X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Farchaeopteryx%2FAptxUtil.java;h=8ceb398a2e08ffaf1bde034aeb7a025662f6ad2b;hb=5c4e24e304f57058fa1c3a3f1256a573b37d89f6;hp=1078656bd7ab1308f9819783c9bc82302df49b23;hpb=ebabb46561f996b5fcd59bd202defd7b189ea5b6;p=jalview.git

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 1078656..8ceb398 100644
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -21,7 +21,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.archaeopteryx;
 
@@ -36,19 +36,26 @@ import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
+import java.io.UnsupportedEncodingException;
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.net.URI;
 import java.net.URL;
+import java.net.URLEncoder;
 import java.text.ParseException;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Set;
+import java.util.SortedMap;
 import java.util.SortedSet;
+import java.util.TreeMap;
 import java.util.TreeSet;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -64,13 +71,18 @@ import javax.swing.text.MaskFormatter;
 
 import org.forester.analysis.TaxonomyDataManager;
 import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
+import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.parsers.nhx.NHXParser.TAXONOMY_EXTRACTION;
 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
 import org.forester.io.parsers.tol.TolParser;
 import org.forester.io.parsers.util.ParserUtils;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
 import org.forester.phylogeny.PhylogenyNode;
 import org.forester.phylogeny.data.Accession;
+import org.forester.phylogeny.data.Annotation;
 import org.forester.phylogeny.data.BranchColor;
 import org.forester.phylogeny.data.Taxonomy;
 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
@@ -79,17 +91,19 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.AsciiHistogram;
 import org.forester.util.DescriptiveStatistics;
+import org.forester.util.ForesterConstants;
 import org.forester.util.ForesterUtil;
+import org.forester.util.SequenceIdParser;
 import org.forester.ws.seqdb.UniProtTaxonomy;
 
 public final class AptxUtil {
 
+    private final static String[] AVAILABLE_FONT_FAMILIES_SORTED = GraphicsEnvironment.getLocalGraphicsEnvironment()
+                                                                         .getAvailableFontFamilyNames();
     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 );
     }
@@ -105,6 +119,69 @@ public final class AptxUtil {
         return formatter;
     }
 
+    public final static String createUriForSeqWeb( final PhylogenyNode node,
+                                                   final Configuration conf,
+                                                   final TreePanel tp ) {
+        String uri_str = null;
+        final String upkb = ForesterUtil.extractUniProtKbProteinSeqIdentifier( node );
+        if ( !ForesterUtil.isEmpty( upkb ) ) {
+            try {
+                uri_str = ForesterUtil.UNIPROT_KB + URLEncoder.encode( upkb, ForesterConstants.UTF8 );
+            }
+            catch ( final UnsupportedEncodingException e ) {
+                showErrorMessage( tp, e.toString() );
+                e.printStackTrace();
+            }
+        }
+        if ( ForesterUtil.isEmpty( uri_str ) ) {
+            final String v = ForesterUtil.extractGenbankAccessor( node );
+            if ( !ForesterUtil.isEmpty( v ) ) {
+                try {
+                    if ( SequenceIdParser.isProtein( v ) ) {
+                        uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 );
+                    }
+                    else {
+                        uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 );
+                    }
+                }
+                catch ( final UnsupportedEncodingException e ) {
+                    showErrorMessage( tp, e.toString() );
+                    e.printStackTrace();
+                }
+            }
+        }
+        if ( ForesterUtil.isEmpty( uri_str ) ) {
+            final String v = ForesterUtil.extractRefSeqAccessorAccessor( node );
+            if ( !ForesterUtil.isEmpty( v ) ) {
+                try {
+                    if ( SequenceIdParser.isProtein( v ) ) {
+                        uri_str = ForesterUtil.NCBI_PROTEIN + URLEncoder.encode( v, ForesterConstants.UTF8 );
+                    }
+                    else {
+                        uri_str = ForesterUtil.NCBI_NUCCORE + URLEncoder.encode( v, ForesterConstants.UTF8 );
+                    }
+                }
+                catch ( final UnsupportedEncodingException e ) {
+                    showErrorMessage( tp, e.toString() );
+                    e.printStackTrace();
+                }
+            }
+        }
+        if ( ForesterUtil.isEmpty( uri_str ) ) {
+            final String v = ForesterUtil.extractGInumber( node );
+            if ( !ForesterUtil.isEmpty( v ) ) {
+                try {
+                    uri_str = ForesterUtil.NCBI_GI + URLEncoder.encode( v, ForesterConstants.UTF8 );
+                }
+                catch ( final UnsupportedEncodingException e ) {
+                    showErrorMessage( tp, e.toString() );
+                    e.printStackTrace();
+                }
+            }
+        }
+        return uri_str;
+    }
+
     final static public boolean isHasAtLeastNodeWithEvent( final Phylogeny phy ) {
         final PhylogenyNodeIterator it = phy.iteratorPostorder();
         while ( it.hasNext() ) {
@@ -182,6 +259,36 @@ public final class AptxUtil {
         }
     }
 
