X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=4bbaa5f4bd21dcc7d2dc28fdd48b03c9d040fd4d;hb=d065bc916cb63af83cdab7319f5177a855724aba;hp=b96c49189127c89c003ce272cda6303098fe204c;hpb=5e8ec77d921ff2d604811e5e4ba7e9211b0f48de;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index b96c491..4bbaa5f 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -37,6 +37,7 @@ import java.awt.Graphics;
 import java.awt.Image;
 import java.awt.Panel;
 import java.beans.PropertyChangeEvent;
+import java.util.List;
 
 public class SeqCanvas extends Panel implements ViewportListenerI
 {
@@ -487,11 +488,10 @@ public class SeqCanvas extends Panel implements ViewportListenerI
         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
         g.setColor(Color.blue);
         int res;
-        for (int i = 0; i < hidden.getHiddenRegions()
-                .size(); i++)
+        List<Integer> positions = hidden.findHiddenRegionPositions();
+        for (int pos : positions)
         {
-          res = hidden.findHiddenRegionPosition(i)
-                  - startRes;
+          res = pos - startRes;
 
           if (res < 0 || res > endx - startRes)
           {
@@ -552,8 +552,8 @@ 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())
@@ -562,15 +562,15 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     }
     else
     {
-
       int screenY = 0;
+      final int screenYMax = endRes - startRes;
       int blockStart = startRes;
       int blockEnd = endRes;
 
       if (av.hasHiddenColumns())
       {
         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-        for (int[] region : hidden)
+        for (int[] region : hidden.getHiddenColumnsCopy())
         {
           int hideStart = region[0];
           int hideEnd = region[1];
@@ -581,13 +581,22 @@ 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,
@@ -600,14 +609,14 @@ 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;