JAL-1432 updated copyright notices

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

diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java
index 215f753..0e7a271 100755 (executable)
--- a/src/MCview/Zsort.java
+++ b/src/MCview/Zsort.java
@@ -1,69 +1,73 @@
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
-*/\r
-\r
-package MCview;\r
-\r
-import java.util.*;\r
-\r
-public class Zsort {\r
-\r
-  public static void Zsort(Vector bonds) {\r
-\r
-    sort(bonds,0,bonds.size()-1);\r
-  }\r
-\r
-\r
-\r
-  public static void sort(Vector bonds,int p, int r) {\r
-    int q;\r
-\r
-    if (p < r) {\r
-      q = partition(bonds,p,r);\r
-      sort(bonds,p,q);\r
-      sort(bonds,q+1,r);\r
-    }\r
-  }\r
-\r
-  private static int partition(Vector bonds, int p, int r) {\r
-    float x = ((Bond)bonds.elementAt(p)).start[2];\r
-    int i = p-1;\r
-    int j = r+1;\r
-\r
-    while(true) {\r
-      do {\r
-        j = j-1;\r
-      }        while (j >= 0  && ((Bond)bonds.elementAt(j)).start[2] > x);\r
-\r
-      do {\r
-        i = i+1;\r
-      } while (i < bonds.size() && ((Bond)bonds.elementAt(i)).start[2] < x);\r
-\r
-      if ( i < j) {\r
-        Bond tmp = (Bond)bonds.elementAt(i);\r
-        bonds.setElementAt(bonds.elementAt(j),i);\r
-        bonds.setElementAt(tmp,j);\r
-      } else {\r
-        return j;\r
-      }\r
-    }\r
-  }\r
-}\r
-\r
-\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.*;
+
+public class Zsort
+{
+  public void Zsort(Vector bonds)
+  {
+    sort(bonds, 0, bonds.size() - 1);
+  }
+
+  public 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 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--;
+      } while ((j >= 0) && (((Bond) bonds.elementAt(j)).start[2] > x));
+
+      do
+      {
+        i++;
+      } 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;
+      }
+    }
+  }
+}