From: cmzmasek <cmzmasek@yahoo.com>
Date: Wed, 27 Jul 2016 22:53:47 +0000 (-0700)
Subject: minor improvements and bug-fixes
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2153d77fe476de9ceeb3b1e7fb3438c2ce373963;p=jalview.git

minor improvements and bug-fixes
---

diff --git a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java
index 4b1c713..19e0697 100644
--- a/forester/java/src/org/forester/archaeopteryx/AptxConstants.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxConstants.java
@@ -38,8 +38,8 @@ public final class AptxConstants {
 
     final static boolean        __ALLOW_PHYLOGENETIC_INFERENCE                                = true;
     public final static String  PRG_NAME                                                      = "Archaeopteryx";
-    final static String         VERSION                                                       = "0.9914 test";
-    final static String         PRG_DATE                                                      = "160714";
+    final static String         VERSION                                                       = "0.9915 test";
+    final static String         PRG_DATE                                                      = "160727";
     final static String         DEFAULT_CONFIGURATION_FILE_NAME                               = "_aptx_configuration_file";
     final static String[]       DEFAULT_FONT_CHOICES                                          = { 
             "Arial Unicode MS", "Dialog", "SansSerif", "Sans", "Arial", "Helvetica" };
@@ -68,6 +68,7 @@ public final class AptxConstants {
     static final int            MAX_TREES_TO_LOAD                                             = 100;
     final static float          PDF_LINE_WIDTH_DEFAULT                                        = 0.5f;
     final static String         APTX_WEB_SITE                                                 = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx";
+    final static String         APTX_MAILING_LIST                                             = "https://groups.google.com/forum/?fromgroups#!forum/archaeopteryx";
     final static String         APTX_DOC_SITE                                                 = "https://sites.google.com/site/cmzmasek/home/software/archaeopteryx/documentation";
     final static String         PHYLOXML_WEB_SITE                                             = ForesterConstants.PHYLO_XML_LOCATION;
     final static String         PHYLOXML_REFERENCE_URL                                        = "http://www.biomedcentral.com/1471-2105/10/356/";
diff --git a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index 958a952..f0da94b 100644
--- a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@ -176,6 +176,17 @@ public final class AptxUtil {
         }
         return false;
     }
+    
+    final static public boolean isHasNoBranchLengthSmallerThanZero( final Phylogeny phy ) {
+        final PhylogenyNodeIterator it = phy.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next(); 
+            if ( n.getDistanceToParent() < 0.0 && !n.isRoot() ) {
+                return false;
+            }
+        }
+        return true;
+    }
 
