X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=e60bc2c43e45fe9ecc4b40139dec46c4f564da09;hb=e8c7440196e8fe798bd5dc2b83cc1e194c77f0d0;hp=ba95034d02f81017973d0ef847b5426285d177b4;hpb=0794f6835ef636577d1bb581f423ac937246586b;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index ba95034..e60bc2c 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -50,6 +50,8 @@ import java.util.Map; import java.util.Set; import java.util.SortedSet; import java.util.TreeSet; +import java.util.regex.Matcher; +import java.util.regex.Pattern; import javax.imageio.IIOImage; import javax.imageio.ImageIO; @@ -60,56 +62,76 @@ import javax.swing.JApplet; import javax.swing.JOptionPane; import javax.swing.text.MaskFormatter; -import org.forester.analysis.AncestralTaxonomyInference; +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; import org.forester.phylogeny.Phylogeny; 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; 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; +import org.forester.ws.seqdb.UniProtTaxonomy; public final class AptxUtil { + 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 void ensurePresenceOfTaxonomy( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasTaxonomy() ) { - node.getNodeData().setTaxonomy( new Taxonomy() ); + public static MaskFormatter createMaskFormatter( final String s ) { + MaskFormatter formatter = null; + try { + formatter = new MaskFormatter( s ); } - } - - public static void ensurePresenceOfSequence( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasSequence() ) { - node.getNodeData().setSequence( new Sequence() ); + catch ( final ParseException e ) { + throw new IllegalArgumentException( e ); } + return formatter; } - final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasDistribution() ) { - node.getNodeData().setDistribution( new Distribution( "" ) ); + 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; } - final public static void ensurePresenceOfDate( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasDate() ) { - node.getNodeData().setDate( new org.forester.phylogeny.data.Date() ); + /** + * 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 ) { @@ -122,6 +144,129 @@ 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() ); + } + 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, @@ -148,41 +293,45 @@ 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.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 ); } - 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, @@ -320,7 +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(); @@ -381,6 +530,26 @@ public final class AptxUtil { } } + 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 ) ) ); + } + } + } + } + } + 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; @@ -434,7 +603,7 @@ public final class AptxUtil { else { UniProtTaxonomy up = null; try { - up = AncestralTaxonomyInference.obtainUniProtTaxonomy( temp_tax, null, null ); + up = TaxonomyDataManager.obtainUniProtTaxonomy( temp_tax, null, null ); } catch ( final Exception e ) { e.printStackTrace(); @@ -457,57 +626,7 @@ public final class AptxUtil { 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 ) ) ); - } - } - } - } - } - - final static String crateBasicInformation( final Phylogeny phy ) { + final static String createBasicInformation( final Phylogeny phy ) { final StringBuilder desc = new StringBuilder(); if ( ( phy != null ) && !phy.isEmpty() ) { if ( !ForesterUtil.isEmpty( phy.getName() ) ) { @@ -544,45 +663,93 @@ public final class AptxUtil { desc.append( "Maximum distance to root: " ); desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) ); desc.append( "\n" ); - desc.append( "Descendants per node statistics: " ); - final DescriptiveStatistics ds = PhylogenyMethods.calculatNumberOfDescendantsPerNodeStatistics( phy ); - desc.append( "\n" ); - desc.append( " Median: " + ForesterUtil.round( ds.median(), 2 ) ); - desc.append( "\n" ); - desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) ); - desc.append( "\n" ); - desc.append( " SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) ); - desc.append( "\n" ); - desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) ); - desc.append( "\n" ); - desc.append( " Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) ); + final Set taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() ); + if ( taxs != null ) { + desc.append( "Distinct external taxonomies: " ); + desc.append( taxs.size() ); + } desc.append( "\n" ); - final DescriptiveStatistics cs = PhylogenyMethods.calculatConfidenceStatistics( phy ); - if ( cs.getN() > 1 ) { - desc.append( "Support statistics: " ); + final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy ); + if ( bs.getN() > 3 ) { + desc.append( "\n" ); + desc.append( "Branch-length