X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=3349825bcbe82581726bcc269f80dbe991cb2c43;hb=197359781e7142ec6bcb53740831fc626c4675cd;hp=ac9368316e96238cb3ac0027b04515b4f32c99da;hpb=eb77addf49f8957e88b61f07ce36414c6619a221;p=jalview.git

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index ac93683..3349825 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -286,6 +286,25 @@ public class SeqPanel extends JPanel implements MouseListener,
     {
       seqCanvas.cursorX += dx;
       seqCanvas.cursorY += dy;
+      if (av.hasHiddenColumns && !av.colSel.isVisible(seqCanvas.cursorX))
+      {
+        int original = seqCanvas.cursorX - dx;
+        int maxWidth = av.alignment.getWidth();
+
+        while(!av.colSel.isVisible(seqCanvas.cursorX)
+              && seqCanvas.cursorX<maxWidth
+              && seqCanvas.cursorX>0)
+        {
+          seqCanvas.cursorX += dx;
+        }
+
+        if(seqCanvas.cursorX>=maxWidth
+           || !av.colSel.isVisible(seqCanvas.cursorX) )
+        {
+          seqCanvas.cursorX = original;
+        }
+      }
+
       scrollToVisible();
     }
 
@@ -319,12 +338,12 @@ public class SeqPanel extends JPanel implements MouseListener,
         }
         if (!av.wrapAlignment)
         {
-          while (seqCanvas.cursorX < av.startRes)
+          while (seqCanvas.cursorX < av.colSel.adjustForHiddenColumns(av.startRes))
           {
             if (!ap.scrollRight(false))
               break;
           }
-          while (seqCanvas.cursorX > av.endRes)
+          while (seqCanvas.cursorX > av.colSel.adjustForHiddenColumns(av.endRes))
           {
             if (!ap.scrollRight(true))
               break;
@@ -1221,7 +1240,7 @@ public class SeqPanel extends JPanel implements MouseListener,
                               features[0].getEnd());
           seqCanvas.highlightSearchResults(highlight);
         }
-        if(features!=null)
+        if(features!=null && features.length>0)
         {
           seqCanvas.getFeatureRenderer().amendFeatures(
               new SequenceI[]
@@ -1430,7 +1449,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
           if (stretchGroup.cs instanceof Blosum62ColourScheme
               || stretchGroup.cs instanceof PIDColourScheme
-              || stretchGroup.cs.conservationApplied())
+              || stretchGroup.cs.conservationApplied()
+              || stretchGroup.cs.getThreshold()>0)
             stretchGroup.recalcConservation();
 
           if (stretchGroup.cs.conservationApplied())