From: cmzmasek@gmail.com Date: Tue, 9 Oct 2012 20:05:43 +0000 (+0000) Subject: 1st fix of embedded applet null pointer "issue"... ^^ X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a07102813fbac79ba1a534dc9954a8500dc5e5ff;p=jalview.git 1st fix of embedded applet null pointer "issue"... ^^ --- diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index 1942bbe..ab8bcf6 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -96,125 +96,6 @@ public final class AptxUtil { Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED ); } - 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 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 ); - 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(); - } - - /** - * 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, @@ -385,6 +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(); ) { @@ -411,6 +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; @@ -487,56 +396,6 @@ 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 createBasicInformation( final Phylogeny phy ) { final StringBuilder desc = new StringBuilder(); if ( ( phy != null ) && !phy.isEmpty() ) { @@ -663,6 +522,17 @@ public final class AptxUtil { 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. * @@ -679,6 +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; } @@ -711,6 +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; @@ -847,6 +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 { @@ -919,6 +893,56 @@ public final class AptxUtil { + "] 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(); @@ -945,6 +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, @@ -1060,71 +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; diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java index 1591e63..d232fdd 100644 --- a/forester/java/src/org/forester/archaeopteryx/Configuration.java +++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java @@ -213,7 +213,7 @@ public final class Configuration { private Color _gui_button_border_color = Constants.BUTTON_BORDER_COLOR_DEFAULT; private Color _domain_structure_font_color = Constants.DOMAIN_STRUCTURE_FONT_COLOR_DEFAULT; private Color _domain_structure_base_color = Constants.DOMAIN_STRUCTURE_BASE_COLOR_DEFAULT; - private NODE_DATA _ext_desc_data_to_return = NODE_DATA.NODE_NAME; + private NODE_DATA _ext_desc_data_to_return = NODE_DATA.UNKNOWN; private String _label_for_get_ext_descendents_data = ""; private EXT_NODE_DATA_RETURN_ON _ext_node_data_return_on = EXT_NODE_DATA_RETURN_ON.WINODW; private static String DEFAULT_FONT_FAMILY = ""; @@ -1315,6 +1315,9 @@ public final class Configuration { else if ( s.equalsIgnoreCase( "taxonomy_code" ) ) { setExtDescNodeDataToReturn( NODE_DATA.TAXONOMY_CODE ); } + else if ( s.equalsIgnoreCase( "user_selected" ) ) { + setExtDescNodeDataToReturn( NODE_DATA.UNKNOWN ); + } else { ForesterUtil.printWarningMessage( Constants.PRG_NAME, "unknown value [" + s + "] for [ext_descendents_data_to_return]" ); diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java index 4a40c7f..d7df705 100644 --- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java +++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java @@ -1415,7 +1415,10 @@ final class ControlPanel extends JPanel implements ActionListener { s = "Taxonomy Codes"; break; case TAXONOMY_SCIENTIFIC_NAME: - s = "Scientific names"; + s = "Scientific Names"; + break; + case UNKNOWN: + s = "User Selected Data"; break; } final String label = _configuration.getClickToTitle( Configuration.get_ext_desc_data ) + " " + s; diff --git a/forester/java/src/org/forester/archaeopteryx/TreePanel.java b/forester/java/src/org/forester/archaeopteryx/TreePanel.java index 17cd7f6..47ca58d 100644 --- a/forester/java/src/org/forester/archaeopteryx/TreePanel.java +++ b/forester/java/src/org/forester/archaeopteryx/TreePanel.java @@ -107,6 +107,7 @@ import org.forester.phylogeny.data.Annotation; import org.forester.phylogeny.data.BranchColor; import org.forester.phylogeny.data.Confidence; import org.forester.phylogeny.data.Event; +import org.forester.phylogeny.data.NodeData.NODE_DATA; import