X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=f06965b16d3e85e5532befc73f3ea1942e5a18b0;hb=97358f7a982d67831aedc14d5ab193727f6bdc83;hp=0e217c44fd67ae9d7cc6161e3fc44388572eefbc;hpb=6726c4b54521e8f4f1ca3e293124776a507cbdfa;p=jalview.git diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java index 0e217c4..f06965b 100644 --- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java +++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java @@ -25,6 +25,7 @@ package org.forester.archaeopteryx; +import java.awt.Color; import java.awt.Component; import java.awt.Graphics2D; import java.awt.GraphicsEnvironment; @@ -35,10 +36,12 @@ import java.io.ByteArrayOutputStream; import java.io.File; import java.io.FileNotFoundException; import java.io.IOException; +import java.io.InputStream; import java.lang.reflect.InvocationTargetException; import java.lang.reflect.Method; import java.net.URI; import java.net.URL; +import java.net.URLConnection; import java.text.ParseException; import java.util.Arrays; import java.util.HashSet; @@ -69,6 +72,7 @@ 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.Confidence; import org.forester.phylogeny.data.Taxonomy; import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory; import org.forester.phylogeny.factories.PhylogenyFactory; @@ -79,12 +83,64 @@ import org.forester.util.ForesterUtil; public final class AptxUtil { + 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(); static { Arrays.sort( AVAILABLE_FONT_FAMILIES_SORTED ); } + 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 ); + } + else { + second = my_str.charAt( my_str.length() - 1 ); + } + if ( is_taxonomy ) { + if ( my_str.length() > 2 ) { + if ( my_str.indexOf( " " ) > 0 ) { + third = my_str.charAt( my_str.indexOf( " " ) + 1 ); + } + else { + third = my_str.charAt( 2 ); + } + } + } + else if ( my_str.length() > 2 ) { + third = my_str.charAt( ( my_str.length() - 1 ) / 2 ); + } + } + 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 new Color( first, second, third ); + } + public static MaskFormatter createMaskFormatter( final String s ) { MaskFormatter formatter = null; try { @@ -108,8 +164,8 @@ 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 ) { @@ -122,6 +178,22 @@ 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() ) { @@ -132,6 +204,30 @@ 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, @@ -188,6 +284,57 @@ public final class AptxUtil { System.out.println( "[" + name + "] > " + message ); } + 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 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 ); + } + } + AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() ); + final URLConnection url_connection = url.openConnection(); + url_connection.setDefaultUseCaches( false ); + final InputStream i = url_connection.getInputStream(); + final Phylogeny[] phys = factory.create( i, parser ); + i.close(); + 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 showErrorMessage( final Component parent, final String error_msg ) { printAppletMessage( Constants.PRG_NAME, error_msg ); JOptionPane.showMessageDialog( parent, error_msg, "[" + Constants.PRG_NAME + " " + Constants.VERSION @@ -227,7 +374,7 @@ 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, @@ -261,6 +408,44 @@ 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, @@ -528,8 +713,8 @@ public final class AptxUtil { /** * Exits with -1. - * - * + * + * * @param message * to message to be printed */ @@ -649,56 +834,15 @@ 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 ); - } - } - AptxUtil.printAppletMessage( "Archaeopteryx", "parser is " + parser.getName() ); - final Phylogeny[] phys = factory.create( url.openStream(), parser ); - 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 ); - } - } + 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 ); } } @@ -747,7 +891,7 @@ public final class AptxUtil { 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.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY() ); tree_panel.resetPreferredSize(); tree_panel.repaint(); } @@ -812,7 +956,7 @@ public final class AptxUtil { 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.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY() ); tree_panel.resetPreferredSize(); tree_panel.repaint(); } @@ -903,73 +1047,4 @@ public final class AptxUtil { final IIOImage iio_image = new IIOImage( image, null, null ); writer.write( null, iio_image, image_write_param ); } - - final private static void openUrlInWebBrowser( final String url ) throws IOException, ClassNotFoundException, - SecurityException, NoSuchMethodException, IllegalArgumentException, IllegalAccessException, - InvocationTargetException, InterruptedException { - final String os = System.getProperty( "os.name" ); - final Runtime runtime = Runtime.getRuntime(); - if ( os.toLowerCase().startsWith( "win" ) ) { - Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url ); - } - else if ( ForesterUtil.isMac() ) { - final Class file_mgr = Class.forName( "com.apple.eio.FileManager" ); - final Method open_url = file_mgr.getDeclaredMethod( "openURL", new Class[] { String.class } ); - open_url.invoke( null, new Object[] { url } ); - } - else { - final String[] browsers = { "firefox", "opera", "konqueror", "mozilla", "netscape", "epiphany" }; - String browser = null; - for( int i = 0; ( i < browsers.length ) && ( browser == null ); ++i ) { - if ( runtime.exec( new String[] { "which", browsers[ i ] } ).waitFor() == 0 ) { - browser = browsers[ i ]; - } - } - if ( browser == null ) { - throw new IOException( "could not find a web browser to open [" + url + "] in" ); - } - else { - runtime.exec( new String[] { browser, url } ); - } - } - } - - // See: http://www.xml.nig.ac.jp/tutorial/rest/index.html#2.2 - // static void openDDBJRest() throws IOException { - // //set URL - // 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 { - 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; - } - } }