X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FBond.java;h=8e95c1b50dda3217f26a82d7ef8bb5740c1c02eb;hb=16af141746661052f9902fe1ee2872ed07929667;hp=c84152a6d13e0d3f832b665940f79f0a20dd5042;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git

diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java
index c84152a..8e95c1b 100755
--- a/src/MCview/Bond.java
+++ b/src/MCview/Bond.java
@@ -1,84 +1,80 @@
 /*
-* 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
-*/
-
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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;
+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;
+    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];
+  /*  public Bond(Bond bond) {
+        this.start = new float[3];
 
-    this.end    = new float[3];
+        this.start[0] = bond.start[0];
+        this.start[1] = bond.start[1];
+        this.start[2] = bond.start[2];
 
-    this.end[0] = bond.end[0];
-    this.end[1] = bond.end[1];
-    this.end[2] = bond.end[2];
+        this.end = new float[3];
 
-    this.startCol = bond.startCol;
-    this.endCol   = bond.endCol;
-  }
+        this.end[0] = bond.end[0];
+        this.end[1] = bond.end[1];
+        this.end[2] = bond.end[2];
 
-  public void print() {
-    System.out.println("Start " + start[0] + " "+ start[1] + " " + start[2]);
-    System.out.println("End   " + end[0] + " "+ end[1] + " " + 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]);
+    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));
+        len = (float) (Math.sqrt(len));
 
-    return len;
-  }
-  public void translate(float x, float y, float z) {
+        return len;
+    }*/
+
+  public void translate(float x, float y, float z)
+  {
     start[0] = (start[0] + x);
-    end[0]   = (end[0] + x);
+    end[0] = (end[0] + x);
 
     start[1] = (start[1] + y);
-    end[1]   = (end[1] + y);
+    end[1] = (end[1] + y);
 
     start[2] = (start[2] + z);
-    end[2]   = (end[2] + z);
+    end[2] = (end[2] + z);
   }
 }