Merge branch 'JAL-1139_proguard' into develop

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

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 729065c..9c5512c 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -17,6 +17,7 @@
  */
 package jalview.schemes;
 
+import jalview.analysis.Conservation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AnnotatedCollectionI;
 import jalview.datamodel.GraphLine;
@@ -24,6 +25,7 @@ import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceI;
 
 import java.awt.Color;
+import java.util.Hashtable;
 import java.util.IdentityHashMap;
 import java.util.Map;
 
@@ -47,9 +49,9 @@ 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;
 
@@ -270,6 +272,16 @@ 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;
@@ -279,4 +291,28 @@ 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);
+    }
+  }
 }