statistics: " ); + desc.append( "\n" ); + desc.append( " Number of branches with non-negative branch-lengths: " + bs.getN() ); desc.append( "\n" ); - desc.append( " Branches with support: " + cs.getN() ); + desc.append( " Median: " + ForesterUtil.round( bs.median(), 6 ) ); desc.append( "\n" ); - desc.append( " Median: " + ForesterUtil.round( cs.median(), 6 ) ); + desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) ); desc.append( "\n" ); - desc.append( " Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) ); + desc.append( " SD: " + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) ); desc.append( "\n" ); - if ( cs.getN() > 2 ) { - desc.append( " SD: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) ); + desc.append( " Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) ); + desc.append( "\n" ); + desc.append( " Maximum: " + ForesterUtil.round( bs.getMax(), 6 ) ); + desc.append( "\n" ); + 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, " " ) ); } - desc.append( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) ); + } + 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( "\n" ); + desc.append( " Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) ); + desc.append( "\n" ); + desc.append( " SD: " + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) ); desc.append( "\n" ); - desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) ); + desc.append( " Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) ); + desc.append( "\n" ); + desc.append( " Maximum: " + ForesterUtil.roundToInt( ds.getMax() ) ); desc.append( "\n" ); } - final Set taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() ); - if ( taxs != null ) { - desc.append( "Distinct external taxonomies: " ); - desc.append( taxs.size() ); + List css = null; + try { + css = PhylogenyMethods.calculatConfidenceStatistics( phy ); } - } - return desc.toString(); + catch ( final IllegalArgumentException e ) { + ForesterUtil.printWarningMessage( Constants.PRG_NAME, e.getMessage() ); + } + if ( ( css != null ) && ( css.size() > 0 ) ) { + desc.append( "\n" ); + for( int i = 0; i < css.size(); ++i ) { + final DescriptiveStatistics cs = css.get( i ); + if ( ( cs != null ) && ( cs.getN() > 1 ) ) { + if ( css.size() > 1 ) { + desc.append( "Support statistics " + ( i + 1 ) + ": " ); + } + else { + desc.append( "Support statistics: " ); + } + if ( !ForesterUtil.isEmpty( cs.getDescription() ) ) { + desc.append( "\n" ); + desc.append( " Type: " + cs.getDescription() ); + } + desc.append( "\n" ); + desc.append( " Branches with support: " + cs.getN() ); + desc.append( "\n" ); + 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( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) ); + desc.append( "\n" ); + desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) ); + desc.append( "\n" ); + } + } + } + } + return desc.toString(); } /** @@ -601,26 +768,30 @@ public final class AptxUtil { System.exit( -1 ); } - final static String[] getAvailableFontFamiliesSorted() { - return AVAILABLE_FONT_FAMILIES_SORTED; + 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; + } + } + return str_array; } - final static void inferCommonPartOfScientificNames( final Phylogeny tree ) { - boolean inferred = false; - for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) { + 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() && !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 ( n.getNodeData().isHasTaxonomy() && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getRank() ) ) { + ranks.add( n.getNodeData().getTaxonomy().getRank() ); } } - if ( inferred ) { - tree.setRerootable( false ); - } + return ForesterUtil.stringSetToArray( ranks ); + } + + final static String[] getAvailableFontFamiliesSorted() { + return AVAILABLE_FONT_FAMILIES_SORTED; } final static boolean isHasAssignedEvent( final PhylogenyNode node ) { @@ -678,47 +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 ) { @@ -761,44 +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; - } - - 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 ); @@ -812,21 +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 ) { @@ -835,12 +947,6 @@ 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 StringBuffer sb = new StringBuffer(); @@ -867,13 +973,13 @@ public final class AptxUtil { + 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" ); @@ -897,10 +1003,6 @@ 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(); @@ -923,72 +1025,26 @@ 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" ); @@ -1012,6 +1068,10 @@ 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(); @@ -1034,13 +1094,18 @@ 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 + "]"; } @@ -1076,6 +1141,52 @@ 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