-/*\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 ($$Version-Rel$$)
+ * 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.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;
+ }
+ }
+ }
+}