This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git.
Pull mirroring updated .
- 19 Mar, 2019 4 commits
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Marek Szuba authored
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Marek Szuba authored
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Marek Szuba authored
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Marek Szuba authored
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- 18 Mar, 2019 9 commits
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Marek Szuba authored
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Marek Szuba authored
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Marek Szuba authored
On the one hand there seems to be no good reason for a MicroRNA object having multiple arm attributes, on the other hand simply taking the first one in the event of it happening may not even return the same value every time (it depends on a lot of factors, from the implementation details of AttributeAdaptor up to and including the underlying database system). There was a warning but who reads those anyway. Just throw an exception instead, if someone decides to allow such a case they can always catch it.
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Marek Szuba authored
There is now a dedicated class, Utils::RNAProductTypeMapper, which provides type_id<->class_name mappings to both RNAProduct constructor (with the side bonus of no longer having to set the type ID in the constructor of each subclass) and RNAProductAdaptor. The latter will likely be used more frequently than the former, therefore the default map uses type IDs as keys; the reverse map is only generated the first time it is needed. In addition to the constructor, the RNAProductTypeMapper.pm defines a function called mapper() which provides a singleton instance of the mapper object. The mappings are hardcoded instead of being retrieved from the database because the latter could in principle result in execution of arbitrary code. Some tests have been defined as well.
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Marek Szuba authored
1. List of arguments passed to the constructor now references the superclass (a'la Feature class hierarchy) instead of listing them explicitly. 2. Arm documentation now correctly lists values this property can take.
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Marek Szuba authored
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Marek Szuba authored
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Marek Szuba authored
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Marek Szuba authored
A minimal extension of Bio::EnsEMBL::RNAProduct, with the only new information being the arm of the hairpin the miRNA has come from. On the storage side, this information is stored as a new type of rnaproduct attribute.
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