+    public static Set<Taxonomy> obtainAllDistinctTaxonomies( final PhylogenyNode node ) {
+        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
+        final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
+        for( final PhylogenyNode n : descs ) {
+            if ( n.getNodeData().isHasTaxonomy() && !n.getNodeData().getTaxonomy().isEmpty() ) {
+                tax_set.add( n.getNodeData().getTaxonomy() );
+            }
+        }
+        return tax_set;
+    }
+
+    /**
+     * Returns the set of distinct taxonomies of
+     * all external nodes of node.
+     * If at least one the external nodes has no taxonomy,
+     * null is returned.
+     * 
+     */
+    public static Set<Taxonomy> obtainDistinctTaxonomies( final PhylogenyNode node ) {
+        final List<PhylogenyNode> descs = node.getAllExternalDescendants();
+        final Set<Taxonomy> tax_set = new HashSet<Taxonomy>();
+        for( final PhylogenyNode n : descs ) {
+            if ( !n.getNodeData().isHasTaxonomy() || n.getNodeData().getTaxonomy().isEmpty() ) {
+                return null;
+            }
+            tax_set.add( n.getNodeData().getTaxonomy() );
+        }
+        return tax_set;
+    }
+
     public final static Accession obtainSequenceAccessionFromName( final String sequence_name ) {
         final String n = sequence_name.trim();
         final Matcher matcher1 = seq_identifier_pattern_1.matcher( n );
@@ -242,6 +349,10 @@ public final class AptxUtil {
                 && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getScientificName() ) ) {
             showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getScientificName(), sb );
         }
+        if ( cp.isShowTaxonomyCommonNames() && node.getNodeData().isHasTaxonomy()
+                && !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) {
+            showExtDescNodeDataUserSelectedHelperHelper( node.getNodeData().getTaxonomy().getCommonName(), sb );
+        }
         if ( ( cp.isShowGeneNames() || cp.isShowGeneSymbols() || cp.isShowSequenceAcc() )
                 && node.getNodeData().isHasSequence()
                 && !ForesterUtil.isEmpty( node.getNodeData().getSequence().getMolecularSequence() ) ) {
@@ -297,7 +408,7 @@ public final class AptxUtil {
                                                                          final ControlPanel ac,
                                                                          final GraphicsExportType type,
                                                                          final Options options ) throws IOException {
-        tree_panel.setParametersForPainting( width, height, true );
+        tree_panel.calcParametersForPainting( width, height, true );
         tree_panel.resetPreferredSize();
         tree_panel.repaint();
         final RenderingHints rendering_hints = new RenderingHints( RenderingHints.KEY_RENDERING,
@@ -432,25 +543,41 @@ public final class AptxUtil {
         lookAtSomeTreePropertiesForAptxControlSettings( phy, main_panel.getControlPanel(), configuration );
     }
 
