X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FOverviewPanel.java;h=3662ec298f88f3d1b8293faf61951b5f37b92c3e;hb=43a9f559bb49f579ce153c812052c149963a99de;hp=7086a5123a712b6b36693a386c50ba24c5af088c;hpb=8878681ec11f85c050248236a96ffbcaf2f0497b;p=jalview.git

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 7086a51..3662ec2 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 +63,16 @@ 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 );
+        fr = new FeatureRenderer(av);
+        fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;
+        fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;
 
         // 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;
 
 
@@ -109,6 +112,7 @@ public class OverviewPanel extends JPanel implements Runnable
             {
                 public void mouseDragged(MouseEvent evt)
                 {
+                  if(!av.wrapAlignment)
                     doMouseDragged(evt);
                 }
             });
@@ -117,11 +121,13 @@ public class OverviewPanel extends JPanel implements Runnable
             {
                 public void mousePressed(MouseEvent evt)
                 {
+                  if(!av.wrapAlignment)
                     doMousePressed(evt);
                 }
 
                 public void mouseReleased(MouseEvent evt)
                 {
+                  if(!av.wrapAlignment)
                     doMouseReleased(evt);
                 }
             });
@@ -254,34 +260,50 @@ 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;
 
+        int lastcol=-1, lastrow=-1;
+        Color color = Color.white;
         for (int col = 0; col < width; col++)
         {
           for (int row = 0; row < sequencesHeight; row++)
           {
-            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((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
+            {
+              miniMe.setRGB(col,row,color.getRGB());
+              continue;
+            }
+
+            lastrow = (int)(row*sampleRow);
+            lastcol = (int)(col*sampleCol);
+
+            color = sr.getResidueBoxColour(
+                av.alignment.getSequenceAt(lastrow), lastcol);
+
+            if(av.showSequenceFeatures)
+            {
+              color = fr.findFeatureColour(color,
+                                                       av.alignment.getSequenceAt(lastrow),
+                                                       lastcol);
+            }
+
+            miniMe.setRGB(col,row,color.getRGB());
 
             if (av.conservation != null)
+            {
+              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();