From 0416a98d6da9e0fbe42a9676d4ef30c234cb7b12 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 17 Oct 2013 13:44:25 +0100
Subject: [PATCH] JAL-643 - abstracted colourscheme components to allow
 consensus/colouring to be propagated from background to a
 group

---
 src/jalview/schemes/AnnotationColourGradient.java |   35 +--------------
 src/jalview/schemes/FollowerColourScheme.java     |   49 +++++++++++++++++++++
 2 files changed, 50 insertions(+), 34 deletions(-)
 create mode 100644 src/jalview/schemes/FollowerColourScheme.java

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 1b23d13..c3357ad 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -18,7 +18,6 @@
  */
 package jalview.schemes;
 
-import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.GraphLine;
@@ -26,11 +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;
 
@@ -48,8 +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;
@@ -157,11 +153,6 @@ public class AnnotationColourGradient extends ResidueColourScheme
     }
   }
 
-  public ColourSchemeI getBaseColour()
-  {
-    return colourScheme;
-  }
-
   public Color getMinColour()
   {
     return new Color((int) r1, (int) g1, (int) b1);
@@ -292,28 +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);
-    }
-  }
 }
diff --git a/src/jalview/schemes/FollowerColourScheme.java b/src/jalview/schemes/FollowerColourScheme.java
new file mode 100644
index 0000000..32e9316
--- /dev/null
+++ b/src/jalview/schemes/FollowerColourScheme.java
@@ -0,0 +1,49 @@
+package jalview.schemes;
+
+import jalview.analysis.Conservation;
+
+import java.util.Hashtable;
+
+/**
+ * Colourscheme that takes its colours from some other colourscheme
+ * @author jimp
+ *
+ */
+public class FollowerColourScheme extends ResidueColourScheme
+{
+
+  protected ColourSchemeI colourScheme;
+
+  public ColourSchemeI getBaseColour()
+  {
+    return colourScheme;
+  }
+
+  @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);
+    }
+  }
+
+}
-- 
1.7.10.2