work in airplane

diff --git a/forester/java/src/org/forester/application/simple_node_processor.java b/forester/java/src/org/forester/application/simple_node_processor.java
index 033bd9f..c7e495a 100644 (file)
--- a/forester/java/src/org/forester/application/simple_node_processor.java
+++ b/forester/java/src/org/forester/application/simple_node_processor.java
@@ -40,18 +40,25 @@ public class simple_node_processor {
     private final static String BASE = "b_";
 
     public static void main( final String args[] ) {
+        File in = null;
+        File out = null;
         if ( ( args.length != 2 ) ) {
-            System.exit( -1 );
+           // System.exit( -1 );
+            if ( ( args.length == 0 ) ) {
+                in = new File("C:\\Users\\zma\\dollo.xml");
+                out = null;
+            }
         }
         try {
+            System.out.println( "...");
             CommandLineArguments cla = null;
             cla = new CommandLineArguments( args );
-            final File in = cla.getFile( 0 );
-            final File out = cla.getFile( 1 );
-            if ( out.exists() ) {
-                System.out.println( out + " already exists" );
-                System.exit( -1 );
-            }
+           // in = cla.getFile( 0 );
+           // out = cla.getFile( 1 );
+           // if ( out.exists() ) {
+          //      System.out.println( out + " already exists" );
+          //      System.exit( -1 );
+          //  }
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final PhyloXmlParser xml_parser = new PhyloXmlParser();
             final Phylogeny[] phylogenies_0 = factory.create( in, xml_parser );

diff --git a/forester/java/src/org/forester/archaeopteryx/Configuration.java b/forester/java/src/org/forester/archaeopteryx/Configuration.java
index 348d29d..3562e10 100644 (file)
--- a/forester/java/src/org/forester/archaeopteryx/Configuration.java
+++ b/forester/java/src/org/forester/archaeopteryx/Configuration.java
@@ -158,11 +158,11 @@ public final class Configuration {
             { "Taxonomy Colorize", "display", "yes" }, { "Colorize Branches", "display", "no" },
             { "Use Branch-Width", "nodisplay", "no" }, { "Show Custom Nodes", "display", "yes" },
             { "Domains", "nodisplay", "no" }, { "Binary Characters", "nodisplay", "no" },
-            { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "no" },
+            { "Binary Char Counts", "nodisplay", "no" }, { "Prot/Gene Name", "display", "yes" },
             { "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
             { "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
             { "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
-            { "Property", "nodisplay", "no" }, { "Prot/Gene Symbol", "display", "no" },
+            { "Property", "nodisplay", "no" }, { "Prot/Gene Symbol", "display", "yes" },
             { "Rollover", "display", "yes" }, { "Relation Confidence", "display", "no" },
             { "Vector Data", "display", "no" }, { "Taxonomy Images", "display", "no" }            };
     final static String                     clickto_options[][]                                    = {

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index 5ef3b5f..dd3dba0 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -420,7 +420,23 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
         if ( isInternal() && !isCollapse() ) {
             throw new UnsupportedOperationException( "attempt to get next external node of an uncollapsed internal node" );
         }
-        else if ( isLastExternalNode() ) {
+        if ( isRoot() ) {
+            return null;
+        }
+        if ( getParent().isCollapse() ) {
+            throw new UnsupportedOperationException( "attempt to get next external node of node with a collapsed parent" );
+        }
+        // This checks if last node.
