Merge branch 'patch/JAL-3700_JAL-3748_JAL-3763_for_2_11_1_3' into releases/Release_2_...

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 47c8453..a2ce2ae 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,23 +1,28 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package MCview;
 
-import java.awt.*;
+import jalview.schemes.ResidueProperties;
+
+import java.awt.Color;
 
 public class Atom
 {
@@ -70,20 +75,22 @@ 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);
+    resNumIns = str.substring(22, 27).trim();
     insCode = str.substring(26, 27).charAt(0);
-    this.x = (float) (new Float(str.substring(30, 38).trim()).floatValue());
-    this.y = (float) (new Float(str.substring(38, 46).trim()).floatValue());
-    this.z = (float) (new Float(str.substring(47, 55).trim()).floatValue());
+    this.x = (Float.valueOf(str.substring(30, 38).trim()).floatValue());
+    this.y = (Float.valueOf(str.substring(38, 46).trim()).floatValue());
+    this.z = (Float.valueOf(str.substring(47, 55).trim()).floatValue());
     // optional entries - see JAL-730
     String tm = str.substring(54, 60).trim();
     if (tm.length() > 0)
     {
-      occupancy = (float) (new Float(tm)).floatValue();
+      occupancy = (Float.valueOf(tm)).floatValue();
     }
     else
     {
@@ -93,7 +100,7 @@ public class Atom
     tm = str.substring(60, 66).trim();
     if (tm.length() > 0)
     {
-      tfactor = (float) (new Float(tm).floatValue());
+      tfactor = (Float.valueOf(tm).floatValue());
     }
     else
     {
@@ -102,13 +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;
-  // }
 }