X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=618ec8a10a8b2b474e6cf36ed90161afc17755ef;hb=df1c58f9669c477db082016aa919d6c6cc9da071;hp=fe8122aece254fe8f63c8b908d4de66b8aefc5d3;hpb=5099540b9d747283036a752baa5ea246e8a5e855;p=jalview.git

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index fe8122a..618ec8a 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -35,8 +35,7 @@ public class SeqCanvas
 
   AlignViewport av;
 
-  boolean displaySearch = false;
-  int[] searchResults = null;
+  SearchResults searchResults = null;
 
   int chunkHeight;
   int chunkWidth;
@@ -155,11 +154,13 @@ public class SeqCanvas
 
   public void fastPaint(int horizontal, int vertical)
   {
-    if (gg == null)
+    if (fastPaint || gg == null)
     {
+      repaint();
       return;
     }
 
+    fastPaint = true;
     gg.copyArea(horizontal * av.charWidth,
                 vertical * av.charHeight,
                 imgWidth,
@@ -169,6 +170,7 @@ public class SeqCanvas
 
     int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq,
         transX = 0, transY = 0;
+
     if (horizontal > 0) // scrollbar pulled right, image to the left
     {
       transX = (er - sr - horizontal) * av.charWidth;
@@ -202,12 +204,9 @@ public class SeqCanvas
 
     gg.translate(transX, transY);
 
-    gg.setColor(Color.white);
-    gg.fillRect(0, 0, (er - sr + 1) * av.charWidth, (es - ss) * av.charHeight);
     drawPanel(gg, sr, er, ss, es, sr, ss, 0);
     gg.translate( -transX, -transY);
 
-    fastPaint = true;
     repaint();
 
   }
@@ -229,7 +228,6 @@ public class SeqCanvas
 
   public void paint(Graphics g)
   {
-    sr.renderGaps(av.renderGaps);
 
     if (fastPaint)
     {
@@ -449,12 +447,27 @@ public class SeqCanvas
 
     if (av.showSequenceFeatures)
     {
-      fr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq), x1, x2,
+      fr.drawSequence(g, nextSeq, x1, x2,
                       (x1 - startx) * av.charWidth,
                       offset +
                       (i - starty) * av.charHeight,
                       av.charWidth, av.charHeight);
     }
+    /// Highlight search Results once all sequences have been drawn
+   //////////////////////////////////////////////////////////
+   if (searchResults != null)
+   {
+     int[] visibleResults = searchResults.getResults(nextSeq, x1, x2);
+     if (visibleResults != null)
+       for (int r = 0; r < visibleResults.length; r += 2)
+       {
+         sr.drawHighlightedText(nextSeq, visibleResults[r],
+                                visibleResults[r + 1],
+                                (visibleResults[r] - startx) * av.charWidth,
+                                offset + ( (i - starty) * av.charHeight),
+                                av.charWidth, av.charHeight);
+       }
+   }
   }
 
     /////////////////////////////////////
@@ -614,58 +627,10 @@ public class SeqCanvas
         }
         while (groupIndex < groups.size());
     }
-
-    /// Highlight search Results once all sequences have been drawn
-    //////////////////////////////////////////////////////////
-    if (displaySearch)
-    {
-      for (int r = 0; r < searchResults.length; r += 3)
-      {
-        int searchSeq = searchResults[r];
-
-        if (searchSeq >= y1 && searchSeq < y2)
-        {
-          SequenceI seq = av.getAlignment().getSequenceAt(searchSeq);
-
-          int searchStart = seq.findIndex(searchResults[r + 1]) - 1;
-          int searchEnd = seq.findIndex(searchResults[r + 2]) - 1;
-
-          SequenceRenderer ssr = (SequenceRenderer) sr;
-          if (searchStart < x1)
-          {
-            searchStart = x1;
-          }
-          if (searchEnd > x2)
-          {
-            searchEnd = x2;
-          }
-
-          ssr.drawHighlightedText(seq,
-                                  searchStart,
-                                  searchEnd,
-                                  (searchStart - startx) * av.charWidth,
-                                  offset +
-                                  (searchSeq-starty)*av.charHeight,
-                                  av.charWidth,
-                                  av.charHeight);
-        }
-      }
-    }
-
   }
 
-  public void highlightSearchResults(int[] results)
+  public void highlightSearchResults(SearchResults results)
   {
-    // results are in the order sequence, startRes, endRes
-    if (results == null)
-    {
-      displaySearch = false;
-    }
-    else
-    {
-      displaySearch = true;
-    }
-
     searchResults = results;
 
     repaint();