New implementation for holding search results

[jalview.git] / src / jalview / appletgui / SeqCanvas.java

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