X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=04defb793cc6d747a095eaddd56f1596b8e5c6bb;hb=82483c09d45298e6f93a7d3d2b537598cc0451b5;hp=e786b114c389cbface8fb50d94108fe81535f551;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index e786b11..04defb7 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -76,7 +76,7 @@ public class SequenceRenderer
   {
     if (cs != null)
     {
-      resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+      resBoxColour = cs.findColour(seq.getCharAt(i), i);
     }
     else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
     {
@@ -99,6 +99,9 @@ public class SequenceRenderer
   public void drawSequence(SequenceI seq, SequenceGroup[] sg,
                            int start, int end,  int y1)
   {
+    if(seq==null)
+      return;
+
     allGroups = sg;
 
     drawBoxes(seq, start, end,  y1);
@@ -164,6 +167,14 @@ public class SequenceRenderer
 
   public void drawText(SequenceI seq, int start, int end, int y1)
   {
+   Font boldFont = null;
+   boolean bold = false;
+   if(av.upperCasebold)
+   {
+     boldFont = new Font(av.getFont().getName(), Font.BOLD, av.charHeight);
+
+     graphics.setFont(av.getFont());
+   }
 
     y1 += av.charHeight - av.charHeight / 5;  // height/5 replaces pady
 
@@ -219,6 +230,26 @@ public class SequenceRenderer
         }
       }
 
+      if (av.upperCasebold)
+      {
+        fm = graphics.getFontMetrics();
+        if ('A' <= s && s <= 'Z')
+        {
+          if(!bold)
+          {
+
+            graphics.setFont(boldFont);
+          }
+          bold = true;
+        }
+        else if(bold)
+        {
+          graphics.setFont(av.font);
+          bold = false;
+        }
+
+      }
+
       charOffset = (av.charWidth - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s),
                          charOffset + av.charWidth * (i - start),
@@ -262,7 +293,7 @@ public class SequenceRenderer
       {
         if (i < seq.getLength())
         {
-          s = seq.getSequence().charAt(i);
+          s = seq.getCharAt(i);
         }
 
         charOffset = (av.charWidth - fm.charWidth(s)) / 2;