X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=958a952089fd87947d7a0cd0a272cecb95e48287;hb=803a2b32992b5944b73c6dfcb80ceb58c09b81c1;hp=3ba5102d0b42735bb8fe6b1d5be524e15a59b818;hpb=680c2b0355ceaf9c5557874fb97330dfc3f92519;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index 3ba5102..958a952 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -36,25 +36,21 @@ import java.io.ByteArrayOutputStream; import java.io.File; import java.io.FileNotFoundException; import java.io.IOException; -import java.io.UnsupportedEncodingException; import java.lang.reflect.InvocationTargetException; import java.lang.reflect.Method; import java.net.URI; import java.net.URL; -import java.net.URLEncoder; +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; -import java.util.regex.Matcher; -import java.util.regex.Pattern; import javax.imageio.IIOImage; import javax.imageio.ImageIO; @@ -65,7 +61,6 @@ import javax.swing.JApplet; import javax.swing.JOptionPane; import javax.swing.text.MaskFormatter; -import org.forester.analysis.TaxonomyDataManager; import org.forester.io.parsers.PhylogenyParser; import org.forester.io.parsers.nexus.NexusPhylogeniesParser; import org.forester.io.parsers.nhx.NHXParser; @@ -77,93 +72,72 @@ 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.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.phylogeny.iterators.PreorderTreeIterator; import org.forester.util.AsciiHistogram; import org.forester.util.DescriptiveStatistics; -import org.forester.util.ForesterConstants; import org.forester.util.ForesterUtil; -import org.forester.util.SequenceIdParser; -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*$" ); - private final static Pattern seq_identifier_pattern_2 = Pattern - .compile( "^([A-Za-z]{2,5})[|=:]([0-9A-Za-z_\\.]{5,40})[|,; ].*$" ); + 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 ); } - public final static String createUriForSeqWeb( final PhylogenyNode node, - final Configuration conf, - final TreePanel tp ) { - String uri_str = null; - final String upkb = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node ); - if ( !ForesterUtil.isEmpty( upkb ) ) { - try { - uri_str = ForesterUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF8 ); + 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 ); } - catch ( final UnsupportedEncodingException e ) { - showErrorMessage( tp, e.toString() ); - e.printStackTrace(); + else { + second = my_str.charAt( my_str.length() - 1 ); } - } - if ( ForesterUtil.isEmpty( uri_str ) ) { - final String v = ForesterUtil.extractGenbankAccessor( node ); - if ( !ForesterUtil.isEmpty( v ) ) { - try { - if ( SequenceIdParser.isProtein( v ) ) { - uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 ); + if ( is_taxonomy ) { + if ( my_str.length() > 2 ) { + if ( my_str.indexOf( " " ) > 0 ) { + third = my_str.charAt( my_str.indexOf( " " ) + 1 ); } else { - uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 ); + third = my_str.charAt( 2 ); } } - catch ( final UnsupportedEncodingException e ) { - showErrorMessage( tp, e.toString() ); - e.printStackTrace(); - } } - } - if ( ForesterUtil.isEmpty( uri_str ) ) { - final String v = ForesterUtil.extractRefSeqAccessorAccessor( node ); - if ( !ForesterUtil.isEmpty( v ) ) { - try { - if ( SequenceIdParser.isProtein( v ) ) { - uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 ); - } - else { - uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 ); - } - } - catch ( final UnsupportedEncodingException e ) { - showErrorMessage( tp, e.toString() ); - e.printStackTrace(); - } + else if ( my_str.length() > 2 ) { + third = my_str.charAt( ( my_str.length() - 1 ) / 2 ); } } - if ( ForesterUtil.isEmpty( uri_str ) ) { - final String v = ForesterUtil.extractGInumber( node ); - if ( !ForesterUtil.isEmpty( v ) ) { - try { - uri_str = ForesterUtil.NCBI_GI + URLEncoder.encode( v, ForesterConstants.UTF8 ); - } - catch ( final UnsupportedEncodingException e ) { - showErrorMessage( tp, e.toString() ); - e.printStackTrace(); - } - } + 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 uri_str; + return new Color( first, second, third ); } public static MaskFormatter createMaskFormatter( final String s ) { @@ -189,8 +163,8 @@ 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 ) { @@ -203,6 +177,22 @@ public final class AptxUtil { return false; } + 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() ) { @@ -213,6 +203,30 @@ public final class AptxUtil { return false; } + 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; + } + } + 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 boolean is_applet, final JApplet applet, @@ -265,109 +279,69 @@ public final class AptxUtil { return tax_set; } - /** - * Returns the set of distinct taxonomies of - * all external nodes of node. - * If at least one the external nodes has no taxonomy, - * null is returned. - * - */ - public static Set obtainDistinctTaxonomies( 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() ) { - return null; - } - tax_set.add( n.getNodeData().getTaxonomy() ); - } - return tax_set; + public