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

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

diff --git a/src/MCview/Residue.java b/src/MCview/Residue.java
index b01d982..2b0159e 100755 (executable)
--- a/src/MCview/Residue.java
+++ b/src/MCview/Residue.java
@@ -1,45 +1,52 @@
-/*\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.util.*;\r
-\r
-\r
-public class Residue {\r
-    Vector atoms = new Vector();\r
-    int number;\r
-    int count;\r
-    int seqnumber;\r
-\r
-    public Residue(Vector atoms, int number, int count) {\r
-        this.atoms = atoms;\r
-        this.number = number;\r
-        this.count = count;\r
-    }\r
-\r
-    public myAtom findAtom(String name) {\r
-        for (int i = 0; i < atoms.size(); i++) {\r
-            if (((myAtom) atoms.elementAt(i)).name.equals(name)) {\r
-                return (myAtom) atoms.elementAt(i);\r
-            }\r
-        }\r
-\r
-        return null;\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 java.util.Vector;
+
+public class Residue
+{
+  Vector<Atom> atoms;
+
+  int number;
+
+  int count;
+
+  public Residue(Vector<Atom> resAtoms, int number, int count)
+  {
+    this.atoms = resAtoms;
+    this.number = number;
+    this.count = count;
+  }
+
+  public Atom findAtom(String name)
+  {
+    for (Atom atom : atoms)
+    {
+      if (atom.name.equals(name))
+      {
+        return atom;
+      }
+    }
+
+    return null;
+  }
+}