-package MCview;\r
-import java.util.*;\r
-import java.awt.*;\r
-\r
-public class Atom {\r
- double x;\r
- double y;\r
- double z;\r
- int number;\r
- String name;\r
- String resName;\r
- int resNumber;\r
- int type;\r
- Color color;\r
- String chain;\r
-\r
- public Atom(StringTokenizer str) {\r
- this.number = (new Integer(str.nextToken())).intValue();\r
- this.name = str.nextToken();\r
- this.resName = str.nextToken();\r
-\r
- String tmpstr = new String();\r
-\r
- try {\r
- tmpstr = str.nextToken();\r
-\r
- this.resNumber = (new Integer(tmpstr).intValue());\r
- this.chain = "A";\r
- this.color = Color.green;\r
-\r
- } catch(NumberFormatException e) {\r
- this.chain = tmpstr;\r
-\r
- if (tmpstr.equals("A")) {\r
- this.color = new Color((float)Math.random(),(float)Math.random(),(float)Math.random());\r
- } else {\r
- this.color = Color.red;\r
- }\r
- this.resNumber = (new Integer(str.nextToken()).intValue());\r
- }\r
-\r
- this.x = (double)(new Double(str.nextToken()).floatValue());\r
- this.y = (double)(new Double(str.nextToken()).floatValue());\r
- this.z = (double)(new Double(str.nextToken()).floatValue());\r
-\r
- }\r
-\r
- public void setColor(Color col) {\r
- this.color = col;\r
- }\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package MCview;
+
+import java.awt.*;
+
+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;
+ public int alignmentMapping = -1;
+ public int atomIndex;
+ public float occupancy=0;
+ public float tfactor=0;
+ 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);
+
+ 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 = (float) (new Float(str.substring(30, 38).trim()).floatValue());
+ this.y = (float) (new Float(str.substring(38, 46).trim()).floatValue());
+ this.z = (float) (new Float(str.substring(47, 55).trim()).floatValue());
+ occupancy = (float) (new Float(str.substring(54,60).trim()).floatValue());
+ tfactor = (float) (new Float(str.substring(60,66).trim()).floatValue());
+ }
+
+ public Atom(float x, float y, float z)
+ {
+ this.x = x;
+ this.y = y;
+ this.z = z;
+ }
+ // public void setColor(Color col) {
+ // this.color = col;
+ // }
+}