X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=d26127a860b254e311998f9ae02031e2d463938f;hb=b4d39d202d7162aed8a41f2e1c42ac81f91c9341;hp=41b7ce44cb88ea911d7e68a5b8a6929620cfe330;hpb=fd4ebf6cb139b472664fee8cb9e74af3933a4ae5;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index 41b7ce4..d26127a 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -21,11 +21,10 @@ // 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; -import java.awt.Color; import java.awt.Component; import java.awt.Graphics2D; import java.awt.GraphicsEnvironment; @@ -42,11 +41,10 @@ import java.net.URI; import java.net.URL; 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; @@ -62,40 +60,137 @@ import javax.swing.JApplet; import javax.swing.JOptionPane; import javax.swing.text.MaskFormatter; -import org.forester.analysis.AncestralTaxonomyInference; 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.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; import org.forester.phylogeny.iterators.PhylogenyNodeIterator; -import org.forester.phylogeny.iterators.PreorderTreeIterator; import org.forester.util.AsciiHistogram; import org.forester.util.DescriptiveStatistics; import org.forester.util.ForesterUtil; -import org.forester.ws.uniprot.UniProtTaxonomy; public final class AptxUtil { + private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment() + .getAvailableFontFamilyNames(); private final static Pattern seq_identifier_pattern_1 = Pattern .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})\\s*$" ); private final static Pattern seq_identifier_pattern_2 = Pattern .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" ); - private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment() - .getAvailableFontFamilyNames(); static { 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 static Set obtainAllDistinctTaxonomies( final PhylogenyNode node ) { + final List descs = node.getAllExternalDescendants(); + final Set tax_set = new HashSet(); + for( final PhylogenyNode n : descs ) { + if ( n.getNodeData().isHasTaxonomy() && !n.getNodeData().getTaxonomy().isEmpty() ) { + tax_set.add( n.getNodeData().getTaxonomy() ); + } + } + return tax_set; + } + public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) { final String n = sequence_name.trim(); final Matcher matcher1 = seq_identifier_pattern_1.matcher( n ); @@ -118,38 +213,14 @@ public final class AptxUtil { return new Accession( group2, group1 ); } - public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasTaxonomy() ) { - node.getNodeData().setTaxonomy( new Taxonomy() ); - } - } - - public static void ensurePresenceOfSequence( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasSequence() ) { - node.getNodeData().setSequence( new Sequence() ); - } - } - - final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasDistribution() ) { - node.getNodeData().setDistribution( new Distribution( "" ) ); - } - } - - final public static void ensurePresenceOfDate( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasDate() ) { - node.getNodeData().setDate( new org.forester.phylogeny.data.Date() ); - } + public final static void printWarningMessage( final String name, final String message ) { + System.out.println( "[" + name + "] > " + message ); } - 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 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 static void writePhylogenyToGraphicsFile( final File intree, @@ -178,41 +249,45 @@ public final class AptxUtil { mf.end(); } - /** - * 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; - } + 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 ); } - return false; - } - - final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) { - final PhylogenyNodeIterator it = phy.iteratorPostorder(); - while ( it.hasNext() ) { - if ( it.next().getNodeData().isHasEvent() ) { - return true; - } + else { + rendering_hints.put( RenderingHints.KEY_TEXT_ANTIALIASING, RenderingHints.VALUE_TEXT_ANTIALIAS_OFF ); + rendering_hints.put( RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_OFF ); } - return false; - } - - public static MaskFormatter createMaskFormatter( final String s ) { - MaskFormatter formatter = null; - try { - formatter = new MaskFormatter( s ); + final Phylogeny phylogeny = tree_panel.getPhylogeny(); + if ( ( phylogeny == null ) || phylogeny.isEmpty() ) { + return; } - catch ( final ParseException e ) { - throw new IllegalArgumentException( e ); + if ( outfile.isDirectory() ) { + throw new IOException( "\"" + outfile + "\" is a directory" ); } - return formatter; + 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, @@ -316,230 +391,29 @@ public final class AptxUtil { lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration ); } - final static Color calculateColorFromString( final String str ) { - final String species_uc = str.toUpperCase(); - char first = species_uc.charAt( 0 ); - char second = ' '; - char third = ' '; - if ( species_uc.length() > 1 ) { - second = species_uc.charAt( 1 ); - if ( species_uc.length() > 2 ) { - if ( species_uc.indexOf( " " ) > 0 ) { - third = species_uc.charAt( species_uc.indexOf( " " ) + 1 ); - } - else { - third = species_uc.charAt( 2 ); - } - } - } - first = AptxUtil.normalizeCharForRGB( first ); - second = AptxUtil.normalizeCharForRGB( second ); - third = AptxUtil.normalizeCharForRGB( third ); - if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) { - first = 0; - } - else if ( ( first < 80 ) && ( second < 80 ) && ( third < 80 ) ) { - second = 255; - } - return new Color( first, second, third ); - } - // Returns true if the specified format name can be written final static boolean canWriteFormat( final String format_name ) { final Iterator iter = ImageIO.getImageWritersByFormatName( format_name ); return iter.hasNext(); } - final public static void collapseSpeciesSpecificSubtrees( final Phylogeny phy ) { - boolean inferred = false; - for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - if ( !n.isExternal() && !n.isCollapse() && ( n.getNumberOfDescendants() > 1 ) ) { - final Set taxs = PhylogenyMethods.obtainDistinctTaxonomies( n ); - if ( ( taxs != null ) && ( taxs.size() == 1 ) ) { - AptxUtil.collapseSubtree( n, true ); - if ( !n.getNodeData().isHasTaxonomy() ) { - n.getNodeData().setTaxonomy( ( Taxonomy ) n.getAllExternalDescendants().get( 0 ).getNodeData() - .getTaxonomy().copy() ); - } - inferred = true; - } - else { - n.setCollapse( false ); - } - } - } - if ( inferred ) { - phy.setRerootable( false ); - } - } - - final static void collapseSubtree( final PhylogenyNode node, final boolean collapse ) { - node.setCollapse( collapse ); - if ( node.isExternal() ) { - return; - } - final PhylogenyNodeIterator it = new PreorderTreeIterator( node ); - while ( it.hasNext() ) { - it.next().setCollapse( collapse ); - } - } - - final static void colorPhylogenyAccordingToConfidenceValues( final Phylogeny tree, final TreePanel tree_panel ) { - double max_conf = 0.0; - for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - n.getBranchData().setBranchColor( null ); - if ( n.getBranchData().isHasConfidences() ) { - final double conf = PhylogenyMethods.getConfidenceValue( n ); - if ( conf > max_conf ) { - max_conf = conf; - } - } - } - if ( max_conf > 0.0 ) { - final Color bg = tree_panel.getTreeColorSet().getBackgroundColor(); - final Color br = tree_panel.getTreeColorSet().getBranchColor(); - for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - if ( n.getBranchData().isHasConfidences() ) { - final double conf = PhylogenyMethods.getConfidenceValue( n ); - final BranchColor c = new BranchColor( ForesterUtil.calcColor( conf, 0.0, max_conf, bg, br ) ); - colorizeSubtree( n, c ); - } - } - } - } - - final static int colorPhylogenyAccordingToRanks( final Phylogeny tree, final String rank, final TreePanel tree_panel ) { - final Map true_lineage_to_color_map = new HashMap(); - int colorizations = 0; - for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - if ( n.getNodeData().isHasTaxonomy() - && ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) - || !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) || !ForesterUtil - .