JAL-1503 update version in GPL header

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

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 1b23d13..301eb73 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -18,19 +18,18 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.GraphLine;
 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;
 
@@ -48,14 +47,32 @@ 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;
 
   IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
-
+  @Override
+  public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+          Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+  {
+    AnnotationColourGradient acg = new AnnotationColourGradient(annotation, colourScheme, aboveAnnotationThreshold);
+    acg.thresholdIsMinMax = thresholdIsMinMax;
+    acg.annotationThreshold = (annotationThreshold==null) ? null : new GraphLine(annotationThreshold);
+    acg.r1 = r1;
+    acg.g1 = g1;
+    acg.b1 = b1;
+    acg.rr = rr;
+    acg.gg = gg;
+    acg.bb = bb;
+    acg.dr = dr;
+    acg.dg = dg;
+    acg.db = db;
+    acg.predefinedColours = predefinedColours;
+    acg.seqAssociated = seqAssociated;
+    
+    return acg;
+  }
   /**
    * Creates a new AnnotationColourGradient object.
    */
@@ -109,7 +126,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
   public void alignmentChanged(AnnotatedCollectionI alignment,
           Map<SequenceI, SequenceCollectionI> hiddenReps)
   {
-    // TODO Auto-generated method stub
     super.alignmentChanged(alignment, hiddenReps);
 
     if (seqAssociated && annotation.getCalcId() != null)
@@ -122,7 +138,9 @@ public class AnnotationColourGradient extends ResidueColourScheme
       {
         seqannot = new IdentityHashMap<SequenceI, AlignmentAnnotation>();
       }
-      for (AlignmentAnnotation alan : alignment.findAnnotation(annotation
+      // resolve the context containing all the annotation for the sequence
+      AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment : alignment.getContext();
+      for (AlignmentAnnotation alan : alcontext.findAnnotation(annotation
               .getCalcId()))
       {
         if (alan.sequenceRef != null
@@ -157,11 +175,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
     }
   }
 
-  public ColourSchemeI getBaseColour()
-  {
-    return colourScheme;
-  }
-
   public Color getMinColour()
   {
     return new Color((int) r1, (int) g1, (int) b1);
@@ -292,28 +305,4 @@ 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);
-    }
-  }
 }