"rio" work

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

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 67e9b52..75250eb 100644 (file)
--- 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();
@@ -1601,9 +1613,10 @@ public class PhylogenyMethods {
      *            a reference Phylogeny
      * @param to_be_stripped
      *            Phylogeny to be stripped
-     * @return number of external nodes removed from to_be_stripped
+     * @return nodes removed from to_be_stripped
      */
-    public static int taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference, final Phylogeny to_be_stripped ) {
+    public static List<PhylogenyNode> taxonomyBasedDeletionOfExternalNodes( final Phylogeny reference,
+                                                                            final Phylogeny to_be_stripped ) {
         final Set<String> ref_ext_taxo = new HashSet<String>();
         for( final PhylogenyNodeIterator it = reference.iteratorExternalForward(); it.hasNext(); ) {
             final PhylogenyNode n = it.next();
@@ -1629,12 +1642,12 @@ public class PhylogenyMethods {
                 nodes_to_delete.add( n );
             }
         }
-        for( final PhylogenyNode phylogenyNode : nodes_to_delete ) {
-            to_be_stripped.deleteSubtree( phylogenyNode, true );
+        for( final PhylogenyNode n : nodes_to_delete ) {
+            to_be_stripped.deleteSubtree( n, true );
         }
         to_be_stripped.clearHashIdToNodeMap();
         to_be_stripped.externalNodesHaveChanged();
-        return nodes_to_delete.size();
+        return nodes_to_delete;
     }
 
     /**
@@ -1692,10 +1705,6 @@ 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;
     }