     final static public boolean isHasAtLeastOneBranchWithSupportSD( final Phylogeny phy ) {
         final PhylogenyNodeIterator it = phy.iteratorPostorder();
@@ -771,12 +782,17 @@ public final class AptxUtil {
                                                                      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 );
+            else {
+                final boolean has_all_bl = AptxUtil.isHasNoBranchLengthSmallerThanZero( t );
+                cp.setDrawPhylogram(  has_all_bl );
+                if ( cp.getDisplayAsPhylogramCb() != null ) {
+                    cp.setDrawPhylogramEnabled( true );
+                }
             }
         }
     }
@@ -789,7 +805,6 @@ public final class AptxUtil {
                 atv_control.setDrawPhylogram( false );
                 atv_control.setDrawPhylogramEnabled( false );
             }
-            
             if ( t.getFirstExternalNode().getBranchData().getBranchColor() != null
                     && atv_control.getUseVisualStylesCb() != null ) {
                 atv_control.getUseVisualStylesCb().setSelected( true );
@@ -805,7 +820,9 @@ public final class AptxUtil {
             if ( configuration.doGuessCheckOption( Configuration.display_as_phylogram ) ) {
                 if ( atv_control.getDisplayAsPhylogramCb() != null ) {
                     if ( has_bl ) {
-                        atv_control.setDrawPhylogram( true );
+                        final boolean has_all_bl = AptxUtil.isHasNoBranchLengthSmallerThanZero( t );
+                        
+                        atv_control.setDrawPhylogram( has_all_bl );
                         atv_control.setDrawPhylogramEnabled( true );
                     }
                     else {
diff --git a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
index 1612aba..ff3ce2f 100644
--- a/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
+++ b/forester/java/src/org/forester/archaeopteryx/ArchaeopteryxE.java
@@ -338,7 +338,7 @@ public class ArchaeopteryxE extends JApplet implements ActionListener {
             updateOptions( getOptions() );
         }
         else if ( o == _about_item ) {
-            MainFrame.about();
+            getMainPanel().getMainFrame().about();
         }
         else if ( o == _help_item ) {
             try {
diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 79fec13..bf28511 100644
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -253,6 +253,7 @@ public final class Configuration {
     private boolean                         _line_up_renderable_node_data                          = true;
     private boolean                         _right_align_domains                                   = false;
     private boolean                         _allow_thick_strokes                                   = false;
+    private boolean                         _could_read_config_file = false;
     static {
         for( final String font_name : AptxConstants.DEFAULT_FONT_CHOICES ) {
             if ( Arrays.binarySearch( AptxUtil.getAvailableFontFamiliesSorted(), font_name ) >= 0 ) {
@@ -276,6 +277,7 @@ public final class Configuration {
         else {
             config_filename = cf;
         }
+        _could_read_config_file = false;
         setDisplayColors( new TreeMap<String, Color>() );
         config_filename = config_filename.trim();
         URL u = null;
@@ -290,6 +292,7 @@ public final class Configuration {
                     bf.close();
                     ForesterUtil.programMessage( AptxConstants.PRG_NAME, "successfully read from configuration url ["
                             + config_filename + "]" );
+                    _could_read_config_file = true;
                 }
                 catch ( final Exception e ) {
                     ForesterUtil.printWarningMessage( AptxConstants.PRG_NAME, "failed to read configuration from ["
@@ -312,6 +315,7 @@ public final class Configuration {
                     final BufferedReader bf = new BufferedReader( new FileReader( f ) );
                     readConfig( bf );
                     bf.close();
+                    _could_read_config_file = true;
                 }
                 catch ( final Exception e ) {
                     if ( verbose ) {
@@ -1793,4 +1797,10 @@ public final class Configuration {
     static String getDefaultFontFamilyName() {
         return DEFAULT_FONT_FAMILY;
     }
+
+    public boolean isCouldReadConfigFile() {
+        return _could_read_config_file;
+    }
+
+    
 }
diff --git a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
index 47a9f72..fb6f98c 100644
--- a/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
+++ b/forester/java/src/org/forester/archaeopteryx/ControlPanel.java
@@ -455,7 +455,7 @@ final class ControlPanel extends JPanel implements ActionListener {
         }
         final ArrayList<String> sequenceNamesToAdd = new ArrayList<String>();
         for( final Sequence seq : sequenceRelationQueries ) {
-            if ( seq.hasSequenceRelations() ) {
+            if ( seq.isHasSequenceRelations() ) {
                 boolean fFoundForCurrentType = false;
                 for( final SequenceRelation sq : seq.getSequenceRelations() ) {
                     if ( sq.getType().equals( relationType ) ) {
diff --git a/forester/java/src/org/forester/archaeopteryx/MainFrame.java b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
index e6309db..0336c92 100644
