X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=3f87b02aded9ca039dd04a2ec37f46ad4adfe2dc;hb=47a3f3d338d24f2a92d8249eede1ed0a6fd43d87;hp=889df36e434f454f93069a039217677291fdfd18;hpb=a0b602a4a6b25d6c1a31905f8aec55ebb9d5ec0b;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 889df36..3f87b02 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -33,6 +33,7 @@ public class SequenceRenderer
   SequenceGroup[] allGroups = null;
   Color resBoxColour;
   Graphics graphics;
+  boolean forOverview = false;
 
   public SequenceRenderer(AlignViewport av)
   {
@@ -69,42 +70,45 @@ public class SequenceRenderer
     {
       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
     }
+    else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
+    {
+        resBoxColour = Color.lightGray;
+    }
     else
     {
       resBoxColour = Color.white;
     }
+
   }
 
   public Color findSequenceColour(SequenceI seq, int i)
   {
     allGroups = av.alignment.findAllGroups(seq);
-    drawBoxes(seq, i,i, 0, 0, 1,1);
+    drawBoxes(seq, i,i, 0);
     return resBoxColour;
   }
 
   public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
-                           int start, int end, int x1, int y1, int width,
-                           int height)
+                           int start, int end,  int y1)
   {
     allGroups = sg;
 
     graphics = g;
 
-    drawBoxes(seq, start, end, x1, y1, (int) width, height);
+    drawBoxes(seq, start, end,  y1);
 
     fm = g.getFontMetrics();
-    drawText(seq, start, end, x1, y1, (int) width, height);
+    drawText(seq, start, end, y1);
 
   }
 
-  public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
-                        int width, int height)
+  public void drawBoxes(SequenceI seq, int start, int end,  int y1)
   {
     int i = start;
     int length = seq.getLength();
 
     int curStart = -1;
-    int curWidth = width;
+    int curWidth = av.charWidth;
 
     Color tempColour = null;
     while (i <= end)
@@ -130,32 +134,31 @@ public class SequenceRenderer
       {
         if (tempColour != null)
         {
-          graphics.fillRect(x1 + width * (curStart - start), y1, curWidth,
-                            height);
+          graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
+                            av.charHeight);
         }
         graphics.setColor(resBoxColour);
 
         curStart = i;
-        curWidth = width;
+        curWidth = av.charWidth;
         tempColour = resBoxColour;
 
       }
       else
       {
-        curWidth += width;
+        curWidth += av.charWidth;
       }
 
       i++;
     }
 
-    graphics.fillRect(x1 + width * (curStart - start), y1, curWidth, height);
+    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth, av.charHeight);
   }
 
-  public void drawText(SequenceI seq, int start, int end, int x1, int y1,
-                       int width, int height)
+  public void drawText(SequenceI seq, int start, int end, int y1)
   {
 
-    y1 += height - height / 5;  // height/5 replaces pady
+    y1 += av.charHeight - av.charHeight / 5;  // height/5 replaces pady
 
     int charOffset = 0;
 
@@ -209,9 +212,9 @@ public class SequenceRenderer
         }
       }
 
-      charOffset = (width - fm.charWidth(s)) / 2;
+      charOffset = (av.charWidth - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s),
-                         charOffset + x1 + width * (i - start),
+                         charOffset + av.charWidth * (i - start),
                         y1 );
     }