X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=daf971d406348f5682cc23ea8c67a66cffcd9768;hb=94e19634c669879ab63bbb82d5489c200cdb18f8;hp=9103c1d3a27d914907cae96557177db5c16f1cfe;hpb=5cd5b6e7864fe435ceb3f5c2f339a436ea0aac93;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 9103c1d..daf971d 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -47,11 +47,11 @@ public class SequenceRenderer
    */
   public void prepare(Graphics g, boolean renderGaps)
   {
-      graphics = g;
-      fm = g.getFontMetrics();
+    graphics = g;
+    fm = g.getFontMetrics();
 
-      this.renderGaps = renderGaps;
-    }
+    this.renderGaps = renderGaps;
+  }
 
   public Color getResidueBoxColour(SequenceI seq, int i)
   {
@@ -66,21 +66,21 @@ public class SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-        getBoxColour(av.globalColourScheme, seq, i);
+      getBoxColour(av.globalColourScheme, seq, i);
     }
 
     return resBoxColour;
-    }
+  }
 
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
     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)))
+    else if (forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
     {
-        resBoxColour = Color.lightGray;
+      resBoxColour = Color.lightGray;
     }
     else
     {
@@ -92,24 +92,29 @@ public class SequenceRenderer
   public Color findSequenceColour(SequenceI seq, int i)
   {
     allGroups = av.alignment.findAllGroups(seq);
-    drawBoxes(seq, i,i, 0);
+    drawBoxes(seq, i, i, 0);
     return resBoxColour;
   }
 
   public void drawSequence(SequenceI seq, SequenceGroup[] sg,
-                           int start, int end,  int y1)
+                           int start, int end, int y1)
   {
+    if (seq == null)
+    {
+      return;
+    }
+
     allGroups = sg;
 
-    drawBoxes(seq, start, end,  y1);
+    drawBoxes(seq, start, end, y1);
 
-    if(av.validCharWidth)
+    if (av.validCharWidth)
     {
       drawText(seq, start, end, y1);
     }
   }
 
-  public void drawBoxes(SequenceI seq, int start, int end,  int y1)
+  public void drawBoxes(SequenceI seq, int start, int end, int y1)
   {
     int i = start;
     int length = seq.getLength();
@@ -121,7 +126,7 @@ public class SequenceRenderer
     while (i <= end)
     {
       resBoxColour = Color.white;
-      if(i < length)
+      if (i < length)
       {
         if (inCurrentSequenceGroup(i))
         {
@@ -136,7 +141,6 @@ public class SequenceRenderer
         }
       }
 
-
       if (resBoxColour != tempColour)
       {
         if (tempColour != null)
@@ -159,19 +163,30 @@ public class SequenceRenderer
       i++;
     }
 
-    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth, av.charHeight);
+    graphics.fillRect(av.charWidth * (curStart - start), y1, curWidth,
+                      av.charHeight);
   }
 
   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);
 
-    y1 += av.charHeight - av.charHeight / 5;  // height/5 replaces pady
+      graphics.setFont(av.getFont());
+    }
+
+    y1 += av.charHeight - av.charHeight / 5; // height/5 replaces pady
 
     int charOffset = 0;
 
     // Need to find the sequence position here.
-    if(end+1>=seq.getLength())
-          end = seq.getLength()-1;
+    if (end + 1 >= seq.getLength())
+    {
+      end = seq.getLength() - 1;
+    }
 
     char s = ' ';
 
@@ -219,10 +234,30 @@ 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),
-                        y1 );
+                          charOffset + av.charWidth * (i - start),
+                          y1);
     }
 
   }
@@ -246,7 +281,8 @@ public class SequenceRenderer
     return false;
   }
 
-  public void drawHighlightedText(SequenceI seq, int start, int end, int x1, int y1)
+  public void drawHighlightedText(SequenceI seq, int start, int end, int x1,
+                                  int y1)
   {
     int pady = av.charHeight / 5;
     int charOffset = 0;
@@ -256,13 +292,13 @@ public class SequenceRenderer
 
     char s = '~';
     // Need to find the sequence position here.
-    if(av.validCharWidth)
+    if (av.validCharWidth)
     {
       for (int i = start; i <= end; i++)
       {
         if (i < seq.getLength())
         {
-          s = seq.getSequence().charAt(i);
+          s = seq.getCharAt(i);
         }
 
         charOffset = (av.charWidth - fm.charWidth(s)) / 2;
@@ -292,6 +328,6 @@ public class SequenceRenderer
                           charOffset + x1,
                           (y1 + av.charHeight) - pady);
     }
-    }
+  }
 
 }