoundException; import java.io.IOException; -import java.io.InputStream; import java.lang.reflect.InvocationTargetException; import java.lang.reflect.Method; import java.net.URI; import java.net.URL; -import java.net.URLConnection; +import java.security.KeyManagementException; +import java.security.NoSuchAlgorithmException; import java.text.ParseException; import java.util.Arrays; +import java.util.HashMap; import java.util.HashSet; import java.util.Iterator; import java.util.List; import java.util.Locale; +import java.util.Map; import java.util.Set; import java.util.SortedSet; import java.util.TreeSet; @@ -57,7 +59,6 @@ import javax.imageio.ImageIO; import javax.imageio.ImageWriteParam; import javax.imageio.ImageWriter; import javax.imageio.stream.ImageOutputStream; -import javax.swing.JApplet; import javax.swing.JOptionPane; import javax.swing.text.MaskFormatter; @@ -65,29 +66,89 @@ 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; import org.forester.phylogeny.Phylogeny; import org.forester.phylogeny.PhylogenyMethods; import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY; import org.forester.phylogeny.PhylogenyNode; +import org.forester.phylogeny.data.BranchWidth; +import org.forester.phylogeny.data.Confidence; import org.forester.phylogeny.data.Taxonomy; -import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; -import org.forester.phylogeny.factories.PhylogenyFactory; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; import org.forester.util.AsciiHistogram; import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterUtil; +import org.forester.util.TaxonomyUtil; public final class AptxUtil { + public static enum GraphicsExportType { + BMP( "bmp" ), + GIF( "gif" ), + JPG( "jpg" ), + PDF( "pdf" ), + PNG( "png" ), + TIFF( "tif" ); + + private final String _suffix; + + private GraphicsExportType( final String suffix ) { + _suffix = suffix; + } + + @Override + public String toString() { + return _suffix; + } + } private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment() - .getAvailableFontFamilyNames(); + .getAvailableFontFamilyNames(); static { Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED ); } + final public static Color calculateColorFromString( final String str, final boolean is_taxonomy ) { + final String my_str = str.toUpperCase(); + char first = my_str.charAt( 0 ); + char second = ' '; + char third = ' '; + if ( my_str.length() > 1 ) { + if ( is_taxonomy ) { + second = my_str.charAt( 1 ); + } + else { + second = my_str.charAt( my_str.length() - 1 ); + } + if ( is_taxonomy ) { + if ( my_str.length() > 2 ) { + if ( my_str.indexOf( " " ) > 0 ) { + third = my_str.charAt( my_str.indexOf( " " ) + 1 ); + } + else { + third = my_str.charAt( 2 ); + } + } + } + else if ( my_str.length() > 2 ) { + third = my_str.charAt( ( my_str.length() - 1 ) / 2 ); + } + } + first = normalizeCharForRGB( first ); + second = normalizeCharForRGB( second ); + third = normalizeCharForRGB( third ); + if ( ( first > 200 ) && ( second > 200 ) && ( third > 200 ) ) { + first = 0; + } + else if ( ( first < 60 ) && ( second < 60 ) && ( third < 60 ) ) { + second = 255; + } + else if ( Math.abs( first - second ) < 40 && Math.abs( second - third ) < 40 ) { + third = 255; + } + return new Color( first, second, third ); + } + public static MaskFormatter createMaskFormatter( final String s ) { MaskFormatter formatter = null; try { @@ -111,8 +172,8 @@ public final class AptxUtil { /** * Returns true if at least one branch has a length larger than zero. - * - * + * + * * @param phy */ final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) { @@ -125,6 +186,49 @@ public final class AptxUtil { return false; } + final static public boolean isHasAtLeast50PercentBranchLengthLargerThanZero( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + int positive = 0; + int total = 0; + while ( it.hasNext() ) { + if ( it.next().getDistanceToParent() > 0.0 ) { + ++positive; + } + ++total; + } + if ( total == 0 ) { + return false; + } + return (((( double ) positive) / total) >= 0.5 ); + } + + final static public boolean isHasNoBranchLengthSmallerThanZero( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + if ( n.getDistanceToParent() < 0.0 && !n.isRoot() ) { + return false; + } + } + return true; + } + + final static public boolean isHasAtLeastOneBranchWithSupportSD( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + if ( n.getBranchData().isHasConfidences() ) { + final List c = n.getBranchData().getConfidences(); + for( final Confidence confidence : c ) { + if ( confidence.getStandardDeviation() > 0 ) { + return true; + } + } + } + } + return false; + } + final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) { final PhylogenyNodeIterator it = phy.iteratorPostorder(); while ( it.hasNext() ) { @@ -135,45 +239,61 @@ public final class AptxUtil { 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() ); + final static public boolean isHasAtLeastOneNodeWithScientificName( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + if ( n.