--- a/forester/java/src/org/forester/archaeopteryx/MainFrame.java
+++ b/forester/java/src/org/forester/archaeopteryx/MainFrame.java
@@ -272,6 +272,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     JMenuItem                        _about_item;
     JMenuItem                        _help_item;
     JMenuItem                        _website_item;
+    JMenuItem                        _mailing_list_item;
     JMenuItem                        _phyloxml_website_item;
     JMenuItem                        _phyloxml_ref_item;
     JMenuItem                        _aptx_ref_item;
@@ -606,6 +607,14 @@ public abstract class MainFrame extends JFrame implements ActionListener {
                 ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
             }
         }
+        else if ( o == _mailing_list_item ) {
+            try {
+                AptxUtil.openWebsite( AptxConstants.APTX_MAILING_LIST, is_applet, applet );
+            }
+            catch ( final IOException e1 ) {
+                ForesterUtil.printErrorMessage( AptxConstants.PRG_NAME, e1.toString() );
+            }
+        }
         else if ( o == _phyloxml_website_item ) {
             try {
                 AptxUtil.openWebsite( AptxConstants.PHYLOXML_WEB_SITE, is_applet, applet );
@@ -1165,6 +1174,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         _help_jmenu.add( _help_item = new JMenuItem( "Documentation" ) );
         _help_jmenu.addSeparator();
         _help_jmenu.add( _website_item = new JMenuItem( "Archaeopteryx Home" ) );
+        _help_jmenu.add( _mailing_list_item = new JMenuItem( "Mailing List" ) );
         _aptx_ref_item = new JMenuItem( "Archaeopteryx Reference" ); //TODO need to add this...
         _help_jmenu.add( _phyloxml_website_item = new JMenuItem( "phyloXML Home" ) );
         _help_jmenu.add( _phyloxml_ref_item = new JMenuItem( "phyloXML Reference" ) );
@@ -1172,6 +1182,7 @@ public abstract class MainFrame extends JFrame implements ActionListener {
         _help_jmenu.add( _about_item = new JMenuItem( "About" ) );
         customizeJMenuItem( _help_item );
         customizeJMenuItem( _website_item );
+        customizeJMenuItem( _mailing_list_item );
         customizeJMenuItem( _phyloxml_website_item );
         customizeJMenuItem( _aptx_ref_item );
         customizeJMenuItem( _phyloxml_ref_item );
@@ -2000,13 +2011,21 @@ public abstract class MainFrame extends JFrame implements ActionListener {
     /**
      * Display the about box.
      */
-    static void about() {
+    void about() {
         final StringBuffer about = new StringBuffer( "Archaeopteryx\nVersion " + AptxConstants.VERSION + "\n" );
         about.append( "Copyright (C) 2016 Christian M Zmasek\n" );
         about.append( "All Rights Reserved\n" );
         about.append( "License: GNU Lesser General Public License (LGPL)\n" );
         about.append( "Last modified: " + AptxConstants.PRG_DATE + "\n" );
         about.append( "Based on: " + ForesterUtil.getForesterLibraryInformation() + "\n" );
+        
+        if  ( _configuration.isCouldReadConfigFile() ) {
+            about.append( "Using configuration file: " + _configuration.config_filename + "\n" );
+        }
+        else {
+            about.append( "Not using a configuration file\n" );
+        }
+        
         about.append( "phyloXML version : " + ForesterConstants.PHYLO_XML_VERSION + "\n" );
         about.append( "phyloXML location: " + ForesterConstants.PHYLO_XML_LOCATION + "\n" );
         if ( !ForesterUtil.isEmpty( ForesterUtil.JAVA_VERSION ) && !ForesterUtil.isEmpty( ForesterUtil.JAVA_VENDOR ) ) {
diff --git a/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java b/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java
index 9faee68..afe47f0 100644
--- a/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java
+++ b/forester/java/src/org/forester/archaeopteryx/tools/ImageLoader.java
@@ -74,8 +74,10 @@ public class ImageLoader implements Runnable {
                     && !node.getNodeData().getTaxonomy().getUris().isEmpty() ) {
                 final List<Uri> us = new ArrayList<Uri>();
                 for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
-                    for( final Uri uri : t.getUris() ) {
-                        us.add( uri );
+                    if ( t.getUris() != null ) {
+                        for( final Uri uri : t.getUris() ) {
+                            us.add( uri );
+                        }
                     }
                 }
                 for( final Uri uri : us ) {
diff --git a/forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java b/forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java
index 88f1d0c..ac5c521 100644
--- a/forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java
+++ b/forester/java/src/org/forester/io/parsers/phyloxml/data/ColorParser.java
@@ -74,7 +74,7 @@ public class ColorParser implements PhylogenyDataPhyloXmlParser {
             color.setValue( new Color( red, green, blue ) );
         }
         else { 
-            color.setValue( new Color( red, green, blue ) );
+            color.setValue( new Color( red, green, blue, alpha ) );
         }
         return color;
     }
diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 3928bc3..6aa0fff 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -468,12 +468,12 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
 
