JAL-3026 MCview -> mc_view

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

diff --git a/src/mc_view/Zsort.java b/src/mc_view/Zsort.java
new file mode 100755 (executable)
index 0000000..a2080eb
--- /dev/null
+++ b/src/mc_view/Zsort.java
@@ -0,0 +1,80 @@
+/*
+ * 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.util.Vector;
+
+public class Zsort
+{
+  /**
+   * Sorts the Bond list in ascending order of the z-value of the bond start
+   * atom
+   * 
+   * @param bonds
+   */
+  public void sort(Vector<Bond> bonds)
+  {
+    sort(bonds, 0, bonds.size() - 1);
+  }
+
+  public void sort(Vector<Bond> bonds, int p, int r)
+  {
+    int q;
+
+    if (p < r)
+    {
+      q = partition(bonds, p, r);
+      sort(bonds, p, q);
+      sort(bonds, q + 1, r);
+    }
+  }
+
+  private int partition(Vector<Bond> bonds, int p, int r)
+  {
+    float x = bonds.elementAt(p).start[2];
+    int i = p - 1;
+    int j = r + 1;
+    Bond tmp;
+    while (true)
+    {
+      do
+      {
+        j--;
+      } while ((j >= 0) && (bonds.elementAt(j).start[2] > x));
+
+      do
+      {
+        i++;
+      } while ((i < bonds.size()) && (bonds.elementAt(i).start[2] < x));
+
+      if (i < j)
+      {
+        tmp = bonds.elementAt(i);
+        bonds.setElementAt(bonds.elementAt(j), i);
+        bonds.setElementAt(tmp, j);
+      }
+      else
+      {
+        return j;
+      }
+    }
+  }
+}