needed for https for treebase

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