JAL-1741 nucleotide-aware colour schemes applied to structures

[jalview.git] / src / jalview / structures / models / AAStructureBindingModel.java

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 653ec2d..3602056 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -1,16 +1,17 @@
 package jalview.structures.models;
 
+import java.util.ArrayList;
+import java.util.List;
+
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
 import jalview.util.MessageManager;
 
-import java.util.ArrayList;
-import java.util.List;
-
 /**
  * 
  * A base class to hold common function for protein structure model binding.
@@ -46,6 +47,8 @@ public abstract class AAStructureBindingModel extends
 
   protected boolean colourBySequence = true;
 
+  private boolean nucleotide;
+
   /**
    * Constructor
    * 
@@ -74,6 +77,7 @@ public abstract class AAStructureBindingModel extends
   {
     this.ssm = ssm;
     this.sequence = sequenceIs;
+    this.nucleotide = Comparison.isNucleotide(sequenceIs);
     this.chains = chains;
     this.pdbEntry = pdbentry;
     this.protocol = protocol;
@@ -375,8 +379,11 @@ public abstract class AAStructureBindingModel extends
     }
   }
 
-  // TODO Jmol and Chimera seem to expect pdbFile, javascript listener pdbId
   protected abstract void highlightAtom(int atomIndex, int pdbResNum,
           String chain, String pdbFile);
 
+  protected boolean isNucleotide()
+  {
+    return this.nucleotide;
+  }
 }
\ No newline at end of file