JAL-1953 redundant tree interface instantiation removed

diff --git a/forester b/forester
index 1706dee..3d5864a 160000 (submodule)
--- a/forester
+++ b/forester
@@ -1 +1 @@
-Subproject commit 1706deea223bc1a30d170596192d726b6847b7eb
+Subproject commit 3d5864a39739960c126f2ab5585162fd52d1f47d

diff --git a/src/jalview/ext/archaeopteryx/AptxFrame.java b/src/jalview/ext/archaeopteryx/AptxFrame.java
index e7a1517..c517ed3 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxFrame.java
+++ b/src/jalview/ext/archaeopteryx/AptxFrame.java
@@ -32,7 +32,10 @@ import javax.swing.JRootPane;
 import javax.swing.JSeparator;
 import javax.swing.event.InternalFrameListener;
 
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.archaeopteryx.Configuration;
 import org.forester.archaeopteryx.MainFrame;
+import org.forester.phylogeny.Phylogeny;
 import org.jibble.epsgraphics.EpsGraphics2D;
 
 public class AptxFrame implements ExternalTreeFrame
@@ -43,8 +46,20 @@ public class AptxFrame implements ExternalTreeFrame
 
   private ExternalTreeControlsI aptxControls;
 
+
+  public AptxFrame(Phylogeny tree, Configuration aptxConfig,
+          String treeTitle)
+  {
+    this(Archaeopteryx.createApplication(tree,
+            aptxConfig,
+            treeTitle));
+
+  }
+
+
   public AptxFrame(MainFrame aptx)
   {
+
     aptxFrame = aptx;
     aptxPanel = new AptxTreePanel(
             aptxFrame.getMainPanel().getCurrentTreePanel());
@@ -53,15 +68,16 @@ public class AptxFrame implements ExternalTreeFrame
     adaptAptxGui(aptxFrame);
 
   }
+  
   /**
    * Hides certain redundant Archaeopteryx GUI elements such as the menu items
    * for reading in trees and adds extra items related to Jalview such as the
-   * tree sorting item.
+   * tree sorting menu item.
    * 
    * 
    * @param aptxFrame
    */
-  private void adaptAptxGui(MainFrame aptxFrame)
+  protected void adaptAptxGui(MainFrame aptxFrame)
   {
     JMenuBar frameBar = aptxFrame.getJMenuBar();
     boolean epsAdded = false;
@@ -151,7 +167,7 @@ public class AptxFrame implements ExternalTreeFrame
       }
 
     }
-    aptxFrame.validate();
+    // aptxFrame.validate();
   }
 
   public void epsTree_actionPerformed(ActionEvent e)

diff --git a/src/jalview/ext/archaeopteryx/AptxInit.java b/src/jalview/ext/archaeopteryx/AptxInit.java
index d0fb9fe..f7ec0ad 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxInit.java
+++ b/src/jalview/ext/archaeopteryx/AptxInit.java
@@ -87,6 +87,7 @@ public final class AptxInit
     return aptxApp;
   }
 
+
   /**
    * Refactored from Archaeopteryx.main
    * 
@@ -155,8 +156,7 @@ public final class AptxInit
       }
       String treeTitle = treeFile.getName() + "[" + i + "]";
       aptxPhylogeny.setName(treeTitle);
-      Tree aptxTree = new Tree(aptxPhylogeny);
-      aptxFrames[i] = createAptxFrame(aptxTree, viewport, treeTitle);
+        aptxFrames[i] = createAptxFrame(aptxPhylogeny, viewport, treeTitle);
 
     }
     if (Desktop.instance != null)
@@ -187,8 +187,7 @@ public final class AptxInit
     for (int i = 0; i < trees.length; i++)
     {
       Phylogeny aptxTree = trees[i];
-      Tree jalviewTree = new Tree(aptxTree);
-      aptxFrames[i] = createAptxFrame(jalviewTree, viewport, treeTitle);
+      aptxFrames[i] = createAptxFrame(aptxTree, viewport, treeTitle);
     }
 
     if (Desktop.instance != null)
@@ -214,6 +213,7 @@ public final class AptxInit
 
     URL url = null;
     Phylogeny[] trees = null;
+    ExternalTreeFrame[] aptxFrames = null;
 
     if ((identifier != null) && (identifier.trim().length() > 0))
     {
@@ -317,6 +317,7 @@ public final class AptxInit
         // _main_frame.getMainPanel().setWaitCursor();
         // }
         trees = ForesterUtil.readPhylogeniesFromUrl(url, parser);
+        aptxFrames = new ExternalTreeFrame[trees.length];
       } catch (final MalformedURLException e)
       {
         exception = true;
@@ -358,6 +359,7 @@ public final class AptxInit
       }
       if ((trees != null) && (trees.length > 0))
       {
+        int i = 0;
         for (final Phylogeny aptxTree : trees)
         {
           if (!aptxTree.isEmpty())
@@ -402,15 +404,14 @@ public final class AptxInit
             // _main_frame.getConfiguration(),
             // new File(url.getFile()).getName(), url.toString());
 
