Merge branch 'features/JAL-2320_closeChimeraAction' into develop

[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 b618bc0..063eacf 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -25,6 +25,7 @@ import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
@@ -71,7 +72,7 @@ public abstract class AAStructureBindingModel extends
   /*
    * datasource protocol for access to PDBEntrylatest
    */
-  String protocol = null;
+  DataSourceType protocol = null;
 
   protected boolean colourBySequence = true;
 
@@ -136,19 +137,14 @@ public abstract class AAStructureBindingModel extends
    * @param protocol
    */
   public AAStructureBindingModel(StructureSelectionManager ssm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
-          String protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+          DataSourceType protocol)
   {
     this.ssm = ssm;
     this.sequence = sequenceIs;
     this.nucleotide = Comparison.isNucleotide(sequenceIs);
-    this.chains = chains;
     this.pdbEntry = pdbentry;
     this.protocol = protocol;
-    if (chains == null)
-    {
-      this.chains = new String[pdbentry.length][];
-    }
   }
 
   public StructureSelectionManager getSsm()
@@ -208,7 +204,7 @@ public abstract class AAStructureBindingModel extends
     return chains;
   }
 
-  public String getProtocol()
+  public DataSourceType getProtocol()
   {
     return protocol;
   }
@@ -677,6 +673,13 @@ public abstract class AAStructureBindingModel extends
   }
 
   /**
+   * Returns a list of chains mapped in this viewer.
+   * 
+   * @return
+   */
+  public abstract List<String> getChainNames();
+
+  /**
    * Returns the Jalview panel hosting the structure viewer (if any)
    * 
    * @return