X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=5b3dafaa1cbdedf0dc85d1e121e7386bbabf92a6;hb=a9e626aa67ff9cb1649c371f9d705eb04498cc33;hp=09effc3e3230709c432077330ddcc1c4a4837835;hpb=87d8c4dedc7e2418f12242986cea67307dd62a7f;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 09effc3..5b3dafa 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;
@@ -39,6 +40,8 @@ import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.net.URI;
 import java.net.URL;
+import java.security.KeyManagementException;
+import java.security.NoSuchAlgorithmException;
 import java.text.ParseException;
 import java.util.Arrays;
 import java.util.HashSet;
@@ -69,9 +72,8 @@ 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;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.util.AsciiHistogram;
 import org.forester.util.DescriptiveStatistics;
@@ -79,12 +81,64 @@ 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();
+            .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 +162,8 @@ 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 +176,22 @@ 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<Confidence> 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 +202,30 @@ 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,
@@ -188,10 +282,65 @@ 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 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() );
+        Phylogeny[] phys = null;
+        try {
+            phys = ForesterUtil.readPhylogeniesFromUrl( url, parser );
+        }
+        catch ( final KeyManagementException e ) {
+            throw new IOException( e.getMessage() );
+        }
+        catch ( final NoSuchAlgorithmException e ) {
+            throw new IOException( e.getMessage() );
+        }
+        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
-                + "] Error", JOptionPane.ERROR_MESSAGE );
+        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,
@@ -216,7 +365,7 @@ 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();
     }
 
@@ -227,7 +376,7 @@ 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,
@@ -261,20 +410,58 @@ 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 ) {
@@ -446,7 +633,7 @@ 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: " );
@@ -468,7 +655,7 @@ 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: " );
@@ -485,10 +672,10 @@ public final class AptxUtil {
             }
             List<DescriptiveStatistics> 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" );
@@ -528,16 +715,16 @@ 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 );
     }
@@ -579,18 +766,31 @@ 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 ( 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 );
                     }
@@ -624,7 +824,7 @@ 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 );
@@ -640,8 +840,8 @@ 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 );
     }
 
@@ -649,53 +849,6 @@ 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 );
-                }
-            }
-        }
-        return phys;
-    }
-
     final static void removeBranchColors( final Phylogeny phy ) {
         for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
             it.next().getBranchData().setBranchColor( null );
@@ -717,11 +870,11 @@ 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 );
     }
@@ -736,10 +889,10 @@ 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,
@@ -753,7 +906,7 @@ 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();
         }
@@ -818,7 +971,7 @@ 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();
         }
@@ -909,73 +1062,4 @@ 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;
-        }
-    }
 }