Merge develop to Release_2_8_3_Branch

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 0a3bd39..9cbcebb 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,23 +1,26 @@
 /*
- * 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 ($$Version-Rel$$)
+ * 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 java.awt.Color;
 
 public class Atom
 {
@@ -45,13 +48,20 @@ 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;
@@ -67,26 +77,31 @@ public class Atom
     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 = (new Float(str.substring(30, 38).trim()).floatValue());
+    this.y = (new Float(str.substring(38, 46).trim()).floatValue());
+    this.z = (new Float(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();
-    } else {
+    if (tm.length() > 0)
+    {
+      occupancy = (new Float(tm)).floatValue();
+    }
+    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 = (new Float(tm).floatValue());
+    }
+    else
     {
-      tfactor = (float) (new Float(tm).floatValue());
-    } else {
       tfactor = 1f;
-      //see note above: tfacset=false;
+      // see note above: tfacset=false;
     }
   }