X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FZsort.java;h=419cb9cb4bc2393910db39bb4e7f396d5237b396;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=f7f2c39274ce18aeaef10f4aeddf36d944cdfcee;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git
diff --git a/src/MCview/Zsort.java b/src/MCview/Zsort.java
index f7f2c39..419cb9c 100755
--- a/src/MCview/Zsort.java
+++ b/src/MCview/Zsort.java
@@ -1,75 +1,80 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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 2.9.0b2)
+ * 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 .
+ * 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;
+ }
+ }
+ }
+}