+        PhylogenyNode n = this;
+        boolean last = true;
+        while ( !n.isRoot() ) {
+            if ( !n.isLastChildNode() ) {
+                last = false;
+                break;
+            }
+            n = n.getParent();
+        }
+        if ( last ) {
             return null;
         }
         int index = getChildNodeIndex();
@@ -431,146 +447,18 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
                         .isLastChildNode() ) ) {
             index = current_node.getChildNodeIndex();
             previous_node = current_node;
-            System.out.println("       " + previous_node.getName());
             current_node = current_node.getParent();
         }
-       // if ( !current_node.isCollapse() ) {
-         current_node = current_node.getChildNode( index + 1 );
-        //}
+        if ( index < current_node.getNumberOfDescendants() - 1 ) {
+            current_node = current_node.getChildNode( index + 1 );
+        }
         while ( current_node.isInternal() && !current_node.isCollapse() ) {
             current_node = current_node.getFirstChildNode();
         }
         return current_node;
     }
     
-    public static void main( final String[] args ) {
-        try {
-            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
-            PhylogenyNode n;
-            List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
-//            final StringBuffer sb0 = new StringBuffer( 
-//            "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
-//            final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
-//            
-//            t0.getNode( "cd" ).setCollapse( true );
-//            t0.getNode( "cde" ).setCollapse( true );
-     //      n = t0.getFirstExternalNode();
-            
-//            while ( n != null ) {
-//                System.out.println( n.getName() );
-//                ext.add( n );
-//                n =  n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
-//            }
-//            
-//           // Archaeopteryx.createApplication( t );
-//            if ( !ext.get( 0 ).getName().equals( "a" ) ) {
-//                System.out.println( "0 fail" );
-//            }
-//            if ( !ext.get( 1 ).getName().equals( "b" ) ) {
-//                System.out.println( "1 fail" );
-//            }
-//            if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
-//                System.out.println( "2 fail" );
-//            }
-//            if ( !ext.get( 3 ).getName().equals( "f" ) ) {
-//                System.out.println( "3 fail" );
-//            }
-//            if ( !ext.get( 4 ).getName().equals( "g" ) ) {
-//                System.out.println( "4 fail" );
-//            }
-//            if ( !ext.get( 5 ).getName().equals( "h" ) ) {
-//                System.out.println( "5 fail" );
-//            }
-          //  if ( !ext.get( 6 ).getName().equals( "a" ) ) {
-          //      System.out.println( "6 fail" );
-           // }
-          //  if ( !ext.get( 7 ).getName().equals( "a" ) ) {
-          //      System.out.println( "7 fail" );
-          //  }
-            
-            
-            final StringBuffer sb1 = new StringBuffer( 
-            "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
-            final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
-           
-            t1.getNode( "ab" ).setCollapse( true );
-            t1.getNode( "cd" ).setCollapse( true );
-            t1.getNode( "cde" ).setCollapse( true );
-           // n = t1.getFirstExternalNode();
-            n = t1.getNode( "ab" );
-            ext = new ArrayList<PhylogenyNode>();
-            while ( n != null ) {
-                System.out.println( n.getName() );
-                ext.add( n );
-                n =  n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
-            }
-            
-           // Archaeopteryx.createApplication( t1 );
-            if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
-                System.out.println( "0 fail" );
-            }
-           
-            if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
-                System.out.println( "1 fail" );
-            }
-            if ( !ext.get( 2 ).getName().equals( "f" ) ) {
-                System.out.println( "2 fail" );
-            }
-            if ( !ext.get( 3 ).getName().equals( "g" ) ) {
-                System.out.println( "3 fail" );
-            }
-            if ( !ext.get( 4 ).getName().equals( "h" ) ) {
-                System.out.println( "4 fail" );
-            }
-            
-            //
-            //
-            final StringBuffer sb2 = new StringBuffer( 
-            "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
-            final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
-           
-            t2.getNode( "ab" ).setCollapse( true );
-            t2.getNode( "cd" ).setCollapse( true );
-            t2.getNode( "cde" ).setCollapse( true );
-            t2.getNode( "c" ).setCollapse( true );
-            t2.getNode( "d" ).setCollapse( true );
-            t2.getNode( "e" ).setCollapse( true );
-            t2.getNode( "gh" ).setCollapse( true );
-           // t2.getNode( "h" ).setCollapse( true );
-           // n = t1.getFirstExternalNode();
-            n = t2.getNode( "ab" );
-            ext = new ArrayList<PhylogenyNode>();
-            while ( n != null ) {
-                System.out.println( n.getName() );
-                ext.add( n );
-                n =  n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
-            }
-            
-           // Archaeopteryx.createApplication( t1 );
-            if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
-                System.out.println( "0 fail" );
-            }
-           
-            if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
-                System.out.println( "1 fail" );
-            }
-            if ( !ext.get( 2 ).getName().equals( "f" ) ) {
-                System.out.println( "2 fail" );
-            }
-            if ( !ext.get( 3 ).getName().equals( "g" ) ) {
