[Cdk-commits] [cdk/cdk] f37ff6: New API for match ChemFormats - instead of checkin...

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

  Branch: refs/heads/master
  Home:   https://github.com/cdk/cdk
  Commit: f37ff6ec969b6ea391333b7ad92f6a9828753613
      https://github.com/cdk/cdk/commit/f37ff6ec969b6ea391333b7ad92f6a9828753613
  Author: John May <joh...@gm...>
  Date:   2013-09-16 (Mon, 16 Sep 2013)

  Changed paths:
    M src/main/org/openscience/cdk/io/formats/IChemFormatMatcher.java

  Log Message:
  -----------
  New API for match ChemFormats - instead of checking line-by-line the entire header is passed. The matcher then indicates whether it matched, where it matched and what format it is.

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


  Commit: 27731549f0e4c42bf6136a9106d680981b720ef9
      https://github.com/cdk/cdk/commit/27731549f0e4c42bf6136a9106d680981b720ef9
  Author: John May <joh...@gm...>
  Date:   2013-09-16 (Mon, 16 Sep 2013)

  Changed paths:
    A src/META-INF/ioformats.libdepends
    M src/META-INF/test-ioformats.libdepends

  Log Message:
  -----------
  Required dependencies.

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


  Commit: 1c8cdb94e9efbf5bc61634f5d5e518f5b5febdfc
      https://github.com/cdk/cdk/commit/1c8cdb94e9efbf5bc61634f5d5e518f5b5febdfc
  Author: John May <joh...@gm...>
  Date:   2013-09-16 (Mon, 16 Sep 2013)

  Changed paths:
    M src/test/org/openscience/cdk/io/formats/ChemFormatMatcherTest.java

  Log Message:
  -----------
  Updating abstract test to use new API.

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


  Commit: 883face3622b4615f7abf86aa19368028a1d0b77
      https://github.com/cdk/cdk/commit/883face3622b4615f7abf86aa19368028a1d0b77
  Author: John May <joh...@gm...>
  Date:   2013-09-16 (Mon, 16 Sep 2013)

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

  Log Message:
  -----------
  Replacing mock method with new implementation.

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


  Commit: f1762d74f49469143dab229ac7c04dd371fa0914
      https://github.com/cdk/cdk/commit/f1762d74f49469143dab229ac7c04dd371fa0914
  Author: John May <joh...@gm...>
  Date:   2013-09-16 (Mon, 16 Sep 2013)

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

  Log Message:
  -----------
  Using new API to guess format

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


  Commit: fba55ebc03a6859d82b5d5198a76e2d27fa19399
      https://github.com/cdk/cdk/commit/fba55ebc03a6859d82b5d5198a76e2d27fa19399
  Author: John May <joh...@gm...>
  Date:   2013-09-16 (Mon, 16 Sep 2013)

  Changed paths:
    A src/main/org/openscience/cdk/io/formats/SimpleChemFormatMatcher.java

  Log Message:
  -----------
  Default implementation to easily adapt existing matchers.

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


  Commit: 95050f74510573432b0add7f1315325cbc38cbb2
      https://github.com/cdk/cdk/commit/95050f74510573432b0add7f1315325cbc38cbb2
  Author: John May <joh...@gm...>
  Date:   2013-09-16 (Mon, 16 Sep 2013)

  Changed paths:
    M src/main/org/openscience/cdk/io/formats/IChemFormatMatcher.java
    M src/main/org/openscience/cdk/io/formats/SimpleChemFormatMatcher.java

  Log Message:
  -----------
  Moving old API method from interface to abstract super-class.

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


  Commit: e55f3739e6aa74e2bbbd8d2387098be133ff8427
      https://github.com/cdk/cdk/commit/e55f3739e6aa74e2bbbd8d2387098be133ff8427
  Author: John May <joh...@gm...>
  Date:   2013-09-16 (Mon, 16 Sep 2013)

