-/*\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
-\r
-package MCview;\r
-\r
-import java.awt.*;\r
-\r
-public class Bond {\r
-\r
- float start[];\r
- float end[];\r
-\r
- Color startCol;\r
- Color endCol;\r
-\r
- public myAtom at1;\r
- public myAtom at2;\r
-\r
- public Bond(float[] start, float[] end, myAtom at1, myAtom 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
- public Bond(Bond bond) {\r
- this.start = new float[3];\r
-\r
- this.start[0] = bond.start[0];\r
- this.start[1] = bond.start[1];\r
- this.start[2] = bond.start[2];\r
-\r
- this.end = new float[3];\r
-\r
- this.end[0] = bond.end[0];\r
- this.end[1] = bond.end[1];\r
- this.end[2] = bond.end[2];\r
-\r
- this.startCol = bond.startCol;\r
- this.endCol = bond.endCol;\r
- }\r
-\r
- public void print() {\r
- System.out.println("Start " + start[0] + " "+ start[1] + " " + 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
- (end[2] - start[2])*(end[2] - start[2]);\r
-\r
- len = (float)(Math.sqrt(len));\r
-\r
- return len;\r
- }\r
- public void translate(float x, float y, float z) {\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
-\r
- start[2] = (start[2] + z);\r
- end[2] = (end[2] + z);\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.awt.Color;
+
+public class Bond
+{
+ float[] start;
+
+ float[] end;
+
+ Color startCol = Color.lightGray;
+
+ Color endCol = Color.lightGray;
+
+ public Atom at1;
+
+ public Atom at2;
+
+ public Bond(Atom at1, Atom at2)
+ {
+ this.start = new float[] { at1.x, at1.y, at1.z };
+ this.end = new float[] { at2.x, at2.y, at2.z };
+ this.startCol = at1.color;
+ this.endCol = at2.color;
+ this.at1 = at1;
+ this.at2 = at2;
+ }
+
+ /*
+ * public Bond(Bond bond) { this.start = new float[3];
+ *
+ * this.start[0] = bond.start[0]; this.start[1] = bond.start[1]; this.start[2]
+ * = bond.start[2];
+ *
+ * this.end = new float[3];
+ *
+ * this.end[0] = bond.end[0]; this.end[1] = bond.end[1]; this.end[2] =
+ * bond.end[2];
+ *
+ * this.startCol = bond.startCol; this.endCol = bond.endCol; }
+ *
+ * public float length() { float len = ((end[0] - start[0]) * (end[0] -
+ * start[0])) + ((end[1] - start[1]) * (end[1] - start[1])) + ((end[2] -
+ * start[2]) * (end[2] - start[2]));
+ *
+ * len = (float) (Math.sqrt(len));
+ *
+ * return len; }
+ */
+
+ public void translate(float x, float y, float z)
+ {
+ start[0] = start[0] + x;
+ end[0] = end[0] + x;
+
+ start[1] = start[1] + y;
+ end[1] = end[1] + y;
+
+ start[2] = start[2] + z;
+ end[2] = end[2] + z;
+ }
+}