X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FAtomSpec.java;fp=src%2Fjalview%2Fstructure%2FAtomSpec.java;h=d3e8d42fe54f7f663d922c29160127f5b015740e;hb=424c56371cd59181b994d7e3e8e91c4b7ba0b507;hp=271c893d1208a58a8b5711fec32abad35702f0f1;hpb=c9f31322ad542be7fab91e0c9f2ff3638a25c5b1;p=jalview.git

diff --git a/src/jalview/structure/AtomSpec.java b/src/jalview/structure/AtomSpec.java
index 271c893..d3e8d42 100644
--- a/src/jalview/structure/AtomSpec.java
+++ b/src/jalview/structure/AtomSpec.java
@@ -8,7 +8,10 @@ package jalview.structure;
  */
 public class AtomSpec
 {
-  private String pdbId;
+  // TODO clarify do we want pdbFile here, or pdbId?
+  // compare highlightAtom in 2.8.2 for JalviewJmolBinding and
+  // javascript.MouseOverStructureListener
+  private String pdbFile;
 
   private String chain;
 
@@ -19,22 +22,22 @@ public class AtomSpec
   /**
    * Constructor
    * 
-   * @param id
+   * @param pdbFile
    * @param chain
    * @param resNo
    * @param atomNo
    */
-  public AtomSpec(String id, String chain, int resNo, int atomNo)
+  public AtomSpec(String pdbFile, String chain, int resNo, int atomNo)
   {
-    this.pdbId = id;
+    this.pdbFile = pdbFile;
     this.chain = chain;
     this.pdbResNum = resNo;
     this.atomIndex = atomNo;
   }
 
-  public String getPdbId()
+  public String getPdbFile()
   {
-    return pdbId;
+    return pdbFile;
   }
 
   public String getChain()
@@ -55,7 +58,7 @@ public class AtomSpec
   @Override
   public String toString()
   {
-    return "pdbId: " + pdbId + ", chain: " + chain + ", res: " + pdbResNum
-            + ", atom: " + atomIndex;
+    return "pdbFile: " + pdbFile + ", chain: " + chain + ", res: "
+            + pdbResNum + ", atom: " + atomIndex;
   }
 }