JAL-2504 use (and update) defaults for new feature only if not supplied

[jalview.git] / src / jalview / appletgui / SeqPanel.java

diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java
index ceae253..d46cc34 100644 (file)
--- a/src/jalview/appletgui/SeqPanel.java
+++ b/src/jalview/appletgui/SeqPanel.java
@@ -237,7 +237,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
       {
         ap.scrollUp(true);
       }
-      while (seqCanvas.cursorY + 1 > ranges.getEndSeq())
+      while (seqCanvas.cursorY > ranges.getEndSeq())
       {
         ap.scrollUp(false);
       }
@@ -965,7 +965,9 @@ public class SeqPanel extends Panel implements MouseMotionListener,
           fontSize = 1;
         }
 
-        av.setFont(new Font(av.font.getName(), av.font.getStyle(), fontSize));
+        av.setFont(
+                new Font(av.font.getName(), av.font.getStyle(), fontSize),
+                true);
         av.setCharWidth(oldWidth);
       }
       else
@@ -1878,7 +1880,8 @@ public class SeqPanel extends Panel implements MouseMotionListener,
         }
         else
         {
-          av.getColumnSelection().setElementsFrom(colsel);
+          av.getColumnSelection().setElementsFrom(colsel,
+                  av.getAlignment().getHiddenColumns());
         }
       }
       repaint |= av.isColSelChanged(true);
@@ -1886,7 +1889,7 @@ public class SeqPanel extends Panel implements MouseMotionListener,
     if (copycolsel
             && av.hasHiddenColumns()
             && (av.getColumnSelection() == null || av.getAlignment()
-                    .getHiddenColumns().getListOfCols() == null))
+                    .getHiddenColumns().getHiddenRegions() == null))
     {
       System.err.println("Bad things");
     }