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Develop #402

Merged
merged 129 commits into from
Oct 31, 2016
Merged

Develop #402

merged 129 commits into from
Oct 31, 2016

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cjmyers
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@cjmyers cjmyers commented Oct 31, 2016

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cjmyers and others added 30 commits May 20, 2016 12:45
@cjmyers
Update pom file to 2.1.1-SNAPSHOT.
65d54de
@cjmyers
Moved version to 2.1.1-SNAPSHOT
0633c40
@mehersam
added toString test to model and renamed class name so maven will run it
e18e325
@mehersam
modified toString() test
ef6e606
@mehersam
added tests for Model methods that were previously untested
718b30e
@mehersam
Merge branch 'develop' of https://github.com/SynBioDex/libSBOLj into …
6633317 
…develop
@mehersam
commented out methods --> Set*x*(Set<x>)
c3ce5e4
@mehersam
fixed some tests
3832ffc
@mehersam
temporary place to put Document tests of previously untested methods.
19747db 
Currently incomplete; will later move to main Document test class
@mehersam
added tests for previously untested methods of SBOLDocument
3ccf6ef
@cjmyers
Fixed bug in clearNamespaces.
f2ce08c
@cjmyers
Added a createCopy for an entire document.
d046416
@cjmyers
Made createCopy of document public
ab8a358
@cjmyers
Added createCopy for document
5e6b7b1
@cjmyers
Made it static
e3d9d5e
@zgzn
Updated CRISPR example tutorial document to use libSBOLj 2.1.0. Updated
5129e5b 
some more JavaDocs in FASTA, GenBank, SBOLDocument, SBOLReader, and
Sequence.
@zgzn
Merge remote-tracking branch 'origin/develop' into develop
c677160 
Conflicts:
	core2/src/main/java/org/sbolstandard/core2/SBOLDocument.java
@mehersam
tested roleMethods in Component class
9fa7868
@mehersam
still adding methods---incomplete
cc4a0f3
@mehersam
tested all previously untested methods except for roleIntegration
2b19b57 
methods in SequenceAnnotation class
Code Coverage: start: 64.8% current: 84.8%
@mehersam
commented out getComponentDefinition method
08b0c89
@mehersam
Merge branch 'develop' of https://github.com/SynBioDex/libSBOLj into …
b586883 
…develop
@zgzn
Major updates on JavaDocs.
475eeb9
@zgzn
Tightened visibility for field variables and methods from AccessType to
3b61f59 
MapsTo.
@zgzn
Tightened visibility for all remaining SBOL core2 classes.
88739d7
@cjmyers
Simplified setOrientation in parseSequenceAnnotationV1
1fac68e
@cjmyers
Fixed several warnings. Simplified SBOLConversionException.
43f723a
@cjmyers
Simplified orientation type in SBOLReader
7d8c824
@zgzn
Removed getExceptionMessage() in SBOLValidationException.
00df30a
@zgzn
Reduced visibility from package to private for all abstract classes.
4109b75
mehersam and others added 29 commits July 24, 2016 21:54
@mehersam
Added basic test for getDecendentNames in EDAMOntology.
d2bb63f 
Shouldn't json be a descendent of FORMAT?
@mehersam
added basic test for getDescendentsNames() in SeqOntology
7921d57
@mehersam
added getDescendentNames() to SystemsBiologyOntology
4e9a04a
@mehersam
cleaned up test
aca3416
@cjmyers
Updated SBO obo file.
2a6bc81
@cjmyers
Merge branch 'develop' of https://github.com/SynBioDex/libSBOLj.git i…
010a03b 
…nto develop
@cjmyers
Fixed error message in validator.
5b25501
@cjmyers
Modifed SBOLReader to check object type from parser before
ebaafc0 
dereferencing.  In some cases, it will support both a Literal or an
inlined TopLevel.
Fixed SBOLTestConversion to point to right example path.
@cjmyers
Now reports object URI for 11905 validation error.
37938b9
@cjmyers
Add validation support for new role/roleIntegration fields.
ea5dc37
@cjmyers
Fixed Role tests.
a97c206
@cjmyers
Removed SMILES parser.
9797d6c
Added provenance examples
3b793b0
@cjmyers
Added linear/circular SO terms in GenBank converter
dc3d146 
Added new terms to SO constants
Conversion messages now go to standard out.
@cjmyers
Merge branch 'develop' of https://github.com/SynBioDex/libSBOLj.git i…
51148b9 
…nto develop
@cjmyers
Updated test files
b37588e
@cjmyers
Added new rules file.
36153c9
@cjmyers
Added support for validation rules 10528 and 10529.
34f2885
@cjmyers
Updated test files.
f77df68 
Conversion to 1.1, sets default of linear.
Changed validation to be at most 1 topology specified.
@mehersam
Updated validation rules file with new validation rules from sbol spe…
22808ec 
…c 2.1.0
@mehersam
Updated validation rules file with new validation rules from sbol spe…
a3e4911 
…c 2.1.0
@cjmyers
Remove
3a86d03
@cjmyers
Added new SBO terms for interactions and participations.
c77cba3
@cjmyers
Removed some fixed TODOs in reader.
8243403 
Fixed validator error messaging to give correct error on each exception.
@cjmyers
Added reference to the specification for validation errors.
7fc3bfa 
Changed rules to 2.1.0.
@cjmyers
Added new method to get "preciseLocations" (i.e., Cuts and Ranges).
690a5e0 
Only consider preciseLocations in GenBank conversion.
@cjmyers
Modified GenBank reader to convert to SAs with no Components.
fa0563a 
Modified GenBank writer to support SAs with no Component.
@cjmyers
Minor changes
f18006f
@cjmyers
Update javadocs
94d7074
@cjmyers cjmyers merged commit edfcc04 into master Oct 31, 2016
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3 participants
@cjmyers @mehersam @zgzn