/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 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
public class Bond {\r
float[] start;\r
float[] end;\r
- Color startCol;\r
- Color endCol;\r
- public myAtom at1;\r
- public myAtom at2;\r
+ Color startCol = Color.lightGray;\r
+ Color endCol= Color.lightGray;\r
+ public Atom at1;\r
+ public Atom at2;\r
\r
- public Bond(float[] start, float[] end, myAtom at1, myAtom at2) {\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.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
this.endCol = bond.endCol;\r
}\r
\r
- public void print() {\r
- System.out.println("Start " + start[0] + " " + start[1] + " " +\r
- start[2]);\r
- System.out.println("End " + end[0] + " " + end[1] + " " + end[2]);\r
- }\r
-\r
public float length() {\r
float len = ((end[0] - start[0]) * (end[0] - start[0])) +\r
((end[1] - start[1]) * (end[1] - start[1])) +\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