X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyMethods.java;h=1532e41e0c0e28e2ac1cb182963a04ed710aa1be;hb=665e671efec73fcb36a9aac45f119330f290fa81;hp=dfe3341531e856040bce2f81b8b4bdbf4ce986f0;hpb=4a71774e563925de62c37378a6c32c3275f2e287;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index dfe3341..1532e41 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -66,6 +66,7 @@ import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.phylogeny.iterators.PreorderTreeIterator;
 import org.forester.util.BasicDescriptiveStatistics;
 import org.forester.util.DescriptiveStatistics;
+import org.forester.util.FailedConditionCheckException;
 import org.forester.util.ForesterUtil;
 import org.forester.util.TaxonomyUtil;
 
@@ -1003,7 +1004,7 @@ public class PhylogenyMethods {
     private static enum NDF {
                              NodeName( "NN" ),
                              TaxonomyCode( "TC" ),
-                             TaxonomyCommonName( "CN" ),
+                             TaxonomyCommonName( "TN" ),
                              TaxonomyScientificName( "TS" ),
                              TaxonomyIdentifier( "TI" ),
                              TaxonomySynonym( "SY" ),
@@ -2126,6 +2127,30 @@ public class PhylogenyMethods {
         }
     }
     
-   
+    public final static PhylogenyNode getFirstExternalNode( final PhylogenyNode node ) {
+        PhylogenyNode n = node;
+        while ( n.isInternal() ) {
+            n = n.getFirstChildNode();
+        }
+        return n;
+    }
+    
+    public final static PhylogenyNode getLastExternalNode( final PhylogenyNode node ) {
+        PhylogenyNode n = node;
+        while ( n.isInternal() ) {
+            n = n.getLastChildNode();
+        }
+        return n;
+    }
+
+    public final static boolean isHasCollapsedNodes( final Phylogeny phy ) {
+        for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( !n.isExternal() && ( n.isCollapse() ) ) {
+                return true;
+            }
+        }
+        return false;
+    }
     
 }