From 9e91d8f8d2a4a3206471356681132eb76952a5c2 Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Fri, 3 Nov 2017 09:23:35 +0000
Subject: [PATCH] JAL-2795 bunch of cleanup and comments

---
 .../archaeopteryx/AlignToArchaeopteryxConverter.java |    6 ------
 ...erBindingI.java => JalviewTreeViewerBinding.java} |    0
 src/jalview/gui/AlignFrame.java                      |    2 +-
 src/jalview/gui/TreePanel.java                       |   18 ++++++++++++++++--
 4 files changed, 17 insertions(+), 9 deletions(-)
 delete mode 100644 src/jalview/ext/archaeopteryx/AlignToArchaeopteryxConverter.java
 rename src/jalview/ext/archaeopteryx/{TreeViewerBindingI.java => JalviewTreeViewerBinding.java} (100%)

diff --git a/src/jalview/ext/archaeopteryx/AlignToArchaeopteryxConverter.java b/src/jalview/ext/archaeopteryx/AlignToArchaeopteryxConverter.java
deleted file mode 100644
index b90cf4b..0000000
--- a/src/jalview/ext/archaeopteryx/AlignToArchaeopteryxConverter.java
+++ /dev/null
@@ -1,6 +0,0 @@
-package jalview.ext.archaeopteryx;
-
-public class AlignToArchaeopteryxConverter
-{
-
-}
diff --git a/src/jalview/ext/archaeopteryx/TreeViewerBindingI.java b/src/jalview/ext/archaeopteryx/JalviewTreeViewerBinding.java
similarity index 100%
rename from src/jalview/ext/archaeopteryx/TreeViewerBindingI.java
rename to src/jalview/ext/archaeopteryx/JalviewTreeViewerBinding.java
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 374ca0e..774a4f1 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3575,7 +3575,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       SequenceGroup sg = viewport.getSelectionGroup();
 
       /* Decide if the selection is a column region */
-      for (SequenceI _s : sg.getSequences())
+      for (SequenceI _s : sg.getSequences()) // port this to Archaeopteryx?
       {
         if (_s.getLength() < sg.getEndRes())
         {
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 57cff8f..55e3a1b 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -128,6 +128,12 @@ public class TreePanel extends GTreePanel
     return treeCanvas.av;
   }
 
+  /**
+   * Initialize a tree panel based on a calculated tree
+   * 
+   * @param ap
+   * @param tree
+   */
   void initTreePanel(AlignmentPanel ap, TreeModel tree)
   {
     buildTreeCanvas(ap);
@@ -136,12 +142,20 @@ public class TreePanel extends GTreePanel
     tl.start();
 
   }
+
+  /**
+   * Initialize a tree panel based on a loaded in tree file.
+   * 
+   * @param ap
+   * @param loadedTree
+   * @param inputData
+   */
   void initTreePanel(AlignmentPanel ap, 
-          NewickFile newTree, AlignmentView inputData)
+          NewickFile loadedTree, AlignmentView inputData)
   {
     buildTreeCanvas(ap);
 
-    TreeLoader tl = new TreeLoader(newTree, inputData);
+    TreeLoader tl = new TreeLoader(loadedTree, inputData);
     tl.start();
   }
 
-- 
1.7.10.2