working on issue of collapsed nodes in circular display

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index c341108..5ef3b5f 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -27,13 +27,17 @@
 
 package org.forester.phylogeny;
 
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.forester.archaeopteryx.Archaeopteryx;
 import org.forester.io.parsers.nhx.NHXFormatException;
 import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.phylogeny.data.BranchData;
 import org.forester.phylogeny.data.NodeData;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.phylogeny.iterators.ChildNodeIteratorForward;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
@@ -413,8 +417,8 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
 
     public final PhylogenyNode getNextExternalNodeWhileTakingIntoAccountCollapsedNodes() {
         //TODO work on me ~~
-        if ( isInternal() ) {
-            throw new UnsupportedOperationException( "attempt to get next external node of an internal node" );
+        if ( isInternal() && !isCollapse() ) {
+            throw new UnsupportedOperationException( "attempt to get next external node of an uncollapsed internal node" );
         }
         else if ( isLastExternalNode() ) {
             return null;
@@ -423,18 +427,152 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
         PhylogenyNode previous_node = this;
         PhylogenyNode current_node = getParent();
         while ( !current_node.isRoot()
-                && ( ( current_node.getNumberOfDescendants() == 1 ) || previous_node.isLastChildNode() ) ) {
+                && ( current_node.isCollapse() || ( current_node.getNumberOfDescendants() == 1 ) || previous_node
+                        .isLastChildNode() ) ) {
             index = current_node.getChildNodeIndex();
             previous_node = current_node;
+            System.out.println("       " + previous_node.getName());
             current_node = current_node.getParent();
         }
-        current_node = current_node.getChildNode( index + 1 );
-        while ( current_node.isInternal() ) {
+       // if ( !current_node.isCollapse() ) {
+         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() {
         if ( _node_data == null ) {
             _node_data = new NodeData();