-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 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
-public class Residue\r
-{\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
- {\r
- this.atoms = atoms;\r
- this.number = number;\r
- this.count = count;\r
- }\r
-\r
- public Atom findAtom(String name)\r
- {\r
- for (int i = 0; i < atoms.size(); i++)\r
- {\r
- if ( ( (Atom) atoms.elementAt(i)).name.equals(name))\r
- {\r
- return (Atom) atoms.elementAt(i);\r
- }\r
- }\r
-\r
- return null;\r
- }\r
-}\r
+/*
+ * 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 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;
+ }
+
+ public Vector<Atom> getAtoms()
+ {
+ return this.atoms;
+ }
+}