Overview displays features

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

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 9c3e908..57150c3 100755 (executable)
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -58,8 +58,8 @@ public class OverviewPanel
     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
+    fr.drawText = false;\r
+\r
 \r
 \r
     // scale the initial size of overviewpanel to shape of alignment\r
@@ -183,6 +183,10 @@ public class OverviewPanel
         return;\r
     }\r
 \r
+    if (av.showSequenceFeatures)\r
+      fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;\r
+\r
+\r
     resizing = true;\r
 \r
     if ( (getSize().width > 0) && (getSize().height > 0))\r
@@ -229,18 +233,29 @@ public class OverviewPanel
     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
+    Color color = Color.yellow;\r
+    int row, col;\r
+    for (col = 0; col < width; col++)\r
     {\r
-      for (int row = 0; row < sequencesHeight; row++)\r
+      for (row = 0; row < sequencesHeight; row++)\r
       {\r
         if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
         {\r
-          mg.setColor(color);\r
-          mg.fillRect(col,row,1,1);\r
+          mg.drawLine(col, row, col, row);\r
           continue;\r
         }\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
+          mg.translate( -col, -sequencesHeight);\r
+        }\r
+\r
         lastrow = (int)(row*sampleRow);\r
         lastcol = (int)(col*sampleCol);\r
 \r
@@ -248,29 +263,20 @@ public class OverviewPanel
         {\r
           color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);\r
 \r
+\r
           if (av.showSequenceFeatures)\r
             color = fr.findFeatureColour(color,\r
-                                         av.alignment.getSequenceAt(lastrow),\r
+                                        av.alignment.getSequenceAt(lastrow),\r
                                          lastcol);\r
         }\r
 \r
-\r
         mg.setColor(color);\r
-        mg.fillRect(col,row,1,1);\r
+        mg.drawLine(col,row,col,row);\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
-          mg.translate(-col, -sequencesHeight);\r
-        }\r
       }\r
     }\r
 \r
+\r
     System.gc();\r
 \r
     resizing = false;\r