JAL-1953 some more comments, moved JalviewBinding

[jalview.git] / src / jalview / ext / treeviewer / TreeViewerUtils.java

diff --git a/src/jalview/ext/treeviewer/TreeViewerUtils.java b/src/jalview/ext/treeviewer/TreeViewerUtils.java
index 9531cf1..7e1a4e9 100644 (file)
--- a/src/jalview/ext/treeviewer/TreeViewerUtils.java
+++ b/src/jalview/ext/treeviewer/TreeViewerUtils.java
@@ -1,7 +1,6 @@
 package jalview.ext.treeviewer;
 
 import jalview.datamodel.SequenceI;
-import jalview.ext.archaeopteryx.JalviewBinding;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
@@ -10,30 +9,32 @@ import java.io.File;
 import java.util.HashMap;
 import java.util.Map;
 
+/**
+ * Static class containing generic methods for communicating between the tree
+ * viewer frame and Jalview, currently includes adding the frame to the Jalview
+ * Desktop and triggering an association between an {@link AlignmentViewport}
+ * and {@link TreeFrameI}.
+ * 
+ * @author kjvanderheide
+ *
+ */
 public final class TreeViewerUtils
 {
+  /**
+   * All tree viewers should be added to this map so that Jalview saves them to
+   * its project.
+   */
   private static Map<TreeFrameI, TreeViewerBindingI> activeViews = new HashMap<>();
 
-  public static TreeViewerBindingI associateNodesWithJalviewSequences(
-          final TreeFrameI treeFrame,
-          final AlignmentViewport jalviewAlignViewport,
-          final Map<SequenceI, TreeNodeI> alignMappedToNodes,
-          final Map<TreeNodeI, SequenceI> nodesMappedToAlign)
-  {
-    TreeViewerBindingI treeBinding = new JalviewBinding(treeFrame,
-            jalviewAlignViewport,
-            alignMappedToNodes, nodesMappedToAlign);
-    jalviewAlignViewport.setCurrentExtTree(treeFrame.getTree());
-    activeViews.put(treeFrame, treeFrame.getViewBinding());
-
-    return treeBinding;
-  }
-
+  /**
+   * Adds the given tree frame to the Jalview {@link Desktop}.
+   * 
+   * @param treeFrame
+   * @return the same tree frame but now as part of Jalview.
+   */
   public static TreeFrameI addTreeViewFrameToJalview(
-          final TreeFrameI treeFrame)
+          final TreeFrameI treeFrame, int width, int height)
   {
-    int width = 400;
-    int height = 550;
     treeFrame.setMinimumSize(new Dimension(width, height));
     // aptxApp.setFont(Desktop.instance.getFont());
     // aptxApp.getMainPanel().setFont(Desktop.instance.getFont());
@@ -41,7 +42,7 @@ public final class TreeViewerUtils
     File treeFile = treeFrame.getTreePanel().getTreeFile();
     if (treeFile != null)
     {
-      frameTitle += MessageManager.formatMessage("label.aptx_title_append",
+      frameTitle += MessageManager.formatMessage("label.of_x",
               new String[]
               { treeFile.getAbsolutePath() });
     }
@@ -51,10 +52,36 @@ public final class TreeViewerUtils
 
     treeFrame.addFrameToJalview(frameTitle, true, width, height, true,
             false);
+    treeFrame.getTreeControls().displayEntireTree();
     return treeFrame;
   
   }
 
+  /**
+   * Convience method for building the association between Jalview's alignment
+   * and the tree frame.
+   * 
+   * @param treeFrame
+   * @param jalviewAlignViewport
+   * @param alignMappedToNodes
+   * @param nodesMappedToAlign
+   * @return
+   */
+  public static TreeViewerBindingI associateNodesWithJalviewSequences(
+          final TreeFrameI treeFrame,
+          final AlignmentViewport jalviewAlignViewport,
+          final Map<SequenceI, TreeNodeI> alignMappedToNodes,
+          final Map<TreeNodeI, SequenceI> nodesMappedToAlign)
+  {
+    TreeViewerBindingI treeBinding = new JalviewBinding(treeFrame,
+            jalviewAlignViewport,
+            alignMappedToNodes, nodesMappedToAlign);
+    jalviewAlignViewport.setCurrentExtTree(treeFrame.getTree());
+    activeViews.put(treeFrame, treeFrame.getViewBinding());
+
+    return treeBinding;
+  }
+
   public static Map<TreeFrameI, TreeViewerBindingI> getActiveTreeViews()
   {
     return activeViews;