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Altered data structure #13

Merged
merged 112 commits into from
Apr 13, 2016
Merged

Altered data structure #13

merged 112 commits into from
Apr 13, 2016

Commits on Apr 2, 2016

  1. Updated poms to dev mode. Interface is now just primitives. Decode st… 

    …ructure updated to follow suit
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  2. Updates to remove Entity and PDBGroup from the DataApi interface

    @abradle
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  3. Updates to remove Bioassembly from the data api and the mmtf-common d… 

    …ependency alltogether
    @abradle
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  4. Altered the groupMap to a groupList. 

    Integration tests pass.
    @abradle
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Commits on Apr 4, 2016

  1. Fixed a bug where the same array was being declared in two places

    @abradle
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  2. Updates to bioassembly handling. However this still fails the tests (… 

    …as some bioassemblies do not have an index).
    @abradle
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  3. Bioassemblies now generate correectly for asym ids. Test - checks to… 

    … see that any missing chain is actually missing from the structure.

    If parsing usign auth ids - bioassemby info isn't available - as no way to pass indices to auth chains.
    @abradle
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Commits on Apr 5, 2016

  1. No longer values for missing resolution/rFree/rWork values 

    Null values are missing from the file now.
For the API 99.0 is the default for resolution and 1.0 for rfree and rwork.
    @abradle
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  2. Update to include the deposition date in ISO date format.

    @abradle
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  3. pdbId renmaed to structureId

    @abradle
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  4. Renamed seqResIdList field to sequenceIdList

    @abradle
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  5. Rename occList field to occupancyList

    @abradle
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  6. no "?" to indicate an empty/unknown value in altLabelList, insCodeList 

    We now use " "
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  7. Updates to the alt label and ins code lists. 

    They are both now int[] not List<String>. First element is the ASCII id for the character. Second elemnet is the number of elements to be repeated.
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  8. Dssp type is now encoded as an Enum.

    @abradle
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  9. Refactored the array decompressor lib to get rid of redundant code

    @abradle
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  10. Added improved tests to the decoder

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  11. Remove unneeded ArrayList references

    @abradle
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  12. Some more cleanup

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  13. Downstream changes from Biojava refactoring

    @abradle
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  14. Turned the groupType map into an enum. 

    Small refactoring in other modules
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  15. Another review session, thanks everyone!

    @josemduarte
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  16. Merge pull request #11 from josemduarte/dev 

    Another review session, thanks everyone!
    @abradle
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Commits on Apr 6, 2016

  1. Updates to the interface from meeting. Fix downstream errors.

    @abradle
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  2. Updates to the documentaion of the functions and some more whitespaci… 

    …ng changes.
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  3. More docs and formatting

    @abradle
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  4. Updates to the tests and the fomrating. Some renaming and refactoring… 

    …. Some changing of whitespace.
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  5. Update the gitignore to track the file generated by mmtf-update

    @abradle
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  6. White space moving

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  7. Added a demo of using the DataApi to move through a structure.

    @abradle
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  8. Some refactoring of the demo

    @abradle
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  9. Updated the MMTF bean altLabelList to altLocList

    @abradle
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  10. Updates and refactoring to the code

    @abradle
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  11. Minor refactoring

    @abradle
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  12. Updates and refactoring of white space

    @abradle
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  13. Updates and some refactoring to the encoder

    @abradle
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  14. Introducing logging in dependencies, now let's use it!

    @josemduarte
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  15. Fairly extensive refactoring and setting of a series of tests to be w… 

    …ritten.
    @abradle
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  16. Merge pull request #12 from josemduarte/dev 

    Introducing logging in dependencies
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  17. Merge branch 'dev' of github.com:rcsb/mmtf-java into dev

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  18. Updates and refactoring to the encoder. Extract an interface from the… 

    … encoder. Biojava is the first implementation of that interface.
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  19. Updates to remove warnings and to refactor

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  20. Refactoring after another group meeting.

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Commits on Apr 7, 2016

  1. Updates to pass the data information through the data chain

    @abradle
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  2. Refactored the array compressors into a single class. 

    I've moved this class into the encoder package.
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  3. Updates to the docs on the decoded data api interface

    @abradle
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  4. First commit of an interface of setters for setting the data into the… 

    … data model
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  5. Added a new array decoders class to hold the array decoders and map o… 

    …ne to one onto arrayencoders
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  6. Minor changes and refactoring

    @abradle
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  7. Some more updates to the decoder library.

    @abradle
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  8. Updates to the tests to remove warnings

    @abradle
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  9. More elegant handling and improvements 

    1) Conversion from and to byte[]
2) Using Biojava to encode data
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  10. Updates and refactoring on the way towards restructuring the Decoder … 

    …and Encoder and removin Biojava as a dependency
    @abradle
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  11. Refactored API as per Alex's suggestions

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  12. New class to fill a get API from an arbitrary data source using the i… 

    …nflator interface
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  13. Make PDBGroup primitive types

    @abradle
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  14. Update the Interface to not require a data setter. 

