JAL-2805 interface comments

[jalview.git] / src / jalview / ext / archaeopteryx / ArchaeopteryxTreeBuilder.java

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
index 02ecdf0..9166497 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
@@ -2,7 +2,7 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
-import jalview.ext.forester.ForesterConversions;
+import jalview.ext.forester.ForesterDataConversions;
 import jalview.ext.forester.ForesterMatrix;
 import jalview.util.MessageManager;
 
@@ -40,9 +40,9 @@ public class ArchaeopteryxTreeBuilder
 
   private PhylogenyNode rootNode;
 
-  private final Map<SequenceI, PhylogenyNode> alignmentBoundNodes;
+  private final Map<SequenceI, PhylogenyNode> alignmentWithNodes;
 
-  private final Map<PhylogenyNode, SequenceI> nodesBoundAlignment;
+  private final Map<PhylogenyNode, SequenceI> nodesWithAlignment;
 
   public ArchaeopteryxTreeBuilder(final TreeBuilder calculatedTree)
   {
@@ -50,10 +50,13 @@ public class ArchaeopteryxTreeBuilder
     sequences = jalviewTree.getSequences();
     distances = ForesterMatrix.convertJalviewToForester(
             jalviewTree.getDistances(), sequences);
+
     aptxTree = new Phylogeny();
     rootNode = new PhylogenyNode();
-    alignmentBoundNodes = new HashMap<>(distances.getSize());
-    nodesBoundAlignment = new HashMap<>(distances.getSize());
+
+    int amountOfSequences = distances.getSize();
+    alignmentWithNodes = new HashMap<>(amountOfSequences);
+    nodesWithAlignment = new HashMap<>(amountOfSequences);
 
 
   }
@@ -80,14 +83,15 @@ public class ArchaeopteryxTreeBuilder
 
     for (SequenceI sequence : sequences)
     {
-      Sequence seq = ForesterConversions
+      Sequence seq = ForesterDataConversions
               .createForesterSequence(sequence, true);
       PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());
+
       NodeData nodeData = sequenceNode.getNodeData();
       nodeData.setSequence(seq);
 
-      nodesBoundAlignment.put(sequenceNode, sequence);
-      alignmentBoundNodes.put(sequence, sequenceNode);
+      nodesWithAlignment.put(sequenceNode, sequence);
+      alignmentWithNodes.put(sequence, sequenceNode);
       rootNode.addAsChild(sequenceNode);
     }
 
@@ -104,13 +108,13 @@ public class ArchaeopteryxTreeBuilder
   @Override
   public Map<SequenceI, PhylogenyNode> getAlignmentBoundNodes()
   {
-    return alignmentBoundNodes;
+    return alignmentWithNodes;
   }
 
   @Override
   public Map<PhylogenyNode, SequenceI> getNodesBoundAlignment()
   {
-    return nodesBoundAlignment;
+    return nodesWithAlignment;
   }
 
   private Phylogeny clusterNodes()