X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fclade_analysis%2FAnalysisSingle.java;h=64f9d5904649e424b6581e8fec570823ca75adc4;hb=1706deea223bc1a30d170596192d726b6847b7eb;hp=5c725b6b525ee543aa45257a1f4b99f003bcc5d4;hpb=31c6a5701649241d2f8a493b09d2871acd146d43;p=jalview.git

diff --git a/forester/java/src/org/forester/clade_analysis/AnalysisSingle.java b/forester/java/src/org/forester/clade_analysis/AnalysisSingle.java
index 5c725b6..64f9d59 100644
--- a/forester/java/src/org/forester/clade_analysis/AnalysisSingle.java
+++ b/forester/java/src/org/forester/clade_analysis/AnalysisSingle.java
@@ -62,7 +62,7 @@ public final class AnalysisSingle {
         final List<PhylogenyNode> qnode_ext_nodes = qnode_pp.getAllExternalDescendants();
         final int lec_ext_nodes = qnode_ext_nodes.size() - 1;
         final int p_ext_nodes = p.getNumberOfExternalNodes() - 1;
-        final List<String> qnode_ext_nodes_names = new ArrayList<>();
+        final List<String> qnode_ext_nodes_names = new ArrayList<String>();
         for( final PhylogenyNode qnode_ext_node : qnode_ext_nodes ) {
             String name = qnode_ext_node.getName();
             if ( ForesterUtil.isEmptyTrimmed( name ) ) {
@@ -87,12 +87,10 @@ public final class AnalysisSingle {
         }
         res.setLeastEncompassingCladeSize( lec_ext_nodes );
         res.setTreeSize( p_ext_nodes );
-       
         final String conf = obtainConfidence( qnode_pp );
         if ( conf != null ) {
-            res.setGreatestCommonCladeSubtreeConfidence(conf);
+            res.setGreatestCommonCladeSubtreeConfidence( conf );
         }
-        
         final String greatest_common_prefix_up[] = analyzeSiblings( qnode_p, qnode_pp, separator );
         res.setGreatestCommonPrefixUp( greatest_common_prefix_up[ 0 ] );
         if ( greatest_common_prefix_up[ 1 ] != null ) {
@@ -106,13 +104,11 @@ public final class AnalysisSingle {
         return res;
     }
 
-   
-
     private final static String[] analyzeSiblings( final PhylogenyNode child,
                                                    final PhylogenyNode parent,
                                                    final String separator ) {
         final int child_index = child.getChildNodeIndex();
-        final List<String> ext_nodes_names = new ArrayList<>();
+        final List<String> ext_nodes_names = new ArrayList<String>();
         final List<PhylogenyNode> descs = parent.getDescendants();
         String conf = null;
         for( int i = 0; i < descs.size(); ++i ) {
@@ -133,9 +129,9 @@ public final class AnalysisSingle {
         final String greatest_common_prefix = ForesterUtil.greatestCommonPrefix( ext_nodes_names, separator );
         return new String[] { greatest_common_prefix, conf };
     }
-    
+
     private final static String obtainConfidence( final PhylogenyNode n ) {
-        if ( n.getBranchData().getConfidences() != null && n.getBranchData().getConfidences().size() > 0 ) {
+        if ( ( n.getBranchData().getConfidences() != null ) && ( n.getBranchData().getConfidences().size() > 0 ) ) {
             final List<Confidence> confidences = n.getBranchData().getConfidences();
             boolean not_first = false;
             Collections.sort( confidences );