X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=cf7db6c302f14dd2200535466b7bb78dd044d2df;hb=8004878db16757b62ee2c35738506bc4509428cf;hp=69db54d3b00590f249de23480df4944af244a9ab;hpb=8220e64aa2718d0f81f39a93df46c3f2265a9fa4;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 69db54d..cf7db6c 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -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)
@@ -98,17 +101,19 @@ public class SequenceRenderer implements RendererI
     int charOffset=0;
     char s;
     // Need to find the sequence position here.
+
+    graphics.setColor(Color.black);
+    String sequence  = seq.getSequence();
     for (int i = start; i <= end; i++)
     {
-        if(i<seq.getLength())
-          s = seq.getSequence().charAt(i);
+        if(i<sequence.length())
+          s = sequence.charAt(i);
         else
           s = ' ';
 
         if(!renderGaps && jalview.util.Comparison.isGap(s))
           continue;
 
-        graphics.setColor(Color.black);
 
         if (inCurrentSequenceGroup(i))
         {
@@ -129,13 +134,18 @@ 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);
            }
         }
 
-      charOffset =  (width - fm.charWidth(s))/2;
-      graphics.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
-    }
+          charOffset =  (width - fm.charWidth(s))/2;
+          graphics.drawString(String.valueOf(s),
+                              charOffset + x1 + width * (i - start),
+                              y1 + height - pady);
+        }
 
 
   }
@@ -170,7 +180,7 @@ public class SequenceRenderer implements RendererI
        if(i<seq.getLength())
           s = seq.getSequence().charAt(i);
 
-      charOffset =  (width - fm.charWidth(s))/2;
+     charOffset =  (width - fm.charWidth(s))/2;
       graphics.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
     }
   }