-            Tree jalviewTree = new Tree(aptxTree);
 
-            ExternalTreeFrame aptxApp = createAptxFrame(jalviewTree,
+            ExternalTreeFrame aptxApp = createAptxFrame(aptxTree,
                     viewport,
                     url.getFile());
             String my_name_for_file = "";
-            if (!ForesterUtil.isEmpty(jalviewTree.getTreeName()))
+            if (!ForesterUtil.isEmpty(aptxTree.getName()))
             {
-              my_name_for_file = new String(jalviewTree.getTreeName())
+              my_name_for_file = new String(aptxTree.getName())
                       .replaceAll(" ", "_");
             }
             else if (aptxTree.getIdentifier() != null)
@@ -434,6 +435,7 @@ public final class AptxInit
             aptxApp.getTreeControls().displayEntireTree();
 
             aptxApp.checkMultipleTrees();
+            aptxFrames[i++] = aptxApp;
           }
         }
       }
@@ -468,40 +470,46 @@ public final class AptxInit
     {
       Desktop.instance.stopLoading();
     }
-    return null;
+    return aptxFrames;
 
 
   }
 
 
 
-
-
-  public static ExternalTreeFrame createAptxFrame(
-          final ExternalTreeI aptxTree,
-          final AlignmentViewport jalviewAlignport, String treeTitle)
+  public static ExternalTreeFrame createAptxFrame(ExternalTreeI aptxTree,
+          AlignmentViewport jalviewAlignport, String treeTitle)
   {
-    if (APTX_CONFIG == null || APTX_CONFIG.isCouldReadConfigFile() == false)
-    {
-      int keepGoing = JvOptionPane.showConfirmDialog(Desktop.desktop,
-              MessageManager.getString("label.aptx_config_not_found"),
-              MessageManager.formatMessage("label.couldnt_locate",
-                      new String[]
-                      { "_aptx_jalview_configuration_file" }),
-              JvOptionPane.YES_NO_CANCEL_OPTION);
+    validateConfig(APTX_CONFIG);
+    ExternalTreeFrame aptxApp = aptxTree
+            .createTreeViewerFromTree(treeTitle);
+    ExternalTreeI jalviewTree = aptxApp.getTree();
+    ExternalLoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
+            jalviewAlignport.getAlignment().getSequencesArray(),
+            jalviewTree);
+    bindAptxNodes.associateLeavesToSequences();
 
-      if (keepGoing == JvOptionPane.CANCEL_OPTION
-              || keepGoing == JvOptionPane.CLOSED_OPTION
-              || keepGoing == JvOptionPane.NO_OPTION)
-      {
-        return null;
-      }
+    bindNodesToJalviewSequences(aptxApp, jalviewAlignport,
+            bindAptxNodes.getAlignmentWithNodes(),
+            bindAptxNodes.getNodesWithAlignment());
+    bindTreeViewFrameToJalview(aptxApp);
 
-    }
-    ExternalTreeFrame aptxApp = aptxTree.createInstanceFromTree(treeTitle);
+    // adaptAptxGui(aptxApp); //moved to AptxFrame
+    return aptxApp;
+  }
 
+
+  protected static ExternalTreeFrame createAptxFrame(
+          final Phylogeny aptxTree,
+          final AlignmentViewport jalviewAlignport, String treeTitle)
+  {
+    validateConfig(APTX_CONFIG);
+    ExternalTreeFrame aptxApp = new AptxFrame(aptxTree, APTX_CONFIG,
+            treeTitle);
+    ExternalTreeI jalviewTree = aptxApp.getTree();
     ExternalLoadedTreeAssociationI bindAptxNodes = new LoadedTreeSequenceAssociation(
-            jalviewAlignport.getAlignment().getSequencesArray(), aptxTree);
+            jalviewAlignport.getAlignment().getSequencesArray(),
+            jalviewTree);
     bindAptxNodes.associateLeavesToSequences();
 
     bindNodesToJalviewSequences(aptxApp, jalviewAlignport,
@@ -514,7 +522,7 @@ public final class AptxInit
   }
 
