X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=f10fabd200983ac545ba2616aa4c5642c52dd694;hb=03e51d179caedf757b09e2872f9500318bd85a53;hp=21a4acecc7055a2851e6ed0ae137d5923b9e8576;hpb=2c2737643b601a33ec1b2854ce29cdd5630808df;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index 21a4ace..f10fabd 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; @@ -60,7 +62,7 @@ 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.phyloxml.PhyloXmlUtil; import org.forester.io.parsers.tol.TolParser; @@ -68,6 +70,7 @@ 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; @@ -76,104 +79,23 @@ 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 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() ); - } - } - - 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; - } - - public static void writePhylogenyToGraphicsFile( final File intree, - final File outfile, - final int width, - final int height, - final GraphicsExportType type, - final Configuration config ) throws IOException { - final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true ); - Phylogeny[] phys = null; - phys = PhylogenyMethods.readPhylogenies( parser, intree ); - final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config ); - AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel() - .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() ); - 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; - } - } - 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; - } - } - return false; - } - - 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 void addPhylogeniesToTabs( final Phylogeny[] phys, final String default_name, final String full_path, @@ -344,6 +266,14 @@ public final class AptxUtil { } } + private static void colorizeSubtree( final PhylogenyNode node, final BranchColor c ) { + node.getBranchData().setBranchColor( c ); + final List descs = PhylogenyMethods.getAllDescendants( node ); + for( final PhylogenyNode desc : descs ) { + desc.getBranchData().setBranchColor( c ); + } + } + final static void colorPhylogenyAccordingToConfidenceValues( final Phylogeny tree, final TreePanel tree_panel ) { double max_conf = 0.0; for( final PhylogenyNodeIterator it = tree.iteratorPreorder(); it.hasNext(); ) { @@ -370,6 +300,26 @@ 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; @@ -378,7 +328,7 @@ public final class AptxUtil { if ( n.getNodeData().isHasTaxonomy() && ( !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) || !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) || !ForesterUtil - .isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) ) { + .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() @@ -423,7 +373,7 @@ 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(); @@ -446,57 +396,7 @@ 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() ) ) { @@ -533,47 +433,106 @@ 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( " Median: " + ForesterUtil.round( bs.median(), 6 ) ); desc.append( "\n" ); - desc.append( " Branches with support: " + cs.getN() ); + desc.append( " Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) ); desc.append( "\n" ); - desc.append( " Median: " + ForesterUtil.round( cs.median(), 6 ) ); + desc.append( " SD: " + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) ); desc.append( "\n" ); - desc.append( " Mean: " + ForesterUtil.round( cs.arithmeticMean(), 6 ) ); + desc.append( " Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) ); desc.append( "\n" ); - if ( cs.getN() > 2 ) { - desc.append( " SD: " + ForesterUtil.round( cs.sampleStandardDeviation(), 6 ) ); + 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( " Maximum: " + ForesterUtil.roundToInt( cs.getMax() ) ); + 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() ) ); 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 ); + } + 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(); } + public static MaskFormatter createMaskFormatter( final String s ) { + MaskFormatter formatter = null; + try { + formatter = new MaskFormatter( s ); + } + catch ( final ParseException e ) { + throw new IllegalArgumentException( e ); + } + return formatter; + } + /** * Exits with -1. * @@ -590,6 +549,52 @@ public final class AptxUtil { System.exit( -1 ); } + final public static void ensurePresenceOfDate( final PhylogenyNode node ) { + if ( !node.getNodeData().isHasDate() ) { + node.getNodeData().setDate( new org.forester.phylogeny.data.Date() ); + } + } + + final public static void ensurePresenceOfDistribution( final PhylogenyNode node ) { + if ( !node.getNodeData().isHasDistribution() ) { + node.getNodeData().setDistribution( new Distribution( "" ) ); + } + } + + public