-                System.out.println( "3 fail" );
-            }
-            if ( !ext.get( 4 ).getName().equals( "h" ) ) {
-                System.out.println( "4 fail" );
-            }
-            
-            
-        }
-        catch ( IOException e ) {
-            // TODO Auto-generated catch block
-            e.printStackTrace();
-        }
-    }
+  
     
     
     public final NodeData getNodeData() {

diff --git a/forester/java/src/org/forester/test/Test.java b/forester/java/src/org/forester/test/Test.java
index 637d05c..b5a3aeb 100644 (file)
--- a/forester/java/src/org/forester/test/Test.java
+++ b/forester/java/src/org/forester/test/Test.java
@@ -38,6 +38,7 @@ import java.util.Locale;
 import java.util.Set;
 
 import org.forester.application.support_transfer;
+import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.development.DevelopmentTools;
 import org.forester.evoinference.TestPhylogenyReconstruction;
 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
@@ -684,6 +685,15 @@ public final class Test {
                 System.out.println( "failed [will not count towards failed tests]" );
             }
         }
+        System.out.print( "Next nodes with collapsed: " );
+        if ( Test.testNextNodeWithCollapsing() ) {
+            System.out.println( "OK." );
+            succeeded++;
+        }
+        else {
+            System.out.println( "failed." );
+            failed++;
+        }
         //        System.out.print( "WABI TxSearch: " );
         //        if ( Test.testWabiTxSearch() ) {
         //            System.out.println( "OK." );
@@ -8100,4 +8110,565 @@ public final class Test {
         }
         return true;
     }
+
+    private static boolean testNextNodeWithCollapsing() {
+        try {
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            PhylogenyNode n;
+            List<PhylogenyNode> ext = new ArrayList<PhylogenyNode>();
+            final StringBuffer sb0 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
+            final Phylogeny t0 = factory.create( sb0, new NHXParser() )[ 0 ];
+            t0.getNode( "cd" ).setCollapse( true );
+            t0.getNode( "cde" ).setCollapse( true );
+            n = t0.getFirstExternalNode();
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( !ext.get( 0 ).getName().equals( "a" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "b" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "cde" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "f" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "g" ) ) {
+                return false;
+            }
+            if ( !ext.get( 5 ).getName().equals( "h" ) ) {
+                return false;
+            }
+            ext.clear();
+            final StringBuffer sb1 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
+            final Phylogeny t1 = factory.create( sb1, new NHXParser() )[ 0 ];
+            t1.getNode( "ab" ).setCollapse( true );
+            t1.getNode( "cd" ).setCollapse( true );
+            t1.getNode( "cde" ).setCollapse( true );
+            n = t1.getNode( "ab" );
+            ext = new ArrayList<PhylogenyNode>();
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "f" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "g" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "h" ) ) {
+                return false;
+            }
+            //
+            //
+            ext.clear();
+            final StringBuffer sb2 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
+            final Phylogeny t2 = factory.create( sb2, new NHXParser() )[ 0 ];
+            t2.getNode( "ab" ).setCollapse( true );
+            t2.getNode( "cd" ).setCollapse( true );
+            t2.getNode( "cde" ).setCollapse( true );
+            t2.getNode( "c" ).setCollapse( true );
+            t2.getNode( "d" ).setCollapse( true );
+            t2.getNode( "e" ).setCollapse( true );
+            t2.getNode( "gh" ).setCollapse( true );
+            n = t2.getNode( "ab" );
+            ext = new ArrayList<PhylogenyNode>();
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "f" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "gh" ) ) {
+                return false;
+            }
+            //
+            //
+            ext.clear();
+            final StringBuffer sb3 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
+            final Phylogeny t3 = factory.create( sb3, new NHXParser() )[ 0 ];
+            t3.getNode( "ab" ).setCollapse( true );
+            t3.getNode( "cd" ).setCollapse( true );
+            t3.getNode( "cde" ).setCollapse( true );
+            t3.getNode( "c" ).setCollapse( true );
+            t3.getNode( "d" ).setCollapse( true );
+            t3.getNode( "e" ).setCollapse( true );
+            t3.getNode( "gh" ).setCollapse( true );
+            t3.getNode( "fgh" ).setCollapse( true );
+            n = t3.getNode( "ab" );
+            ext = new ArrayList<PhylogenyNode>();
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "fgh" ) ) {
+                return false;
+            }
+            //
+            //
+            ext.clear();
+            final StringBuffer sb4 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
+            final Phylogeny t4 = factory.create( sb4, new NHXParser() )[ 0 ];
+            t4.getNode( "ab" ).setCollapse( true );
+            t4.getNode( "cd" ).setCollapse( true );
+            t4.getNode( "cde" ).setCollapse( true );
+            t4.getNode( "c" ).setCollapse( true );
+            t4.getNode( "d" ).setCollapse( true );
+            t4.getNode( "e" ).setCollapse( true );
+            t4.getNode( "gh" ).setCollapse( true );
+            t4.getNode( "fgh" ).setCollapse( true );
+            t4.getNode( "abcdefgh" ).setCollapse( true );
+            n = t4.getNode( "abcdefgh" );
+            if ( n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() != null ) {
+                return false;
+            }
+            //
+            //
+            final StringBuffer sb5 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
+            final Phylogeny t5 = factory.create( sb5, new NHXParser() )[ 0 ];
