Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge

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

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 71aaa55..8ca4420 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -18,6 +18,7 @@
  */
 package jalview.schemes;
 
+import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.GraphLine;
@@ -25,6 +26,7 @@ import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
+import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Map;
 
@@ -48,9 +50,9 @@ public class AnnotationColourGradient extends ResidueColourScheme
 
   ColourSchemeI colourScheme;
 
-  public boolean predefinedColours = false;
+  private boolean predefinedColours = false;
 
-  public boolean seqAssociated = false;
+  private boolean seqAssociated = false;
 
   IdentityHashMap<SequenceI, AlignmentAnnotation> seqannot = null;
 
@@ -271,6 +273,16 @@ public class AnnotationColourGradient extends ResidueColourScheme
     return currentColour;
   }
 
+  public boolean isPredefinedColours()
+  {
+    return predefinedColours;
+  }
+
+  public void setPredefinedColours(boolean predefinedColours)
+  {
+    this.predefinedColours = predefinedColours;
+  }
+
   public boolean isSeqAssociated()
   {
     return seqAssociated;
@@ -280,4 +292,28 @@ 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);
+    }
+  }
 }