after merge

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 7910f2d..23bfd09 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -39,7 +39,8 @@ public class OverviewPanel
 \r
   // Can set different properties in this seqCanvas than\r
   // main visible SeqCanvas\r
-  SeqCanvas overviewSeq;\r
+  SequenceRenderer sr;\r
+  //FeatureRenderer fr;\r
 \r
 \r
   Frame nullFrame;\r
@@ -52,9 +53,14 @@ public class OverviewPanel
     nullFrame = new Frame();\r
     nullFrame.addNotify();\r
 \r
-    overviewSeq = new SeqCanvas(av);\r
-    overviewSeq.isOverview = true;\r
-    overviewSeq.sr.renderGaps = false;\r
+\r
+    sr = new SequenceRenderer(av);\r
+    sr.graphics = nullFrame.getGraphics();\r
+    sr.renderGaps( false );\r
+    //fr = new FeatureRenderer(av);\r
+    //fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\r
+    //fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;\r
+\r
 \r
 \r
     // scale the initial size of overviewpanel to shape of alignment\r
@@ -231,31 +237,40 @@ public class OverviewPanel
     float sampleCol = (float) alwidth / (float) width;\r
     float sampleRow = (float) alheight / (float) sequencesHeight;\r
 \r
+    int lastcol=-1, lastrow=-1;\r
+    Color color = Color.white;\r
     for (int col = 0; col < width; col++)\r
     {\r
       for (int row = 0; row < sequencesHeight; row++)\r
       {\r
-        overviewSeq.drawPanel(mg,\r
-                                        (int) (col * sampleCol),\r
-                                        (int) (col * sampleCol),\r
-                                        (int) (row * sampleRow),\r
-                                        (int) (row * sampleRow) + 1,\r
-                                        (int) (col * sampleCol),\r
-                                        (int) (row * sampleRow), 0);\r
-        mg.translate(0, 1);\r
+        if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
+        {\r
+          mg.setColor(color);\r
+          mg.fillRect(col,row,1,1);\r
+          continue;\r
+        }\r
+\r
+        lastrow = (int)(row*sampleRow);\r
+        lastcol = (int)(col*sampleCol);\r
+\r
+        color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);\r
+\r
+        mg.setColor(color);\r
+        mg.fillRect(col,row,1,1);\r
 \r
         if (av.conservation != null)\r
+        {\r
+          mg.translate(col, sequencesHeight);\r
           ap.annotationPanel.drawGraph(mg, av.conservation,\r
                                        (int) (sampleCol) + 1,\r
                                        graphHeight,\r
                                        (int) (col * sampleCol),\r
                                        (int) (col * sampleCol) + 1);\r
-\r
+          mg.translate(-col, -sequencesHeight);\r
+        }\r
       }\r
-      mg.translate(0, -sequencesHeight);\r
-      mg.translate(1, 0);\r
+    }\r
 \r
-        }\r
     System.gc();\r
 \r
     resizing = false;\r