X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyMethods.java;h=f839fd6ce43d34017dfff00a7164d9f2a2843304;hb=5b11e68cf46c363bd5ae256f794871c194776bd7;hp=67e9b52751885f8acc3603d4e7997a0c88399c74;hpb=b0fc7a39bd4bdbe8ba7b576a14ce1aaae645ea1b;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 67e9b52..f839fd6 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -159,6 +159,12 @@ public class PhylogenyMethods {
      * @return LCA of node1 and node2
      */
     public final static PhylogenyNode calculateLCA( PhylogenyNode node1, PhylogenyNode node2 ) {
+        if ( node1 == null ) {
+            throw new IllegalArgumentException( "first argument (node) is null" );
+        }
+        if ( node2 == null ) {
+            throw new IllegalArgumentException( "second argument (node) is null" );
+        }
         if ( node1 == node2 ) {
             return node1;
         }
@@ -211,6 +217,12 @@ public class PhylogenyMethods {
      * @return LCA of node1 and node2
      */
     public final static PhylogenyNode calculateLCAonTreeWithIdsInPreOrder( PhylogenyNode node1, PhylogenyNode node2 ) {
+        if ( node1 == null ) {
+            throw new IllegalArgumentException( "first argument (node) is null" );
+        }
+        if ( node2 == null ) {
+            throw new IllegalArgumentException( "second argument (node) is null" );
+        }
         while ( node1 != node2 ) {
             if ( node1.getId() > node2.getId() ) {
                 node1 = node1.getParent();
@@ -1692,10 +1704,6 @@ public class PhylogenyMethods {
         TAXONOMY_ID;
     }
 
-    public static enum TAXONOMY_EXTRACTION {
-        NO, YES, PFAM_STYLE_ONLY;
-    }
-
     public static enum DESCENDANT_SORT_PRIORITY {
         TAXONOMY, SEQUENCE, NODE_NAME;
     }