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Fixed issues around reduced format #41

Merged
merged 10 commits into from
Jun 14, 2017
Merged

Fixed issues around reduced format #41

merged 10 commits into from
Jun 14, 2017

Commits on Jun 13, 2017

  1. Removed dead code in addEntityInfo. Closes #38

    @pwrose
    pwrose committed Jun 13, 2017
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  2. Made classes serializable for use in Spark.

    @pwrose
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  3. Made serializable for use in Spark, clear transient entities, and 

    declared List<Entity> entities transient to avoid serializing temporary
data structures, added setMmtfProducer method.
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    pwrose committed Jun 13, 2017
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  4. Resolved incorrect indexing in the data structure. Create a 

    comprehensive test for the reduced data structure.
    @pwrose
    pwrose committed Jun 13, 2017
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  5. Added check for solvent DOD.

    @pwrose
    pwrose committed Jun 13, 2017
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  6. Added test cases from MMTF project, as well as special case to test for 

    DOD as a solvent. Now also checking for DOD in the ReducedEncoder.
    @pwrose
    pwrose committed Jun 13, 2017
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  7. Updated 4CUP pdbId to upper case so all test files are in consistent 

    case.
    @pwrose
    pwrose committed Jun 13, 2017
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  8. Converted PdbID 4cup to upper case so it matches the test files.

    @pwrose
    pwrose committed Jun 13, 2017
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  9. Corrected initialization of reducedAtomCount, needs to start at -1, not 

    0.
    @pwrose
    pwrose committed Jun 13, 2017
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  10. Merge branch 'master' of https://github.com/pwrose/mmtf-java 

    Updating ReducedEncoder
    @pwrose
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