Allow subclasses to AbstractFlatFileParser to participate in auto-detection of file format
|Reported by:||Nicklas Nordborg||Owned by:||Nicklas Nordborg|
This is currently an affair for the AbstractFlatFileParser only. The issue arised because the PrintMapFlatFileImporter detected the Illumina raw data files as print maps. This problem can only partly be solved with regular expressions. It would be useful if the subclass was allowed to inspect headers or control the auto-detection in a more powerful way.
This requires that the AbstractFlatFileParser.isImportable() method changes:
- It must handle sections in the same way as the doImport() method does. The doImport() starts with a call to nextSection() but the isImportable() doesn't.
- It must allow a subclass to inspect headers
- It must allow a subclass to continue parsing if it needs to