JAL-3026 MCview -> mc_view

[jalview.git] / src / mc_view / Bond.java

diff --git a/src/mc_view/Bond.java b/src/mc_view/Bond.java
new file mode 100755 (executable)
index 0000000..e609506
--- /dev/null
+++ b/src/mc_view/Bond.java
@@ -0,0 +1,82 @@
+/*
+ * 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 mc_view;
+
+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;
+  }
+}