-    final static Color calculateColorFromString( final String str ) {
-        final String species_uc = str.toUpperCase();
-        char first = species_uc.charAt( 0 );
+    final 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 ( species_uc.length() > 1 ) {
-            second = species_uc.charAt( 1 );
-            if ( species_uc.length() > 2 ) {
-                if ( species_uc.indexOf( " " ) > 0 ) {
-                    third = species_uc.charAt( species_uc.indexOf( " " ) + 1 );
-                }
-                else {
-                    third = species_uc.charAt( 2 );
+        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 = ( char ) ( Math.abs( str.hashCode() / 16909320 ) );
+                System.out.println( str.hashCode() );
+            }
         }
         first = AptxUtil.normalizeCharForRGB( first );
         second = AptxUtil.normalizeCharForRGB( second );
-        third = AptxUtil.normalizeCharForRGB( third );
+        if ( is_taxonomy ) {
+            third = AptxUtil.normalizeCharForRGB( third );
+        }
+        else {
+            third = third > 255 ? 255 : third;
+        }
         if ( ( first > 235 ) && ( second > 235 ) && ( third > 235 ) ) {
             first = 0;
         }
@@ -471,7 +598,7 @@ public final class AptxUtil {
         for( final PhylogenyNodeIterator it = phy.iteratorPreorder(); it.hasNext(); ) {
             final PhylogenyNode n = it.next();
             if ( !n.isExternal() && !n.isCollapse() && ( n.getNumberOfDescendants() > 1 ) ) {
-                final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( n );
+                final Set<Taxonomy> taxs = obtainDistinctTaxonomies( n );
                 if ( ( taxs != null ) && ( taxs.size() == 1 ) ) {
                     AptxUtil.collapseSubtree( n, true );
                     if ( !n.getNodeData().isHasTaxonomy() ) {
@@ -623,6 +750,49 @@ public final class AptxUtil {
         return colorizations;
     }
 
