JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / src / MCview / Atom.java

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 9cbcebb..b2fb5f5 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,8 @@
  */
 package MCview;
 
+import jalview.schemes.ResidueProperties;
+
 import java.awt.Color;
 
 public class Atom
@@ -73,11 +75,13 @@ 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);
 
     resNumber = Integer.parseInt(str.substring(22, 26).trim());
-    resNumIns = str.substring(22, 27).trim();
+    resNumIns = str.substring(22, 27);
     insCode = str.substring(26, 27).charAt(0);
     this.x = (new Float(str.substring(30, 38).trim()).floatValue());
     this.y = (new Float(str.substring(38, 46).trim()).floatValue());
@@ -111,7 +115,4 @@ public class Atom
     this.y = y;
     this.z = z;
   }
-  // public void setColor(Color col) {
-  // this.color = col;
-  // }
 }