2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
30 public String resName;
32 public char insCode=' ';
33 public String resNumIns=null;
35 Color color = Color.lightGray;
37 int alignmentMapping=-1;
39 public boolean isSelected = false;
41 public Atom(String str)
43 name = str.substring(12,15).trim();
45 resName = str.substring(17,20);
47 chain = str.substring(21,22);
49 resNumber = Integer.parseInt(str.substring(22,26).trim());
50 resNumIns=str.substring(22,27);
51 insCode = str.substring(26,27).charAt(0);
52 this.x = (float) (new Float(str.substring(30,38).trim()).floatValue());
53 this.y = (float) (new Float(str.substring(38,46).trim()).floatValue());
54 this.z = (float) (new Float(str.substring(47,55).trim()).floatValue());
57 public Atom(float x,float y, float z) {
62 // public void setColor(Color col) {