+    final static String createAnnotationString( final SortedSet<Annotation> annotations ) {
+        final SortedMap<String, List<Annotation>> m = new TreeMap<String, List<Annotation>>();
+        for( final Annotation an : annotations ) {
+            final String ref_source = ForesterUtil.isEmpty( an.getRefSource() ) ? "?" : an.getRefSource();
+            if ( !m.containsKey( ref_source ) ) {
+                m.put( ref_source, new ArrayList<Annotation>() );
+            }
+            m.get( ref_source ).add( an );
+        }
+        final StringBuilder sb = new StringBuilder();
+        for( final Entry<String, List<Annotation>> e : m.entrySet() ) {
+            final String ref_source = e.getKey();
+            final List<Annotation> ans = e.getValue();
+            if ( m.size() > 1 ) {
+                sb.append( "[" );
+            }
+            if ( !ref_source.equals( "?" ) ) {
+                sb.append( ref_source );
+                sb.append( ": " );
+            }
+            for( int i = 0; i < ans.size(); ++i ) {
+                final Annotation an = ans.get( i );
+                if ( !ForesterUtil.isEmpty( an.getRefValue() ) ) {
+                    sb.append( an.getRefValue() );
+                    sb.append( " " );
+                }
+                if ( !ForesterUtil.isEmpty( an.getDesc() ) ) {
+                    sb.append( an.getDesc() );
+                }
+                if ( sb.charAt( sb.length() - 1 ) == ' ' ) {
+                    sb.deleteCharAt( sb.length() - 1 );
+                }
+                if ( i < ans.size() - 1 ) {
+                    sb.append( ", " );
+                }
+            }
+            if ( m.size() > 1 ) {
+                sb.append( "] " );
+            }
+        }
+        return sb.toString();
+    }
+
     final static String createBasicInformation( final Phylogeny phy ) {
         final StringBuilder desc = new StringBuilder();
         if ( ( phy != null ) && !phy.isEmpty() ) {
@@ -633,7 +803,22 @@ public final class AptxUtil {
             }
             if ( phy.getIdentifier() != null ) {
                 desc.append( "Id: " );
-                desc.append( phy.getIdentifier() );
+                desc.append( phy.getIdentifier().toString() );
+                desc.append( "\n" );
+            }
+            if ( !ForesterUtil.isEmpty( phy.getDescription() ) ) {
+                desc.append( "Description: " );
+                desc.append( phy.getDescription() );
+                desc.append( "\n" );
+            }
+            if ( !ForesterUtil.isEmpty( phy.getDistanceUnit() ) ) {
+                desc.append( "Distance Unit: " );
+                desc.append( phy.getDistanceUnit() );
+                desc.append( "\n" );
+            }
+            if ( !ForesterUtil.isEmpty( phy.getType() ) ) {
+                desc.append( "Type: " );
+                desc.append( phy.getType() );
                 desc.append( "\n" );
             }
             desc.append( "Rooted: " );
@@ -642,16 +827,19 @@ public final class AptxUtil {
             desc.append( "Rerootable: " );
             desc.append( phy.isRerootable() );
             desc.append( "\n" );
-            desc.append( "Node sum: " );
+            desc.append( "Nodes: " );
             desc.append( phy.getNodeCount() );
             desc.append( "\n" );
-            desc.append( "External node sum: " );
+            desc.append( "External nodes: " );
             desc.append( phy.getNumberOfExternalNodes() );
             desc.append( "\n" );
-            desc.append( "Internal node sum: " );
+            desc.append( "Internal nodes: " );
             desc.append( phy.getNodeCount() - phy.getNumberOfExternalNodes() );
             desc.append( "\n" );
-            desc.append( "Branche sum: " );
+            desc.append( "Internal nodes with polytomies: " );
+            desc.append( PhylogenyMethods.countNumberOfPolytomies( phy ) );
+            desc.append( "\n" );
+            desc.append( "Branches: " );
             desc.append( phy.getNumberOfBranches() );
             desc.append( "\n" );
             desc.append( "Depth: " );
@@ -660,11 +848,14 @@ public final class AptxUtil {
             desc.append( "Maximum distance to root: " );
             desc.append( ForesterUtil.round( PhylogenyMethods.calculateMaxDistanceToRoot( phy ), 6 ) );
             desc.append( "\n" );
-            final Set<Taxonomy> taxs = PhylogenyMethods.obtainDistinctTaxonomies( phy.getRoot() );
+            final Set<Taxonomy> taxs = obtainAllDistinctTaxonomies( phy.getRoot() );
             if ( taxs != null ) {
                 desc.append( "Distinct external taxonomies: " );
                 desc.append( taxs.size() );
             }
+            for( final Taxonomy t : taxs ) {
+                System.out.println( t.toString() );
+            }
             desc.append( "\n" );
             final DescriptiveStatistics bs = PhylogenyMethods.calculatBranchLengthStatistics( phy );
             if ( bs.getN() > 3 ) {
@@ -675,9 +866,8 @@ public final class AptxUtil {
                 desc.append( "\n" );
                 desc.append( "    Median: " + ForesterUtil.round( bs.median(), 6 ) );
                 desc.append( "\n" );
-                desc.append( "    Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) );
-                desc.append( "\n" );
-                desc.append( "    SD: " + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) );
+                desc.append( "    Mean: " + ForesterUtil.round( bs.arithmeticMean(), 6 ) + " (stdev: "
+                        + ForesterUtil.round( bs.sampleStandardDeviation(), 6 ) + ")" );
                 desc.append( "\n" );
                 desc.append( "    Minimum: " + ForesterUtil.round( bs.getMin(), 6 ) );
                 desc.append( "\n" );
@@ -696,9 +886,8 @@ public final class AptxUtil {
                 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( "    Mean: " + ForesterUtil.round( ds.arithmeticMean(), 2 ) + " (stdev: "
+                        + ForesterUtil.round( ds.sampleStandardDeviation(), 2 ) + ")" );
                 desc.append( "\n" );
                 desc.append( "    Minimum: " + ForesterUtil.roundToInt( ds.getMin() ) );
                 desc.append( "\n" );
@@ -733,11 +922,10 @@ public final class AptxUtil {
                         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( " (stdev: " + 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() ) );
@@ -791,24 +979,6 @@ public final class AptxUtil {
         return AVAILABLE_FONT_FAMILIES_SORTED;
     }
 
