Open for more bug fixing

Change-Id: I8d9a836aef161059b8e9e2f130ac0391f771d9fe
unit test for bug 1269 (atom... not placed by SDG, causing NPE), remove catch statements, set expected

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
unit test

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
unit test

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added a field to the bond order enumeration allow access to the numeric value for that order.

Change-Id: I69b108218a127dad9ca73994de76558f977a304d
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Replaced IBond.Order.ordinal() usages with IBond.Order.numeric()
Updated the @cdk.bugs taglet to support the new SourceForge project pages

Change-Id: I080fe6433b361a22a054f1d92724ee10291c9679
Added accessor for the bond length in StructureDiagramGenerator

Signed-off-by: John May <john.wilkinsonmay@gmail.com>
A few unit tests uncovering some issues with == comparisons

Change-Id: Ib013c284e1f742a6d7655ec2c81ae01ca2757b07
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>
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>
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>
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>
Replaced subtraction based comparator. This comparator is unlikely to overflow but the safety of using the equalities ensures the proper behaviour of this comparator.

Change-Id: I4cf311f327e53754e189c5734147a245446495ac
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Corrected null handling on AtomContainer 2D centre comparison. Previous if either container was null the comparator would incorrectly return '0' indicating they were equal. The method was changed to always provide a minimum Point2d when an atom container is null. This will sort all null containers lower then non-null containers.

Change-Id: I49d919c7d0cf0ea17a65e2a031c1a827bdbbbb50
Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Updated comparator on AtomPlacer. The comparator now uses the built in Integer comparator. To avoid null pointer exceptions the access to the weight value is wrapped in a private method which return the minimum integer value when the weight is not set (i.e. null).
Updated PMD to version 5.0.1

Change-Id: Ibb369c1eefdf6e65ad5d32cc99495f82ad9c0908