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Altered data structure #13

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merged 112 commits into from
Apr 13, 2016
Merged

Altered data structure #13

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7023ffb
Updated poms to dev mode. Interface is now just primitives. Decode st…
abradle Apr 2, 2016
a01d4dd
Updates to remove Entity and PDBGroup from the DataApi interface
abradle Apr 2, 2016
78c0b1f
Updates to remove Bioassembly from the data api and the mmtf-common d…
abradle Apr 2, 2016
3b23493
Altered the groupMap to a groupList.
abradle Apr 2, 2016
61b749d
Fixed a bug where the same array was being declared in two places
abradle Apr 2, 2016
fa92ea6
Updates to bioassembly handling. However this still fails the tests (…
abradle Apr 4, 2016
88ca101
Bioassemblies now generate correectly for asym ids. Test - checks…
abradle Apr 4, 2016
950b785
No longer values for missing resolution/rFree/rWork values
abradle Apr 5, 2016
04980af
Update to include the deposition date in ISO date format.
abradle Apr 5, 2016
bcc881e
pdbId renmaed to structureId
abradle Apr 5, 2016
ad1d951
Renamed seqResIdList field to sequenceIdList
abradle Apr 5, 2016
2a8abe9
Rename occList field to occupancyList
abradle Apr 5, 2016
a250522
no "?" to indicate an empty/unknown value in altLabelList, insCodeList
abradle Apr 5, 2016
09da648
Updates to the alt label and ins code lists.
abradle Apr 5, 2016
1dc3e1f
Dssp type is now encoded as an Enum.
abradle Apr 5, 2016
b8c1d15
Refactored the array decompressor lib to get rid of redundant code
abradle Apr 5, 2016
fd07dd9
Added improved tests to the decoder
abradle Apr 5, 2016
88af555
Remove unneeded ArrayList references
abradle Apr 5, 2016
5caa76f
Some more cleanup
abradle Apr 5, 2016
ce44086
Downstream changes from Biojava refactoring
abradle Apr 5, 2016
08393fe
Turned the groupType map into an enum.
abradle Apr 5, 2016
1aede7a
Another review session, thanks everyone!
josemduarte Apr 5, 2016
e5d6043
Merge pull request #11 from josemduarte/dev
abradle Apr 5, 2016
a477d8b
Updates to the interface from meeting. Fix downstream errors.
abradle Apr 6, 2016
5de2874
Updates to the documentaion of the functions and some more whitespaci…
abradle Apr 6, 2016
f58f428
More docs and formatting
abradle Apr 6, 2016
df7e06f
Updates to the tests and the fomrating. Some renaming and refactoring…
abradle Apr 6, 2016
a00e19e
Update the gitignore to track the file generated by mmtf-update
abradle Apr 6, 2016
72e1358
White space moving
abradle Apr 6, 2016
f6ea3bd
Added a demo of using the DataApi to move through a structure.
abradle Apr 6, 2016
ffdc193
Some refactoring of the demo
abradle Apr 6, 2016
63a3fc1
Updated the MMTF bean altLabelList to altLocList
abradle Apr 6, 2016
00fb2a3
Updates and refactoring to the code
abradle Apr 6, 2016
fde6dd9
Minor refactoring
abradle Apr 6, 2016
d2c81bd
Updates and refactoring of white space
abradle Apr 6, 2016
f0921f0
Updates and some refactoring to the encoder
abradle Apr 6, 2016
90c02f6
Introducing logging in dependencies, now let's use it!
josemduarte Apr 6, 2016
fadbd6b
Fairly extensive refactoring and setting of a series of tests to be w…
abradle Apr 6, 2016
b27823f
Merge pull request #12 from josemduarte/dev
abradle Apr 6, 2016
fab7f3a
Merge branch 'dev' of github.com:rcsb/mmtf-java into dev
abradle Apr 6, 2016
68fe3be
Updates and refactoring to the encoder. Extract an interface from the…
abradle Apr 6, 2016
1c729ac
Updates to remove warnings and to refactor
abradle Apr 6, 2016
adf06cd
Refactoring after another group meeting.
abradle Apr 6, 2016
b206168
Updates to pass the data information through the data chain
abradle Apr 7, 2016
e8953af
Refactored the array compressors into a single class.
abradle Apr 7, 2016
00e1f38
Updates to the docs on the decoded data api interface
abradle Apr 7, 2016
a6a532a
First commit of an interface of setters for setting the data into the…
abradle Apr 7, 2016
825ce34
Added a new array decoders class to hold the array decoders and map o…
abradle Apr 7, 2016
7044be2
Minor changes and refactoring
abradle Apr 7, 2016
7e8aa5e
Some more updates to the decoder library.
abradle Apr 7, 2016
155d0f9
Updates to the tests to remove warnings
abradle Apr 7, 2016
015731d
More elegant handling and improvements
abradle Apr 7, 2016
759458e
Updates and refactoring on the way towards restructuring the Decoder …
abradle Apr 7, 2016
b383256
Refactored API as per Alex's suggestions
abradle Apr 7, 2016
9b2cbea
New class to fill a get API from an arbitrary data source using the i…
abradle Apr 7, 2016
c6f9ee1
Make PDBGroup primitive types
abradle Apr 7, 2016
13d4627
Update the Interface to not require a data setter.
abradle Apr 7, 2016
3cd83bf
Extensive refactoring and cleanup of the decoder and the PDBGroup.
abradle Apr 7, 2016
f586496
