X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=7ffac1e9da0eab40d69def91c86ddd147cc832ae;hb=9807ea8cc4e867378c52d51b832168d4bc611d29;hp=635e4550591766e076fb979312246ccb701981fe;hpb=2ffe2deedb1527c067060646055bddd18d41d367;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 635e455..7ffac1e 100755
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -49,7 +49,8 @@ public class OverviewPanel extends JPanel implements Runnable
 
     // Can set different properties in this seqCanvas than
     // main visible SeqCanvas
-    SeqCanvas overviewSeq;
+    SequenceRenderer sr;
+    FeatureRenderer fr;
 
     /**
      * Creates a new OverviewPanel object.
@@ -62,14 +63,17 @@ public class OverviewPanel extends JPanel implements Runnable
         this.ap = ap;
         setLayout(null);
 
-        overviewSeq = new SeqCanvas(av);
-        overviewSeq.isOverview = true;
-        overviewSeq.sr.renderGaps = false;
+        sr = new SequenceRenderer(av);
+        sr.renderGaps( false );
+        sr.forOverview = true;
+        fr = new FeatureRenderer(av);
+        fr.overview = true;
+
 
         // scale the initial size of overviewpanel to shape of alignment
         float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();
 
-        if(av.vconsensus==null)
+        if(av.conservation==null)
           graphHeight = 0;
 
 
@@ -241,6 +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();
 
@@ -257,36 +269,64 @@ public class OverviewPanel extends JPanel implements Runnable
 
 
         Graphics mg = miniMe.getGraphics();
+        mg.setColor(Color.orange);
+        mg.fillRect(0,0,width, miniMe.getHeight());
 
         float sampleCol = (float) alwidth / (float) width;
         float sampleRow = (float) alheight / (float) sequencesHeight;
 
-        for (int col = 0; col < width; col++)
+        int lastcol=-1, lastrow=-1;
+        int color = Color.white.getRGB();
+        int row, col;
+        for (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);
+              continue;
+            }
+
+            lastrow = (int)(row*sampleRow);
+            lastcol = (int)(col*sampleCol);
+
+            if(av.alignment.getSequenceAt(lastrow).getLength()>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);
+
+
+          }
+        }
+
+        if (av.conservation != null)
         {
-          for (int row = 0; row < sequencesHeight; row++)
+          for (col = 0; col < width; col++)
           {
-            overviewSeq.drawPanel(mg,
-                                            (int) (col * sampleCol),
-                                            (int) (col * sampleCol),
-                                            (int) (row * sampleRow),
-                                            (int) (row * sampleRow) + 1,
-                                            (int) (col * sampleCol),
-                                            (int) (row * sampleRow), 0);
-            mg.translate(0, 1);
-
-            if (av.conservation != null)
+            lastcol = (int) (col * sampleCol);
+            {
+              mg.translate(col, sequencesHeight);
               ap.annotationPanel.drawGraph(mg, av.conservation,
                                            (int) (sampleCol) + 1,
                                            graphHeight,
                                            (int) (col * sampleCol),
                                            (int) (col * sampleCol) + 1);
-
+              mg.translate( -col, -sequencesHeight);
+            }
           }
-          mg.translate(0, -sequencesHeight);
-          mg.translate(1, 0);
-
         }
-
         System.gc();
 
         resizing = false;