JAL-2794 most method parameters/class variables made final

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

diff --git a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
index 9542397..0bdd4e2 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeConverter.java
@@ -2,82 +2,114 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
+import jalview.ext.forester.ForesterConversions;
+import jalview.ext.forester.ForesterMatrix;
 import jalview.util.MessageManager;
 
+import java.util.HashMap;
+import java.util.Map;
+
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyNode;
-
+import org.forester.phylogeny.data.NodeData;
+import org.forester.phylogeny.data.Sequence;
+
+/**
+ * Note that this currently demands a 1:1 relationship between nodes and
+ * sequences
+ * 
+ * @author kjvanderheide
+ *
+ */
 public class ArchaeopteryxTreeConverter
 {
-  protected SequenceI[] sequences;
-
-  private Phylogeny aptxTree;
-
-  private PhylogenyNode rootNode;
+  protected final SequenceI[] sequences;
 
-  protected DistanceMatrix distances;
+  protected final DistanceMatrix distances;
   
-  protected TreeBuilder jalviewTree;
+  protected final TreeBuilder jalviewTree;
   
   public String treeTitle;
 
+  private final Phylogeny aptxTree;
 
+  private PhylogenyNode rootNode;
 
-  public ArchaeopteryxTreeConverter(TreeBuilder calculatedTree)
-  {
-    this.jalviewTree = calculatedTree;
-    this.sequences = jalviewTree.getSequences();
-    this.distances = MatrixConverter.convertJalviewToForester(
-            jalviewTree.getDistances(), jalviewTree.getSequences());
+  private final Map<SequenceI, PhylogenyNode> alignmentBoundNodes;
 
-  }
+  private final Map<PhylogenyNode, SequenceI> nodesBoundAlignment;
 
-  public Phylogeny buildAptxTree()
+  public ArchaeopteryxTreeConverter(final TreeBuilder calculatedTree)
   {
-    this.rootNode = new PhylogenyNode();
+    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());
 
-    return buildAptxTree(rootNode);
 
   }
 
-  public Phylogeny buildAptxTree(PhylogenyNode treeRoot)
+  public Phylogeny buildAptxTree(final PhylogenyNode treeRoot)
   {
 
-    this.rootNode = treeRoot;
-
-    this.aptxTree = new Phylogeny();
-
-    this.treeTitle = generateTreeName();
-    this.aptxTree.setName(treeTitle);
-
-    // final NeighborJoiningF nj = NeighborJoiningF.createInstance(false, 5);
+    if (treeRoot != null)
+    {
+      rootNode = treeRoot;
+    }
 
-    //
-    // final Phylogeny phy = nj.execute(JalviewMatrixToForesterMatrix
-    // .convertJalviewToForester(distances));
+    buildAptxTree();
 
-    return buildAptxTree(sequences);
+    return aptxTree;
 
   }
 
-  // testing method to be removed
-  public Phylogeny buildAptxTree(SequenceI[] sequences)
+
+  public Phylogeny buildAptxTree()
   {
 
     for (SequenceI sequence : sequences)
     {
-      PhylogenyNode treeNode = new PhylogenyNode(sequence.getName());
-      rootNode.addAsChild(treeNode);
-
+      Sequence seq = ForesterConversions
+              .createForesterSequence(sequence, true);
+      PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());
+      NodeData nodeData = sequenceNode.getNodeData();
+      nodeData.setSequence(seq);
+
+      nodesBoundAlignment.put(sequenceNode, sequence);
+      alignmentBoundNodes.put(sequence, sequenceNode);
+      rootNode.addAsChild(sequenceNode);
     }
 
+
     aptxTree.setRoot(rootNode);
+
+    treeTitle = generateTreeName();
+    aptxTree.setName(treeTitle);
+
     return aptxTree;
 
   }
 
+  public Map<SequenceI, PhylogenyNode> getAlignmentBoundNodes()
+  {
+    return alignmentBoundNodes;
+  }
 
+  public Map<PhylogenyNode, SequenceI> getNodesBoundAlignment()
+  {
+    return nodesBoundAlignment;
+  }
+
+  private Phylogeny clusterNodes()
+  {
+    return aptxTree;
+
+  }
   /**
    * Formats a localised title for the tree panel, like
    * <p>
@@ -87,7 +119,8 @@ public class ArchaeopteryxTreeConverter
    * 
    * @return
    */
-  public String generateTreeName()
+  public String generateTreeName() // Move this and add selection region to the
+                                   // title when applicable
   {
     if (treeTitle != null) // will currently never happen, loaded tree file will
                            // take a different path