/*\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
+ * 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.awt.*;\r
\r
+public class Bond\r
+{\r
+ float[] start;\r
+ float[] end;\r
+ Color startCol = Color.lightGray;\r
+ Color endCol = Color.lightGray;\r
+ public Atom at1;\r
+ public Atom at2;\r
\r
-public class Bond {\r
- float[] start;\r
- float[] end;\r
- Color startCol;\r
- Color endCol;\r
- public Atom at1;\r
- public Atom at2;\r
+ public Bond(float[] start, float[] end, Atom at1, Atom at2)\r
+ {\r
+ this.start = start;\r
+ this.end = end;\r
+ this.startCol = at1.color;\r
+ this.endCol = at2.color;\r
+ this.at1 = at1;\r
+ this.at2 = at2;\r
+ }\r
\r
- public Bond(float[] start, float[] end, Atom at1, Atom at2) {\r
- this.start = start;\r
- this.end = end;\r
- this.startCol = at1.color;\r
- this.endCol = at2.color;\r
- this.at1 = at1;\r
- this.at2 = at2;\r
- }\r
-\r
- public Bond(Bond bond) {\r
+ /* public Bond(Bond bond) {\r
this.start = new float[3];\r
\r
this.start[0] = bond.start[0];\r
len = (float) (Math.sqrt(len));\r
\r
return len;\r
- }\r
+ }*/\r
\r
- public void translate(float x, float y, float z) {\r
- start[0] = (start[0] + x);\r
- end[0] = (end[0] + x);\r
+ public void translate(float x, float y, float z)\r
+ {\r
+ start[0] = (start[0] + x);\r
+ end[0] = (end[0] + x);\r
\r
- start[1] = (start[1] + y);\r
- end[1] = (end[1] + y);\r
+ start[1] = (start[1] + y);\r
+ end[1] = (end[1] + y);\r
\r
- start[2] = (start[2] + z);\r
- end[2] = (end[2] + z);\r
- }\r
+ start[2] = (start[2] + z);\r
+ end[2] = (end[2] + z);\r
+ }\r
}\r