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) { - if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) - && n.getNodeData().getTaxonomy().getRank().equalsIgnoreCase( rank ) ) { - final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( n.getNodeData() - .getTaxonomy() ) ); - colorizeSubtree( n, c ); - ++colorizations; - if ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) { - true_lineage_to_color_map.put( n.getNodeData().getTaxonomy().getScientificName(), c.getValue() ); - } - } - } - } - for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) { - final PhylogenyNode node = it.next(); - if ( ( node.getBranchData().getBranchColor() == null ) && node.getNodeData().isHasTaxonomy() - && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getLineage() ) ) { - boolean success = false; - if ( !true_lineage_to_color_map.isEmpty() ) { - for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) { - if ( true_lineage_to_color_map.containsKey( lin ) ) { - colorizeSubtree( node, new BranchColor( true_lineage_to_color_map.get( lin ) ) ); - ++colorizations; - success = true; - break; - } - } + final static String createBasicInformation( final Phylogeny phy, final File treefile ) { + final StringBuilder desc = new StringBuilder(); + if ( ( phy != null ) && !phy.isEmpty() ) { + String f = null; + if ( treefile != null ) { + try { + f = treefile.getCanonicalPath(); } - if ( !success ) { - final Map lineage_to_rank_map = MainPanel.getLineageToRankMap(); - for( final String lin : node.getNodeData().getTaxonomy().getLineage() ) { - final Taxonomy temp_tax = new Taxonomy(); - temp_tax.setScientificName( lin ); - if ( lineage_to_rank_map.containsKey( lin ) - && !ForesterUtil.isEmpty( lineage_to_rank_map.get( lin ) ) - && lineage_to_rank_map.get( lin ).equalsIgnoreCase( rank ) ) { - final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( temp_tax ) ); - colorizeSubtree( node, c ); - ++colorizations; - true_lineage_to_color_map.put( lin, c.getValue() ); - break; - } - else { - UniProtTaxonomy up = null; - try { - up = AncestralTaxonomyInference.obtainUniProtTaxonomy( temp_tax, null, null ); - } - catch ( final Exception e ) { - e.printStackTrace(); - } - if ( ( up != null ) && !ForesterUtil.isEmpty( up.getRank() ) ) { - lineage_to_rank_map.put( lin, up.getRank() ); - if ( up.getRank().equalsIgnoreCase( rank ) ) { - final BranchColor c = new BranchColor( tree_panel.calculateTaxonomyBasedColor( temp_tax ) ); - colorizeSubtree( node, c ); - ++colorizations; - true_lineage_to_color_map.put( lin, c.getValue() ); - break; - } - } - } - } + catch ( final IOException e ) { + //Not important, ignore. } - } - } - return colorizations; - } - - 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 String[] getAllRanks( final Phylogeny tree ) { - final SortedSet ranks = new TreeSet(); - for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) { - ranks.add( n.getNodeData().getTaxonomy().getRank() ); - } - } - return ForesterUtil.stringSetToArray( ranks ); - } - - public 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 ) { - if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) { - str_array[ i++ ] = e; - } - } - return str_array; - } - - final static void colorPhylogenyAccordingToExternalTaxonomy( final Phylogeny tree, final TreePanel tree_panel ) { - for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) { - it.next().getBranchData().setBranchColor( null ); - } - for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) { - final PhylogenyNode n = it.next(); - if ( !n.getBranchData().isHasBranchColor() ) { - final Taxonomy tax = PhylogenyMethods.getExternalDescendantsTaxonomy( n ); - if ( tax != null ) { - n.getBranchData().setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) ); - final List descs = PhylogenyMethods.getAllDescendants( n ); - for( final PhylogenyNode desc : descs ) { - desc.getBranchData() - .setBranchColor( new BranchColor( tree_panel.calculateTaxonomyBasedColor( tax ) ) ); - } + if ( !ForesterUtil.isEmpty( f ) ) { + desc.append( "Path: " ); + desc.append( f ); + desc.append( "\n" ); } } - } - } - - final static String createBasicInformation( final Phylogeny phy ) { - final StringBuilder desc = new StringBuilder(); - if ( ( phy != null ) && !phy.isEmpty() ) { if ( !ForesterUtil.isEmpty( phy.getName() ) ) { desc.append( "Name: " ); desc.append( phy.getName() ); @@ -547,7 +421,22 @@ public final class AptxUtil { } if ( phy.getIdentifier() != null ) { desc.append( "Id: " ); - desc.append( phy.getIdentifier() ); + desc.append( phy.getIdentifier().toString() ); + desc.append( "\n" ); + } + if ( !ForesterUtil.isEmpty( phy.getDescription() ) ) { + desc.append( "Description: " ); + desc.append( phy.getDescription() ); + desc.append( "\n" ); + } + if ( !ForesterUtil.isEmpty( phy.getDistanceUnit() ) ) { + desc.append( "Distance Unit: " ); + desc.append( phy.getDistanceUnit() ); + desc.append( "\n" ); + } + if ( !ForesterUtil.isEmpty( phy.getType() ) ) { + desc.append( "Type: " ); + desc.append( phy.getType() ); desc.append( "\n" ); } desc.append( "Rooted: " ); @@ -556,16 +445,19 @@ public final class AptxUtil { desc.append( "Rerootable: " ); desc.append( phy.isRerootable() ); desc.append( "\n" ); - desc.append( "Node sum: " ); + desc.append( "Nodes: " ); desc.append( phy.getNodeCount() ); desc.append( "\n" ); - desc.append( "External node sum: " ); + desc.append( "External nodes: " ); desc.append( phy.getNumberOfExternalNodes() ); desc.append( "\n" ); - desc.append( "Internal node sum: " ); + desc.append( "Internal nodes: " ); desc.append( phy.getNodeCount() - phy.getNumberOfExternalNodes() ); desc.append( "\n" ); - desc.append( "Branche sum: " ); + desc.append( "Internal nodes with polytomies: " ); + desc.append( PhylogenyMethods.countNumberOfPolytomies( phy ) ); + desc.append( "\n" ); + desc.append( "Branches: " ); desc.append( phy.getNumberOfBranches() ); desc.append( "\n" ); desc.append( "Depth: " ); @@ -574,14 +466,17 @@ public final class AptxUtil { desc.append( "Maximum distance to root: " ); desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) ); desc.append( "\n" ); - final Set taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() ); + final Set taxs = obtainAllDistinctTaxonomies( phy.getRoot() ); if ( taxs != null ) { desc.append( "Distinct external taxonomies: " ); desc.append( taxs.size() ); } + for( final Taxonomy t : taxs ) { + System.out.println( t.toString() ); + } desc.append( "\n" ); final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy ); - if ( bs.getN() > 2 ) { + if ( bs.getN() > 3 ) { desc.append( "\n" ); desc.append( "Branch-length statistics: " ); desc.append( "\n" ); @@ -589,28 +484,28 @@ public final class AptxUtil { desc.append( "\n" ); desc.append( " Median: " + ForesterUtil.round( bs.median(), 6 ) ); desc.append( "\n" ); - desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) ); - desc.append( "\n" ); - desc.append( " SD: " + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) ); + desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (stdev: " + + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) + ")" ); desc.append( "\n" ); desc.append( " Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) ); desc.append( "\n" ); desc.append( " Maximum: " + ForesterUtil.round( bs.getMax(), 6 ) ); desc.append( "\n" ); - desc.append( "\n" ); - final AsciiHistogram histo = new AsciiHistogram( bs ); - desc.append( histo.toStringBuffer( 12, '#', 40, 7, " " ) ); + if ( Math.abs( bs.getMax() - bs.getMin() ) > 0.0001 ) { + desc.append( "\n" ); + final AsciiHistogram histo = new AsciiHistogram( bs ); + desc.append( histo.toStringBuffer( 12, '#', 40, 7, " " ) ); + } } final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy ); if ( ds.getN() > 2 ) { desc.append( "\n" ); desc.append( "Descendants per node statistics: " ); desc.append( "\n" ); - desc.append( " Median: " + ForesterUtil.round( ds.median(), 2 ) ); + desc.append( " Median: " + ForesterUtil.round( ds.median(), 6 ) ); desc.append( "\n" ); - desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) ); - desc.append( "\n" ); - desc.append( " SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) ); + desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 6 ) + " (stdev: " + + ForesterUtil.round( ds.sampleStandardDeviation(), 6 ) + ")" ); desc.append( "\n" ); desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) ); desc.append( "\n" ); @@ -645,14 +540,13 @@ public final