-    final static void inferCommonPartOfScientificNames( final Phylogeny tree ) {
-        boolean inferred = false;
-        for( final PhylogenyNodeIterator it = tree.iteratorPostorder(); it.hasNext(); ) {
-            final PhylogenyNode n = it.next();
-            if ( !n.getNodeData().isHasTaxonomy() && !n.isExternal() ) {
-                final String sn = PhylogenyMethods.inferCommonPartOfScientificNameOfDescendants( n );
-                if ( !ForesterUtil.isEmpty( sn ) ) {
-                    n.getNodeData().setTaxonomy( new Taxonomy() );
-                    n.getNodeData().getTaxonomy().setScientificName( sn );
-                    inferred = true;
-                }
-            }
-        }
-        if ( inferred ) {
-            tree.setRerootable( false );
-        }
-    }
-
     final static boolean isHasAssignedEvent( final PhylogenyNode node ) {
         if ( !node.getNodeData().isHasEvent() ) {
             return false;
@@ -819,28 +989,6 @@ public final class AptxUtil {
         return true;
     }
 
-    final static boolean isJava15() {
-        try {
-            final String s = ForesterUtil.JAVA_VERSION;
-            return s.startsWith( "1.5" );
-        }
-        catch ( final Exception e ) {
-            ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
-            return false;
-        }
-    }
-
-    final static boolean isMac() {
-        try {
-            final String s = ForesterUtil.OS_NAME.toLowerCase();
-            return s.startsWith( "mac" );
-        }
-        catch ( final Exception e ) {
-            ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
-            return false;
-        }
-    }
-
     final static boolean isUsOrCanada() {
         try {
             if ( ( Locale.getDefault().equals( Locale.CANADA ) ) || ( Locale.getDefault().equals( Locale.US ) ) ) {
@@ -853,17 +1001,6 @@ public final class AptxUtil {
         return false;
     }
 
-    final static boolean isWindows() {
-        try {
-            final String s = ForesterUtil.OS_NAME.toLowerCase();
-            return s.indexOf( "win" ) > -1;
-        }
-        catch ( final Exception e ) {
-            ForesterUtil.printWarningMessage( Constants.PRG_NAME, "minor error: " + e );
-            return false;
-        }
-    }
-
     final static void lookAtSomeTreePropertiesForAptxControlSettings( final Phylogeny t,
                                                                       final ControlPanel atv_control,
                                                                       final Configuration configuration ) {
@@ -915,21 +1052,66 @@ public final class AptxUtil {
         }
     }
 
+    final static void outOfMemoryError( final OutOfMemoryError e ) {
+        System.err.println();
+        System.err.println( "Java memory allocation might be too small, try \"-Xmx2048m\" java command line option" );
+        System.err.println();
+        e.printStackTrace();
+        System.err.println();
+        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 );
+        System.exit( -1 );
+    }
+
     final static void printAppletMessage( final String applet_name, final String message ) {
         System.out.println( "[" + applet_name + "] > " + message );
     }
 
-    final static Phylogeny[] readPhylogeniesFromUrl( final URL url, final boolean phyloxml_validate_against_xsd )
-            throws FileNotFoundException, IOException {
+    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();
-        PhylogenyParser parser = null;
+        final PhylogenyParser parser;
+        boolean nhx_or_nexus = false;
         if ( url.getHost().toLowerCase().indexOf( "tolweb" ) >= 0 ) {
             parser = new TolParser();
         }
         else {
             parser = ParserUtils.createParserDependingOnUrlContents( url, phyloxml_validate_against_xsd );
+            if ( parser instanceof NHXParser ) {
+                nhx_or_nexus = true;
+                final NHXParser nhx = ( NHXParser ) parser;
+                nhx.setReplaceUnderscores( replace_underscores );
+                nhx.setIgnoreQuotes( false );
+                nhx.setTaxonomyExtraction( taxonomy_extraction );
+            }
+            else if ( parser instanceof NexusPhylogeniesParser ) {
+                nhx_or_nexus = true;
+                final NexusPhylogeniesParser nex = ( NexusPhylogeniesParser ) parser;
+                nex.setReplaceUnderscores( replace_underscores );
+                nex.setIgnoreQuotes( false );
+            }
+        }
+        final Phylogeny[] phys = factory.create( url.openStream(), parser );
+        if ( nhx_or_nexus && internal_numbers_are_confidences ) {
+            for( final Phylogeny phy : phys ) {
+                PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
+            }
+        }
+        if ( midpoint_reroot ) {
+            for( final Phylogeny phy : phys ) {
+                PhylogenyMethods.midpointRoot( phy );
+                PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+            }
         }
-        return factory.create( url.openStream(), parser );
+        return phys;
     }
 
     final static void removeBranchColors( final Phylogeny phy ) {
@@ -938,30 +1120,38 @@ public final class AptxUtil {
         }
     }
 
