X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAtom.java;h=b1fe59f037308c3a8943f6b0a2f20f759024514b;hb=02e9934037787599aefda03a6af9b7501e867dc3;hp=e22b94ef5687016e7bdeae39b8b8e82691724c27;hpb=ff33b2ff68aed0d69ac1a4edf860141dc9402592;p=jalview.git

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
index e22b94e..b1fe59f 100755
--- 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 2.8)
+ * 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 
+ * 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;
 
@@ -23,21 +22,45 @@ 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;
+
+  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)
@@ -56,8 +79,27 @@ 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)
@@ -66,7 +108,7 @@ 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;
+  // }
 }