From 8136b9b35478ec46e2f2064c32506b6bcdd85533 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 4 Apr 2016 15:22:56 +0100
Subject: [PATCH] JAL-969 refactor columnselection operation (during JAL-2001)

---
 src/jalview/appletgui/AlignViewport.java     |   33 --------------------------
 src/jalview/gui/AlignViewport.java           |   33 --------------------------
 src/jalview/viewmodel/AlignmentViewport.java |   33 ++++++++++++++++++++++++++
 3 files changed, 33 insertions(+), 66 deletions(-)

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 09e6562..e5178cb 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -348,39 +348,6 @@ public class AlignViewport extends AlignmentViewport implements
             .getStructureSelectionManager(applet);
   }
 
-  /**
-   * synthesize a column selection if none exists so it covers the given
-   * selection group. if wholewidth is false, no column selection is made if the
-   * selection group covers the whole alignment width.
-   * 
-   * @param sg
-   * @param wholewidth
-   */
-  public void expandColSelection(SequenceGroup sg, boolean wholewidth)
-  {
-    int sgs, sge;
-    if (sg != null
-            && (sgs = sg.getStartRes()) >= 0
-            && sg.getStartRes() <= (sge = sg.getEndRes())
-            && (colSel == null || colSel.getSelected() == null || colSel
-                    .getSelected().size() == 0))
-    {
-      if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
-      {
-        // do nothing
-        return;
-      }
-      if (colSel == null)
-      {
-        colSel = new ColumnSelection();
-      }
-      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
-      {
-        colSel.addElement(cspos);
-      }
-    }
-  }
-
   @Override
   public boolean isNormaliseSequenceLogo()
   {
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7d8d4fe..692cd18 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -663,39 +663,6 @@ public class AlignViewport extends AlignmentViewport implements
   }
 
   /**
-   * synthesize a column selection if none exists so it covers the given
-   * selection group. if wholewidth is false, no column selection is made if the
-   * selection group covers the whole alignment width.
-   * 
-   * @param sg
-   * @param wholewidth
-   */
-  public void expandColSelection(SequenceGroup sg, boolean wholewidth)
-  {
-    int sgs, sge;
-    if (sg != null
-            && (sgs = sg.getStartRes()) >= 0
-            && sg.getStartRes() <= (sge = sg.getEndRes())
-            && (colSel == null || colSel.getSelected() == null || colSel
-                    .getSelected().size() == 0))
-    {
-      if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
-      {
-        // do nothing
-        return;
-      }
-      if (colSel == null)
-      {
-        colSel = new ColumnSelection();
-      }
-      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
-      {
-        colSel.addElement(cspos);
-      }
-    }
-  }
-
-  /**
    * Returns the (Desktop) instance of the StructureSelectionManager
    */
   @Override
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 6322243..b70e92b 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2655,4 +2655,37 @@ public abstract class AlignmentViewport implements AlignViewportI,
             sequence.findPosition(middleColumn), mappings);
     return seqOffset;
   }
+
+  /**
+   * synthesize a column selection if none exists so it covers the given
+   * selection group. if wholewidth is false, no column selection is made if the
+   * selection group covers the whole alignment width.
+   * 
+   * @param sg
+   * @param wholewidth
+   */
+  public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+  {
+    int sgs, sge;
+    if (sg != null
+            && (sgs = sg.getStartRes()) >= 0
+            && sg.getStartRes() <= (sge = sg.getEndRes())
+            && (colSel == null || colSel.getSelected() == null || colSel
+                    .getSelected().size() == 0))
+    {
+      if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+      {
+        // do nothing
+        return;
+      }
+      if (colSel == null)
+      {
+        colSel = new ColumnSelection();
+      }
+      for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+      {
+        colSel.addElement(cspos);
+      }
+    }
+  }
 }
-- 
1.7.10.2