/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* 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
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;
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;
}
}