update author list in license for (JAL-826)

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index f8fb9b4..1502f4e 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,20 +1,19 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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
+ * 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.
+ * 
+ * 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 
+ * 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/>.
  */
 package MCview;
 
@@ -23,20 +22,41 @@ 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;
+
+  /**
+   * 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)
@@ -55,7 +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());
-
+    // 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)
@@ -64,7 +99,7 @@ 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;
+  // }
 }