final static void printWarningMessage( final String name, final String message ) { + System.out.println( "[" + name + "] > " + message ); } - 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 ); + 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 { - final Matcher matcher2 = seq_identifier_pattern_2.matcher( n ); - if ( matcher2.matches() ) { - group1 = matcher2.group( 1 ); - group2 = matcher2.group( 2 ); + 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 ); } } - if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) { - return null; + AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() ); + Phylogeny[] phys = null; + try { + phys = ForesterUtil.readPhylogeniesFromUrl( url, parser ); } - 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.isShowTaxonomyCommonNames() && node.getNodeData().isHasTaxonomy() - && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) { - showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), 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 ); + catch ( final KeyManagementException e ) { + throw new IOException( e.getMessage() ); } - } - - public final static void showExtDescNodeDataUserSelectedHelperHelper( final String s, final StringBuilder sb ) { - if ( sb.length() > 0 ) { - sb.append( "\t" ); + catch ( final NoSuchAlgorithmException e ) { + throw new IOException( e.getMessage() ); } - sb.append( s ); + 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 showInformationMessage( final Component parent, final String title, final String msg ) { - JOptionPane.showMessageDialog( parent, msg, title, JOptionPane.INFORMATION_MESSAGE ); + final public static void showErrorMessage( final Component parent, final String error_msg ) { + 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, @@ -392,7 +366,7 @@ public final class AptxUtil { phys[ 0 ] = phy; final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config ); AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel() - .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() ); + .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() ); mf.end(); } @@ -403,7 +377,7 @@ public final class AptxUtil { final ControlPanel ac, final GraphicsExportType type, final Options options ) throws IOException { - tree_panel.calcParametersForPainting( width, height, true ); + tree_panel.calcParametersForPainting( width, height ); tree_panel.resetPreferredSize(); tree_panel.repaint(); final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING, @@ -437,20 +411,58 @@ 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 ) { + if ( phys.length > AptxConstants.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 ); + + " 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 ) { @@ -538,200 +550,29 @@ 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 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 = 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 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 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(); } - } - } - } - - 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() ); - } + catch ( final IOException e ) { + //Not important, ignore. } - } - } - 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; - } - } - } - 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 = TaxonomyDataManager.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; - } - } - } - } + if ( !ForesterUtil.isEmpty( f ) ) { + desc.append( "Path: " ); + desc.append( f ); + desc.append( "\n" ); } } - } - return colorizations; - } - - 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() ); @@ -793,7 +634,7 @@ 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: " ); @@ -815,15 +656,15 @@ 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: " ); 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 ) + " (stdev: " - + 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" ); @@ -832,10 +673,10 @@ 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" ); @@ -862,9 +703,9 @@ public final class AptxUtil { desc.append( " (stdev: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) + ")" ); } desc.append( "\n" ); - desc.append( " Minimum: " + ForesterUtil.roundToInt( cs.getMin() ) ); + desc.append( " Minimum: " + ForesterUtil.round( cs.getMin(), 6 ) ); desc.append( "\n" ); - desc.append( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) ); + desc.append( " Maximum: " + ForesterUtil.round( cs.getMax(), 6 ) ); desc.append( "\n" ); } } @@ -875,16 +716,16 @@ 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 ); } @@ -915,16 +756,6 @@ public final class AptxUtil { return AVAILABLE_FONT_FAMILIES_SORTED; } - final static boolean isHasAssignedEvent( final PhylogenyNode node ) { - if ( !node.getNodeData().isHasEvent() ) { - return false; - } - if ( ( node.getNodeData().getEvent() ).isUnassigned() ) { - return false; - } - return true; - } - final static boolean isUsOrCanada() { try { if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) { @@ -936,18 +767,44 @@ public final class AptxUtil { } return false; } - + 