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { + return true; } - catch ( final Exception e ) { - throw new IOException( e ); + } + return false; + } + + final static public boolean isHasAtLeastOneNodeWithSequenceAnnotation( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + while ( it.hasNext() ) { + final PhylogenyNode n = it.next(); + if ( n.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAnnotations() ) ) { + return true; } - // } } + return false; + } + + final public static void launchWebBrowser( final URI uri, final String frame_name ) throws IOException { + // 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 static Set obtainAllDistinctTaxonomies( final PhylogenyNode node ) { @@ -191,10 +311,67 @@ public final class AptxUtil { System.out.println( "[" + name + "] > " + message ); } + final public 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, + final boolean midpoint_reroot ) + throws FileNotFoundException, IOException { + 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 ); + } + } + AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() ); + Phylogeny[] phys = null; + try { + phys = ForesterUtil.readPhylogeniesFromUrl( url, parser ); + } + catch ( final KeyManagementException e ) { + throw new IOException( e.getMessage() ); + } + catch ( final NoSuchAlgorithmException e ) { + throw new IOException( e.getMessage() ); + } + if ( phys != null ) { + if ( nhx_or_nexus && internal_numbers_are_confidences ) { + for( final Phylogeny phy : phys ) { + PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" ); + } + } + if ( midpoint_reroot ) { + for( final Phylogeny phy : phys ) { + PhylogenyMethods.midpointRoot( phy ); + PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME ); + } + } + } + return phys; + } + 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 ); + printAppletMessage( AptxConstants.PRG_NAME, error_msg ); + JOptionPane.showMessageDialog( parent, + error_msg, + "[" + AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + "] Error", + JOptionPane.ERROR_MESSAGE ); } public static void writePhylogenyToGraphicsFile( final File intree, @@ -202,7 +379,8 @@ public final class AptxUtil { final int width, final int height, final GraphicsExportType type, - final Configuration config ) throws IOException { + final Configuration config ) + throws IOException { final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true ); Phylogeny[] phys = null; phys = PhylogenyMethods.readPhylogenies( parser, intree ); @@ -214,12 +392,18 @@ public final class AptxUtil { final int width, final int height, final GraphicsExportType type, - final Configuration config ) throws IOException { + 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() ); + AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, + width, + height, + mf.getMainPanel().getCurrentTreePanel(), + mf.getMainPanel().getControlPanel(), + type, + mf.getOptions() ); mf.end(); } @@ -229,8 +413,9 @@ public final class AptxUtil { final TreePanel tree_panel, final ControlPanel ac, final GraphicsExportType type, - final Options options ) throws IOException { - tree_panel.calcParametersForPainting( width, height, true ); + final Options options ) + throws IOException { + tree_panel.calcParametersForPainting( width, height ); tree_panel.resetPreferredSize(); tree_panel.repaint(); final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING, @@ -264,20 +449,62 @@ public final class AptxUtil { g2d.dispose(); } + 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 ( ForesterUtil.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 addPhylogeniesToTabs( final Phylogeny[] phys, final String default_name, final String full_path, final Configuration configuration, final MainPanel main_panel ) { - if ( phys.length > Constants.MAX_TREES_TO_LOAD ) { - JOptionPane.showMessageDialog( main_panel, "Attempt to load " + phys.length - + " phylogenies,\ngoing to load only the first " + Constants.MAX_TREES_TO_LOAD, Constants.PRG_NAME - + " more than " + Constants.MAX_TREES_TO_LOAD + " phylogenies", JOptionPane.WARNING_MESSAGE ); + if ( phys.length > AptxConstants.MAX_TREES_TO_LOAD ) { + JOptionPane.showMessageDialog( main_panel, + "Attempt to load " + phys.length + + " phylogenies,\ngoing to load only the first " + + AptxConstants.MAX_TREES_TO_LOAD, + AptxConstants.PRG_NAME + " more than " + AptxConstants.MAX_TREES_TO_LOAD + + " phylogenies", + JOptionPane.WARNING_MESSAGE ); } int i = 1; for( final Phylogeny phy : phys ) { if ( !phy.isEmpty() ) { - if ( i <= Constants.MAX_TREES_TO_LOAD ) { + if ( i <= AptxConstants.MAX_TREES_TO_LOAD ) { String my_name = ""; String my_name_for_file = ""; if ( phys.length > 1 ) { @@ -449,7 +676,7 @@ public final class AptxUtil { System.out.println( t.toString() ); } desc.append( "\n" ); - final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy ); + final DescriptiveStatistics bs = PhylogenyMethods.calculateBranchLengthStatistics( phy ); if ( bs.getN() > 3 ) { desc.append( "\n" ); desc.append( "Branch-length statistics: " ); @@ -471,7 +698,7 @@ public final class AptxUtil { desc.append( histo.toStringBuffer( 12, '#', 40, 7, " " ) ); } } - final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy ); + final DescriptiveStatistics ds = PhylogenyMethods.calculateNumberOfDescendantsPerNodeStatistics( phy ); if ( ds.getN() > 2 ) { desc.append( "\n" ); desc.append( "Descendants per node statistics: " ); @@ -488,10 +715,10 @@ public final class AptxUtil { } List css = null; try { - css = PhylogenyMethods.calculatConfidenceStatistics( phy ); + css = PhylogenyMethods.calculateConfidenceStatistics( phy ); } catch ( final IllegalArgumentException e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, e.getMessage() ); + ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, e.getMessage() ); } if ( ( css != null ) && ( css.size() > 0 ) ) { desc.append( "\n" ); @@ -531,31 +758,47 @@ public final class AptxUtil { /** * Exits with -1. - * - * + * + * * @param message * to message to be printed */ final static void dieWithSystemError( final String message ) { System.out.println(); - System.out.println( Constants.PRG_NAME + " encountered the following system error: " + message ); + System.out.println( AptxConstants.PRG_NAME + " encountered the following system error: " + message ); System.out.println( "Please contact the authors." ); - System.out.println( Constants.PRG_NAME + " needs to close." ); + System.out.println( AptxConstants.PRG_NAME + " needs to close." ); System.out.println(); System.exit( -1 ); } final static String[] getAllPossibleRanks() { - final String[] str_array = new String[ PhyloXmlUtil.TAXONOMY_RANKS_LIST.size() - 2 ]; + final String[] str_array = new String[ TaxonomyUtil.TAXONOMY_RANKS_LIST.size() - 2 ]; int i = 0; - for( final String e : PhyloXmlUtil.TAXONOMY_RANKS_LIST ) { - if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) { + for( final String e : TaxonomyUtil.TAXONOMY_RANKS_LIST ) { + if ( !e.equals( TaxonomyUtil.UNKNOWN ) && !e.equals( TaxonomyUtil.OTHER ) ) { str_array[ i++ ] = e; } } return str_array; } + final static String[] getAllPossibleRanks( final Map present_ranks ) { + final String[] str_array = new String[ TaxonomyUtil.TAXONOMY_RANKS_LIST.size() - 2 ]; + int i = 0; + for( final String e : TaxonomyUtil.TAXONOMY_RANKS_LIST ) { + if ( !e.equals( TaxonomyUtil.UNKNOWN ) && !e.equals( TaxonomyUtil.OTHER ) ) { + if ( present_ranks != null && present_ranks.containsKey( e ) ) { + str_array[ i++ ] = e + " (" + present_ranks.get( e ) + ")"; + } + else { + str_array[ i++ ] = e; + } + } + } + return str_array; + } + final static String[] getAllRanks( final Phylogeny tree ) { final SortedSet ranks = new TreeSet(); for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) { @@ -583,51 +826,84 @@ public final class AptxUtil { return false; } - final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t, - final ControlPanel atv_control, + final static void lookAtRealBranchLengthsForAptxControlSettings( final Phylogeny t, final ControlPanel cp ) { + if ( ( t != null ) && !t.isEmpty() ) { + final boolean has_bl = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ); + if ( !has_bl ) { + cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM ); + cp.setDrawPhylogramEnabled( false ); + } + else { + final boolean has_all_bl = AptxUtil.isHasNoBranchLengthSmallerThanZero( t ); + if ( has_all_bl ) { + cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM ); + } + if ( cp.getDisplayAsUnalignedPhylogramRb() != null ) { + cp.setDrawPhylogramEnabled( true ); + } + } + } + } + + public final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t, + final ControlPanel cp, final Configuration configuration ) { if ( ( t != null ) && !t.isEmpty() ) { - if ( !AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) { - atv_control.setDrawPhylogram( false ); - atv_control.setDrawPhylogramEnabled( false ); + final boolean has_bl = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ); + if ( !has_bl ) { + cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM ); + cp.setDrawPhylogramEnabled( false ); + } + if ( t.getFirstExternalNode().getBranchData().getBranchColor() != null + && cp.getUseVisualStylesCb() != null ) { + cp.getUseVisualStylesCb().setSelected( true ); + } + if ( t.getFirstExternalNode().getBranchData().getBranchWidth() != null + && t.getFirstExternalNode().getBranchData().getBranchWidth() + .getValue() != