Altered data structure #13

abradle · 2016-04-13T11:38:06Z

Altered data structure so that:

Decoder and encoder are symmetric
We can accommodate different serializers, not just MessagePack
Can accommodate different codec strategies

…ructure updated to follow suit

…ependency alltogether

Integration tests pass.

…as some bioassemblies do not have an index).

… 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.

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.

We now use " "

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.

Small refactoring in other modules

Another review session, thanks everyone!

…ng changes.

…. Some changing of whitespace.

…ectly

…izer

…he dependency issues. It will be moved to mmtf-update repo

coveralls · 2016-04-13T11:41:01Z

Coverage decreased (-32.8%) to 16.245% when pulling 407e6d4 on alter_data_struct into b09bc3a on master.

coveralls · 2016-04-13T11:45:32Z

Coverage decreased (-32.8%) to 16.245% when pulling 403e905 on alter_data_struct into b09bc3a on master.

…tests

… writer

coveralls · 2016-04-13T22:21:22Z

Coverage increased (+41.7%) to 90.759% when pulling 8f43dba on alter_data_struct into b09bc3a on master.

abradle and others added 30 commits April 1, 2016 17:39

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

7023ffb

…ructure updated to follow suit

Updates to remove Entity and PDBGroup from the DataApi interface

a01d4dd

Updates to remove Bioassembly from the data api and the mmtf-common d…

78c0b1f

…ependency alltogether

Altered the groupMap to a groupList.

3b23493

Integration tests pass.

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

61b749d

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

fa92ea6

…as some bioassemblies do not have an index).

Bioassemblies now generate correectly for asym ids. Test - checks to…

88ca101

… 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.

No longer values for missing resolution/rFree/rWork values

950b785

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.

Update to include the deposition date in ISO date format.

04980af

pdbId renmaed to structureId

bcc881e

Renamed seqResIdList field to sequenceIdList

ad1d951

Rename occList field to occupancyList

2a8abe9

no "?" to indicate an empty/unknown value in altLabelList, insCodeList

a250522

We now use " "

Updates to the alt label and ins code lists.

09da648

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.

Dssp type is now encoded as an Enum.

1dc3e1f

Refactored the array decompressor lib to get rid of redundant code

b8c1d15

Added improved tests to the decoder

fd07dd9

Remove unneeded ArrayList references

88af555

Some more cleanup

5caa76f

Downstream changes from Biojava refactoring

ce44086

Turned the groupType map into an enum.

08393fe

Small refactoring in other modules

Another review session, thanks everyone!

1aede7a

Merge pull request #11 from josemduarte/dev

e5d6043

Another review session, thanks everyone!

Updates to the interface from meeting. Fix downstream errors.

a477d8b

Updates to the documentaion of the functions and some more whitespaci…

5de2874

…ng changes.

More docs and formatting

f58f428

Updates to the tests and the fomrating. Some renaming and refactoring…

df7e06f

…. Some changing of whitespace.

Update the gitignore to track the file generated by mmtf-update

a00e19e

White space moving

72e1358

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

f6ea3bd

abradle added 12 commits April 12, 2016 10:08

Updates to the naming of bioassembly related fields

84e6edf

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

aa8d070

…ectly

Updates to incluide release date into the format

4c38e19

Rename sequenceIdList to sequenceIndexList

a817843

Update to include to pass releaseDate into the mmtf bean

5bef90b

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

7aa7991

…izer

Added coveralls integration

a3ff0b5

Added cobertura integration

46ffe47

Run cobertura on travis

44807e6

Update README.md

4a2d185

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

db82cca

…he dependency issues. It will be moved to mmtf-update repo

Refactoring of the names of the interfaces and decoder/encoder classes.

407e6d4

Removed pointless SeDeserializer interfaces

403e905

abradle added 12 commits April 13, 2016 04:49

Some more refactoring and docs for the encoder

b7b44b8

Added new tests for hte decoder

38e0f39

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

ddb0955

…tests

Updates and refactoring to the encoder to fix data inconsistencies in…

eb712d5

… writer

Change to the DummAPIimpl to increase code coverage

fec2df8

Add test dataholder class

0cd57c0

Added tests for the message pack serializer / deserializers

712cea3

Remove unuseful try catch

c1e6b75

Check PDBGroup equals method works

917c482

Added new tests for the encoder decoder and common

2f01599

Some more tests and test more cases. ReaderUtils still not tested

5a23868

Merge branch 'master' into alter_data_struct

8f43dba

abradle merged commit c68481c into master Apr 13, 2016

abradle deleted the alter_data_struct branch April 22, 2016 12:53

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Altered data structure #13

Altered data structure #13

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Altered data structure #13

Altered data structure #13

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abradle commented Apr 13, 2016

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