[Cdk-commits] [cdk/cdk] b2dbc1: IteratingMDLReader Skip Patch

[GitHub <no...@gi...>]

  Branch: refs/heads/master
  Home:   https://github.com/cdk/cdk
  Commit: b2dbc1a23900c2dc6766815db5fba2cffc6118e3
      https://github.com/cdk/cdk/commit/b2dbc1a23900c2dc6766815db5fba2cffc6118e3
  Author: John May <joh...@gm...>
  Date:   2012-03-23 (Fri, 23 Mar 2012)

  Changed paths:
    M src/main/org/openscience/cdk/io/iterator/IteratingSDFReader.java
  A src/test/data/mdl/bug3488307.sdf
  M src/test/org/openscience/cdk/io/iterator/IteratingSDFReaderTest.java

  Log Message:
  -----------
  IteratingMDLReader Skip Patch

Provides skip functionality to IteratingMDLReader. If a molecule is null the reader
can skip over it (if 'skip' boolean is set true). The skip property is set via an
mutator 'setSkip' or in the constructor. If a null molecule is read the read will
skip forward until the next record separator ($$$$). The commit include a unit test
for the patch which uses some molecules from the HMDB sdf file.

Change-Id: Ie116eb1d5119357bec049a66e2d1a0a2a3dcb620
Signed-off-by: Egon Willighagen <eg...@us...>

Conflicts:

	src/main/org/openscience/cdk/io/iterator/IteratingSDFReader.java
	src/test/org/openscience/cdk/io/iterator/IteratingSDFReaderTest.java


  Commit: a51b2aef147962d39889e2eac5bf99d7c9deb4d2
      https://github.com/cdk/cdk/commit/a51b2aef147962d39889e2eac5bf99d7c9deb4d2
  Author: Egon Willighagen <eg...@us...>
  Date:   2012-03-23 (Fri, 23 Mar 2012)

  Changed paths:
    M src/main/org/openscience/cdk/smsd/algorithm/rgraph/CDKMCSHandler.java
  M src/main/org/openscience/cdk/smsd/algorithm/rgraph/CDKSubGraphHandler.java

  Log Message:
  -----------
  Fixed link to the CDKMCS class, which is now in a different package

Change-Id: I357116a906d44821d2bf55c9ea406f8af73a5f3f


  Commit: fd86c19d1e9191a6ac57bf174f19ef46a50a79ca
      https://github.com/cdk/cdk/commit/fd86c19d1e9191a6ac57bf174f19ef46a50a79ca
  Author: Egon Willighagen <eg...@us...>
  Date:   2012-03-23 (Fri, 23 Mar 2012)

  Changed paths:
    M src/main/org/openscience/cdk/controller/IMouseEventRelay.java

  Log Message:
  -----------
  Synchronized variable names in the API and JavaDoc

Change-Id: Ie337970d25e85ae0af7049ff4bb0e8047e1413ed


  Commit: fa405ecc4df29c33936ea10423f44c0e42d50001
      https://github.com/cdk/cdk/commit/fa405ecc4df29c33936ea10423f44c0e42d50001
  Author: Egon Willighagen <eg...@us...>
  Date:   2012-03-23 (Fri, 23 Mar 2012)

  Changed paths:
    M src/main/org/openscience/cdk/io/iterator/IteratingSDFReader.java

  Log Message:
  -----------
  Inline linking is done with @link, not @see

Change-Id: I62438e365c11b0f774673ddc6c72efec336aa7d3


  Commit: 3523643de407a9b2522dc4183354af12cb12e1cd
      https://github.com/cdk/cdk/commit/3523643de407a9b2522dc4183354af12cb12e1cd
  Author: Egon Willighagen <eg...@us...>
  Date:   2012-03-23 (Fri, 23 Mar 2012)

  Changed paths:
    M src/main/org/openscience/cdk/tools/manipulator/MolecularFormulaManipulator.java

  Log Message:
  -----------
  Added a missing # in the @see (needed for methods)

Change-Id: I179e27073da3086cb8d367a982dfba51c1ce5679


  Commit: a68fcc2ce4f792b1c8fa307e9aebc646de4e5e88
      https://github.com/cdk/cdk/commit/a68fcc2ce4f792b1c8fa307e9aebc646de4e5e88
  Author: Egon Willighagen <eg...@us...>
  Date:   2012-03-23 (Fri, 23 Mar 2012)

  Changed paths:
    M src/main/org/openscience/cdk/smsd/algorithm/matchers/DefaultMCSPlusAtomMatcher.java
  M src/main/org/openscience/cdk/smsd/algorithm/matchers/DefaultRGraphAtomMatcher.java
  M src/main/org/openscience/cdk/smsd/algorithm/matchers/DefaultVFAtomMatcher.java
  M src/main/org/openscience/cdk/smsd/algorithm/mcsplus/ExactMapping.java
  M src/main/org/openscience/cdk/smsd/filters/ChemicalFilters.java
  M src/main/org/openscience/cdk/smsd/labelling/ICanonicalReactionLabeller.java
  M src/main/org/openscience/cdk/smsd/ring/HanserRingFinder.java

  Log Message:
  -----------
  Fixed empty @return javadoc tags: some removed (e.g. with @inheritDoc), some now got a description

Change-Id: I646a1f0107943e9d9b9c224a1ca219b18972eb2f


  Commit: 53c14901262793819a242f54db0141f73cf36bc7
      https://github.com/cdk/cdk/commit/53c14901262793819a242f54db0141f73cf36bc7
  Author: John May <joh...@gm...>
  Date:   2012-03-23 (Fri, 23 Mar 2012)

  Changed paths:
    M src/test/org/openscience/cdk/io/iterator/IteratingSDFReaderTest.java

  Log Message:
  -----------
  Removing redundant code

Removes code that was used when writing the test and is not used any
more

Signed-off-by: Rajarshi Guha <raj...@gm...>


  Commit: 07d42e123a542ff9e54fe468d2302ed717344049
      https://github.com/cdk/cdk/commit/07d42e123a542ff9e54fe468d2302ed717344049
  Author: Egon Willighagen <ego...@gm...>
  Date:   2012-03-23 (Fri, 23 Mar 2012)

  Changed paths:
    M src/test/org/openscience/cdk/coverage/CoverageAnnotationTest.java

  Log Message:
  -----------
  Bridge methods are methods introduced by compilers in relation to methods that use generics. Various renderer related method trigger test methods for just bridge methods, but are never really implemented.

For example, the below interface code causes the coverage test before
this patch to expect the bridge generate(IChemObject object, RendererModel model)
method to be tested:

public interface IGenerator<T extends IChemObject>  {
  public IRenderingElement generate(T object, RendererModel model);
}

This fix now skips these bridge methods from coverage testing.

(Thanx to Arvid Berg for pointing me to the Method.isBridge() method!)


Compare: https://github.com/cdk/cdk/compare/6d051a6...07d42e1