Migrating NomParser to 'cdk-legacy'.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Move all 'cdk-qm' code to 'cdk-legacy'. The custom PMD rulesets (no removed) seem no different from '/pmd/custom-data.xml' and was not specific to 'qm' code.

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

Conflicts:
	legacy/src/test/java/org/openscience/cdk/math/GaussiansCalculationTest.java
	misc/qm/src/test/java/org/openscience/cdk/coverage/QmCoverageTest.java
	misc/qm/src/test/java/org/openscience/cdk/modulesuites/MqmTests.java

Change-Id: Icf6b051d50a0931e23fa16ea08b4a039a6eac219
Resolve review comments. Ensure copyright is intact and added a hyperlink.

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Synchronise bits in IntArrayFingerprint, old pre-maven patch (pull/34).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Double check locking of chem object builders. Follows on from a jonalv pre-maven patch (pull/34).

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
Parameterized generic types

Change-Id: I2bbc37af6e0f0c04a3d9f3e8a0adaaf66461b8d1
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Parameterized generic types

Change-Id: I0d7e19c187f5f45be94d09232ae678809e9cddf8
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Typed the Comparator

Change-Id: I010ca701c13010fc50d91d8a5584b44929321f3b
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Added more closing of IO resources

Change-Id: I68cd72f7a2c761c969cc707f0492b0f0f87c9591
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removed redundant, floating JavaDoc

Change-Id: Ic77fc2855efcc34b9b4888e769e1e088b4982f8c
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removed unused imports

Change-Id: If4342394f117be2b6d5d3567e4d22c8d046f83dc
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removed redundant, floating JavaDoc

Change-Id: I3b4b36d2ebba8db78c3b1c11a3da83ca730f222e
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Synchronized the APIs with the changes introduced in commit 5baedfeec823813395bffdaf14dbd0c4fc19f395

Change-Id: I2e3b403b2d70f216314c64efaa99503095551120
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Use Integer|Double.valueof()

Change-Id: Idba9d882c9fd1cf22b7a336e3d6920db09ae1647
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Removed redundant check

Change-Id: Ib4bb3fd098d25dc1f9a1d916c62a325a6a5fda37
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Simpler and/or more efficient String handling

Change-Id: Ib46973c7f67ea8345ac13d347bed0febeae43780
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Use equals() to compare String's

Change-Id: I7f9ec954265ef1771e6f4ce66788f5d464b25505
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Use indexOf(char) instead of indexOf(String) whenever possible

Change-Id: I6aee376b35df4b61abbdde8551281e937110bb7e
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Various optimizations.

- the ILoggingTool allows you to pass an arbitrary number of parameters, which it will concatenate
  only when that logging level is turned on. In many cases it means less String concatenation.
- use charAt(chat) instead of startsWith(char)
- removed a needless String instantiation

Change-Id: I9da89d4d51c704c4615e03db5a63678926459f56
Signed-off-by: John May <john.wilkinsonmay@gmail.com>
Also updated the silent MolecularFormula class

Change-Id: If5b5c2c5179ddc8dedb32a89da76cd2110bc768d
Signed-off-by: John May <john.wilkinsonmay@gmail.com>