Merge branch 'docs/2_8_1_Release' into Release_2_8_1_Branch

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 25a3dc6..6140ed0 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,19 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 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.
- * 
+ *  
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package MCview;
 
@@ -46,15 +47,19 @@ public class Atom
   public String chain;
 
   /**
-   * this is a temporary value - designed to store the position in sequence that this atom corresponds to after aligning the chain to a SequenceI object. Do not rely on its value being correct when visualizing sequence colourings on the structure - use the StructureSelectionManager's mapping instead.
+   * this is a temporary value - designed to store the position in sequence that
+   * this atom corresponds to after aligning the chain to a SequenceI object. Do
+   * not rely on its value being correct when visualizing sequence colourings on
+   * the structure - use the StructureSelectionManager's mapping instead.
    */
   public int alignmentMapping = -1;
 
   public int atomIndex;
 
   public float occupancy = 0;
-  
+
   public float tfactor = 0;
+
   // need these if we ever want to export Atom data
   // public boolean tfacset=true,occset=true;
   public boolean isSelected = false;
@@ -77,19 +82,24 @@ public class Atom
     this.z = (float) (new Float(str.substring(47, 55).trim()).floatValue());
     // optional entries - see JAL-730
     String tm = str.substring(54, 60).trim();
-    if (tm.length()>0) {
+    if (tm.length() > 0)
+    {
       occupancy = (float) (new Float(tm)).floatValue();
-    } else {
+    }
+    else
+    {
       occupancy = 1f; // default occupancy
       // see note above: occset=false;
     }
     tm = str.substring(60, 66).trim();
-    if (tm.length()>0)
+    if (tm.length() > 0)
     {
       tfactor = (float) (new Float(tm).floatValue());
-    } else {
+    }
+    else
+    {
       tfactor = 1f;
-      //see note above: tfacset=false;
+      // see note above: tfacset=false;
     }
   }