X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=54785ef0e4bbc42237350d9ef5367ecbe4e1147b;hb=00f6edbbdddf16f77142e98e375363675be807fe;hp=5b5a392f5ed445a6de169df6fe24f77421d3d4e6;hpb=e71a5d2b1e0025a8e23eb637f12f6f5665c91feb;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 5b5a392..54785ef 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -35,7 +35,7 @@ public class SequenceRenderer implements RendererI
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
    if (cs != null)
-       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i, av.getConsensus(false));
+       resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
    else
        resBoxColour = Color.white;
   }
@@ -46,18 +46,18 @@ public class SequenceRenderer implements RendererI
 
     graphics = g;
 
-    drawBoxes(seq, start, end, x1, y1, (int) width, height, pid);
+    drawBoxes(seq, start, end, x1, y1, (int) width, height);
 
     fm = g.getFontMetrics();
     drawText(seq,start,end,x1,y1,(int)width,height);
 
   }
 
-  public void drawBoxes(SequenceI seq,int start, int end, int x1, int y1, int width, int height,Vector freq) {
+  public void drawBoxes(SequenceI seq,int start, int end, int x1, int y1, int width, int height) {
     int i      = start;
     int length = seq.getLength();
 
-    int curStart = x1;
+    int curStart = -1;
     int curWidth = width;
 
     Color tempColour = null;
@@ -76,7 +76,8 @@ public class SequenceRenderer implements RendererI
 
       if (resBoxColour != tempColour)
       {
-        graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+        if(tempColour!=null)
+          graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
         graphics.setColor(resBoxColour);
 
         curStart = i;
@@ -89,7 +90,9 @@ public class SequenceRenderer implements RendererI
 
       i++;
     }
-    graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
+
+
+     graphics.fillRect(x1+width*(curStart-start),y1,curWidth,height);
   }
 
   public void drawText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)
@@ -131,7 +134,10 @@ public class SequenceRenderer implements RendererI
           if(av.getColourText())
            {
              getBoxColour(av.getGlobalColourScheme(), seq, i);
-             graphics.setColor(resBoxColour.darker());
+             if(av.getShowBoxes())
+              graphics.setColor(resBoxColour.darker());
+            else
+              graphics.setColor(resBoxColour);
            }
         }