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 21a4e30..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;
 
@@ -25,7 +25,8 @@ import org.forester.phylogeny.data.Sequence;
  * @author kjvanderheide
  *
  */
-public class ArchaeopteryxTreeConverter
+public class ArchaeopteryxTreeBuilder
+        implements ExternalTreeBuilderI<Phylogeny, PhylogenyNode>
 {
   protected final SequenceI[] sequences;
 
@@ -39,25 +40,29 @@ public class ArchaeopteryxTreeConverter
 
   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 ArchaeopteryxTreeConverter(final TreeBuilder calculatedTree)
+  public ArchaeopteryxTreeBuilder(final TreeBuilder calculatedTree)
   {
     jalviewTree = calculatedTree;
     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);
 
 
   }
 
-  public Phylogeny buildAptxTree(final PhylogenyNode treeRoot)
+  @Override
+  public Phylogeny buildTree(final PhylogenyNode treeRoot)
   {
 
     if (treeRoot != null)
@@ -65,26 +70,28 @@ public class ArchaeopteryxTreeConverter
       rootNode = treeRoot;
     }
 
-    buildAptxTree();
+    buildTree();
 
     return aptxTree;
 
   }
 
 
-  public Phylogeny buildAptxTree()
+  @Override
+  public Phylogeny buildTree()
   {
 
     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);
     }
 
@@ -98,14 +105,16 @@ public class ArchaeopteryxTreeConverter
 
   }
 
+  @Override
   public Map<SequenceI, PhylogenyNode> getAlignmentBoundNodes()
   {
-    return alignmentBoundNodes;
+    return alignmentWithNodes;
   }
 
+  @Override
   public Map<PhylogenyNode, SequenceI> getNodesBoundAlignment()
   {
-    return nodesBoundAlignment;
+    return nodesWithAlignment;
   }
 
   private Phylogeny clusterNodes()
@@ -122,6 +131,7 @@ public class ArchaeopteryxTreeConverter
    * 
    * @return
    */
+  @Override
   public String generateTreeName() // Move this and add selection region to the
                                    // title when applicable
   {