  Changed paths:
    M src/main/org/openscience/cdk/io/formats/ABINITFormat.java
    M src/main/org/openscience/cdk/io/formats/ADFFormat.java
    M src/main/org/openscience/cdk/io/formats/Aces2Format.java
    M src/main/org/openscience/cdk/io/formats/CACheFormat.java
    M src/main/org/openscience/cdk/io/formats/CDKOWLFormat.java
    M src/main/org/openscience/cdk/io/formats/CIFFormat.java
    M src/main/org/openscience/cdk/io/formats/CMLFormat.java
    M src/main/org/openscience/cdk/io/formats/CTXFormat.java
    M src/main/org/openscience/cdk/io/formats/CrystClustFormat.java
    M src/main/org/openscience/cdk/io/formats/DaltonFormat.java
    M src/main/org/openscience/cdk/io/formats/GamessFormat.java
    M src/main/org/openscience/cdk/io/formats/Gaussian03Format.java
    M src/main/org/openscience/cdk/io/formats/Gaussian90Format.java
    M src/main/org/openscience/cdk/io/formats/Gaussian92Format.java
    M src/main/org/openscience/cdk/io/formats/Gaussian94Format.java
    M src/main/org/openscience/cdk/io/formats/Gaussian95Format.java
    M src/main/org/openscience/cdk/io/formats/Gaussian98Format.java
    M src/main/org/openscience/cdk/io/formats/GhemicalMMFormat.java
    M src/main/org/openscience/cdk/io/formats/GhemicalSPMFormat.java
    M src/main/org/openscience/cdk/io/formats/HINFormat.java
    M src/main/org/openscience/cdk/io/formats/INChIFormat.java
    M src/main/org/openscience/cdk/io/formats/INChIPlainTextFormat.java
    M src/main/org/openscience/cdk/io/formats/JaguarFormat.java
    M src/main/org/openscience/cdk/io/formats/MDLFormat.java
    M src/main/org/openscience/cdk/io/formats/MDLRXNFormat.java
    M src/main/org/openscience/cdk/io/formats/MDLRXNV3000Format.java
    M src/main/org/openscience/cdk/io/formats/MDLV2000Format.java
    M src/main/org/openscience/cdk/io/formats/MDLV3000Format.java
    M src/main/org/openscience/cdk/io/formats/MOPAC2002Format.java
    M src/main/org/openscience/cdk/io/formats/MOPAC7Format.java
    M src/main/org/openscience/cdk/io/formats/MOPAC7InputFormat.java
    M src/main/org/openscience/cdk/io/formats/MOPAC93Format.java
    M src/main/org/openscience/cdk/io/formats/MOPAC97Format.java
    M src/main/org/openscience/cdk/io/formats/MoSSOutputFormat.java
    M src/main/org/openscience/cdk/io/formats/Mol2Format.java
    M src/main/org/openscience/cdk/io/formats/NWChemFormat.java
    M src/main/org/openscience/cdk/io/formats/PDBFormat.java
    M src/main/org/openscience/cdk/io/formats/PMPFormat.java
    M src/main/org/openscience/cdk/io/formats/PubChemASNFormat.java
    M src/main/org/openscience/cdk/io/formats/PubChemCompoundXMLFormat.java
    M src/main/org/openscience/cdk/io/formats/PubChemCompoundsXMLFormat.java
    M src/main/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormat.java
    M src/main/org/openscience/cdk/io/formats/PubChemSubstancesASNFormat.java
    M src/main/org/openscience/cdk/io/formats/PubChemSubstancesXMLFormat.java
    M src/main/org/openscience/cdk/io/formats/QChemFormat.java
    M src/main/org/openscience/cdk/io/formats/RGroupQueryFormat.java
    M src/main/org/openscience/cdk/io/formats/SDFFormat.java
    M src/main/org/openscience/cdk/io/formats/ShelXFormat.java
    M src/main/org/openscience/cdk/io/formats/SpartanFormat.java
    M src/main/org/openscience/cdk/io/formats/VASPFormat.java
    M src/main/org/openscience/cdk/io/formats/ZMatrixFormat.java

  Log Message:
  -----------
  Adapting existing formats to new API.

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


  Commit: 073aeb4953f58e7d9afb0f4d16f3c1cb65ee78ae
      https://github.com/cdk/cdk/commit/073aeb4953f58e7d9afb0f4d16f3c1cb65ee78ae
  Author: John May <joh...@gm...>
  Date:   2013-09-16 (Mon, 16 Sep 2013)

  Changed paths:
    M src/main/org/openscience/cdk/io/formats/PubChemCompoundXMLFormat.java

  Log Message:
  -----------
  Updating PubChem Compound XML format to not match PubChem Compounds (plural).

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


  Commit: 5800444297cbf42c7064170238af4dea73fa1e23
      https://github.com/cdk/cdk/commit/5800444297cbf42c7064170238af4dea73fa1e23
  Author: John May <joh...@gm...>
  Date:   2013-09-16 (Mon, 16 Sep 2013)

  Changed paths:
    M src/main/org/openscience/cdk/io/formats/PubChemSubstanceXMLFormat.java

  Log Message:
  -----------
  Allow PubChem Substance to not match PubChem Substances (plural).

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


  Commit: f07a7077ebe56623ce93ea9bafb9a0d170c9e538
      https://github.com/cdk/cdk/commit/f07a7077ebe56623ce93ea9bafb9a0d170c9e538
  Author: John May <joh...@gm...>
  Date:   2013-09-16 (Mon, 16 Sep 2013)

  Changed paths:
    M src/main/org/openscience/cdk/io/formats/MDLRXNV3000Format.java

  Log Message:
  -----------
  Removing matching state from MDLRXN3000 format.

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


  Commit: 16e96a3938ef2331b3fc1c9052231d111a94e699
      https://github.com/cdk/cdk/commit/16e96a3938ef2331b3fc1c9052231d111a94e699
  Author: John May <joh...@gm...>
  Date:   2013-09-16 (Mon, 16 Sep 2013)

  Changed paths:
    M src/META-INF/pdb.libdepends
    M src/META-INF/test-pdb.libdepends

  Log Message:
  -----------
  Dependencies not inherited from ioformats.

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


Compare: https://github.com/cdk/cdk/compare/84edd5d4b366...16e96a3938ef