DESIGN: Add SequenceContigsInterface class - Githubissues

HenrikBengtsson / aroma.seq

🔬 R package: aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

https://github.com/HenrikBengtsson/aroma.seq

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DESIGN: Add SequenceContigsInterface class #17

Closed HenrikBengtsson closed 9 years ago

HenrikBengtsson commented 9 years ago

Add SequenceContigsInterface class with corresponding methods such as:

nbrOfSeqs()
getSeqNames()
hasSeqLengths()
getSeqLengths()
getTotalSeqLength()
typeOfSeqOrdering()
getSeqsGenericSummary()
isCompatibleWithBySeqNames(..., other)
isCompatibleWithBySeqLengths(..., other)
isCompatibleWithBySeqs(..., other)

Have the following classes inherit from/implement this interface:

BamDataFile
FastaReferenceFile
FastaReferenceIndexFile
GcBaseFile
GtfDataFile
Bowtie2IndexSet
...

This will reduce the amount of redundant code noticeably.

HenrikBengtsson commented 9 years ago

Done. Got a working setup now.