merge from 2_4_Release branch

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index c15455e..e69e1ce 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * This program 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 2
  * of the License, or (at your option) any later version.
- *
+ * 
  * This program 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 this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -23,23 +23,43 @@ import java.awt.*;
 public class Atom
 {
   public float x;
+
   public float y;
+
   public float z;
+
   public int number;
+
   public String name;
+
   public String resName;
+
   public int resNumber;
+
   public char insCode = ' ';
+
   public String resNumIns = null;
+
   public int type;
+
   Color color = Color.lightGray;
+
   public String chain;
-  int alignmentMapping = -1;
+
+  public int alignmentMapping = -1;
+
+  public int atomIndex;
+
+  public float occupancy = 0;
+
+  public float tfactor = 0;
 
   public boolean isSelected = false;
 
   public Atom(String str)
   {
+    atomIndex = Integer.parseInt(str.substring(6, 11).trim());
+
     name = str.substring(12, 15).trim();
 
     resName = str.substring(17, 20);
@@ -52,7 +72,9 @@ 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());
   }
 
   public Atom(float x, float y, float z)
@@ -61,7 +83,7 @@ public class Atom
     this.y = y;
     this.z = z;
   }
-  //  public void setColor(Color col) {
-  //      this.color = col;
-  //  }
+  // public void setColor(Color col) {
+  // this.color = col;
+  // }
 }