X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FBond.java;h=e3f36f7415a5ccd05c7b8cabe6032120fd08b30b;hb=5b9d104db221e9796918183ca901012bd5a31695;hp=60b2f21529783568efc993be17f24fbeb47c4252;hpb=9b22c11a0e12a9320e41eca2cbcbe30f81eb1cb4;p=jalview.git

diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java
index 60b2f21..e3f36f7 100755
--- a/src/MCview/Bond.java
+++ b/src/MCview/Bond.java
@@ -1,65 +1,84 @@
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* 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 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.
+*
+* 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
+*/
 package MCview;
 
 import java.awt.*;
 
-public class Bond {
-
-  float start[];
-  float end[];
-
-  Color startCol;
-  Color endCol;
-
-  public myAtom at1;
-  public myAtom at2;
-
-  public Bond(float[] start, float[] end, myAtom at1, myAtom 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 void print() {
-    System.out.println("Start " + start[0] + " "+ start[1] + " " + start[2]);
-    System.out.println("End   " + end[0] + " "+ end[1] + " " + end[2]);
-  }
-
-  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);
-  }
+public class Bond {
+    float[] start;
+    float[] end;
+    Color startCol;
+    Color endCol;
+    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 void print() {
+        System.out.println("Start " + start[0] + " " + start[1] + " " +
+            start[2]);
+        System.out.println("End   " + end[0] + " " + end[1] + " " + end[2]);
+    }
+
+    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);
+    }
 }