X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FZsort.java;h=d57ee550a3212178a06cd31e0e354516e2c00ba3;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=1e7ac4162f489bfe5cd41a2d4307a496c8f7fa16;hpb=4266cb41bf11ee3fdac840e25a8159f6796276a3;p=jalview.git

diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java
index 1e7ac41..d57ee55 100755
--- a/src/MCview/Zsort.java
+++ b/src/MCview/Zsort.java
@@ -1,63 +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
-*/
-package MCview;
-
-import java.util.*;
-
-
-public class Zsort {
-    public static void Zsort(Vector bonds) {
-        sort(bonds, 0, bonds.size() - 1);
-    }
-
-    public static void sort(Vector 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 static int partition(Vector bonds, int p, int r) {
-        float x = ((Bond) bonds.elementAt(p)).start[2];
-        int i = p - 1;
-        int j = r + 1;
-        Bond tmp;
-        while (true) {
-            do {
-                j = j - 1;
-            } while ((j >= 0) && (((Bond) bonds.elementAt(j)).start[2] > x));
-
-            do {
-                i = i + 1;
-            } while ((i < bonds.size()) &&
-                    (((Bond) bonds.elementAt(i)).start[2] < x));
-
-            if (i < j) {
-                tmp = (Bond) bonds.elementAt(i);
-                bonds.setElementAt(bonds.elementAt(j), i);
-                bonds.setElementAt(tmp, j);
-            } else {
-                return j;
-            }
-        }
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.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;
+      }
+    }
+  }
+}