class AptxUtil { desc.append( " Median: " + ForesterUtil.round( cs.median(), 6 ) ); desc.append( "\n" ); desc.append( " Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) ); - desc.append( "\n" ); if ( cs.getN() > 2 ) { - desc.append( " SD: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) ); - desc.append( "\n" ); + desc.append( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" ); } - desc.append( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) ); desc.append( "\n" ); - desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) ); + desc.append( " Minimum: " + ForesterUtil.round( cs.getMin(), 6 ) ); + desc.append( "\n" ); + desc.append( " Maximum: " + ForesterUtil.round( cs.getMax(), 6 ) ); desc.append( "\n" ); } } @@ -674,61 +568,33 @@ public final class AptxUtil { System.out.println( "Please contact the authors." ); System.out.println( Constants.PRG_NAME + " needs to close." ); System.out.println(); - System.exit( -1 ); - } - - final static String[] getAvailableFontFamiliesSorted() { - return AVAILABLE_FONT_FAMILIES_SORTED; + System.exit( -1 ); } - 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; - } + 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 ) { + if ( !e.equals( PhyloXmlUtil.UNKNOWN ) && !e.equals( PhyloXmlUtil.OTHER ) ) { + str_array[ i++ ] = e; } } - if ( inferred ) { - tree.setRerootable( false ); - } - } - - final static boolean isHasAssignedEvent( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasEvent() ) { - return false; - } - if ( ( node.getNodeData().getEvent() ).isUnassigned() ) { - return false; - } - return true; + return str_array; } - final static boolean isJava15() { - try { - final String s = ForesterUtil.JAVA_VERSION; - return s.startsWith( "1.5" ); - } - catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e ); - return false; + final static String[] getAllRanks( final Phylogeny tree ) { + final SortedSet ranks = new TreeSet(); + for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) { + final PhylogenyNode n = it.next(); + if ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) { + ranks.add( n.getNodeData().getTaxonomy().getRank() ); + } } + return ForesterUtil.stringSetToArray( ranks ); } - final static boolean isMac() { - try { - final String s = ForesterUtil.OS_NAME.toLowerCase(); - return s.startsWith( "mac" ); - } - catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e ); - return false; - } + final static String[] getAvailableFontFamiliesSorted() { + return AVAILABLE_FONT_FAMILIES_SORTED; } final static boolean isUsOrCanada() { @@ -743,58 +609,6 @@ public final class AptxUtil { return false; } - final static boolean isWindows() { - try { - final String s = ForesterUtil.OS_NAME.toLowerCase(); - return s.indexOf( "win" ) > -1; - } - catch ( final Exception e ) { - ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e ); - 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 ); - } - // } - } - } - final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t, final ControlPanel atv_control, final Configuration configuration ) { @@ -837,44 +651,6 @@ 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; - } - - 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 ); @@ -884,25 +660,66 @@ public final class AptxUtil { } } - final static void printAppletMessage( final String applet_name, final String message ) { - System.out.println( "[" + applet_name + "] > " + message ); + 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 ); } - public final static void printWarningMessage( final String name, final String message ) { - System.out.println( "[" + name + "] > " + message ); + final static void printAppletMessage( final String applet_name, final String message ) { + System.out.println( "[" + applet_name + "] > " + message ); } - final static Phylogeny[] readPhylogeniesFromUrl( final URL url, final boolean phyloxml_validate_against_xsd ) - throws FileNotFoundException, IOException { + 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, + final boolean midpoint_reroot ) 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 ); + } + } + if ( midpoint_reroot ) { + for( final Phylogeny