X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FBond.java;h=371ccd5280ae124657d3748b03d883d8d8e8687a;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=cc5e67c5982ed5b8475850769bcbcb2f6786000f;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java
index cc5e67c..371ccd5 100755
--- a/src/MCview/Bond.java
+++ b/src/MCview/Bond.java
@@ -1,24 +1,26 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * 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.*;
+import java.awt.Color;
 
 public class Bond
 {
@@ -34,10 +36,10 @@ public class Bond
 
   public Atom at2;
 
-  public Bond(float[] start, float[] end, Atom at1, Atom at2)
+  public Bond(Atom at1, Atom at2)
   {
-    this.start = start;
-    this.end = end;
+    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;
@@ -47,8 +49,8 @@ public class Bond
   /*
    * 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.start[0] = bond.start[0]; this.start[1] = bond.start[1]; this.start[2]
+   * = bond.start[2];
    * 
    * this.end = new float[3];
    * 
@@ -68,13 +70,13 @@ public class Bond
 
   public void translate(float x, float y, float z)
   {
-    start[0] = (start[0] + x);
-    end[0] = (end[0] + x);
+    start[0] = start[0] + x;
+    end[0] = end[0] + x;
 
-    start[1] = (start[1] + y);
-    end[1] = (end[1] + y);
+    start[1] = start[1] + y;
+    end[1] = end[1] + y;
 
-    start[2] = (start[2] + z);
-    end[2] = (end[2] + z);
+    start[2] = start[2] + z;
+    end[2] = end[2] + z;
   }
 }