X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignViewport.java;h=e9829bb7d31ce7d454483915e0fd43cad1f5d7a4;hb=260c50cca8fff9b7e15e311dfc9fd9dda685950b;hp=49fe522346186f12583860243773206aa4078106;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 49fe522..e9829bb 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
@@ -138,8 +139,6 @@ public class AlignViewport extends AlignmentViewport implements
 
   Stack redoList = new Stack();
 
-  Hashtable sequenceColours;
-
   int thresholdTextColour = 0;
 
   Color textColour = Color.black;
@@ -934,35 +933,6 @@ public class AlignViewport extends AlignmentViewport implements
     showHiddenMarkers = show;
   }
 
-  public Color getSequenceColour(SequenceI seq)
-  {
-    if (sequenceColours == null || !sequenceColours.containsKey(seq))
-    {
-      return Color.white;
-    }
-    else
-    {
-      return (Color) sequenceColours.get(seq);
-    }
-  }
-
-  public void setSequenceColour(SequenceI seq, Color col)
-  {
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
-
-    if (col == null)
-    {
-      sequenceColours.remove(seq);
-    }
-    else
-    {
-      sequenceColours.put(seq, col);
-    }
-  }
-
   /**
    * returns the visible column regions of the alignment
    * 
@@ -1044,23 +1014,6 @@ public class AlignViewport extends AlignmentViewport implements
     centreColumnLabels = centrecolumnlabels;
   }
 
-  public void updateSequenceIdColours()
-  {
-    if (sequenceColours == null)
-    {
-      sequenceColours = new Hashtable();
-    }
-    for (SequenceGroup sg : alignment.getGroups())
-    {
-      if (sg.idColour != null)
-      {
-        for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
-        {
-          sequenceColours.put(s, sg.idColour);
-        }
-      }
-    }
-  }
 
   /**
    * enable or disable the display of Database Cross References in the sequence