Affy -> Oligo schema and API changes.
Can now support oligonucleotide microarrays other than Affy. The three affy_* tables are changed to oligo_* tables. New fields are: oligo_array.type (currently either AFFY or OLIGO) oligo_probe.length oligo_probe.description The existing Affy objects become subclasses of new Oligo objects, but the API is backwards compatible, so existing pipeline and Web code won't need changing.
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- modules/Bio/EnsEMBL/AffyArray.pm 54 additions, 156 deletionsmodules/Bio/EnsEMBL/AffyArray.pm
- modules/Bio/EnsEMBL/AffyFeature.pm 76 additions, 188 deletionsmodules/Bio/EnsEMBL/AffyFeature.pm
- modules/Bio/EnsEMBL/AffyProbe.pm 99 additions, 310 deletionsmodules/Bio/EnsEMBL/AffyProbe.pm
- modules/Bio/EnsEMBL/DBSQL/AffyArrayAdaptor.pm 86 additions, 194 deletionsmodules/Bio/EnsEMBL/DBSQL/AffyArrayAdaptor.pm
- modules/Bio/EnsEMBL/DBSQL/AffyFeatureAdaptor.pm 94 additions, 369 deletionsmodules/Bio/EnsEMBL/DBSQL/AffyFeatureAdaptor.pm
- modules/Bio/EnsEMBL/DBSQL/AffyProbeAdaptor.pm 116 additions, 274 deletionsmodules/Bio/EnsEMBL/DBSQL/AffyProbeAdaptor.pm
- modules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm 1 addition, 0 deletionsmodules/Bio/EnsEMBL/DBSQL/AnalysisAdaptor.pm
- modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm 2 additions, 1 deletionmodules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm
- modules/Bio/EnsEMBL/DBSQL/OligoArrayAdaptor.pm 276 additions, 0 deletionsmodules/Bio/EnsEMBL/DBSQL/OligoArrayAdaptor.pm
- modules/Bio/EnsEMBL/DBSQL/OligoFeatureAdaptor.pm 510 additions, 0 deletionsmodules/Bio/EnsEMBL/DBSQL/OligoFeatureAdaptor.pm
- modules/Bio/EnsEMBL/DBSQL/OligoProbeAdaptor.pm 371 additions, 0 deletionsmodules/Bio/EnsEMBL/DBSQL/OligoProbeAdaptor.pm
- modules/Bio/EnsEMBL/OligoArray.pm 243 additions, 0 deletionsmodules/Bio/EnsEMBL/OligoArray.pm
- modules/Bio/EnsEMBL/OligoFeature.pm 230 additions, 0 deletionsmodules/Bio/EnsEMBL/OligoFeature.pm
- modules/Bio/EnsEMBL/OligoProbe.pm 426 additions, 0 deletionsmodules/Bio/EnsEMBL/OligoProbe.pm
- modules/Bio/EnsEMBL/Slice.pm 74 additions, 8 deletionsmodules/Bio/EnsEMBL/Slice.pm
- modules/t/affy.t 3 additions, 3 deletionsmodules/t/affy.t
- modules/t/affyAdaptors.t 15 additions, 4 deletionsmodules/t/affyAdaptors.t
- modules/t/oligo.t 124 additions, 0 deletionsmodules/t/oligo.t
- modules/t/oligoAdaptors.t 185 additions, 0 deletionsmodules/t/oligoAdaptors.t
- modules/t/test_genome.zip 0 additions, 0 deletionsmodules/t/test_genome.zip
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