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Cleaned up documentation, reworded and added example usage. Update tu…

…torial link to a site which has backed up the now missing web page.
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1 parent e6f3e8a commit 15735a4146d3a6ed8b3420946ed9b660cc0da41b @johnmay committed
Showing with 24 additions and 19 deletions.
  1. +24 −19 src/main/org/openscience/cdk/graph/AtomContainerAtomPermutor.java
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43 src/main/org/openscience/cdk/graph/AtomContainerAtomPermutor.java
@@ -1,10 +1,5 @@
/*
- * $RCSfile$
- * $Author$
- * $Date$
- * $Revision$
- *
- * Copyright (C) 1997-2007 The Chemistry Development Kit (CDK) project
+ * Copyright (C) 1997-2012 The Chemistry Development Kit (CDK) project
*
* Contact: cdk-devel@lists.sourceforge.net
*
@@ -25,7 +20,6 @@
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
- *
*/
package org.openscience.cdk.graph;
@@ -34,21 +28,32 @@
import org.openscience.cdk.Atom;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.tools.LoggingTool;
/**
- * This class allows to iterate trough the set of all possible
- * permutations of the atom order in a given atom container.
- * It allows to check for a dependency of algorithm results
- * on the atom order.
- *
- * <p>The permutation code here is based on a pseudo code example
- * on a tutorial site created and maintained by Phillip P. Fuchs:
- * <a href="http://www.geocities.com/permute_it/pseudo2.html">http://www.geocities.com/permute_it/pseudo2.html</a>.
- *
- *@author steinbeck
+ * This class iterates through all possible permutations of the atom order in a
+ * given atom container. These permutations ensure that the results of an
+ * algorithm are independent of atom order.
+ * <p/>
+ * <pre>{@code
+ *
+ * IAtomContainer container = ...;
+ * AtomContainerPermutor permutor = new AtomContainerAtomPermutor(container);
+ *
+ * while (permutor.hasNext()) {
+ * IAtomContainer permutation = permutor.next();
+ * }
+ *
+ * }</pre>
+ * <p/>
+ * The permutation code here is based on a tutorial by Phillip P. Fuchs.
+ *
@egonw
egonw added a note

Ah, this is a nice example where you can use {@cdk.cite XXXX} ... the URL goes in as bibtexml into

doc/refs/cheminf.bibx

E.g. like:

< bibtex:entry id="BER2001">
< bibtex:misc>
< bibtex:author>Bernstein, H.J./bibtex:author
< bibtex:title>Manual RasMol 2.7.2.1 - CPK Colours/bibtex:title
< bibtex:url>http://www.openrasmol.org/doc/rasmol.html#cpkcolours/bibtex:url
< /bibtex:misc>
< /bibtex:entry>

@johnmay Owner
johnmay added a note

Is this right: 71c3f3b

@egonw
egonw added a note

Link does not work...

@johnmay Owner
johnmay added a note

Hmm... it works for me. Or do you mean in the javadoc?

@egonw
egonw added a note

This one: 71c3f3b

(not away for the party yet?)

@johnmay Owner
johnmay added a note

Not yet, hmm? You mean the commit is missing? I think I squished it...

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+ * @author steinbeck
+ * @see <a href="http://www.oocities.org/permute_it/pseudo2.html">
+ * Phillip P. Fuchs Tutorial</a>
* @cdk.githash
- *@cdk.created 2005-05-04
- *@cdk.keyword permutation
+ * @cdk.created 2005-05-04
+ * @cdk.keyword permutation
*/
public class AtomContainerAtomPermutor extends AtomContainerPermutor
{

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