     public final PhylogenyNode getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() {
         //TODO work on me ~~
-        if ( isInternal() && !isCollapse() ) {
-            throw new UnsupportedOperationException( "attempt to get next external node of an uncollapsed internal node" );
-        }
         if ( isRoot() ) {
             return null;
         }
+        if ( isInternal() && !isCollapse() ) {
+            throw new UnsupportedOperationException( "attempt to get next external node of an uncollapsed internal node" );
+        }
         if ( getParent().isCollapse() ) {
             throw new UnsupportedOperationException( "attempt to get next external node of node with a collapsed parent" );
         }
@@ -617,9 +617,10 @@ public final class PhylogenyNode implements Comparable<PhylogenyNode> {
 
     /**
      * Returns whether this PhylogenyNode should be drawn as collapsed.
+     * Root can not be collapsed.
      */
     final public boolean isCollapse() {
-        return _collapse;
+        return _collapse && _parent != null;
     }
 
     /**
diff --git a/forester/java/src/org/forester/phylogeny/data/Confidence.java b/forester/java/src/org/forester/phylogeny/data/Confidence.java
index 8b12491..1d490ff 100644
--- a/forester/java/src/org/forester/phylogeny/data/Confidence.java
+++ b/forester/java/src/org/forester/phylogeny/data/Confidence.java
@@ -38,7 +38,7 @@ import org.forester.util.ForesterUtil;
 
 public class Confidence implements PhylogenyData, Comparable<Confidence> {
 
-    public final static int          CONFIDENCE_DEFAULT_VALUE = -9999;
+    public final static int          CONFIDENCE_DEFAULT_VALUE = -Integer.MAX_VALUE;
     private double                   _value;
     private double                   _sd;
     private String                   _type;
diff --git a/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java b/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java
index 48da0e0..f40b507 100644
--- a/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java
+++ b/forester/java/src/org/forester/phylogeny/data/PhylogenyDataUtil.java
@@ -35,7 +35,7 @@ import org.forester.util.ForesterUtil;
 
 public final class PhylogenyDataUtil {
 
-    /** Value of -99.0 is used as default value. */
+    /** Value of -1024.0 is used as default value. */
     public final static double BRANCH_LENGTH_DEFAULT = -1024.0;
 
     public static void appendClose( final Writer w, final String element_name ) throws IOException {
diff --git a/forester/java/src/org/forester/phylogeny/data/Sequence.java b/forester/java/src/org/forester/phylogeny/data/Sequence.java
index fd366c6..3561edc 100644
--- a/forester/java/src/org/forester/phylogeny/data/Sequence.java
+++ b/forester/java/src/org/forester/phylogeny/data/Sequence.java
@@ -315,8 +315,8 @@ public class Sequence implements PhylogenyData, MultipleUris, Comparable<Sequenc
         return result;
     }
 
-    public boolean hasSequenceRelations() {
-        return _seq_relations.size() > 0;
+    public boolean isHasSequenceRelations() {
+        return _seq_relations != null && _seq_relations.size() > 0;
     }
 
