X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fext%2Farchaeopteryx%2FAptxTreeBuilder.java;fp=src%2Fjalview%2Fext%2Farchaeopteryx%2FAptxTreeBuilder.java;h=1be7da33842b7aad4feda67b55450004ff366a03;hp=74d89d200f6f5ff9e094df7901e7f9fe0c41e397;hb=4a3def9f59cefe629c9a33d87483283aee085928;hpb=eca4795050a0f7eca3d5dece68eaa54987cebd15

diff --git a/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
index 74d89d2..1be7da3 100644
--- a/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
@@ -1,170 +1,167 @@
-package jalview.ext.archaeopteryx;
-
-import jalview.analysis.TreeBuilder;
-import jalview.datamodel.SequenceI;
-import jalview.ext.forester.DataConversions;
-import jalview.ext.forester.ForesterMatrix;
-import jalview.ext.treeviewer.ExternalTreeBuilderI;
-import jalview.util.MappingUtils;
-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;
-
-/**
- * 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 AptxTreeBuilder
-        implements ExternalTreeBuilderI<Phylogeny, PhylogenyNode>
-{
-  protected final SequenceI[] sequences;
-
-  protected final DistanceMatrix distances;
-  
-  protected final TreeBuilder jalviewTree;
-  
-  public String treeTitle;
-
-  private final Phylogeny aptxTree;
-
-  private PhylogenyNode rootNode;
-
-  private final Map<SequenceI, PhylogenyNode> alignmentWithNodes;
-
-  private final Map<PhylogenyNode, SequenceI> nodesWithAlignment;
-
-  public AptxTreeBuilder(final TreeBuilder calculatedTree)
-  {
-    jalviewTree = calculatedTree;
-    sequences = jalviewTree.getSequences();
-    distances = ForesterMatrix.convertJalviewToForester(
-            jalviewTree.getDistances(), sequences);
-
-    aptxTree = new Phylogeny();
-    rootNode = new PhylogenyNode();
-
-    int amountOfSequences = distances.getSize();
-    alignmentWithNodes = new HashMap<>(amountOfSequences);
-    nodesWithAlignment = new HashMap<>(amountOfSequences);
-
-
-  }
-
-  @Override
-  public Phylogeny buildTree(final PhylogenyNode treeRoot)
-  {
-
-    if (treeRoot != null)
-    {
-      rootNode = treeRoot;
-    }
-
-    buildTree();
-
-    return aptxTree;
-
-  }
-
-
-  @Override
-  public Phylogeny buildTree()
-  {
-
-    for (SequenceI sequence : sequences)
-    {
-      Sequence seq = DataConversions
-              .createForesterSequence(sequence, true);
-      PhylogenyNode sequenceNode = new PhylogenyNode(sequence.getName());
-
-      NodeData nodeData = sequenceNode.getNodeData();
-      nodeData.setSequence(seq);
-
-      MappingUtils.putWithDuplicationCheck(nodesWithAlignment,
-              sequenceNode, sequence);
-      MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
-              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>
-   * Neighbour Joining Using BLOSUM62
-   * <p>
-   * For a tree loaded from file, just uses the file name
-   * 
-   * @return
-   */
-  @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;
-    }
-  }
-  
-
-}
+// package jalview.ext.archaeopteryx;
+//
+// import jalview.analysis.TreeBuilder;
+// import jalview.datamodel.SequenceI;
+// import jalview.ext.forester.ForesterMatrix;
+// import jalview.ext.treeviewer.TreeBuilderI;
+// import jalview.ext.treeviewer.TreeI;
+// import jalview.ext.treeviewer.TreeNodeI;
+// import jalview.util.MappingUtils;
+// 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;
+//
+/// **
+// * 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 AptxTreeBuilder
+// implements TreeBuilderI
+// {
+// protected final SequenceI[] sequences;
+//
+// protected final DistanceMatrix distances;
+//
+// protected final TreeBuilder jalviewTree;
+//
+// public String treeTitle;
+//
+// private final TreeI aptxTree;
+//
+// private TreeNodeI rootNode;
+//
+// private final Map<SequenceI, TreeNodeI> alignmentWithNodes;
+//
+// private final Map<TreeNodeI, SequenceI> nodesWithAlignment;
+//
+// public AptxTreeBuilder(final TreeBuilder calculatedTree)
+// {
+// jalviewTree = calculatedTree;
+// sequences = jalviewTree.getSequences();
+// distances = ForesterMatrix.convertJalviewToForester(
+// jalviewTree.getDistances(), sequences);
+//
+// aptxTree = new Tree(new Phylogeny());
+// rootNode = TreeNode.getUniqueWrapper(new PhylogenyNode());
+//
+// int amountOfSequences = distances.getSize();
+// alignmentWithNodes = new HashMap<>(amountOfSequences);
+// nodesWithAlignment = new HashMap<>(amountOfSequences);
+//
+//
+// }
+//
+// @Override
+// public TreeI buildTree(final TreeNodeI treeRoot)
+// {
+//
+// if (treeRoot != null)
+// {
+// rootNode = treeRoot;
+// }
+//
+// buildTree();
+//
+// return aptxTree;
+//
+// }
+//
+//
+// @Override
+// public TreeI buildTree()
+// {
+//
+// for (SequenceI sequence : sequences)
+// {
+//
+// TreeNodeI sequenceNode = TreeNode
+// .getUniqueWrapper(
+// new PhylogenyNode(sequence.getName()));
+//
+// sequenceNode.setSequence(sequence);
+//
+// MappingUtils.putWithDuplicationCheck(nodesWithAlignment,
+// sequenceNode, sequence);
+// MappingUtils.putWithDuplicationCheck(alignmentWithNodes,
+// sequence, sequenceNode);
+// rootNode.addAsChild(sequenceNode);
+// }
+//
+//
+// aptxTree.setRoot(rootNode);
+//
+// treeTitle = generateTreeName();
+// aptxTree.setTreeName(treeTitle);
+//
+// return aptxTree;
+//
+// }
+//
+// @Override
+// public Map<SequenceI, TreeNodeI> getAlignmentBoundNodes()
+// {
+// return alignmentWithNodes;
+// }
+//
+// @Override
+// public Map<TreeNodeI, SequenceI> getNodesBoundAlignment()
+// {
+// return nodesWithAlignment;
+// }
+//
+//
+// /**
+// * Formats a localised title for the tree panel, like
+// * <p>
+// * Neighbour Joining Using BLOSUM62
+// * <p>
+// * For a tree loaded from file, just uses the file name
+// *
+// * @return
+// */
+// @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;
+// }
+// }
+//
+//
+//
+//
+// }