-    final static void unexpectedError( final Error err ) {
-        err.printStackTrace();
+    final static void unexpectedError( final Error e ) {
+        System.err.println();
+        e.printStackTrace( System.err );
+        System.err.println();
         final StringBuffer sb = new StringBuffer();
-        for( final StackTraceElement s : err.getStackTrace() ) {
+        for( final StackTraceElement s : e.getStackTrace() ) {
             sb.append( s + "\n" );
         }
         JOptionPane
                 .showMessageDialog( null,
                                     "An unexpected (possibly severe) error has occured - terminating. \nPlease contact: "
-                                            + Constants.AUTHOR_EMAIL + " \nError: " + err + "\n" + sb,
+                                            + Constants.AUTHOR_EMAIL + " \nError: " + e.getLocalizedMessage() + "\n"
+                                            + sb,
                                     "Unexpected Severe Error [" + Constants.PRG_NAME + " " + Constants.VERSION + "]",
                                     JOptionPane.ERROR_MESSAGE );
         System.exit( -1 );
     }
 
-    final static void unexpectedException( final Exception ex ) {
-        ex.printStackTrace();
+    final static void unexpectedException( final Exception e ) {
+        System.err.println();
+        e.printStackTrace( System.err );
+        System.err.println();
         final StringBuffer sb = new StringBuffer();
-        for( final StackTraceElement s : ex.getStackTrace() ) {
+        for( final StackTraceElement s : e.getStackTrace() ) {
             sb.append( s + "\n" );
         }
-        JOptionPane.showMessageDialog( null, "An unexpected exception has occured. \nPlease contact: "
-                + Constants.AUTHOR_EMAIL + " \nException: " + ex + "\n" + sb, "Unexpected Exception ["
-                + Constants.PRG_NAME + Constants.VERSION + "]", JOptionPane.ERROR_MESSAGE );
+        JOptionPane.showMessageDialog( null,
+                                       "An unexpected exception has occured. \nPlease contact: "
+                                               + Constants.AUTHOR_EMAIL + " \nException: " + e.getLocalizedMessage()
+                                               + "\n" + sb,
+                                       "Unexpected Exception [" + Constants.PRG_NAME + Constants.VERSION + "]",
+                                       JOptionPane.ERROR_MESSAGE );
     }
 
     final static String writePhylogenyToGraphicsByteArrayOutputStream( final ByteArrayOutputStream baos,
@@ -975,7 +1165,7 @@ public final class AptxUtil {
             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.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
             tree_panel.resetPreferredSize();
             tree_panel.repaint();
         }
@@ -1040,7 +1230,7 @@ public final class AptxUtil {
             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.calcParametersForPainting( options.getPrintSizeX(), options.getPrintSizeY(), true );
             tree_panel.resetPreferredSize();
             tree_panel.repaint();
         }
@@ -1156,7 +1346,7 @@ public final class AptxUtil {
         if ( os.toLowerCase().startsWith( "win" ) ) {
             Runtime.getRuntime().exec( "rundll32 url.dll,FileProtocolHandler " + url );
         }
-        else if ( isMac() ) {
+        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 } );
@@ -1203,7 +1393,7 @@ public final class AptxUtil {
     // br.close();
     // }
     public static enum GraphicsExportType {
-        GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" ), BMP( "bmp" );
+        BMP( "bmp" ), GIF( "gif" ), JPG( "jpg" ), PDF( "pdf" ), PNG( "png" ), TIFF( "tif" );
 
         private final String _suffix;