     public void init() {
diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 8e40249..5d8854d 100644
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -479,6 +479,15 @@ public final class Test {
             System.out.println( "failed." );
             failed++;
         }
+        System.out.print( "phyloXML parsing (validating against schema): " );
+        if ( testPhyloXMLparsingValidating() ) {
+            System.out.println( "OK." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
         System.out.print( "Roundtrip phyloXML parsing (validating against schema): " );
         if ( Test.testBasicPhyloXMLparsingRoundtrip() ) {
             System.out.println( "OK." );
@@ -2740,6 +2749,42 @@ public final class Test {
         }
         return true;
     }
+    
+    private static boolean testPhyloXMLparsingValidating() {
+        try {
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            PhyloXmlParser xml_parser = null;
+            try {
+                xml_parser = PhyloXmlParser.createPhyloXmlParserXsdValidating();
+            }
+            catch ( final Exception e ) {
+                // Do nothing -- means were not running from jar.
+            }
+            if ( xml_parser == null ) {
+                xml_parser = PhyloXmlParser.createPhyloXmlParser();
+                if ( USE_LOCAL_PHYLOXML_SCHEMA ) {
+                    xml_parser.setValidateAgainstSchema( PHYLOXML_LOCAL_XSD );
+                }
+                else {
+                    xml_parser.setValidateAgainstSchema( PHYLOXML_REMOTE_XSD );
+                }
+            }
+            final Phylogeny[] phylogenies_0 = factory.create( new File( Test.PATH_TO_TEST_DATA + "phyloxml_test_1.xml" ),
+                                                              xml_parser );
+            if ( xml_parser.getErrorCount() > 0 ) {
+                System.out.println( xml_parser.getErrorMessages().toString() );
+                return false;
+            }
+            if ( phylogenies_0.length != 3 ) {
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
 
