Merge remote-tracking branch 'origin/develop' into

[jalview.git] / src / jalview / structure / AtomSpec.java

diff --git a/src/jalview/structure/AtomSpec.java b/src/jalview/structure/AtomSpec.java
index 271c893..d3e8d42 100644 (file)
--- 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;
   }
 }