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 fb1ebe3..9166497 100644 (file)
--- a/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/ArchaeopteryxTreeBuilder.java
@@ -2,73 +2,126 @@ package jalview.ext.archaeopteryx;
 
 import jalview.analysis.TreeBuilder;
 import jalview.datamodel.SequenceI;
-import jalview.math.MatrixI;
+import jalview.ext.forester.ForesterDataConversions;
+import jalview.ext.forester.ForesterMatrix;
+import jalview.util.MessageManager;
 
-import org.forester.io.parsers.SymmetricalDistanceMatrixParser;
-import org.forester.msa.Msa;
+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;
-
-public class ArchaeopteryxTreeBuilder // cannot inherit
-                                                        // TreeBuilder as that
-                                                        // demands the use of
-                                                        // SequenceNode (instead
-                                                        // of PhylogenyNode)
+import org.forester.phylogeny.data.NodeData;
+import org.forester.phylogeny.data.Sequence;
+
+/**
+ * Class for converting trees made in Jalview (through TreeBuilder) to trees
+ * compatible with Forester (Phylogeny objects).
+ * 
+ * Note that this currently demands a 1:1 relationship between tree nodes and
+ * the sequences used for generating them.
+ * 
+ * @author kjvanderheide
+ *
+ */
+public class ArchaeopteryxTreeBuilder
+        implements ExternalTreeBuilderI<Phylogeny, PhylogenyNode>
 {
-  protected SequenceI[] sequences;
+  protected final SequenceI[] sequences;
 
-  private Phylogeny aptxTree;
+  protected final DistanceMatrix distances;
+  
+  protected final TreeBuilder jalviewTree;
+  
+  public String treeTitle;
+
+  private final Phylogeny aptxTree;
 
   private PhylogenyNode rootNode;
 
-  protected MatrixI distances;
+  private final Map<SequenceI, PhylogenyNode> alignmentWithNodes;
 
-  protected Msa msa;
+  private final Map<PhylogenyNode, SequenceI> nodesWithAlignment;
 
-  protected SymmetricalDistanceMatrixParser distanceParser = SymmetricalDistanceMatrixParser
-          .createInstance();
+  public ArchaeopteryxTreeBuilder(final TreeBuilder calculatedTree)
+  {
+    jalviewTree = calculatedTree;
+    sequences = jalviewTree.getSequences();
+    distances = ForesterMatrix.convertJalviewToForester(
+            jalviewTree.getDistances(), sequences);
 
+    aptxTree = new Phylogeny();
+    rootNode = new PhylogenyNode();
 
-  public ArchaeopteryxTreeBuilder()
-  {
+    int amountOfSequences = distances.getSize();
+    alignmentWithNodes = new HashMap<>(amountOfSequences);
+    nodesWithAlignment = new HashMap<>(amountOfSequences);
 
-    this.rootNode = new PhylogenyNode();
-    this.aptxTree = new Phylogeny();
 
   }
 
-  public ArchaeopteryxTreeBuilder(PhylogenyNode treeRoot)
+  @Override
+  public Phylogeny buildTree(final PhylogenyNode treeRoot)
   {
 
-    this.rootNode = treeRoot;
-    this.aptxTree = new Phylogeny();
+    if (treeRoot != null)
+    {
+      rootNode = treeRoot;
+    }
 
-  }
+    buildTree();
 
-  public Phylogeny buildAptxTree(TreeBuilder tree)
-  {
-    this.sequences = tree.getSequences();
-    aptxTree.setName("word");
-    return buildAptxTree(sequences);
+    return aptxTree;
 
   }
 
-  public Phylogeny buildAptxTree(SequenceI[] sequences)
+
+  @Override
+  public Phylogeny buildTree()
   {
 
     for (SequenceI sequence : sequences)
     {
-      PhylogenyNode treeNode = new PhylogenyNode();
-      treeNode.setName(sequence.getName());
-      rootNode.addAsChild(treeNode);
+      Sequence seq = ForesterDataConversions
+              .createForesterSequence(sequence, true);
+      PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());
+
+      NodeData nodeData = sequenceNode.getNodeData();
+      nodeData.setSequence(seq);
 
+      nodesWithAlignment.put(sequenceNode, sequence);
+      alignmentWithNodes.put(sequence, sequenceNode);
+      rootNode.addAsChild(sequenceNode);
     }
 
+
     aptxTree.setRoot(rootNode);
+
+    treeTitle = generateTreeName();
+    aptxTree.setName(treeTitle);
+
     return aptxTree;
 
   }
 
+  @Override
+  public Map<SequenceI, PhylogenyNode> getAlignmentBoundNodes()
+  {
+    return alignmentWithNodes;
+  }
+
+  @Override
+  public Map<PhylogenyNode, SequenceI> getNodesBoundAlignment()
+  {
+    return nodesWithAlignment;
+  }
+
+  private Phylogeny clusterNodes()
+  {
+    return aptxTree;
+
+  }
   /**
    * Formats a localised title for the tree panel, like
    * <p>
@@ -78,31 +131,34 @@ public class ArchaeopteryxTreeBuilder // cannot inherit
    * 
    * @return
    */
-  // public String getPanelTitle()
-  // {
-  // if (treeTitle != null)
-  // {
-  // return treeTitle;
-  // }
-  // else
-  // {
-  // /*
-  // * i18n description of Neighbour Joining or Average Distance method
-  // */
-  // String treecalcnm = MessageManager
-  // .getString("label.tree_calc_" + treeType.toLowerCase());
-  //
-  // /*
-  // * short score model name (long description can be too long)
-  // */
-  // String smn = substitutionMatrix;
-  //
-  // /*
-  // * put them together as <method> Using <model>
-  // */
-  // final String ttl = MessageManager
-  // .formatMessage("label.treecalc_title", treecalcnm, smn);
-  // return ttl;
-  // }
-  // }
+  @Override
+  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
+    {
+      return treeTitle;
+    }
+    else
+    {
+      /*
+      * i18n description of Neighbour Joining or Average Distance method
+      */
+      String treecalcnm = MessageManager
+              .getString("label.tree_calc_" + jalviewTree.getClass()
+                      .getSimpleName().substring(0, 2).toLowerCase());
+      /*
+      * short score model name (long description can be too long)
+      */
+      String smn = jalviewTree.getScoreModel().getName();
+
+      /*
+      * put them together as <method> Using <model>
+      */
+      final String ttl = MessageManager
+              .formatMessage("label.treecalc_title", treecalcnm, smn);
+      return ttl;
+    }
+  }
 }