     private static boolean testBasicProtein() {
         try {
diff --git a/forester/test_data/phyloxml_test_1.xml b/forester/test_data/phyloxml_test_1.xml
new file mode 100644
index 0000000..83c400d
--- /dev/null
+++ b/forester/test_data/phyloxml_test_1.xml
@@ -0,0 +1,265 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<phyloxml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+          xsi:schemaLocation="http://www.phyloxml.org http://www.phyloxml.org/1.20/phyloxml.xsd"
+          xmlns="http://www.phyloxml.org">
+    <phylogeny branch_length_unit="c" rooted="true" rerootable="true" type="gene_tree">
+        <name>tree 0</name>
+        <id provider="treebank">1-1</id>
+        <description>test phylogeny</description>
+        <date>2002-05-30T09:00:00</date>
+        <confidence type="ml">0.999</confidence>
+        <confidence type="pp">0.955</confidence>
+        <clade branch_length="0.1" id_source="id111" collapse="true">
+            <name>root node</name>
+            <confidence type="bootstrap">90</confidence>
+            <confidence type="ml" stddev="1.1E-10">1e-3</confidence>
+            <confidence type="decay">2</confidence>
+            <width>10.5</width>
+            <color>
+                <red>2</red>
+                <green>22</green>
+                <blue>33</blue>
+                <alpha>123</alpha>
+            </color>
+            <taxonomy id_source="qwerty1">
+                <id provider="ncbi">1</id>
+                <code>ECDYS</code>
+                <scientific_name>ecdysozoa</scientific_name>
+                <authority>authority, 1999</authority>
+                <common_name>molting animals</common_name>
+                <synonym>Ecdy</synonym>
+                <synonym>The Ecdysozoa</synonym>
+                <rank>phylum</rank>
+                <uri type="img">http://www.molting.org/m.jpg</uri>
+                <uri type="source" desc="original source">http://www.ecdysozoa.org/</uri>
+            </taxonomy>
+            <taxonomy>
+                <id provider="ncbi">123</id>
+                <synonym>Æ Ä ä, ö and ü>– —</synonym>
+                <synonym>한글</synonym>
+                <synonym>日本語ひらがなカタカナ</synonym>
+                <synonym>русский алфавит</synonym>
+                <synonym>繁體字</synonym>
+                <synonym>ภาษาไทย</synonym>
+                <synonym>Tiếng Việt</synonym>
+            </taxonomy>
+            <sequence type="protein" id_source="idsource">
+                <symbol>BCL2L14</symbol>
+                <accession source="UniProtKB" comment="outdated">Q9BZR8</accession>
+                <name>Apoptosis facilitator Bcl-2-like 14 protein</name>
+                <gene_name>bcl2l14</gene_name>
+                <location>12p13-p12</location>
+                <mol_seq is_aligned="true">MCSTSGCDLEEIPLDDDDLNTIEFKILAYY</mol_seq>
+                <uri type="source" desc="UniProt link">http://www.pir.uniprot.org/cgi-bin/upEntry?id=B2L14_HUMAN</uri>
+                <annotation>
+                    <desc>intracellular organelle</desc>
+                </annotation>
+                <annotation ref="GO:0005829"/>
+                <annotation ref="GO:0006915" source="UniProtKB" evidence="experimental" type="function">
+                    <desc>apoptosis</desc>
+                    <confidence type="ml" stddev="0.3">1</confidence>
+                    <property datatype="xsd:double" applies_to="annotation" ref="AFFY:expression" unit="AFFY:x">0.2
+                    </property>
+                    <property datatype="xsd:string" applies_to="annotation" ref="MED:disease">lymphoma</property>
+                    <uri type="source" desc="google">http://www.google.com</uri>
+                    <uri type="source2" desc="bing">http://www.bing.com</uri>
+                </annotation>
+                <cross_references>
+                    <accession source="UNIPROTKB">383</accession>
+                    <accession source="PDB">1G5M</accession>
+                    <accession source="KEGG">hsa:596</accession>
+                    <accession source="PDB" comment="?">2G5M</accession>
+                </cross_references>
+            </sequence>
+            <sequence type="protein">
+                <symbol>BCL2</symbol>
+            </sequence>
+            <events>
+                <type>mixed</type>
+                <duplications>1</duplications>
+                <confidence type="bs">99</confidence>
+            </events>
+            <distribution>
+                <desc>irgendwo</desc>
+                <point geodetic_datum="WGS84" alt_unit="m">
+                    <lat>35.9296730123456789</lat>
+                    <long>-78.9482370123456789</long>
+                    <alt>1303</alt>
+                </point>
+                <point geodetic_datum="WGS84" alt_unit="m">
+                    <lat>129.549495485834893</lat>
+                    <long>-78.00000000000000</long>
+                    <alt>1400</alt>
+                </point>
+            </distribution>
+            <distribution>
+                <desc>anderswo</desc>
+            </distribution>
+            <date unit="MYA">
+                <desc>Silurian</desc>
+            </date>
+            <reference doi="10.1038/387489a0">
+                <desc>
+                    Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, &amp;
+                    J. A. Lake (1997). "Evidence for a clade of nematodes, arthropods and other moulting animals".
+                    Nature 387 (6632): 489–493.
+                </desc>
+            </reference>
+            <reference doi="10.1036/59494">
+            </reference>
+            <property ref="F:foo" datatype="xsd:int" applies_to="clade">2</property>
+            <property ref="F:bar" datatype="xsd:int" applies_to="clade">33</property>
+            <clade>
+                <name>node a</name>
+                <branch_length>0.2</branch_length>
+                <color>
+                    <red>12</red>
+                    <green>14</green>
+                    <blue>16</blue>
+                </color>
+                <taxonomy>
+                    <id provider="ncbi">123</id>
