X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2FMCview%2FAtom.java;h=1502f4e72da9798ecf8270ddaec1dc016d205868;hb=61df2ddd377ad0171a6d203fb9db2e1fa8ba5be6;hp=8e5cc4d12581d8d2ac45267e50cdb75f35e2c733;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index 8e5cc4d..1502f4e 100755
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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.
  * 
@@ -45,14 +45,18 @@ 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;
 
   public Atom(String str)
@@ -71,9 +75,22 @@ public class Atom
     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());
-    occupancy = (float) (new Float(str.substring(54, 60).trim())
-            .floatValue());
-    tfactor = (float) (new Float(str.substring(60, 66).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 {
+      occupancy = 1f; // default occupancy
+      // see note above: occset=false;
+    }
+    tm = str.substring(60, 66).trim();
+    if (tm.length()>0)
+    {
+      tfactor = (float) (new Float(tm).floatValue());
+    } else {
+      tfactor = 1f;
+      //see note above: tfacset=false;
+    }
   }
 
   public Atom(float x, float y, float z)