X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2FMCview%2FZsort.java;h=6bdbafa14a3d8d7e32ae01f29ff28bd6f10c1f11;hb=4a43369c96bc932961492509c4008972d4d566e5;hp=8325f9a5d468ad10cf2a62581ad4c8d92e53bcf7;hpb=fbf0a6e1eb4869dc676334a30c9e40b60a7659ac;p=jalview.git
diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java
index 8325f9a..6bdbafa 100755
--- a/src/MCview/Zsort.java
+++ b/src/MCview/Zsort.java
@@ -1,63 +1,80 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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 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;
- }
- }
- }
-}
+/*
+ * 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 .
+ * 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 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 = 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;
+ }
+ }
+ }
+}