X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=7ffac1e9da0eab40d69def91c86ddd147cc832ae;hb=9807ea8cc4e867378c52d51b832168d4bc611d29;hp=3662ec298f88f3d1b8293faf61951b5f37b92c3e;hpb=9c5d69ef1e102b1eac18ec13c362522f40c9000d;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 3662ec2..7ffac1e 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -65,9 +65,10 @@ public class OverviewPanel extends JPanel implements Runnable
 
         sr = new SequenceRenderer(av);
         sr.renderGaps( false );
+        sr.forOverview = true;
         fr = new FeatureRenderer(av);
-        fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
-        fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;
+        fr.overview = true;
+
 
         // scale the initial size of overviewpanel to shape of alignment
         float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();
@@ -244,6 +245,14 @@ public class OverviewPanel extends JPanel implements Runnable
     {
         miniMe = null;
 
+       if (av.showSequenceFeatures)
+       {
+         fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
+         fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+         fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
+         fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;
+       }
+
         int alwidth = av.alignment.getWidth();
         int alheight = av.alignment.getHeight();
 
@@ -267,33 +276,46 @@ public class OverviewPanel extends JPanel implements Runnable
         float sampleRow = (float) alheight / (float) sequencesHeight;
 
         int lastcol=-1, lastrow=-1;
-        Color color = Color.white;
-        for (int col = 0; col < width; col++)
+        int color = Color.white.getRGB();
+        int row, col;
+        for (row = 0; row < sequencesHeight; row++)
         {
-          for (int row = 0; row < sequencesHeight; row++)
-          {
+            for (col = 0; col < width; col++)
+            {
             if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
             {
-              miniMe.setRGB(col,row,color.getRGB());
+              miniMe.setRGB(col,row,color);
               continue;
             }
 
             lastrow = (int)(row*sampleRow);
             lastcol = (int)(col*sampleCol);
 
-            color = sr.getResidueBoxColour(
-                av.alignment.getSequenceAt(lastrow), lastcol);
-
-            if(av.showSequenceFeatures)
+            if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)
             {
-              color = fr.findFeatureColour(color,
-                                                       av.alignment.getSequenceAt(lastrow),
-                                                       lastcol);
-            }
+             color = sr.getResidueBoxColour(
+                av.alignment.getSequenceAt(lastrow), lastcol).getRGB();
+
+             if(av.showSequenceFeatures)
+                 color = fr.findFeatureColour(color,  lastrow, lastcol);
+
+             }
+             else
+             {
+               color = -1; //White
+             }
 
-            miniMe.setRGB(col,row,color.getRGB());
+            miniMe.setRGB(col,row,color);
 
-            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,
@@ -301,11 +323,10 @@ public class OverviewPanel extends JPanel implements Runnable
                                            graphHeight,
                                            (int) (col * sampleCol),
                                            (int) (col * sampleCol) + 1);
-              mg.translate(-col, -sequencesHeight);
+              mg.translate( -col, -sequencesHeight);
             }
           }
         }
-
         System.gc();
 
         resizing = false;