X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=57cd0fc93c2b0aaa5188066818cf668517c49d69;hb=c24071f7b9e6b70c94743214677871ae2dc88499;hp=e36160a939d13b843aa20a86dbad19a2116a7115;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index e36160a..57cd0fc 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -24,7 +24,6 @@ import jalview.schemes.*;
 
 import java.awt.*;
 
-
 /**
  * DOCUMENT ME!
  *
@@ -61,22 +60,27 @@ public class SequenceRenderer
         renderGaps = b;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param cs DOCUMENT ME!
-     * @param seq DOCUMENT ME!
-     * @param i DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)
+
+    public Color getResidueBoxColour(SequenceI seq, int i)
     {
-        getBoxColour(cs, seq, i);
+      allGroups = av.alignment.findAllGroups(seq);
+
+      if (inCurrentSequenceGroup(i))
+      {
+        if (currentSequenceGroup.getDisplayBoxes())
+        {
+          getBoxColour(currentSequenceGroup.cs, seq, i);
+        }
+      }
+      else if (av.getShowBoxes())
+      {
+          getBoxColour(av.globalColourScheme, seq, i);
+      }
 
-        return resBoxColour;
+      return resBoxColour;
     }
 
+
     /**
      * DOCUMENT ME!
      *
@@ -133,63 +137,62 @@ public class SequenceRenderer
      * @param width DOCUMENT ME!
      * @param height DOCUMENT ME!
      */
-    public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
+    public synchronized void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,
         int width, int height)
     {
-        int i = start;
-        int length = seq.getLength();
+      int i = start;
+      int length = seq.getLength();
 
-        int curStart = -1;
-        int curWidth = width;
+      int curStart = -1;
+      int curWidth = width;
 
-        Color tempColour = null;
+      Color tempColour = null;
 
-        while ((i <= end) && (i < length))
+      while (i <= end)
+      {
+        resBoxColour = Color.white;
+
+        if (i < length)
         {
-            if (inCurrentSequenceGroup(i))
-            {
-                if (currentSequenceGroup.getDisplayBoxes())
-                {
-                    getBoxColour(currentSequenceGroup.cs, seq, i);
-                }
-                else
-                {
-                    resBoxColour = Color.white;
-                }
-            }
-            else if (av.getShowBoxes())
+          if (inCurrentSequenceGroup(i))
+          {
+            if (currentSequenceGroup.getDisplayBoxes())
             {
-                getBoxColour(av.getGlobalColourScheme(), seq, i);
-            }
-            else
-            {
-                resBoxColour = Color.white;
+              getBoxColour(currentSequenceGroup.cs, seq, i);
             }
+          }
+          else if (av.getShowBoxes())
+          {
+            getBoxColour(av.globalColourScheme, seq, i);
+          }
 
-            if (resBoxColour != tempColour)
-            {
-                if (tempColour != null)
-                {
-                    graphics.fillRect(x1 + (width * (curStart - start)), y1,
-                        curWidth, height);
-                }
+        }
 
-                graphics.setColor(resBoxColour);
+          if (resBoxColour != tempColour)
+          {
+              if (tempColour != null)
+              {
+                  graphics.fillRect(x1 + (width * (curStart - start)), y1,
+                      curWidth, height);
+              }
 
-                curStart = i;
-                curWidth = width;
-                tempColour = resBoxColour;
-            }
-            else
-            {
-                curWidth += width;
-            }
+              graphics.setColor(resBoxColour);
 
-            i++;
-        }
+              curStart = i;
+              curWidth = width;
+              tempColour = resBoxColour;
+          }
+          else
+          {
+              curWidth += width;
+          }
+
+          i++;
+      }
+
+      graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,
+          height);
 
-        graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,
-            height);
     }
 
     /**
@@ -210,21 +213,18 @@ public class SequenceRenderer
         int charOffset = 0;
         char s;
 
+
         // Need to find the sequence position here.
         String sequence = seq.getSequence();
 
+        if(end+1>=seq.getLength())
+          end = seq.getLength()-1;
+
         for (int i = start; i <= end; i++)
         {
             graphics.setColor(Color.black);
 
-            if (i < sequence.length())
-            {
-                s = sequence.charAt(i);
-            }
-            else
-            {
-                s = ' ';
-            }
+            s = sequence.charAt(i);
 
             if (!renderGaps && jalview.util.Comparison.isGap(s))
             {
@@ -253,7 +253,7 @@ public class SequenceRenderer
 
                 if (av.getColourText())
                 {
-                    getBoxColour(av.getGlobalColourScheme(), seq, i);
+                    getBoxColour(av.globalColourScheme, seq, i);
 
                     if (av.getShowBoxes())
                     {
@@ -268,7 +268,8 @@ public class SequenceRenderer
 
             charOffset = (width - fm.charWidth(s)) / 2;
             graphics.drawString(String.valueOf(s),
-                charOffset + x1 + (width * (i - start)), (y1 + height) - pady);
+                charOffset + x1 + (int)(width * (i - start)), (y1 + height) - pady);
+
         }
     }