X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=8d8472e90a71ed8d335a99aaae3ce9946707f35f;hb=42ae188a9819c341cd345baeab442cd0606ff157;hp=c5789fe0ba3eb555cd9b318a920c3597e376baf1;hpb=de468b0bf50850a89c6a8a7acfa4ff5b689ffed1;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index c5789fe..8d8472e 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -40,7 +40,7 @@ public class OverviewPanel
   // Can set different properties in this seqCanvas than
   // main visible SeqCanvas
   SequenceRenderer sr;
-  //FeatureRenderer fr;
+  FeatureRenderer fr;
 
 
   Frame nullFrame;
@@ -57,9 +57,10 @@ public class OverviewPanel
     sr = new SequenceRenderer(av);
     sr.graphics = nullFrame.getGraphics();
     sr.renderGaps( false );
-    //fr = new FeatureRenderer(av);
-    //fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
-    //fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;
+    sr.forOverview = true;
+    fr = new FeatureRenderer(av);
+    fr.drawText = false;
+    fr.overview = true;
 
 
 
@@ -184,6 +185,14 @@ public class OverviewPanel
         return;
     }
 
+    if (av.showSequenceFeatures)
+   {
+     fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
+     fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+     fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;
+   }
+
+
     resizing = true;
 
     if ( (getSize().width > 0) && (getSize().height > 0))
@@ -229,28 +238,46 @@ public class OverviewPanel
     float sampleCol = (float) alwidth / (float) width;
     float sampleRow = (float) alheight / (float) sequencesHeight;
 
-    int lastcol=-1, lastrow=-1;
-    Color color = Color.white;
-    for (int col = 0; col < width; col++)
+    int lastcol=-1, lastrow=0;
+    Color color = Color.yellow;
+    int row, col;
+    jalview.datamodel.SequenceI sequence;
+    for (row = 0; row < sequencesHeight; row++)
     {
-      for (int row = 0; row < sequencesHeight; row++)
+      sequence = av.getAlignment().getSequenceAt(lastrow);
+      for (col = 0; col < width; col++)
       {
         if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
         {
-          mg.setColor(color);
-          mg.fillRect(col,row,1,1);
+          mg.drawLine(col, row, col, row);
           continue;
         }
 
         lastrow = (int)(row*sampleRow);
         lastcol = (int)(col*sampleCol);
 
-        color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);
+        if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)
+        {
+
+          color = sr.findSequenceColour(sequence, lastcol);
+
+          if (av.showSequenceFeatures)
+            color = fr.findFeatureColour(color,
+                                        sequence,
+                                        lastcol);
+        }
 
         mg.setColor(color);
-        mg.fillRect(col,row,1,1);
+        mg.drawLine(col,row,col,row);
 
-        if (av.conservation != null)
+      }
+    }
+
+    if (av.conservation != null)
+    {
+      for (col = 0; col < width; col++)
+      {
+        lastcol = (int) (col * sampleCol);
         {
           mg.translate(col, sequencesHeight);
           ap.annotationPanel.drawGraph(mg, av.conservation,
@@ -258,11 +285,13 @@ public class OverviewPanel
                                        graphHeight,
                                        (int) (col * sampleCol),
                                        (int) (col * sampleCol) + 1);
-          mg.translate(-col, -sequencesHeight);
+          mg.translate( -col, -sequencesHeight);
         }
       }
     }
 
+
+
     System.gc();
 
     resizing = false;