+                    <code>CAEEL</code>
+                    <scientific_name>C elegans</scientific_name>
+                    <common_name>elegant nematode worm</common_name>
+                    <rank>species</rank>
+                    <uri>http://www.wormbase.org/</uri>
+                </taxonomy>
+                <sequence id_source="xyz">
+                    <name>CAEEL_XYZ</name>
+                </sequence>
+                <sequence id_source="abc">
+                    <name>CAEEL_ABC</name>
+                </sequence>
+                <events>
+                    <type>other</type>
+                    <duplications>58</duplications>
+                    <speciations>59403</speciations>
+                    <losses>58485</losses>
+                    <confidence type="p">0.9901</confidence>
+                </events>
+            </clade>
+            <clade>
+                <name>node b</name>
+                <events>
+                    <duplications>1</duplications>
+                    <confidence type="">80</confidence>
+                </events>
+                <binary_characters type="characters" present_count="2" lost_count="3" gained_count="1">
+                    <gained>
+                        <bc>c</bc>
+                    </gained>
+                    <lost>
+                        <bc>d</bc>
+                        <bc>e</bc>
+                        <bc>f</bc>
+                    </lost>
+                    <present>
+                        <bc>a</bc>
+                        <bc>b</bc>
+                    </present>
+                </binary_characters>
+                <clade>
+                    <name>node ba</name>
+                    <distribution>
+                        <desc>Africa</desc>
+                    </distribution>
+                    <date unit="mya">
+                        <desc>Silurian</desc>
+                        <value>435</value>
+                        <minimum>416</minimum>
+                        <maximum>443.7</maximum>
+                    </date>
+                </clade>
+                <clade collapse="false">
+                    <name>node bb</name>
+                    <taxonomy>
+                        <id provider="EOL">704294</id>
+                        <code>NEMVE</code>
+                        <scientific_name>Nematostella vectensis</scientific_name>
+                        <authority>Stephenson, 1935</authority>
+                        <common_name>starlet sea anemone</common_name>
+                        <synonym>Nematostella vectensis Stephenson1935</synonym>
+                        <synonym>See
+                            Anemone
+                        </synonym>
+                        <synonym></synonym>
+                        <rank>species</rank>
+                        <uri desc="EOL" type="linkout">http://www.eol.org/pages/704294</uri>
+                    </taxonomy>
+                    <binary_characters type="domains">
+                        <gained>
+                            <bc>A</bc>
+                            <bc>B</bc>
+                            <bc>C</bc>
+                        </gained>
+                        <lost>
+                            <bc>D</bc>
+                        </lost>
+                        <present>
+                            <bc>X</bc>
+                            <bc>M</bc>
+                        </present>
+                    </binary_characters>
+                    <date>
+                        <desc>Triassic</desc>
+                    </date>
+                </clade>
+                <clade>
+                    <name>node bc</name>
+                    <sequence>
+                        <name>bc seq</name>
+                        <domain_architecture length="124">
+                            <domain from="120" to="130" confidence="0.9">A</domain>
+                            <domain from="21" to="44" confidence="0" id="pfam">B</domain>
+                            <domain to="43" confidence="1.0E-89" from="34" id="">C</domain>
+                            <domain id="123" from="34" to="43" confidence="1.3e-34">D</domain>
+                        </domain_architecture>
+                    </sequence>
+                    <events>
+                        <speciations>1</speciations>
+                    </events>
+                    <date>
+                        <value>433</value>
+                    </date>
+                </clade>
+            </clade>
+        </clade>
+        <sequence_relation id_ref_0="abc" id_ref_1="xyz" distance="0.34" type="ultra_paralogy">
+            <confidence type="pp" stddev="1.1E-10">1e-3</confidence>
+        </sequence_relation>
+        <sequence_relation id_ref_0="xyz" id_ref_1="abc" distance="2" type="unknown">
+            <confidence type="pp" stddev="1.245836">99.0000001</confidence>
+        </sequence_relation>
+        <property datatype="xsd:double" applies_to="phylogeny" ref="TIME:time" unit="TIME:MYA">2</property>
+        <property datatype="xsd:string" applies_to="phylogeny" ref="GO:function">cell death</property>
+    </phylogeny>
+    <phylogeny rooted="true" rerootable="true">
+        <name>phylogeny2</name>
+        <clade>
+            <clade>
+                <name>A</name>
+            </clade>
+            <clade>
+                <name>B</name>
+            </clade>
+        </clade>
+    </phylogeny>
+    <phylogeny rooted="true" rerootable="true">
+        <name>phylogeny3</name>
+        <clade>
+            <clade id_source="i0">
+                <name>C</name>
+            </clade>
+            <clade id_source="i1">
+                <name>D</name>
+            </clade>
+        </clade>
+        <clade_relation id_ref_0="i0" id_ref_1="i1" distance="0.34" type="parent">
+            <confidence type="pp" stddev="1.1E-10">1e-3</confidence>
+        </clade_relation>
+        <clade_relation id_ref_0="i1" id_ref_1="i0" distance="2" type="child">
+            <confidence type="pp" stddev="1.1E-20">1e-4</confidence>
+        </clade_relation>
+    </phylogeny>
+</phyloxml>
\ No newline at end of file