JAL-2591 Removed getHiddenRegions()==null checks which are always false

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

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 6773611..7651eb4 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -394,8 +394,7 @@ public class SeqPanel extends JPanel implements MouseListener,
     }
     else
     {
-      av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY,
-              av);
+      av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY);
     }
     setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY),
             seqCanvas.cursorX, seqCanvas.cursorY);
@@ -804,7 +803,9 @@ public class SeqPanel extends JPanel implements MouseListener,
   /**
    * Removes from the list of features any that start after, or end before, the
    * given column position. This allows us to retain only those features
-   * adjacent to a gapped position that straddle the position.
+   * adjacent to a gapped position that straddle the position. Contact features
+   * that 'straddle' the position are also removed, since they are not 'at' the
+   * position.
    * 
    * @param features
    * @param column
@@ -819,7 +820,8 @@ public class SeqPanel extends JPanel implements MouseListener,
     while (it.hasNext())
     {
       SequenceFeature sf = it.next();
-      if (sequence.findIndex(sf.getBegin()) > column
+      if (sf.isContactFeature()
+              || sequence.findIndex(sf.getBegin()) > column
               || sequence.findIndex(sf.getEnd()) < column)
       {
         it.remove();
@@ -2143,8 +2145,7 @@ public class SeqPanel extends JPanel implements MouseListener,
 
     if (copycolsel
             && av.hasHiddenColumns()
-            && (av.getAlignment().getHiddenColumns() == null || av
-                    .getAlignment().getHiddenColumns().getHiddenRegions() == null))
+            && (av.getAlignment().getHiddenColumns() == null))
     {
       System.err.println("Bad things");
     }