Downstream refactoring the update
abradle Apr 8, 2016
f15d295
Further refactoring and modifications.
abradle Apr 8, 2016
93ba67c
Removed all dependeices on Biojava from the encoder.
abradle Apr 8, 2016
d35310e
Downstream refactoring of the update module.
abradle Apr 8, 2016
7514650
Culling of all the data beans and moving around of tests.
abradle Apr 8, 2016
b5ec23f
Refactoring and restructuring.
abradle Apr 8, 2016
b276a24
Updated the decoder to the new static methods
abradle Apr 8, 2016
3d10c62
Update to the encoder to follow the same path as the decoder.
abradle Apr 8, 2016
c0b0fde
Finished writing unit tests (tests pass) and the Encoder converters a…
abradle Apr 8, 2016
4fb0aea
Set the group to sequence mapping indices better.
abradle Apr 8, 2016
b4fcd11
Remove setter repetition
abradle Apr 8, 2016
7fe0b97
Moved the serializer tests to update
abradle Apr 8, 2016
c49bfe7
Added a reader and writer interface.
abradle Apr 8, 2016
2f179c0
Refactoring of the code and tests in mmtf-update.
abradle Apr 9, 2016
830ae39
Some more refactoring and lyering to get the update module to work.
abradle Apr 9, 2016
5ac1829
Integration tests now pass for all structures.
abradle Apr 11, 2016
92baac2
Update the pom to compile junit
abradle Apr 11, 2016
3ff3541
Updates to the dataholder tests and mmtfbean so that tests pass.
abradle Apr 11, 2016
2821aa6
Make the mapper static
abradle Apr 11, 2016
db1960a
Added tests for the codec utils class
abradle Apr 11, 2016
56fb1d1
Refactored the names of the Decoding and Encoding functions
abradle Apr 11, 2016
a878fd5
Some more refactoring and addtion of comments
abradle Apr 11, 2016
7a1cbe2
Refactored the git version packaged into mmtf-common
abradle Apr 11, 2016
b105b9e
Refacotred the examples package into mmtf-update
abradle Apr 11, 2016
e56bdce
Refactored functions out of DataApiToReader into a Utils class
abradle Apr 11, 2016
e3b2c22
Updated the names of test.
abradle Apr 11, 2016
1bd09f1
Updates to consider alt loc and insertion code information better.
abradle Apr 12, 2016
d2623c6
Refactored removed the pointless Reader and Writer interfaces
abradle Apr 12, 2016
d4cc255
Update to store insCodeList & altLocList as byte arrays
abradle Apr 12, 2016
84e6edf
Updates to the naming of bioassembly related fields
abradle Apr 12, 2016
aa8d070
Unit tests that check array encoder/decoders handle empty arrays corr…
abradle Apr 12, 2016
4c38e19
Updates to incluide release date into the format
abradle Apr 12, 2016
a817843
Rename sequenceIdList to sequenceIndexList
abradle Apr 12, 2016
5bef90b
Update to include to pass releaseDate into the mmtf bean
abradle Apr 12, 2016
7aa7991
Updates to remove any mention of the Messagepack serializer /deserial…
abradle Apr 12, 2016
a3ff0b5
Added coveralls integration
abradle Apr 13, 2016
46ffe47
Added cobertura integration
abradle Apr 13, 2016
44807e6
Run cobertura on travis
abradle Apr 13, 2016
4a2d185
Update README.md
abradle Apr 13, 2016
db82cca
Refactored the mmtf-update project out of mmtf-java. This is due to t…
abradle Apr 13, 2016
407e6d4
Refactoring of the names of the interfaces and decoder/encoder classes.
abradle Apr 13, 2016
403e905
Removed pointless SeDeserializer interfaces
abradle Apr 13, 2016
b7b44b8
Some more refactoring and docs for the encoder
abradle Apr 13, 2016
38e0f39
Added new tests for hte decoder
abradle Apr 13, 2016
ddb0955
Updates to the encoder tests and fixed a couple of bugs found by the …
abradle Apr 13, 2016
eb712d5
Updates and refactoring to the encoder to fix data inconsistencies in…
abradle Apr 13, 2016
fec2df8
Change to the DummAPIimpl to increase code coverage
abradle Apr 13, 2016
0cd57c0
Add test dataholder class
abradle Apr 13, 2016
712cea3
Added tests for the message pack serializer / deserializers
abradle Apr 13, 2016
c1e6b75
Remove unuseful try catch
abradle Apr 13, 2016
917c482
Check PDBGroup equals method works
abradle Apr 13, 2016
2f01599
Added new tests for the encoder decoder and common
abradle Apr 13, 2016
5a23868
Some more tests and test more cases. ReaderUtils still not tested
abradle Apr 13, 2016
8f43dba
Merge branch 'master' into alter_data_struct
abradle Apr 13, 2016
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -4,3 +4,4 @@
*.project
*.swp
release.*
mmtf-update/pathname
7 changes: 0 additions & 7 deletions mmtf-api/pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,16 +19,9 @@
</properties>

<dependencies>
<dependency>
<groupId>org.rcsb</groupId>
<artifactId>mmtf-common</artifactId>
<version>0.0.1-alpha4-SNAPSHOT</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.11</version>
<scope>test</scope>
</dependency>
</dependencies>
<build>
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263 changes: 0 additions & 263 deletions mmtf-api/src/main/java/org/rcsb/mmtf/api/DataApiInterface.java
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