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE + && cp.getUseBranchWidthsCb() != null ) { + cp.getUseBranchWidthsCb().setSelected( true ); } if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) { - if ( atv_control.getDisplayAsPhylogramCb() != null ) { - if ( AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) { - atv_control.setDrawPhylogram( true ); - atv_control.setDrawPhylogramEnabled( true ); + if ( cp.getDisplayAsAlignedPhylogramRb() != null ) { + if ( has_bl ) { + final boolean has_mostly_bl = AptxUtil.isHasAtLeast50PercentBranchLengthLargerThanZero( t ); + if ( has_mostly_bl ) { + cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.UNALIGNED_PHYLOGRAM ); + } + cp.setDrawPhylogramEnabled( true ); } else { - atv_control.setDrawPhylogram( false ); + cp.setTreeDisplayType( Options.PHYLOGENY_DISPLAY_TYPE.CLADOGRAM ); } } } if ( configuration.doGuessCheckOption( Configuration.write_confidence_values ) ) { - if ( atv_control.getWriteConfidenceCb() != null ) { + if ( cp.getWriteConfidenceCb() != null ) { if ( AptxUtil.isHasAtLeastOneBranchWithSupportValues( t ) ) { - atv_control.setCheckbox( Configuration.write_confidence_values, true ); + cp.setCheckbox( Configuration.write_confidence_values, true ); } else { - atv_control.setCheckbox( Configuration.write_confidence_values, false ); + cp.setCheckbox( Configuration.write_confidence_values, false ); } } } if ( configuration.doGuessCheckOption( Configuration.write_events ) ) { - if ( atv_control.getShowEventsCb() != null ) { + if ( cp.getShowEventsCb() != null ) { if ( AptxUtil.isHasAtLeastNodeWithEvent( t ) ) { - atv_control.setCheckbox( Configuration.write_events, true ); + cp.setCheckbox( Configuration.write_events, true ); } else { - atv_control.setCheckbox( Configuration.write_events, false ); + cp.setCheckbox( Configuration.write_events, false ); } } } } } - final static void openWebsite( final String url, final boolean is_applet, final JApplet applet ) throws IOException { + final static void openWebsite( final String url ) throws IOException { try { - AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, Constants.PRG_NAME ); + AptxUtil.launchWebBrowser( new URI( url ), AptxConstants.PRG_NAME ); } catch ( final Exception e ) { throw new IOException( e ); @@ -643,7 +919,8 @@ public final class AptxUtil { 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 + "]", + "Out of Memory Error [" + AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + + "]", JOptionPane.ERROR_MESSAGE ); System.exit( -1 ); } @@ -652,57 +929,6 @@ public final class AptxUtil { System.out.println( "[" + applet_name + "] > " + message ); } - final public 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, - final boolean midpoint_reroot ) - throws FileNotFoundException, IOException { - final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance(); - 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 ); - } - } - AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() ); - final URLConnection url_connection = url.openConnection(); - url_connection.setDefaultUseCaches( false ); - final InputStream i = url_connection.getInputStream(); - final Phylogeny[] phys = factory.create( i, parser ); - i.close(); - if ( phys != null ) { - if ( nhx_or_nexus && internal_numbers_are_confidences ) { - for( final Phylogeny phy : phys ) { - PhylogenyMethods.transferInternalNodeNamesToConfidence( phy, "" ); - } - } - if ( midpoint_reroot ) { - for( final Phylogeny phy : phys ) { - PhylogenyMethods.midpointRoot( phy ); - PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME ); - } - } - } - return phys; - } - final static void removeBranchColors( final Phylogeny phy ) { for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) { it.next().getBranchData().setBranchColor( null ); @@ -723,13 +949,13 @@ public final class AptxUtil { 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: " + e.getLocalizedMessage() + "\n" - + sb, - "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]", - JOptionPane.ERROR_MESSAGE ); + JOptionPane.showMessageDialog( null, + "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: " + + AptxConstants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + + "\n" + sb, + "Unexpected Severe Error [" + AptxConstants.PRG_NAME + " " + + AptxConstants.VERSION + "]", + JOptionPane.ERROR_MESSAGE ); System.exit( -1 ); } @@ -743,9 +969,9 @@ public final class AptxUtil { } JOptionPane.showMessageDialog( null, "An unexpected exception has occured. \nPlease contact: " - + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage() + + AptxConstants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage() + "\n" + sb, - "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]", + "Unexpected