Added a method to order the cells of a partition

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added a method to check that two elements are in the same cell of a partition

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Fixed a bug in the fromString static method of Partition, and test for the case that caused it

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
The second half of the group module, containing the majority of the important stuff : The key classes are the Atom and Bond Discrete Partition Refiners.

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Additional patch for aromatic support, and test cases borowed from bug 1250

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Additional patch that calls refine before returning the automorphism partition

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Post-review fixes; javadocs, making permutation final, improvement to partition refiner

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Alter the data representation in the refiners, and fix some test cases for the Bond Refiner

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added a missing dependency

Change-Id: I02c34ec7e205186868cab24fd28418535b556eca
Added more unit tests for the MDLV2000Writer - including corner cases such as multiline RGPs, atom aliases, truncated atom aliases and pseudo atoms with null labels. The MDLV2000Writer can now handle all of these cases correctly.

Change-Id: I3d134d23fc6252d7425fa2a8c50fb308d058ec7d
Signed-off-by: Stephan Beisken <beisken@ebi.ac.uk>
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Revert "Added more unit tests for the MDLV2000Writer - including corner cases such as multiline RGPs, atom aliases, truncated atom aliases and pseudo atoms with null labels. The MDLV2000Writer can now handle all of these cases correctly."

This reverts commit e3b1c8e8b75325b8fd72cfcfda49fa5176ff60d9.
Added more unit tests for the MDLV2000Writer - including corner cases such as multiline RGPs, atom aliases, truncated atom aliases and pseudo atoms with null labels. The MDLV2000Writer can now handle all of these cases correctly.

Change-Id: I3d134d23fc6252d7425fa2a8c50fb308d058ec7d
Signed-off-by: Stephan Beisken <beisken@ebi.ac.uk>
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Proper modules (wasn't this fixed earlier already??)

Change-Id: I5598c9f4b68699081958e257e3062affe820f40b
Corrected comparator in InvPair sorting. The current comparison was in violation of the comparable contract which was throwing an IllegalArgumentException on JRE 7.

Change-Id: I5d3753a51afcb38585f2f17dac0c769c564ebac8
Signed-off-by: maclean <gilleain.torrance@gmail.com>
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Generified comparators, removing redundant casts

Change-Id: I266c7c45501f91c04577d572870e858d2140b171
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

Conflicts:
	src/main/org/openscience/cdk/smiles/SmilesGenerator.java
corrected handling of null value in the TreeNodeComparator. Previous if any node or atom were null the comparator would return '0' which is incorrect. If one is null and the other is not the objects are not equal.

Change-Id: I928a6832ec15cdf5fad67a9dec41bcec51b05db1
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

Conflicts:
	src/main/org/openscience/cdk/tools/HOSECodeGenerator.java
Corrected canonical label sorting in the SmilesGenerator. This canonical labels are long and thus when the difference between two values is taken the result may be larger then the largest possible integer. This in rare cases cause the value to overflow and thus make the comparator non-transitive.

Change-Id: Ibaba56bb5e559bbf250459689e6b0cc5b286fa03
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>

Conflicts:
	src/main/org/openscience/cdk/smiles/SmilesGenerator.java
Make sure the tests are also run with JUnit4

Change-Id: Ie304f2f8ea4cba60e4f02f899b9ec70c236912aa
OK, simple fix: reset the test graph before each test method call

Change-Id: Ic581d65471ce29e55f9680a3345158970c346f4a
Replaced subtraction based comparison. When the difference (which is a double) is converted to an integer the result may overflow. This overflow can occur in rare cases but would cause the comparator to be non-transitive.

Change-Id: Ic7deea389f63273202288e6d11cc19af94f08d63
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>