JAL-1953 first pass of adding javadoc, some methods renamed

[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 23118cf..d5c1327 100644 (file)
--- a/src/jalview/ext/treeviewer/TreeViewerUtils.java
+++ b/src/jalview/ext/treeviewer/TreeViewerUtils.java
@@ -14,20 +14,6 @@ public final class TreeViewerUtils
 {
   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);
-    activeViews.put(treeFrame, treeBinding);
-    jalviewAlignViewport.setCurrentExtTree(treeFrame.getTree());
-    return treeBinding;
-  }
-
   public static TreeFrameI addTreeViewFrameToJalview(
           final TreeFrameI treeFrame)
   {
@@ -40,16 +26,36 @@ 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() });
     }
+    // Usually redundant as this is done when associating nodes as well but that
+    // step could be bypassed
+    activeViews.put(treeFrame, treeFrame.getViewBinding());
+
     treeFrame.addFrameToJalview(frameTitle, true, width, height, true,
-            true);
+            false);
+    treeFrame.getTreeControls().displayEntireTree();
     return treeFrame;
   
   }
 
+  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;