static void ensurePresenceOfSequence( final PhylogenyNode node ) { + if ( !node.getNodeData().isHasSequence() ) { + node.getNodeData().setSequence( new Sequence() ); + } + } + + public static void ensurePresenceOfTaxonomy( final PhylogenyNode node ) { + if ( !node.getNodeData().isHasTaxonomy() ) { + node.getNodeData().setTaxonomy( new Taxonomy() ); + } + } + + public static String[] getAllPossibleRanks() { + final 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 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 String[] getAvailableFontFamiliesSorted() { return AVAILABLE_FONT_FAMILIES_SORTED; } @@ -622,6 +627,42 @@ public final class AptxUtil { return true; } + final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + while ( it.hasNext() ) { + if ( it.next().getNodeData().isHasEvent() ) { + return true; + } + } + return false; + } + + /** + * Returns true if at least one branch has a length larger than zero. + * + * + * @param phy + */ + final static public boolean isHasAtLeastOneBranchLengthLargerThanZero( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + while ( it.hasNext() ) { + if ( it.next().getDistanceToParent() > 0.0 ) { + return true; + } + } + return false; + } + + final static public boolean isHasAtLeastOneBranchWithSupportValues( final Phylogeny phy ) { + final PhylogenyNodeIterator it = phy.iteratorPostorder(); + while ( it.hasNext() ) { + if ( it.next().getBranchData().isHasConfidences() ) { + return true; + } + } + return false; + } + final static boolean isJava15() { try { final String s = ForesterUtil.JAVA_VERSION; @@ -667,10 +708,10 @@ public final class AptxUtil { } } - final static void launchWebBrowser( final URI uri, - final boolean is_applet, - final JApplet applet, - final String frame_name ) throws IOException { + 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 ); } @@ -758,6 +799,28 @@ public final class AptxUtil { return c; } + public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) { + final String n = sequence_name.trim(); + final Matcher matcher1 = seq_identifier_pattern_1.matcher( n ); + String group1 = ""; + String group2 = ""; + if ( matcher1.matches() ) { + group1 = matcher1.group( 1 ); + group2 = matcher1.group( 2 ); + } + else { + final Matcher matcher2 = seq_identifier_pattern_2.matcher( n ); + if ( matcher2.matches() ) { + group1 = matcher2.group( 1 ); + group2 = matcher2.group( 2 ); + } + } + if ( ForesterUtil.isEmpty( group1 ) || ForesterUtil.isEmpty( group2 ) ) { + return null; + } + return new Accession( group2, group1 ); + } + final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException, SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException, InvocationTargetException, InterruptedException { @@ -824,12 +887,62 @@ public final class AptxUtil { } } - final static void showErrorMessage( final Component parent, final String error_msg ) { + final public static void showErrorMessage( final Component parent, final String error_msg ) { printAppletMessage( Constants.PRG_NAME, error_msg ); JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION + "] Error", JOptionPane.ERROR_MESSAGE ); } + public final static void showExtDescNodeDataUserSelectedHelper( final ControlPanel cp, + final PhylogenyNode node, + final List data ) { + final StringBuilder sb = new StringBuilder(); + if ( cp.isShowNodeNames() && !ForesterUtil.isEmpty( node.getName() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getName(), sb ); + } + if ( cp.isShowGeneNames() && node.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getName(), sb ); + } + if ( cp.isShowGeneSymbols() && node.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getSymbol(), sb ); + } + if ( cp.isShowSequenceAcc() && node.getNodeData().isHasSequence() + && ( node.getNodeData().getSequence().getAccession() != null ) + && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getAccession().toString() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getAccession().toString(), sb ); + } + if ( cp.isShowTaxonomyCode() && node.