JAL-2795 calculated trees are now passed along as Newick strings

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index ba34213..11ee71e 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -1,15 +1,14 @@
 package jalview.ext.archaeopteryx;
 
-import jalview.analysis.TreeBuilder;
 import jalview.ext.forester.io.UtilityMethods;
 import jalview.ext.treeviewer.LoadedTreeAssociationI;
 import jalview.ext.treeviewer.LoadedTreeSequenceAssociation;
-import jalview.ext.treeviewer.TreeBuilderI;
 import jalview.ext.treeviewer.TreeFrameI;
 import jalview.ext.treeviewer.TreeI;
 import jalview.ext.treeviewer.TreeViewerUtils;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
+import jalview.io.NewickFile;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -34,6 +33,8 @@ import org.forester.io.parsers.util.ParserUtils;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.data.Identifier;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
 import org.forester.util.ForesterUtil;
 
 /**
@@ -74,20 +75,60 @@ public final class AptxInit
   private final static NHXParser.TAXONOMY_EXTRACTION TAXONOMY_EXTRACTION = APTX_CONFIG
           .getTaxonomyExtraction();
 
-  public static TreeFrameI createInstanceFromCalculation(
-          final TreeBuilder calculatedTree)
+  // public static TreeFrameI createInstanceFromCalculation(
+  // final TreeBuilder calculatedTree)
+  // {
+  // TreeBuilderI aptxTreeBuilder = new AptxTreeBuilder(
+  // calculatedTree);
+  //
+  // TreeI aptxTree = aptxTreeBuilder.buildTree();
+  //
+  // TreeFrameI aptxApp = createAptxFrame(aptxTree,
+  // calculatedTree.getAvport(), null);
+  //
+  // return aptxApp;
+  // }
+
+  public static TreeFrameI[] createInstances(String treeTitle,
+          Object source, PhylogenyParser parser, AlignmentViewport viewport)
+          throws IOException
   {
-    TreeBuilderI aptxTreeBuilder = new AptxTreeBuilder(
-            calculatedTree);
+    TreeFrameI[] aptxFrames = null;
+    PhylogenyFactory parserFact = ParserBasedPhylogenyFactory.getInstance();
+    Phylogeny[] trees = parserFact.create(source, parser);
+    aptxFrames = new TreeFrameI[trees.length];
+
+    for (int i = 0; i < trees.length; i++)
+    {
+      Phylogeny aptxPhylogeny = trees[i];
 
-    TreeI aptxTree = aptxTreeBuilder.buildTree();
+      // if (nhx_or_nexus && INTERNAL_NUMBERS_AS_CONFIDENCE)
+      // {
+      // PhylogenyMethods
+      // .transferInternalNodeNamesToConfidence(aptxPhylogeny, "");
+      // }
+      aptxPhylogeny.setName(treeTitle);
+      aptxFrames[i] = createAptxFrame(aptxPhylogeny, viewport, treeTitle);
+
+    }
+    if (Desktop.instance != null)
+    {
+      Desktop.instance.stopLoading();
+    }
+
+    return aptxFrames;
 
-    TreeFrameI aptxApp = createAptxFrame(aptxTree,
-            calculatedTree.getAvport(), null);
-            
-    return aptxApp;
   }
 
+  /**
+   * Refactored from Archaeopteryx.main
+   * 
+   * @param filePath
+   * @param viewport
+   * @return
+   * @throws IOException
+   * @throws FileNotFoundException
+   */
   public static TreeFrameI[] createInstancesFromFile(File treeFile,
           AlignmentViewport viewport)
           throws FileNotFoundException, IOException
@@ -155,15 +196,7 @@ public final class AptxInit
     return aptxFrames;
   }
 
-  /**
-   * Refactored from Archaeopteryx.main
-   * 
-   * @param filePath
-   * @param viewport
-   * @return
-   * @throws IOException
-   * @throws FileNotFoundException
-   */
+
   public static TreeFrameI[] createInstancesFromFile(
           String filePath,
           AlignmentViewport viewport)
@@ -174,6 +207,12 @@ public final class AptxInit
 
     }
 
+  public static TreeFrameI[] createInstancesFromFile(NewickFile newickFile,
+          AlignmentViewport viewport)
+  {
+    return null;
+  }
+
 
   public static TreeFrameI[] createInstancesFromUrl(URL treeUrl,
           AlignmentViewport viewport)

diff --git a/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
index 9dff141..1be7da3 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
+++ b/src/jalview/ext/archaeopteryx/AptxTreeBuilder.java
@@ -1,167 +1,167 @@
-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;
-    }
-  }
-
-
-  
-
-}
+// 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;
+// }
+// }
+//
+//
+//
+//
+// }

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index f092e40..b973572 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -46,6 +46,7 @@ import java.awt.event.FocusListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.beans.PropertyVetoException;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -63,6 +64,8 @@ import javax.swing.JRadioButton;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
 
+import org.forester.io.parsers.nhx.NHXParser;
+
 /**
  * A dialog where a user can choose and action Tree or PCA calculation options
  */
@@ -464,6 +467,8 @@ public class CalculationChooser extends JPanel
 
   /**
    * Open and calculate the selected tree or PCA on 'OK'
+   * 
+   * @throws IOException
    */
   protected void calculate_actionPerformed()
   {
@@ -477,7 +482,14 @@ public class CalculationChooser extends JPanel
     }
     else
     {
-      createTree(substitutionMatrix, params);
+      try
+      {
+        createTree(substitutionMatrix, params);
+      } catch (IOException e)
+      {
+        // TODO Auto-generated catch block
+        e.printStackTrace();
+      }
 
 
 
@@ -490,17 +502,23 @@ public class CalculationChooser extends JPanel
   }
 
   protected void createTree(String substitutionMatrix,
-          SimilarityParamsI params)
+          SimilarityParamsI params) throws IOException
   {
     String treeAlgo = determineTreeAlgo();
     TreeCalculator treeCalculator = new TreeCalculator(treeAlgo,
             substitutionMatrix, params);
     TreeBuilder calculatedTree = treeCalculator.makeTree(af.getViewport());
 
-    AptxInit.createInstanceFromCalculation(calculatedTree);
+    // AptxInit.createInstanceFromCalculation(calculatedTree);
 
     TreeModel tree = new TreeModel(calculatedTree);
-    openTreePanel(tree, treeAlgo, substitutionMatrix);
+    jalview.io.NewickFile newick = new jalview.io.NewickFile(
+            tree.getTopNode());
+    String output = newick.print(tree.hasBootstrap(), tree.hasDistances(),
+            tree.hasRootDistance());
+    AptxInit.createInstances(af.getTitle(), output, new NHXParser(),
+            af.getViewport());
+    // openTreePanel(tree, treeAlgo, substitutionMatrix);
   }