Merge branch 'develop' into trialMerge

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

diff --git a/src/MCview/Atom.java b/src/MCview/Atom.java
old mode 100755 (executable)
new mode 100644 (file)
index a2ce2ae..eb91e4e
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,136 +1,6 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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.
- *  
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
 package MCview;
 
-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;
-
-  /**
-   * 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).trim();
-    insCode = str.substring(26, 27).charAt(0);
-    this.x = (Float.valueOf(str.substring(30, 38).trim()).floatValue());
-    this.y = (Float.valueOf(str.substring(38, 46).trim()).floatValue());
-    this.z = (Float.valueOf(str.substring(47, 55).trim()).floatValue());
-    // optional entries - see JAL-730
-    String tm = str.substring(54, 60).trim();
-    if (tm.length() > 0)
-    {
-      occupancy = (Float.valueOf(tm)).floatValue();
-    }
-    else
-    {
-      occupancy = 1f; // default occupancy
-      // see note above: occset=false;
-    }
-    tm = str.substring(60, 66).trim();
-    if (tm.length() > 0)
-    {
-      tfactor = (Float.valueOf(tm).floatValue());
-    }
-    else
-    {
-      tfactor = 1f;
-      // see note above: tfacset=false;
-    }
-  }
-
-  @Override
-  public boolean equals(Object that)
-  {
-    if (this == that || that == null)
-    {
-      return true;
-    }
-    if (that instanceof Atom)
-    {
-      Atom other = (Atom) that;
-      return other.resName.equals(this.resName)
-              && other.resNumber == this.resNumber
-              && other.resNumIns.equals(this.resNumIns)
-              && other.chain.equals(this.chain);
-    }
-    return false;
-  }
 
-  public Atom(float x, float y, float z)
-  {
-    this.x = x;
-    this.y = y;
-    this.z = z;
-  }
 }