X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=69db54d3b00590f249de23480df4944af244a9ab;hb=5f7d80cd8b01e051a6175b0ce8db0ad94d73df2f;hp=6483e8b39d7a972f4c3f212a6d309514d7602417;hpb=f59f68c0a389bef51cfc9397dc0c4b645be51c05;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 6483e8b..69db54d 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -11,7 +11,8 @@ public class SequenceRenderer implements RendererI
   FontMetrics fm;
   boolean renderGaps = true;
   SequenceGroup currentSequenceGroup = null;
-  Color resBoxColour = Color.white;
+  SequenceGroup [] allGroups = null;
+  Color resBoxColour;
   Graphics graphics;
 
   public SequenceRenderer(AlignViewport av)
@@ -33,16 +34,15 @@ public class SequenceRenderer implements RendererI
 
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)
   {
-
    if (cs != null)
        resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i, av.getConsensus(false));
    else
        resBoxColour = Color.white;
   }
 
-  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)
+  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)
   {
-    currentSequenceGroup = sg;
+    allGroups = sg;
 
     graphics = g;
 
@@ -60,7 +60,7 @@ public class SequenceRenderer implements RendererI
     int curStart = x1;
     int curWidth = width;
 
-    Color tempColour = Color.red;
+    Color tempColour = null;
     while (i <= end && i < length)
     {
       if(inCurrentSequenceGroup(i))
@@ -69,7 +69,10 @@ public class SequenceRenderer implements RendererI
              getBoxColour(currentSequenceGroup.cs, seq, i);
       }
       else if(av.getShowBoxes())
-           getBoxColour(av.getGlobalColourScheme(), seq, i);
+            getBoxColour(av.getGlobalColourScheme(), seq, i);
+      else
+        resBoxColour = Color.white;
+
 
       if (resBoxColour != tempColour)
       {
@@ -112,8 +115,11 @@ public class SequenceRenderer implements RendererI
           if(!currentSequenceGroup.getDisplayText())
             continue;
 
-          if(currentSequenceGroup.getColourText())
-            graphics.setColor(resBoxColour.darker());
+            if (currentSequenceGroup.getColourText())
+            {
+              getBoxColour(currentSequenceGroup.cs, seq, i);
+              graphics.setColor(resBoxColour.darker());
+            }
         }
         else
         {
@@ -121,7 +127,10 @@ public class SequenceRenderer implements RendererI
             continue;
 
           if(av.getColourText())
-            graphics.setColor(resBoxColour.darker());
+           {
+             getBoxColour(av.getGlobalColourScheme(), seq, i);
+             graphics.setColor(resBoxColour.darker());
+           }
         }
 
       charOffset =  (width - fm.charWidth(s))/2;
@@ -133,10 +142,17 @@ public class SequenceRenderer implements RendererI
 
   boolean inCurrentSequenceGroup(int res)
   {
-    if(currentSequenceGroup==null)
+    if(allGroups ==null)
       return false;
 
-    return (currentSequenceGroup.getStartRes()<=res && currentSequenceGroup.getEndRes()>=res)?true:false;
+    for(int i=0; i<allGroups.length; i++)
+      if(allGroups[i].getStartRes()<=res && allGroups[i].getEndRes()>=res)
+      {
+         currentSequenceGroup = allGroups[i];
+         return true;
+      }
+
+    return false;
   }
 
   public void drawHighlightedText(SequenceI seq,int start, int end, int x1, int y1, int width, int height)