phy : phys ) { + PhylogenyMethods.midpointRoot( phy ); + PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME ); + } } - return factory.create( url.openStream(), parser ); + return phys; } final static void removeBranchColors( final Phylogeny phy ) { @@ -911,50 +728,52 @@ 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 ); - } - - 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 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 writePhylogenyToGraphicsFile( final String file_name, - int width, - int height, - final TreePanel tree_panel, - final ControlPanel ac, - final GraphicsExportType type, - final Options options ) throws IOException { + final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos, + int width, + int height, + 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.setParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true ); + tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true ); tree_panel.resetPreferredSize(); tree_panel.repaint(); } @@ -973,10 +792,6 @@ public final class AptxUtil { if ( ( phylogeny == null ) || phylogeny.isEmpty() ) { return ""; } - final File file = new File( file_name ); - if ( file.isDirectory() ) { - throw new IOException( "\"" + file_name + "\" is a directory" ); - } Rectangle visible = null; if ( !options.isGraphicsExportUsingActualSize() ) { width = options.getPrintSizeX(); @@ -999,77 +814,31 @@ public final class AptxUtil { y = visible.y; } tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y ); - if ( type == GraphicsExportType.TIFF ) { - writeToTiff( file, buffered_img ); - } - else { - ImageIO.write( buffered_img, type.toString(), file ); - } + ImageIO.write( buffered_img, type.toString(), baos ); g2d.dispose(); System.gc(); if ( !options.isGraphicsExportUsingActualSize() ) { tree_panel.getMainPanel().getControlPanel().showWhole(); } - String msg = file.toString(); + String msg = baos.toString(); if ( ( width > 0 ) && ( height > 0 ) ) { msg += " [size: " + width + ", " + height + "]"; } 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 String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos, - int width, - int height, - final TreePanel tree_panel, - final ControlPanel ac, - final GraphicsExportType type, - final Options options ) throws IOException { + final static String writePhylogenyToGraphicsFile( final String file_name, + int width, + int height, + 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.setParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true ); + tree_panel.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true ); tree_panel.resetPreferredSize(); tree_panel.repaint(); } @@ -1088,6 +857,10 @@ public final class AptxUtil { if ( ( phylogeny == null ) || phylogeny.isEmpty() ) { return ""; } + final File file = new File( file_name ); + if ( file.isDirectory() ) { + throw new IOException( "\"" + file_name + "\" is a directory" ); + } Rectangle visible = null; if ( !options.isGraphicsExportUsingActualSize() ) { width = options.getPrintSizeX(); @@ -1110,13 +883,18 @@ public final class AptxUtil { y = visible.y; } tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y ); - ImageIO.write( buffered_img, type.toString(), baos ); + if ( type == GraphicsExportType.TIFF ) { + writeToTiff( file, buffered_img ); + } + else { + ImageIO.write( buffered_img, type.toString(), file ); + } g2d.dispose(); System.gc(); if ( !options.isGraphicsExportUsingActualSize() ) { tree_panel.getMainPanel().getControlPanel().showWhole(); } - String msg = baos.toString(); + String msg = file.toString(); if ( ( width > 0 ) && ( height > 0 ) ) { msg += " [size: " + width + ", " + height + "]"; } @@ -1152,6 +930,36 @@ 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 } ); + } + } + } + // See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2 // static void openDDBJRest() throws IOException { // //set URL @@ -1177,7 +985,7 @@ public final class AptxUtil { // br.close(); // } public static enum GraphicsExportType { - GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" ), BMP( "bmp" ); + BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" ); private final String _suffix;