 
-  public static ExternalTreeViewerBindingI bindNodesToJalviewSequences(
+  protected static ExternalTreeViewerBindingI bindNodesToJalviewSequences(
           final ExternalTreeFrame aptxApp,
           final AlignmentViewport jalviewAlignViewport,
           final Map<SequenceI, ExternalTreeNodeI> alignMappedToNodes,
@@ -528,7 +536,7 @@ public final class AptxInit
   }
 
 
-  public static ExternalTreeFrame bindTreeViewFrameToJalview(
+  protected static ExternalTreeFrame bindTreeViewFrameToJalview(
           final ExternalTreeFrame aptxApp)
   {
     int width = 400;
@@ -550,6 +558,28 @@ public final class AptxInit
 
   }
 
+  private static boolean validateConfig(Configuration aptxConfig)
+  {
+    if (aptxConfig == null || aptxConfig.isCouldReadConfigFile() == false)
+    {
+      int keepGoing = JvOptionPane.showConfirmDialog(Desktop.desktop,
+              MessageManager.getString("label.aptx_config_not_found"),
+              MessageManager.formatMessage("label.couldnt_locate",
+                      new String[]
+                      { "_aptx_jalview_configuration_file" }),
+              JvOptionPane.YES_NO_CANCEL_OPTION);
+
+      if (keepGoing == JvOptionPane.CANCEL_OPTION
+              || keepGoing == JvOptionPane.CLOSED_OPTION
+              || keepGoing == JvOptionPane.NO_OPTION)
+      {
+        return false;
+      }
+
+    }
+    return true;
+  }
+
 
 
   public static Map<ExternalTreeFrame, ExternalTreeViewerBindingI> getAllAptxFrames()

diff --git a/src/jalview/ext/archaeopteryx/AptxTreePanel.java b/src/jalview/ext/archaeopteryx/AptxTreePanel.java
index 620d95b..f811c3b 100644 (file)
--- a/src/jalview/ext/archaeopteryx/AptxTreePanel.java
+++ b/src/jalview/ext/archaeopteryx/AptxTreePanel.java
@@ -19,7 +19,7 @@ public class AptxTreePanel implements ExternalTreePanel
 {
   private final org.forester.archaeopteryx.TreePanel treeView;
 
-  private final Tree tree;
+  private final ExternalTreeI tree;
 
   private String sequenceSetId;
 
@@ -30,6 +30,15 @@ public class AptxTreePanel implements ExternalTreePanel
     tree = new Tree(treeView.getPhylogeny());
   }
 
+  protected AptxTreePanel(
+          org.forester.archaeopteryx.TreePanel aptxTreePanel,
+          ExternalTreeI aptxTree)
+  {
+    treeView = aptxTreePanel;
+    tree = aptxTree;
+
+  }
+
   @Override
   public void setTreeFile(File file)
   {

diff --git a/src/jalview/ext/archaeopteryx/Tree.java b/src/jalview/ext/archaeopteryx/Tree.java
index e9bfb9b..93091b7 100644 (file)
--- a/src/jalview/ext/archaeopteryx/Tree.java
+++ b/src/jalview/ext/archaeopteryx/Tree.java
@@ -139,7 +139,7 @@ public class Tree implements ExternalTreeI
   }
 
   @Override
-  public ExternalTreeFrame createInstanceFromTree(String instanceTitle)
+  public ExternalTreeFrame createTreeViewerFromTree(String instanceTitle)
   {
     return new AptxFrame(Archaeopteryx.createApplication(tree,
             AptxInit.APTX_CONFIG,

diff --git a/src/jalview/ext/treeviewer/ExternalTreeI.java b/src/jalview/ext/treeviewer/ExternalTreeI.java
index 3f28043..820995f 100644 (file)
--- a/src/jalview/ext/treeviewer/ExternalTreeI.java
+++ b/src/jalview/ext/treeviewer/ExternalTreeI.java
@@ -32,7 +32,6 @@ public interface ExternalTreeI
 
   public Iterator<ExternalTreeNodeI> iterateInPostOrder();
 
-  public ExternalTreeFrame createInstanceFromTree(String instanceTitle);
-
+  ExternalTreeFrame createTreeViewerFromTree(String instanceTitle);
 
 }