X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=5667b6ef318d0326046b884169e0748d549b1734;hb=584c1b0136786968958e22e52b6ce51bd24511e5;hp=28c52919c44cc338940d22a325217f6fa2e80870;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 28c5291..5667b6e 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -491,16 +491,12 @@ public class SeqCanvas extends Panel implements ViewportListenerI
         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
         g.setColor(Color.blue);
         int res;
-        List<Integer> positions = hidden.findHiddenRegionPositions();
+        List<Integer> positions = hidden.findHiddenRegionPositions(startRes,
+                endx + 1);
         for (int pos : positions)
         {
           res = pos - startRes;
 
-          if (res < 0 || res > endx - startRes)
-          {
-            continue;
-          }
-
           gg.fillPolygon(
                   new int[]
                   { res * avcharWidth - avcharHeight / 4,
@@ -510,7 +506,6 @@ public class SeqCanvas extends Panel implements ViewportListenerI
                   { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
                       ypos - (avcharHeight / 2) + 8 },
                   3);
-
         }
       }
 
@@ -559,8 +554,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     return annotations.adjustPanelHeight();
   }
 
-  private void drawPanel(Graphics g1, int startRes, int endRes,
-          int startSeq, int endSeq, int offset)
+  private void drawPanel(Graphics g1, final int startRes, final int endRes,
+          final int startSeq, final int endSeq, final int offset)
   {
 
     if (!av.hasHiddenColumns())
@@ -569,8 +564,8 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     }
     else
     {
-
       int screenY = 0;
+      final int screenYMax = endRes - startRes;
       int blockStart = startRes;
       int blockEnd = endRes;
 
@@ -588,13 +583,22 @@ public class SeqCanvas extends Panel implements ViewportListenerI
             continue;
           }
 
-          blockEnd = hideStart - 1;
+          /*
+           * draw up to just before the next hidden region, or the end of
+           * the visible region, whichever comes first
+           */
+          blockEnd = Math.min(hideStart - 1, blockStart + screenYMax
+                  - screenY);
 
           g1.translate(screenY * avcharWidth, 0);
 
           draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
 
-          if (av.getShowHiddenMarkers())
+          /*
+           * draw the downline of the hidden column marker (ScalePanel draws the
+           * triangle on top) if we reached it
+           */
+          if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
           {
             g1.setColor(Color.blue);
             g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
@@ -607,14 +611,14 @@ public class SeqCanvas extends Panel implements ViewportListenerI
           screenY += blockEnd - blockStart + 1;
           blockStart = hideEnd + 1;
 
-          if (screenY > (endRes - startRes))
+          if (screenY > screenYMax)
           {
             // already rendered last block
             return;
           }
         }
       }
-      if (screenY <= (endRes - startRes))
+      if (screenY <= screenYMax)
       {
         // remaining visible region to render
         blockEnd = blockStart + (endRes - startRes) - screenY;