+            ext.clear();
+            n = t5.getFirstExternalNode();
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( ext.size() != 8 ) {
+                return false;
+            }
+            if ( !ext.get( 0 ).getName().equals( "a" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "b" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "c" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "d" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "e" ) ) {
+                return false;
+            }
+            if ( !ext.get( 5 ).getName().equals( "f" ) ) {
+                return false;
+            }
+            if ( !ext.get( 6 ).getName().equals( "g" ) ) {
+                return false;
+            }
+            if ( !ext.get( 7 ).getName().equals( "h" ) ) {
+                return false;
+            }
+            //
+            //
+            final StringBuffer sb6 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
+            final Phylogeny t6 = factory.create( sb6, new NHXParser() )[ 0 ];
+            ext.clear();
+            t6.getNode( "ab" ).setCollapse( true );
+            n = t6.getNode( "ab" );
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( ext.size() != 7 ) {
+                return false;
+            }
+            if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "c" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "d" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "e" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "f" ) ) {
+                return false;
+            }
+            if ( !ext.get( 5 ).getName().equals( "g" ) ) {
+                return false;
+            }
+            if ( !ext.get( 6 ).getName().equals( "h" ) ) {
+                return false;
+            }
+            //
+            //
+            final StringBuffer sb7 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
+            final Phylogeny t7 = factory.create( sb7, new NHXParser() )[ 0 ];
+            ext.clear();
+            t7.getNode( "cd" ).setCollapse( true );
+            n = t7.getNode( "a" );
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( ext.size() != 7 ) {
+                return false;
+            }
+            if ( !ext.get( 0 ).getName().equals( "a" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "b" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "e" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "f" ) ) {
+                return false;
+            }
+            if ( !ext.get( 5 ).getName().equals( "g" ) ) {
+                return false;
+            }
+            if ( !ext.get( 6 ).getName().equals( "h" ) ) {
+                return false;
+            }
+            //
+            //
+            final StringBuffer sb8 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h))fgh)cdefgh)abcdefgh" );
+            final Phylogeny t8 = factory.create( sb8, new NHXParser() )[ 0 ];
+            ext.clear();
+            t8.getNode( "cd" ).setCollapse( true );
+            t8.getNode( "c" ).setCollapse( true );
+            t8.getNode( "d" ).setCollapse( true );
+            n = t8.getNode( "a" );
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( ext.size() != 7 ) {
+                return false;
+            }
+            if ( !ext.get( 0 ).getName().equals( "a" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "b" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "cd" ) ) {
+                System.out.println( "2 fail" );
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "e" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "f" ) ) {
+                return false;
+            }
+            if ( !ext.get( 5 ).getName().equals( "g" ) ) {
+                return false;
+            }
+            if ( !ext.get( 6 ).getName().equals( "h" ) ) {
+                return false;
+            }
+            //
+            //
+            final StringBuffer sb9 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
+            final Phylogeny t9 = factory.create( sb9, new NHXParser() )[ 0 ];
+            ext.clear();
+            t9.getNode( "gh" ).setCollapse( true );
+            n = t9.getNode( "a" );
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( ext.size() != 7 ) {
+                return false;
+            }
+            if ( !ext.get( 0 ).getName().equals( "a" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "b" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "c" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "d" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "e" ) ) {
+                return false;
+            }
+            if ( !ext.get( 5 ).getName().equals( "f" ) ) {
+                return false;
+            }
+            if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
+                return false;
+            }
+            //
+            //
+            final StringBuffer sb10 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
+            final Phylogeny t10 = factory.create( sb10, new NHXParser() )[ 0 ];
+            ext.clear();
+            t10.getNode( "gh" ).setCollapse( true );
+            t10.getNode( "g" ).setCollapse( true );
+            t10.getNode( "h" ).setCollapse( true );
+            n = t10.getNode( "a" );
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( ext.size() != 7 ) {
+                return false;
+            }
+            if ( !ext.get( 0 ).getName().equals( "a" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "b" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "c" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "d" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "e" ) ) {
+                return false;
+            }
+            if ( !ext.get( 5 ).getName().equals( "f" ) ) {
+                return false;
+            }
+            if ( !ext.get( 6 ).getName().equals( "gh" ) ) {
+                return false;
+            }
+            //
+            //
+            final StringBuffer sb11 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
+            final Phylogeny t11 = factory.create( sb11, new NHXParser() )[ 0 ];
