X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=889df36e434f454f93069a039217677291fdfd18;hb=0201d2b630e06a75fd9522f24863e9cecf8810fd;hp=9a722f279ad171fa1c0305db395dc52f5629ceb9;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 9a722f2..889df36 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -44,11 +44,24 @@ public class SequenceRenderer
     renderGaps = b;
   }
 
-  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;
-  }
+    }
 
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
@@ -62,6 +75,13 @@ public class SequenceRenderer
     }
   }
 
+  public Color findSequenceColour(SequenceI seq, int i)
+  {
+    allGroups = av.alignment.findAllGroups(seq);
+    drawBoxes(seq, i,i, 0, 0, 1,1);
+    return resBoxColour;
+  }
+
   public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
                            int start, int end, int x1, int y1, int width,
                            int height)
@@ -87,27 +107,24 @@ public class SequenceRenderer
     int curWidth = width;
 
     Color tempColour = null;
-    while (i <= end && i < length)
+    while (i <= end)
     {
-      if (inCurrentSequenceGroup(i))
+      resBoxColour = Color.white;
+      if(i < length)
       {
-        if (currentSequenceGroup.getDisplayBoxes())
+        if (inCurrentSequenceGroup(i))
         {
-          getBoxColour(currentSequenceGroup.cs, seq, i);
+          if (currentSequenceGroup.getDisplayBoxes())
+          {
+            getBoxColour(currentSequenceGroup.cs, seq, i);
+          }
         }
-        else
+        else if (av.getShowBoxes())
         {
-          resBoxColour = Color.white;
+          getBoxColour(av.getGlobalColourScheme(), seq, i);
         }
       }
-      else if (av.getShowBoxes())
-      {
-        getBoxColour(av.getGlobalColourScheme(), seq, i);
-      }
-      else
-      {
-        resBoxColour = Color.white;
-      }
+
 
       if (resBoxColour != tempColour)
       {
@@ -137,24 +154,22 @@ public class SequenceRenderer
   public void drawText(SequenceI seq, int start, int end, int x1, int y1,
                        int width, int height)
   {
-    int pady = height / 5;
+
+    y1 += height - height / 5;  // height/5 replaces pady
+
     int charOffset = 0;
-    char s;
+
     // Need to find the sequence position here.
+    if(end+1>=seq.getLength())
+          end = seq.getLength()-1;
+
+    char s = ' ';
 
-    String sequence = seq.getSequence();
     for (int i = start; i <= end; i++)
     {
       graphics.setColor(Color.black);
-      if (i < sequence.length())
-      {
-        s = sequence.charAt(i);
-      }
-      else
-      {
-        s = ' ';
-      }
 
+      s = seq.getCharAt(i);
       if (!renderGaps && jalview.util.Comparison.isGap(s))
       {
         continue;
@@ -196,8 +211,8 @@ public class SequenceRenderer
 
       charOffset = (width - fm.charWidth(s)) / 2;
       graphics.drawString(String.valueOf(s),
-                          charOffset + x1 + width * (i - start),
-                          y1 + height - pady);
+                         charOffset + x1 + width * (i - start),
+                        y1 );
     }
 
   }