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.setDrawPhylogram( false ); + cp.setDrawPhylogramEnabled( false ); + } + else if ( cp.getDisplayAsPhylogramCb() != null ) { + cp.setDrawPhylogramEnabled( true ); + } + } + } final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t, final ControlPanel atv_control, final Configuration configuration ) { if ( ( t != null ) && !t.isEmpty() ) { - if ( !AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) { + final boolean has_bl = AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ); + if ( !has_bl ) { atv_control.setDrawPhylogram( false ); atv_control.setDrawPhylogramEnabled( false ); } + + if ( t.getFirstExternalNode().getBranchData().getBranchColor() != null + && atv_control.getUseVisualStylesCb() != null ) { + atv_control.getUseVisualStylesCb().setSelected( true ); + } + if ( t.getFirstExternalNode().getBranchData().getBranchWidth() != null + && t.getFirstExternalNode().getBranchData().getBranchWidth().getValue() + != BranchWidth.BRANCH_WIDTH_DEFAULT_VALUE + && atv_control.getUseBranchWidthsCb() != null ) { + atv_control.getUseBranchWidthsCb().setSelected( true ); + } + + if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) { if ( atv_control.getDisplayAsPhylogramCb() != null ) { - if ( AptxUtil.isHasAtLeastOneBranchLengthLargerThanZero( t ) ) { + if ( has_bl ) { atv_control.setDrawPhylogram( true ); atv_control.setDrawPhylogramEnabled( true ); } @@ -981,7 +838,7 @@ public final class AptxUtil { 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 ); + AptxUtil.launchWebBrowser( new URI( url ), is_applet, applet, AptxConstants.PRG_NAME ); } catch ( final Exception e ) { throw new IOException( e ); @@ -997,8 +854,8 @@ 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 + "]", - JOptionPane.ERROR_MESSAGE ); + "Out of Memory Error [" + AptxConstants.PRG_NAME + " " + AptxConstants.VERSION + "]", + JOptionPane.ERROR_MESSAGE ); System.exit( -1 ); } @@ -1006,53 +863,15 @@ public final class AptxUtil { System.out.println( "[" + applet_name + "] > " + message ); } - 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(); - 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 ); - } + final static void removeBranchColors( final Phylogeny phy ) { + for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) { + it.next().getBranchData().setBranchColor( null ); } - return phys; } - final static void removeBranchColors( final Phylogeny phy ) { + final static void removeVisualStyles( final Phylogeny phy ) { for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) { - it.next().getBranchData().setBranchColor( null ); + it.next().getNodeData().setNodeVisualData( null ); } } @@ -1065,11 +884,11 @@ public final class AptxUtil { 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 + "]", + .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 ); } @@ -1084,10 +903,10 @@ 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 + "]", - JOptionPane.ERROR_MESSAGE ); + "Unexpected Exception [" + AptxConstants.PRG_NAME + AptxConstants.VERSION + "]", + JOptionPane.ERROR_MESSAGE ); } final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos, @@ -1097,14 +916,7 @@ public final class AptxUtil { 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 RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY ); rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY ); @@ -1121,11 +933,11 @@ 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; @@ -1162,14 +974,7 @@ public final class AptxUtil { 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 RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING, RenderingHints.VALUE_RENDER_QUALITY ); rendering_hints.put( RenderingHints.KEY_COLOR_RENDERING, RenderingHints.VALUE_COLOR_RENDER_QUALITY ); @@ -1190,11 +995,11 @@ 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; @@ -1257,89 +1062,4 @@ public final class AptxUtil { final IIOImage iio_image = new IIOImage( image, null, null ); 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 ( 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 - // URL url = new URL( "http://xml.nig.ac.jp/rest/Invoke" ); - // //set parameter - // String query = "service=GetEntry&method=getDDBJEntry&accession=AB000100"; - // //make connection - // URLConnection urlc = url.openConnection(); - // //use post mode - // urlc.setDoOutput( true ); - // urlc.setAllowUserInteraction( false ); - // //send query - // PrintStream ps = new PrintStream( urlc.getOutputStream() ); - // ps.print( query ); - // ps.close(); - // //get result - // BufferedReader br = new BufferedReader( new InputStreamReader( - // urlc.getInputStream() ) ); - // String l = null; - // while ( ( l = br.readLine() ) != null ) { - // System.out.println( l ); - // } - // br.close(); - // } - public static enum GraphicsExportType { - GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" ), BMP( "bmp" ); - - private final String _suffix; - - private GraphicsExportType( final String suffix ) { - _suffix = suffix; - } - - @Override - public String toString() { - return _suffix; - } - } }