X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=f72acae6c36cdf037c7a0836c0ab2010a49b28fb;hb=8213e48c6973494f7a6e22e1a97290520a461d1b;hp=1df6ae3b120fd2cc061650b946b8b8c7e7d015b1;hpb=a6789f8a91ca11fac840b958ee9207581ea4d14f;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 1df6ae3..f72acae 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.HiddenColumns.VisibleBlocksVisBoundsIterator;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -698,7 +699,7 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
 
         Iterator<Integer> it = hidden.getBoundedStartIterator(startRes,
-                endx + 1, true);
+                endx + 1);
         while (it.hasNext())
         {
           res = it.next() - startRes;
@@ -851,29 +852,23 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     else
     {
       int screenY = 0;
-      final int screenYMax = endRes - startRes;
-      int blockStart = startRes;
-      int blockEnd = endRes;
+      int blockStart;
+      int blockEnd;
 
-      for (int[] region : av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy())
-      {
-        int hideStart = region[0];
-        int hideEnd = region[1];
+      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+      VisibleBlocksVisBoundsIterator regions = (VisibleBlocksVisBoundsIterator) hidden
+              .getVisibleBlocksIterator(startRes, endRes, true);
 
-        if (hideStart <= blockStart)
-        {
-          blockStart += (hideEnd - hideStart) + 1;
-          continue;
-        }
+      while (regions.hasNext())
+      {
+        int[] region = regions.next();
+        blockEnd = region[1];
+        blockStart = region[0];
 
         /*
          * 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 * charWidth, 0);
 
         draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
@@ -882,7 +877,8 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
          * draw the downline of the hidden column marker (ScalePanel draws the
          * triangle on top) if we reached it
          */
-        if (av.getShowHiddenMarkers() && blockEnd == hideStart - 1)
+        if (av.getShowHiddenMarkers()
+                && (regions.hasNext() || regions.endsAtHidden()))
         {
           g1.setColor(Color.blue);
 
@@ -893,23 +889,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
         g1.translate(-screenY * charWidth, 0);
         screenY += blockEnd - blockStart + 1;
-        blockStart = hideEnd + 1;
-
-        if (screenY > screenYMax)
-        {
-          // already rendered last block
-          return;
-        }
-      }
-
-      if (screenY <= screenYMax)
-      {
-        // remaining visible region to render
-        blockEnd = blockStart + screenYMax - screenY;
-        g1.translate(screenY * charWidth, 0);
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, yOffset);
-
-        g1.translate(-screenY * charWidth, 0);
       }
     }
 
@@ -1121,22 +1100,17 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
     {
       // package into blocks of visible columns
       int screenY = 0;
-      int blockStart = startRes;
-      int blockEnd = endRes;
+      int blockStart;
+      int blockEnd;
 
-      for (int[] region : av.getAlignment().getHiddenColumns()
-              .getHiddenColumnsCopy())
+      HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+      VisibleBlocksVisBoundsIterator regions = (VisibleBlocksVisBoundsIterator) hidden
+              .getVisibleBlocksIterator(startRes, endRes, true);
+      while (regions.hasNext())
       {
-        int hideStart = region[0];
-        int hideEnd = region[1];
-
-        if (hideStart <= blockStart)
-        {
-          blockStart += (hideEnd - hideStart) + 1;
-          continue;
-        }
-
-        blockEnd = hideStart - 1;
+        int[] region = regions.next();
+        blockEnd = region[1];
+        blockStart = region[0];
 
         g.translate(screenY * charWidth, 0);
         drawPartialGroupOutline(g, group,
@@ -1144,24 +1118,6 @@ public class SeqCanvas extends JComponent implements ViewportListenerI
 
         g.translate(-screenY * charWidth, 0);
         screenY += blockEnd - blockStart + 1;
-        blockStart = hideEnd + 1;
-
-        if (screenY > (endRes - startRes))
-        {
-          // already rendered last block
-          break;
-        }
-      }
-
-      if (screenY <= (endRes - startRes))
-      {
-        // remaining visible region to render
-        blockEnd = blockStart + (endRes - startRes) - screenY;
-        g.translate(screenY * charWidth, 0);
-        drawPartialGroupOutline(g, group,
-                blockStart, blockEnd, startSeq, endSeq, offset);
-        
-        g.translate(-screenY * charWidth, 0);
       }
     }
   }