Exception [" + AptxConstants.PRG_NAME + AptxConstants.VERSION + "]", JOptionPane.ERROR_MESSAGE ); } @@ -755,15 +981,8 @@ public final class AptxUtil { final TreePanel tree_panel, final ControlPanel ac, final GraphicsExportType type, - final Options options ) throws IOException { - if ( !options.isGraphicsExportUsingActualSize() ) { - if ( options.isGraphicsExportVisibleOnly() ) { - throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" ); - } - tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true ); - tree_panel.resetPreferredSize(); - tree_panel.repaint(); - } + final Options options ) + throws IOException { 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 ); @@ -780,11 +999,11 @@ public final class AptxUtil { return ""; } Rectangle visible = null; - if ( !options.isGraphicsExportUsingActualSize() ) { - width = options.getPrintSizeX(); - height = options.getPrintSizeY(); - } - else if ( options.isGraphicsExportVisibleOnly() ) { + // if ( !options.isGraphicsExportUsingActualSize() ) { + // width = options.getPrintSizeX(); + // height = options.getPrintSizeY(); + // } + /* else*/ if ( options.isGraphicsExportVisibleOnly() ) { visible = tree_panel.getVisibleRect(); width = visible.width; height = visible.height; @@ -820,15 +1039,8 @@ public final class AptxUtil { final TreePanel tree_panel, final ControlPanel ac, final GraphicsExportType type, - final Options options ) throws IOException { - if ( !options.isGraphicsExportUsingActualSize() ) { - if ( options.isGraphicsExportVisibleOnly() ) { - throw new IllegalArgumentException( "cannot export visible rectangle only without exporting in actual size" ); - } - tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true ); - tree_panel.resetPreferredSize(); - tree_panel.repaint(); - } + final Options options ) + throws IOException { 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 ); @@ -849,11 +1061,11 @@ public final class AptxUtil { throw new IOException( "\"" + file_name + "\" is a directory" ); } Rectangle visible = null; - if ( !options.isGraphicsExportUsingActualSize() ) { - width = options.getPrintSizeX(); - height = options.getPrintSizeY(); - } - else if ( options.isGraphicsExportVisibleOnly() ) { + // if ( !options.isGraphicsExportUsingActualSize() ) { + // width = options.getPrintSizeX(); + // height = options.getPrintSizeY(); + // } + /*else*/ if ( options.isGraphicsExportVisibleOnly() ) { visible = tree_panel.getVisibleRect(); width = visible.width; height = visible.height; @@ -917,94 +1129,23 @@ public final class AptxUtil { writer.write( null, iio_image, image_write_param ); } - 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 ( ForesterUtil.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 } ); - } - } - } - - public static enum GraphicsExportType { - BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" ); - - private final String _suffix; - - private GraphicsExportType( final String suffix ) { - _suffix = suffix; - } - - @Override - public String toString() { - return _suffix; - } - } - - final public static Color calculateColorFromString( final String str, final boolean is_taxonomy ) { - final String my_str = str.toUpperCase(); - char first = my_str.charAt( 0 ); - char second = ' '; - char third = ' '; - if ( my_str.length() > 1 ) { - if ( is_taxonomy ) { - second = my_str.charAt( 1 ); - } - else { - second = my_str.charAt( my_str.length() - 1 ); - } - if ( is_taxonomy ) { - if ( my_str.length() > 2 ) { - if ( my_str.indexOf( " " ) > 0 ) { - third = my_str.charAt( my_str.indexOf( " " ) + 1 ); + final static Map getRankCounts( final Phylogeny tree ) { + final Map present_ranks = new HashMap(); + if ( ( tree != null ) && !tree.isEmpty() ) { + for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + if ( !n.isExternal() && n.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) && !n.isRoot() ) { + final String rank = n.getNodeData().getTaxonomy().getRank().toLowerCase(); + if ( present_ranks.containsKey( rank ) ) { + present_ranks.put( rank, present_ranks.get( rank ) + 1 ); } else { - third = my_str.charAt( 2 ); + present_ranks.put( rank, 1 ); } } } - else if ( my_str.length() > 2 ) { - third = my_str.charAt( ( my_str.length() - 1 ) / 2 ); - } } - first = normalizeCharForRGB( first ); - second = normalizeCharForRGB( second ); - third = normalizeCharForRGB( third ); - if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) { - first = 0; - } - else if ( ( first < 60 ) && ( second < 60 ) && ( third < 60 ) ) { - second = 255; - } - return new Color( first, second, third ); - } - - final private static char normalizeCharForRGB( char c ) { - c -= 65; - c *= 10.2; - c = c > 255 ? 255 : c; - c = c < 0 ? 0 : c; - return c; + return present_ranks; } }