+            ext.clear();
+            t11.getNode( "gh" ).setCollapse( true );
+            t11.getNode( "fgh" ).setCollapse( true );
+            n = t11.getNode( "a" );
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( ext.size() != 6 ) {
+                return false;
+            }
+            if ( !ext.get( 0 ).getName().equals( "a" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "b" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "c" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "d" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "e" ) ) {
+                return false;
+            }
+            if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
+                return false;
+            }
+            //
+            //
+            final StringBuffer sb12 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
+            final Phylogeny t12 = factory.create( sb12, new NHXParser() )[ 0 ];
+            ext.clear();
+            t12.getNode( "gh" ).setCollapse( true );
+            t12.getNode( "fgh" ).setCollapse( true );
+            t12.getNode( "g" ).setCollapse( true );
+            t12.getNode( "h" ).setCollapse( true );
+            t12.getNode( "f" ).setCollapse( true );
+            n = t12.getNode( "a" );
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( ext.size() != 6 ) {
+                return false;
+            }
+            if ( !ext.get( 0 ).getName().equals( "a" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "b" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "c" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "d" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "e" ) ) {
+                return false;
+            }
+            if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
+                return false;
+            }
+            //
+            //
+            final StringBuffer sb13 = new StringBuffer( "((a,b)ab,(((c,d)cd,e)cde,(f,(g,h)gh)fgh)cdefgh)abcdefgh" );
+            final Phylogeny t13 = factory.create( sb13, new NHXParser() )[ 0 ];
+            ext.clear();
+            t13.getNode( "ab" ).setCollapse( true );
+            t13.getNode( "b" ).setCollapse( true );
+            t13.getNode( "fgh" ).setCollapse( true );
+            t13.getNode( "gh" ).setCollapse( true );
+            n = t13.getNode( "ab" );
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( ext.size() != 5 ) {
+                return false;
+            }
+            if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "c" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "d" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "e" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
+                return false;
+            }
+            //
+            //
+            final StringBuffer sb14 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
+            final Phylogeny t14 = factory.create( sb14, new NHXParser() )[ 0 ];
+            ext.clear();
+            t14.getNode( "ab" ).setCollapse( true );
+            t14.getNode( "a" ).setCollapse( true );
+            t14.getNode( "fgh" ).setCollapse( true );
+            t14.getNode( "gh" ).setCollapse( true );
+            n = t14.getNode( "ab" );
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( ext.size() != 5 ) {
+                return false;
+            }
+            if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "c" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "d" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "e" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "fgh" ) ) {
+                return false;
+            }
+            //
+            //
+            final StringBuffer sb15 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
+            final Phylogeny t15 = factory.create( sb15, new NHXParser() )[ 0 ];
+            ext.clear();
+            t15.getNode( "ab" ).setCollapse( true );
+            t15.getNode( "a" ).setCollapse( true );
+            t15.getNode( "fgh" ).setCollapse( true );
+            t15.getNode( "gh" ).setCollapse( true );
+            n = t15.getNode( "ab" );
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( ext.size() != 6 ) {
+                return false;
+            }
+            if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "c" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "d" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "e" ) ) {
+                return false;
+            }
+            if ( !ext.get( 4 ).getName().equals( "x" ) ) {
+                return false;
+            }
+            if ( !ext.get( 5 ).getName().equals( "fgh" ) ) {
+                return false;
+            }
+            //
+            //
+            final StringBuffer sb16 = new StringBuffer( "((a,b,0)ab,(((c,d)cd,e)cde,x,(f,(g,h,1,2)gh,0)fgh)cdefgh)abcdefgh" );
+            final Phylogeny t16 = factory.create( sb16, new NHXParser() )[ 0 ];
+            ext.clear();
+            t16.getNode( "ab" ).setCollapse( true );
+            t16.getNode( "a" ).setCollapse( true );
+            t16.getNode( "fgh" ).setCollapse( true );
+            t16.getNode( "gh" ).setCollapse( true );
+            t16.getNode( "cd" ).setCollapse( true );
+            t16.getNode( "cde" ).setCollapse( true );
+            t16.getNode( "d" ).setCollapse( true );
+            t16.getNode( "x" ).setCollapse( true );
+            n = t16.getNode( "ab" );
+            while ( n != null ) {
+                ext.add( n );
+                n = n.getNextExternalNodeWhileTakingIntoAccountCollapsedNodes();
+            }
+            if ( ext.size() != 4 ) {
+                return false;
+            }
+            if ( !ext.get( 0 ).getName().equals( "ab" ) ) {
+                return false;
+            }
+            if ( !ext.get( 1 ).getName().equals( "cde" ) ) {
+                return false;
+            }
+            if ( !ext.get( 2 ).getName().equals( "x" ) ) {
+                return false;
+            }
+            if ( !ext.get( 3 ).getName().equals( "fgh" ) ) {
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
 }