in progress

[jalview.git] / forester / java / src / org / forester / phylogeny / PhylogenyNode.java

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
index c341108..7bf60ef 100644 (file)
--- a/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyNode.java
@@ -413,28 +413,47 @@ 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() ) {
+        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();
         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;
             current_node = current_node.getParent();
         }
-        current_node = current_node.getChildNode( index + 1 );
-        while ( current_node.isInternal() ) {
+        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 final NodeData getNodeData() {
         if ( _node_data == null ) {
             _node_data = new NodeData();
@@ -1030,24 +1049,24 @@ public class PhylogenyNode implements PhylogenyNodeI, Comparable<PhylogenyNode>
     }
 
     public static PhylogenyNode createInstanceFromNhxString( final String nhx ) throws NHXFormatException {
-        return new PhylogenyNode( nhx, ForesterUtil.TAXONOMY_EXTRACTION.NO, false );
+        return new PhylogenyNode( nhx, PhylogenyMethods.TAXONOMY_EXTRACTION.NO, false );
     }
 
     public static PhylogenyNode createInstanceFromNhxString( final String nhx,
-                                                             final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction )
+                                                             final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction )
             throws NHXFormatException {
         return new PhylogenyNode( nhx, taxonomy_extraction, false );
     }
 
     public static PhylogenyNode createInstanceFromNhxString( final String nhx,
-                                                             final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction,
+                                                             final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
                                                              final boolean replace_underscores )
             throws NHXFormatException {
         return new PhylogenyNode( nhx, taxonomy_extraction, replace_underscores );
     }
 
     private PhylogenyNode( final String nhx,
-                           final ForesterUtil.TAXONOMY_EXTRACTION taxonomy_extraction,
+                           final PhylogenyMethods.TAXONOMY_EXTRACTION taxonomy_extraction,
                            final boolean replace_underscores ) throws NHXFormatException {
         init();
         NHXParser.parseNHX( nhx, this, taxonomy_extraction, replace_underscores );