org.forester.phylogeny.data.NodeVisualization; import org.forester.phylogeny.data.NodeVisualization.NodeFill; import org.forester.phylogeny.data.NodeVisualization.NodeShape; @@ -1343,14 +1344,14 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee sortDescendants( node ); break; case GET_EXT_DESC_DATA: - getExtDescNodeData( node ); + showExtDescNodeData( node ); break; default: throw new IllegalArgumentException( "unknown action: " + action ); } } - private void getExtDescNodeData( final PhylogenyNode node ) { + private void showExtDescNodeData( final PhylogenyNode node ) { final List data = new ArrayList(); for( final PhylogenyNode n : node.getAllExternalDescendants() ) { switch ( getOptions().getExtDescNodeDataToReturn() ) { @@ -1378,7 +1379,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } break; case SEQUENCE_ACC: - if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null ) ) { + if ( n.getNodeData().isHasSequence() && ( n.getNodeData().getSequence().getAccession() != null ) + && !ForesterUtil.isEmpty( n.getNodeData().getSequence().getAccession().toString() ) ) { data.add( n.getNodeData().getSequence().getAccession().toString() ); } break; @@ -1394,6 +1396,9 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee data.add( n.getNodeData().getTaxonomy().getTaxonomyCode() ); } break; + case UNKNOWN: + AptxUtil.showExtDescNodeDataUserSelectedHelper( getControlPanel(), n, data ); + break; default: throw new IllegalArgumentException( "unknown data element: " + getOptions().getExtDescNodeDataToReturn() ); @@ -1401,23 +1406,37 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee } // for loop if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.CONSOLE ) { for( final String d : data ) { - System.out.println( d ); + if ( !ForesterUtil.isEmpty( d ) ) { + System.out.println( d ); + } } } else if ( getConfiguration().getExtNodeDataReturnOn() == EXT_NODE_DATA_RETURN_ON.WINODW ) { final StringBuilder sb = new StringBuilder(); for( final String d : data ) { - sb.append( d ); - sb.append( "\n" ); + if ( !ForesterUtil.isEmpty( d ) ) { + sb.append( d ); + sb.append( "\n" ); + } } - if ( getMainPanel().getMainFrame() == null ) { - // Must be "E" applet version. - ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ) - .showTextFrame( sb.toString(), node + " " + obtainTitleForExtDescNodeData() ); + if ( sb.length() < 1 ) { + AptxUtil.showInformationMessage( this, + "No Appropriate Data (" + obtainTitleForExtDescNodeData() + ")", + "Descendants of selected node do not contain selected data" ); } else { - getMainPanel().getMainFrame().showTextFrame( sb.toString(), - node + " " + obtainTitleForExtDescNodeData() ); + final String title = "External Descendants " + + ( getOptions().getExtDescNodeDataToReturn() == NODE_DATA.UNKNOWN ? "Data" + : obtainTitleForExtDescNodeData() ) + " (" + data.size() + "/" + + node.getNumberOfExternalNodes() + ") For Node " + node; + if ( getMainPanel().getMainFrame() == null ) { + // Must be "E" applet version. + ( ( ArchaeopteryxE ) ( ( MainPanelApplets ) getMainPanel() ).getApplet() ).showTextFrame( sb + .toString(), title ); + } + else { + getMainPanel().getMainFrame().showTextFrame( sb.toString(), title ); + } } } } @@ -1438,6 +1457,8 @@ public final class TreePanel extends JPanel implements ActionListener, MouseWhee return "Scientific Names"; case TAXONOMY_CODE: return "Taxonomy Codes"; + case UNKNOWN: + return "User Selected Data"; default: throw new IllegalArgumentException( "unknown data element: " + getOptions().getExtDescNodeDataToReturn() ); diff --git a/forester/java/src/org/forester/phylogeny/data/NodeData.java b/forester/java/src/org/forester/phylogeny/data/NodeData.java index daa9d13..bc7e8b9 100644 --- a/forester/java/src/org/forester/phylogeny/data/NodeData.java +++ b/forester/java/src/org/forester/phylogeny/data/NodeData.java @@ -46,7 +46,8 @@ public class NodeData implements PhylogenyData { SEQUENCE_MOL_SEQ, SEQUENCE_ACC, TAXONOMY_SCIENTIFIC_NAME, - TAXONOMY_CODE; + TAXONOMY_CODE, + UNKNOWN; } private String _node_name; private Event _event;