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getTaxonomyCode() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getTaxonomyCode(), sb ); + } + if ( cp.isShowTaxonomyScientificNames() && node.getNodeData().isHasTaxonomy() + && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getScientificName(), sb ); + } + if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() ) + && node.getNodeData().isHasSequence() + && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) { + showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getSequence().getMolecularSequence(), sb ); + } + final String s = sb.toString().trim(); + if ( !ForesterUtil.isEmpty( s ) ) { + data.add( s ); + } + } + + public final static void showExtDescNodeDataUserSelectedHelperHelper( final String s, final StringBuilder sb ) { + if ( sb.length() > 0 ) { + sb.append( "\t" ); + } + sb.append( s ); + } + + final public static void showInformationMessage( final Component parent, final String title, final String msg ) { + JOptionPane.showMessageDialog( parent, msg, title, JOptionPane.INFORMATION_MESSAGE ); + } + final static void unexpectedError( final Error err ) { err.printStackTrace(); final StringBuffer sb = new StringBuffer(); @@ -856,6 +969,97 @@ public final class AptxUtil { + Constants.PRG_NAME + Constants.VERSION + "]", JOptionPane.ERROR_MESSAGE ); } + 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.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 ""; + } + Rectangle visible = null; + if ( !options.isGraphicsExportUsingActualSize() ) { + width = options.getPrintSizeX(); + height = options.getPrintSizeY(); + } + else if ( options.isGraphicsExportVisibleOnly() ) { + visible = tree_panel.getVisibleRect(); + width = visible.width; + height = visible.height; + } + final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB ); + Graphics2D g2d = buffered_img.createGraphics(); + g2d.setRenderingHints( rendering_hints ); + int x = 0; + int y = 0; + if ( options.isGraphicsExportVisibleOnly() ) { + g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height ); + g2d.setClip( null ); + x = visible.x; + y = visible.y; + } + tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y ); + ImageIO.write( buffered_img, type.toString(), baos ); + g2d.dispose(); + System.gc(); + if ( !options.isGraphicsExportUsingActualSize() ) { + tree_panel.getMainPanel().getControlPanel().showWhole(); + } + String msg = baos.toString(); + if ( ( width > 0 ) && ( height > 0 ) ) { + msg += " [size: " + width + ", " + height + "]"; + } + return msg; + } + + public static void writePhylogenyToGraphicsFile( final File intree, + final File outfile, + final int width, + final int height, + final GraphicsExportType type, + final Configuration config ) throws IOException { + final PhylogenyParser parser = ParserUtils.createParserDependingOnFileType( intree, true ); + Phylogeny[] phys = null; + phys = PhylogenyMethods.readPhylogenies( parser, intree ); + writePhylogenyToGraphicsFile( phys[ 0 ], outfile, width, height, type, config ); + } + + public static void writePhylogenyToGraphicsFile( final Phylogeny phy, + final File outfile, + final int width, + final int height, + final GraphicsExportType type, + final Configuration config ) throws IOException { + final Phylogeny[] phys = new Phylogeny[ 1 ]; + phys[ 0 ] = phy; + final MainFrameApplication mf = MainFrameApplication.createInstance( phys, config ); + AptxUtil.writePhylogenyToGraphicsFileNonInteractive( outfile, width, height, mf.getMainPanel() + .getCurrentTreePanel(), mf.getMainPanel().getControlPanel(), type, mf.getOptions() ); + mf.end(); + } + final static String writePhylogenyToGraphicsFile( final String file_name, int width, int height, @@ -971,71 +1175,6 @@ public final class AptxUtil { 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 { - 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.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 ""; - } - Rectangle visible = null; - if ( !options.isGraphicsExportUsingActualSize() ) { - width = options.getPrintSizeX(); - height = options.getPrintSizeY(); - } - else if ( options.isGraphicsExportVisibleOnly() ) { - visible = tree_panel.getVisibleRect(); - width = visible.width; - height = visible.height; - } - final BufferedImage buffered_img = new BufferedImage( width, height, BufferedImage.TYPE_INT_RGB ); - Graphics2D g2d = buffered_img.createGraphics(); - g2d.setRenderingHints( rendering_hints ); - int x = 0; - int y = 0; - if ( options.isGraphicsExportVisibleOnly() ) { - g2d = ( Graphics2D ) g2d.create( -visible.x, -visible.y, visible.width, visible.height ); - g2d.setClip( null ); - x = visible.x; - y = visible.y; - } - tree_panel.paintPhylogeny( g2d, false, true, width, height, x, y ); - ImageIO.write( buffered_img, type.toString(), baos ); - g2d.dispose(); - System.gc(); - if ( !options.isGraphicsExportUsingActualSize() ) { - tree_panel.getMainPanel().getControlPanel().showWhole(); - } - String msg = baos.toString(); - if ( ( width > 0 ) && ( height > 0 ) ) { - msg += " [size: " + width + ", " + height + "]"; - } - return msg; - } - final static void writeToTiff( final File file, final BufferedImage image ) throws IOException { // See: http://log.robmeek.com/2005/08/write-tiff-in-java.html ImageWriter writer = null;