    Updated the Implementation to have proper getters.
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  15. Extensive refactoring and cleanup of the decoder and the PDBGroup. 

    Upstream changes to the APIs based on spotting some missing data.
    @abradle
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Commits on Apr 8, 2016

  1. Downstream refactoring the update

    @abradle
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  2. Further refactoring and modifications. 

    Added the map of group to sequence.
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  3. Removed all dependeices on Biojava from the encoder. 

    Moved some tests to the integration tests.
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  4. Downstream refactoring of the update module. 

    Altered the two serializer apis intio one interface.
    @abradle
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  5. Culling of all the data beans and moving around of tests.

    @abradle
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  6. Refactoring and restructuring. 

    Addition of unit testing to map onto the new Decoders,Encoders and Converters
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  7. Updated the decoder to the new static methods

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  8. Update to the encoder to follow the same path as the decoder. 

    Upstream refactoring too.
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  9. Finished writing unit tests (tests pass) and the Encoder converters a… 

    …nd encoders.
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  10. Set the group to sequence mapping indices better.

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  11. Remove setter repetition

    @abradle
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  12. Moved the serializer tests to update

    @abradle
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  13. Added a reader and writer interface. 

    GettoInflator now implements the reader interface
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Commits on Apr 9, 2016

  1. Refactoring of the code and tests in mmtf-update. 

    All compile errors and warnings removed.
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  2. Some more refactoring and lyering to get the update module to work. 

    Improvements in te deflator and  some debugging.
    @abradle
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Commits on Apr 11, 2016

  1. Integration tests now pass for all structures. 

    Added secondary structure information to the setGroupInfo and an API function to get the secStructList.
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  2. Update the pom to compile junit 

    Added the new test roundtrip
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  3. Updates to the dataholder tests and mmtfbean so that tests pass.

    @abradle
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  4. Make the mapper static

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  5. Added tests for the codec utils class

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  6. Refactored the names of the Decoding and Encoding functions

    @abradle
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  7. Some more refactoring and addtion of comments

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  8. Refactored the git version packaged into mmtf-common

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  9. Refacotred the examples package into mmtf-update

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  10. Refactored functions out of DataApiToReader into a Utils class

    @abradle
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  11. Updated the names of test. 

    Made a new download utils class in common for downloading data.
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Commits on Apr 12, 2016

  1. Updates to consider alt loc and insertion code information better.

    @abradle
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  2. Refactored removed the pointless Reader and Writer interfaces

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  3. Update to store insCodeList & altLocList as byte arrays

    @abradle
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  4. Updates to the naming of bioassembly related fields

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  5. Unit tests that check array encoder/decoders handle empty arrays corr… 

    …ectly
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  6. Updates to incluide release date into the format

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  7. Rename sequenceIdList to sequenceIndexList

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  8. Update to include to pass releaseDate into the mmtf bean

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  9. Updates to remove any mention of the Messagepack serializer /deserial… 

    …izer
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Commits on Apr 13, 2016

  1. Added coveralls integration

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  2. Added cobertura integration

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  3. Run cobertura on travis

    @abradle
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  4. Update README.md

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  5. Refactored the mmtf-update project out of mmtf-java. This is due to t… 

    …he dependency issues.

It will be moved to mmtf-update repo
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  6. Refactoring of the names of the interfaces and decoder/encoder classes.

    @abradle
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  7. Removed pointless SeDeserializer interfaces

    @abradle
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  8. Some more refactoring and docs for the encoder

    @abradle
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  9. Added new tests for hte decoder

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  10. Updates to the encoder tests and fixed a couple of bugs found by the … 

    …tests
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  11. Updates and refactoring to the encoder to fix data inconsistencies in… 

    … writer
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  12. Change to the DummAPIimpl to increase code coverage

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  13. Add test dataholder class

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    abradle committed Apr 13, 2016
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  14. Added tests for the message pack serializer / deserializers

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    abradle committed Apr 13, 2016
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  15. Remove unuseful try catch

    @abradle
    abradle committed Apr 13, 2016
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  16. Check PDBGroup equals method works

    @abradle
    abradle committed Apr 13, 2016
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  17. Added new tests for the encoder decoder and common

    @abradle
    abradle committed Apr 13, 2016
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  18. Some more tests and test more cases. ReaderUtils still not tested

    @abradle
    abradle committed Apr 13, 2016
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  19. Merge branch 'master' into alter_data_struct

    @abradle
    abradle committed Apr 13, 2016
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