X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fphylogeny%2FPhylogenyMethods.java;h=c3fbc95cb6b32731f0ee22c3525775f5cf7a21a9;hb=b528989f688291ba7615867e5322090ec42096d8;hp=4f55278f3149b4ac4d719e3073058d9c7389b72c;hpb=d05da53bffa2a6c9089467e3f14ed69064f2cd9a;p=jalview.git

diff --git a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
index 4f55278..c3fbc95 100644
--- a/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
+++ b/forester/java/src/org/forester/phylogeny/PhylogenyMethods.java
@@ -107,7 +107,7 @@ public class PhylogenyMethods {
         return could_extract;
     }
 
-    public static DescriptiveStatistics calculatBranchLengthStatistics( final Phylogeny phy ) {
+    public static DescriptiveStatistics calculateBranchLengthStatistics( final Phylogeny phy ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
@@ -118,7 +118,7 @@ public class PhylogenyMethods {
         return stats;
     }
 
-    public static List<DescriptiveStatistics> calculatConfidenceStatistics( final Phylogeny phy ) {
+    public static List<DescriptiveStatistics> calculateConfidenceStatistics( final Phylogeny phy ) {
         final List<DescriptiveStatistics> stats = new ArrayList<DescriptiveStatistics>();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
@@ -305,7 +305,7 @@ public class PhylogenyMethods {
         return x;
     }
 
-    public static DescriptiveStatistics calculatNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
+    public static DescriptiveStatistics calculateNumberOfDescendantsPerNodeStatistics( final Phylogeny phy ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final PhylogenyNodeIterator iter = phy.iteratorPreorder(); iter.hasNext(); ) {
             final PhylogenyNode n = iter.next();
@@ -1158,6 +1158,10 @@ public class PhylogenyMethods {
             final PhylogenyNode node = iter.next();
             boolean all_matched = true;
             for( String query : queries ) {
+                if ( query == null ) {
+                    continue;
+                }
+                query = query.trim();
                 NDF ndf = null;
                 if ( ( query.length() > 2 ) && ( query.indexOf( ":" ) == 2 ) ) {
                     ndf = NDF.fromString( query );