X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAtom.java;h=904e3070c626cf00a1689be96aad34da9cdfbb0d;hb=af65be61ff37a024b694150efed2c6c9b81382ef;hp=9cbcebb004f3b992cd829f2a5594528e7aca2adf;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 9cbcebb..904e307 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -20,6 +20,8 @@
  */
 package MCview;
 
+import jalview.schemes.ResidueProperties;
+
 import java.awt.Color;
 
 public class Atom
@@ -73,6 +75,8 @@ public class Atom
     name = str.substring(12, 15).trim();
 
     resName = str.substring(17, 20);
+    // JAL-1828 treat MSE Selenomethionine as MET (etc)
+    resName = ResidueProperties.getCanonicalAminoAcid(resName);
 
     chain = str.substring(21, 22);
 
@@ -105,13 +109,28 @@ public class Atom
     }
   }
 
+  @Override
+  public boolean equals(Object that)
+  {
+    if (this == that || that == null)
+    {
+      return true;
+    }
+    if (that instanceof Atom)
+    {
+      Atom other = (Atom) that;
+      return other.resName.equals(this.resName)
+              && other.resNumber == this.resNumber
+              && other.resNumIns.equals(this.resNumIns)
+              && other.chain.equals(this.chain);
+    }
+    return false;
+  }
+
   public Atom(float x, float y, float z)
   {
     this.x = x;
     this.y = y;
     this.z = z;
   }
-  // public void setColor(Color col) {
-  // this.color = col;
-  // }
 }