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 5265bc2..b2fb5f5 100755 (executable)
--- a/src/MCview/Atom.java
+++ b/src/MCview/Atom.java
@@ -1,58 +1,118 @@
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
-package MCview;\r
-\r
-import java.awt.*;\r
-\r
-\r
-public class Atom {\r
-    float x;\r
-    float y;\r
-    float z;\r
-    int number;\r
-    String name;\r
-    String resName;\r
-    int resNumber;\r
-    int type;\r
-    Color color = Color.lightGray;\r
-    String chain;\r
-    int alignmentMapping=-1;\r
-\r
-    public boolean isSelected = false;\r
-\r
-    public Atom(String str)\r
-    {\r
-        name =  str.substring(12,15).trim();\r
-\r
-        resName = str.substring(17,20);\r
-\r
-        chain = str.substring(21,22);\r
-\r
-        resNumber = Integer.parseInt(str.substring(22,26).trim());\r
-\r
-        this.x = (float) (new Float(str.substring(30,38).trim()).floatValue());\r
-        this.y = (float) (new Float(str.substring(38,46).trim()).floatValue());\r
-        this.z = (float) (new Float(str.substring(47,55).trim()).floatValue());\r
-\r
-    }\r
-\r
-  //  public void setColor(Color col) {\r
-  //      this.color = col;\r
-  //  }\r
-}\r
+/*
+ * 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.
+ *  
+ * 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);
+    insCode = str.substring(26, 27).charAt(0);
+    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)
+  {
+    this.x = x;
+    this.y = y;
+    this.z = z;
+  }
+}