X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=a4b7f06bef72dfbd9d385662896aaecb5ef6c41e;hb=bf2bf43c980b18a26b724d2a2d51dddc1a79a185;hp=57150c39777d1535d414adb7999912cd3aed54fd;hpb=d355ad106f73e0de0abc3fb3f375af4eaf352591;p=jalview.git

diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 57150c3..a4b7f06 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -57,8 +57,9 @@ public class OverviewPanel
     sr = new SequenceRenderer(av);
     sr.graphics = nullFrame.getGraphics();
     sr.renderGaps( false );
+    sr.forOverview = true;
     fr = new FeatureRenderer(av);
-    fr.drawText = false;
+    fr.overview = true;
 
 
 
@@ -184,8 +185,10 @@ public class OverviewPanel
     }
 
     if (av.showSequenceFeatures)
-      fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;
-
+   {
+     fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
+     fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+   }
 
     resizing = true;
 
@@ -212,6 +215,14 @@ public class OverviewPanel
     int alwidth = av.alignment.getWidth();
     int alheight = av.alignment.getHeight();
 
+    if (av.showSequenceFeatures)
+    {
+      fr.renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+      fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
+      fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+      fr.sequenceFeatures = ap.seqPanel.seqCanvas.getFeatureRenderer().sequenceFeatures;
+    }
+
     if (getSize().width > 0 && getSize().height > 0)
     {
       width = getSize().width;
@@ -232,50 +243,78 @@ public class OverviewPanel
     float sampleCol = (float) alwidth / (float) width;
     float sampleRow = (float) alheight / (float) sequencesHeight;
 
-    int lastcol=-1, lastrow=-1;
+    int lastcol=0, lastseq=0;
+    int xstart=0, ystart=0;
     Color color = Color.yellow;
-    int row, col;
-    for (col = 0; col < width; col++)
+    int col, sameRow = 0, sameCol = 0;
+    jalview.datamodel.SequenceI sequence;
+
+    for (int row = 0; row <= sequencesHeight; row++)
     {
-      for (row = 0; row < sequencesHeight; row++)
+      if((int)(row*sampleRow)==lastseq)
       {
-        if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)
-        {
-          mg.drawLine(col, row, col, row);
-          continue;
-        }
+        sameRow ++;
+        continue;
+      }
 
-        if (av.conservation != null)
+      sequence = av.getAlignment().getSequenceAt(lastseq);
+
+      for (col = 0; col < width; col++)
+      {
+        if((int)(col*sampleCol) == lastcol)
         {
-          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);
+          sameCol ++;
+          continue;
         }
 
-        lastrow = (int)(row*sampleRow);
         lastcol = (int)(col*sampleCol);
 
-        if(av.alignment.getSequenceAt(lastrow).getLength()>lastcol)
+        if(sequence.getLength()>lastcol)
         {
-          color = sr.findSequenceColour(av.alignment.getSequenceAt(lastrow), lastcol);
-
+          color = sr.findSequenceColour(sequence, lastcol);
 
           if (av.showSequenceFeatures)
             color = fr.findFeatureColour(color,
-                                        av.alignment.getSequenceAt(lastrow),
-                                         lastcol);
+                                        sequence,
+                                        lastcol);
         }
+        else
+          color = color.white;
 
         mg.setColor(color);
-        mg.drawLine(col,row,col,row);
+        if (sameCol == 1 && sameRow == 1)
+          mg.drawLine(xstart, ystart, xstart, ystart);
+        else
+          mg.fillRect(xstart, ystart, sameCol, sameRow);
 
+        xstart = col;
+        sameCol = 1;
       }
+
+
+      lastseq = (int)(row*sampleRow);
+      ystart = row;
+      sameRow = 1;
     }
 
+    if (av.conservation != null)
+    {
+      for (col = 0; col < width; col++)
+      {
+        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);
+        }
+      }
+    }
+
+
 
     System.gc();