X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FBond.java;h=9d22b6aaa5c9bcb34467b2f70d2b5eea12709743;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=60b2f21529783568efc993be17f24fbeb47c4252;hpb=9b22c11a0e12a9320e41eca2cbcbe30f81eb1cb4;p=jalview.git

diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java
index 60b2f21..9d22b6a 100755
--- a/src/MCview/Bond.java
+++ b/src/MCview/Bond.java
@@ -1,65 +1,79 @@
-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);
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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);
+  }
+}