JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index c15455e..b2fb5f5 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,58 +1,112 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
- * 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.
- *
+ *  
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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 jalview.schemes.ResidueProperties;
+
+import java.awt.Color;
 
 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;
 
+  /**
+   * 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)
   {
+    atomIndex = Integer.parseInt(str.substring(6, 11).trim());
+
     name = str.substring(12, 15).trim();
 
     resName = str.substring(17, 20);
+    // JAL-1828 treat MSE Selenomethionine as MET (etc)
+    resName = ResidueProperties.getCanonicalAminoAcid(resName);
 
     chain = str.substring(21, 22);
 
     resNumber = Integer.parseInt(str.substring(22, 26).trim());
     resNumIns = str.substring(22, 27);
     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 = (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 = (new Float(tm).floatValue());
+    }
+    else
+    {
+      tfactor = 1f;
+      // see note above: tfacset=false;
+    }
   }
 
   public Atom(float x, float y, float z)
@@ -61,7 +115,4 @@ public class Atom
     this.y = y;
     this.z = z;
   }
-  //  public void setColor(Color col) {
-  //      this.color = col;
-  //  }
 }