JAL-643 - abstracted colourscheme components to allow consensus/colouring to be propa...

[jalview.git] / src / jalview / schemes / AnnotationColourGradient.java

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 9c5512c..c3357ad 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.
  * 
@@ -14,10 +14,10 @@
  * 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.
  */
 package jalview.schemes;
 
-import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.GraphLine;
@@ -25,11 +25,10 @@ import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
-import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Map;
 
-public class AnnotationColourGradient extends ResidueColourScheme
+public class AnnotationColourGradient extends FollowerColourScheme
 {
   public static final int NO_THRESHOLD = -1;
 
@@ -47,8 +46,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
   float r1, g1, b1, rr, gg, bb, dr, dg, db;
 
-  ColourSchemeI colourScheme;
-
   private boolean predefinedColours = false;
 
   private boolean seqAssociated = false;
@@ -156,11 +153,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
     }
   }
 
-  public ColourSchemeI getBaseColour()
-  {
-    return colourScheme;
-  }
-
   public Color getMinColour()
   {
     return new Color((int) r1, (int) g1, (int) b1);
@@ -206,7 +198,7 @@ public class AnnotationColourGradient extends ResidueColourScheme
     }
     if ((threshold == 0) || aboveThreshold(c, j))
     {
-      if (j < annotation.annotations.length
+      if (annotation.annotations!=null && j < annotation.annotations.length
               && annotation.annotations[j] != null
               && !jalview.util.Comparison.isGap(c))
       {
@@ -291,28 +283,4 @@ public class AnnotationColourGradient extends ResidueColourScheme
   {
     seqAssociated = sassoc;
   }
-  @Override
-  public void setConsensus(Hashtable[] consensus)
-  {
-    if (colourScheme!=null)
-    {
-      colourScheme.setConsensus(consensus);
-    }
-  }
-  @Override
-  public void setConservation(Conservation cons)
-  {
-    if (colourScheme!=null)
-    {
-      colourScheme.setConservation(cons);
-    }
-  }
-  @Override
-  public void setConservationInc(int i)
-  {
-    if (colourScheme!=null)
-    {
-      colourScheme.setConservationInc(i);
-    }
-  }
 }