formatting

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 0a3bd39..47c8453 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,6 +1,6 @@
 /*
- * 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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -45,13 +45,20 @@ 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.
+   */
   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;
@@ -74,19 +81,24 @@ 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;
     }
   }