X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=96eb6b98ed49d548f95be0c449a257495393dda3;hb=8c0db65da2a81d3cae2bb5cbde02b1af407061b8;hp=74a9f7f4e0087cb1ddebe57cde70067bff58f7d1;hpb=14aeb3c39e60a604bdeed33949ba05e0c8c8be5d;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 74a9f7f..96eb6b9 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -25,6 +25,7 @@ import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
 import jalview.renderer.ScaleRenderer;
 import jalview.renderer.ScaleRenderer.ScaleMark;
 import jalview.viewmodel.AlignmentViewport;
@@ -130,16 +131,9 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       startx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(startx);
+              .visibleToAbsoluteColumn(startx);
       endx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(endx);
-    }
-
-    int maxwidth = av.getAlignment().getWidth();
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth) - 1;
+              .visibleToAbsoluteColumn(endx);
     }
 
     // WEST SCALE
@@ -180,7 +174,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     if (av.hasHiddenColumns())
     {
       endx = av.getAlignment().getHiddenColumns()
-              .adjustForHiddenColumns(endx);
+              .visibleToAbsoluteColumn(endx);
     }
 
     SequenceI seq;
@@ -449,13 +443,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     int endx;
     int ypos = hgap;
   
-    int maxwidth = av.getAlignment().getWidth();
-  
-    if (av.hasHiddenColumns())
-    {
-      maxwidth = av.getAlignment().getHiddenColumns()
-              .findColumnPosition(maxwidth);
-    }
+    int maxwidth = av.getAlignment().getVisibleWidth();
   
     while ((ypos <= canvasHeight) && (startRes < maxwidth))
     {
@@ -491,7 +479,7 @@ public class SeqCanvas extends Panel implements ViewportListenerI
         HiddenColumns hidden = av.getAlignment().getHiddenColumns();
         g.setColor(Color.blue);
         int res;
-        Iterator<Integer> it = hidden.getBoundedStartIterator(startRes,
+        Iterator<Integer> it = hidden.getStartRegionIterator(startRes,
                 endx + 1);
         while (it.hasNext())
         {
@@ -560,30 +548,23 @@ public class SeqCanvas extends Panel implements ViewportListenerI
     else
     {
       int screenY = 0;
-      final int screenYMax = endRes - startRes;
-      int blockStart = startRes;
-      int blockEnd = endRes;
+      int blockStart;
+      int blockEnd;
 
       HiddenColumns hidden = av.getAlignment().getHiddenColumns();
-      Iterator<int[]> regions = hidden.iterator();
+      VisibleContigsIterator regions = hidden
+              .getVisContigsIterator(startRes, endRes + 1, true);
+
       while (regions.hasNext())
       {
         int[] region = regions.next();
-        int hideStart = region[0];
-        int hideEnd = region[1];
-
-        if (hideStart <= blockStart)
-        {
-          blockStart += (hideEnd - hideStart) + 1;
-          continue;
-        }
+        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 * avcharWidth, 0);
 
         draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
@@ -592,7 +573,8 @@ public class SeqCanvas extends Panel 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);
           g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
@@ -602,23 +584,6 @@ public class SeqCanvas extends Panel implements ViewportListenerI
 
         g1.translate(-screenY * avcharWidth, 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 * avcharWidth, 0);
-        draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
-        g1.translate(-screenY * avcharWidth, 0);
       }
     }
   }
@@ -876,15 +841,37 @@ public class SeqCanvas extends Panel implements ViewportListenerI
   {
     String eventName = evt.getPropertyName();
 
+    if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
+    {
+      fastPaint = true;
+      repaint();
+      return;
+    }
+    else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
+    {
+      fastPaint = false;
+      repaint();
+      return;
+    }
+
     if (!av.getWrapAlignment())
     {
       int scrollX = 0;
-      if (eventName.equals(ViewportRanges.STARTRES))
+      if (eventName.equals(ViewportRanges.STARTRES)
+              || eventName.equals(ViewportRanges.STARTRESANDSEQ))
       {
         // Make sure we're not trying to draw a panel
         // larger than the visible window
+        if (eventName.equals(ViewportRanges.STARTRES))
+        {
+          scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+        }
+        else
+        {
+          scrollX = ((int[]) evt.getNewValue())[0]
+                  - ((int[]) evt.getOldValue())[0];
+        }
         ViewportRanges vpRanges = av.getRanges();
-        scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
         int range = vpRanges.getEndRes() - vpRanges.getStartRes();
         if (scrollX > range)
         {
@@ -911,6 +898,10 @@ public class SeqCanvas extends Panel implements ViewportListenerI
         // scroll
         fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
       }
+      else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+      {
+        fastPaint(scrollX, 0);
+      }
     }
   }