From 86fd4dbafd6175d651fe569c0861de10029cc7b8 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Wed, 3 May 2017 16:31:14 +0100
Subject: [PATCH] JAL-2491 Tidies

---
 src/jalview/gui/AlignmentPanel.java |   51 ++++++++++++++++++++++-------------
 1 file changed, 33 insertions(+), 18 deletions(-)

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index a2773e8..0a128c8 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -477,7 +477,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
             || res >= (vpRanges.getStartRes() + cwidth))
     {
       vscroll.setValue((res / cwidth));
-      // vpRanges.setStartRes(vscroll.getValue() * cwidth);
     }
 
   }
@@ -705,7 +704,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     if (av.getWrapAlignment())
     {
-      setScrollingForWrappedPanel(x, y);
+      setScrollingForWrappedPanel(x);
     }
     else
     {
@@ -752,14 +751,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
         x = 0;
       }
 
-      /*
-       * each scroll adjustment triggers adjustmentValueChanged, which resets the
-       * 'do not scroll complement' flag; ensure it is the same for both
-       * operations
-       */
-      // boolean flag = isDontScrollComplement();
+      // update the scroll values
       hscroll.setValues(x, hextent, 0, width);
-      // setDontScrollComplement(flag);
       vscroll.setValues(y, vextent, 0, height);
     }
   }
@@ -787,6 +780,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
         int offy = vscroll.getValue();
         int rowSize = getSeqPanel().seqCanvas
                 .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
+
+        // if we're scrolling to the position we're already at, stop
+        // this prevents infinite recursion of events when the scroll/viewport
+        // ranges values are the same
         if (offy * rowSize == oldX)
         {
           return;
@@ -819,6 +816,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
       if (evt.getSource() == hscroll)
       {
         int x = hscroll.getValue();
+
+        // if we're scrolling to the position we're already at, stop
+        // this prevents infinite recursion of events when the scroll/viewport
+        // ranges values are the same
         if (x == oldX)
         {
           return;
@@ -830,6 +831,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
       else if (evt.getSource() == vscroll)
       {
         int offy = vscroll.getValue();
+
+        // if we're scrolling to the position we're already at, stop
+        // this prevents infinite recursion of events when the scroll/viewport
+        // ranges values are the same
         if (offy == oldY)
         {
           return;
@@ -889,35 +894,37 @@ public class AlignmentPanel extends GAlignmentPanel implements
     validate();
 
     /*
-     * set scroll bar positions; first suppress this being 'followed' in any
-     * complementary split pane
+     * set scroll bar positions
      */
-
-    // setDontScrollComplement(true);
     setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
   }
 
   /*
    * Set vertical scroll bar parameters for wrapped panel
+   * @param res 
+   *    the residue to scroll to
    */
-  private void setScrollingForWrappedPanel(int x, int y)
+  private void setScrollingForWrappedPanel(int res)
   {
+    // get the width of the alignment in residues
     int maxwidth = av.getAlignment().getWidth();
-
     if (av.hasHiddenColumns())
     {
       maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
     }
 
+    // get the width of the canvas in residues
     int canvasWidth = getSeqPanel().seqCanvas
             .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
     if (canvasWidth > 0)
     {
-      int current = x / canvasWidth;
+      // position we want to scroll to is number of canvasWidth's to get there
+      int current = res / canvasWidth;
+
+      // max scroll position: add one because extent is 1 and scrollbar value
+      // can only be set to at most max - extent
       int max = maxwidth / canvasWidth + 1;
-      vscroll.setMaximum(max);
       vscroll.setUnitIncrement(1);
-      vscroll.setVisibleAmount(1);
       vscroll.setValues(current, 1, 0, max);
     }
   }
@@ -1891,11 +1898,19 @@ public class AlignmentPanel extends GAlignmentPanel implements
   }
 
   @Override
+  /**
+   * Property change event fired when a change is made to the viewport ranges 
+   * object associated with this alignment panel's viewport
+   */
   public void propertyChange(PropertyChangeEvent evt)
   {
+    // update this panel's scroll values based on the new viewport ranges values
     int x = vpRanges.getStartRes();
     int y = vpRanges.getStartSeq();
     setScrollValues(x, y);
+
+    // now update any complementary alignment (its viewport ranges object
+    // is different so does not get automatically updated)
     av.scrollComplementaryAlignment();
   }
 }
-- 
1.7.10.2