update author list in license for (JAL-826)

[jalview.git] / src / MCview / Bond.java

diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java
index 5f162b0..2979cd1 100755 (executable)
--- a/src/MCview/Bond.java
+++ b/src/MCview/Bond.java
@@ -1,78 +1,79 @@
-/*\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
-package MCview;\r
-\r
-import java.awt.*;\r
-\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
-\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
-        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 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
-\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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+package MCview;
+
+import java.awt.*;
+
+public class Bond
+{
+  float[] start;
+
+  float[] end;
+
+  Color startCol = Color.lightGray;
+
+  Color endCol = Color.lightGray;
+
+  public Atom at1;
+
+  public Atom at2;
+
+  public Bond(float[] start, float[] end, Atom at1, Atom at2)
+  {
+    this.start = start;
+    this.end = end;
+    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);
+  }
+}