X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FBond.java;h=371ccd5280ae124657d3748b03d883d8d8e8687a;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=17f66bba2f5ab5028bdfcb9ac0061ebe34e70c53;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/MCview/Bond.java b/src/MCview/Bond.java
index 17f66bb..371ccd5 100755
--- a/src/MCview/Bond.java
+++ b/src/MCview/Bond.java
@@ -1,84 +1,82 @@
-/*
-* 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);
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package MCview;
+
+import java.awt.Color;
+
+public class Bond
+{
+  float[] start;
+
+  float[] end;
+
+  Color startCol = Color.lightGray;
+
+  Color endCol = Color.lightGray;
+
+  public Atom at1;
+
+  public Atom at2;
+
+  public Bond(Atom at1, Atom at2)
+  {
+    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;
+    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;
+  }
+}