Implement BFS exporter for spot data

[Nicklas Nordborg]

This ticket is about implementing the plug-in for exporting bioassay set data in BFS format. A description of the file format is found in #1440. The implementation of the plug-in should build on/use the generic writers that are implemented as part of #1444.

This ticket in itself can also be split in two parts. First, a working export implementation (not a plug-in) is created, then a plug-in is created that uses the exporter. This is similar to how the BASEfile export and plug-in was setup as part of #742.

[Nicklas Nordborg]

(In [5199]) References #1448: Implement BFS exporter for spot data

The exporter implementation should now be usable and it should be possible to start implementating the plug-in that will use this export.

[Nicklas Nordborg]

(In [5209]) References #1448: Implement BFS exporter for spot data

First version of the exporter. It is limited to save the files in a directory in the BASE file system and needs more error handling. Assay annotations are not yet supported.

[Nicklas Nordborg]

(In [5210]) References #1448: Implement BFS exporter for spot data

Changes that should have been included in [5209] but for some reason wasn't. I'm sorry if anyone has had compilation problems...

[Nicklas Nordborg]

(In [5211]) References #1448: Implement BFS exporter for spot data

Added experimental factors as assay fields.

[Nicklas Nordborg]

(In [5213]) References #1448: Implement BFS exporter for spot data

The exporter now uses the new file name generation implementations. Added parameter in the plug-in to let the user select a file naming strategy.

[Nicklas Nordborg]

(In [5214]) References #1448: Implement BFS exporter for spot data

Renamed the plug-in to make it consistent with the naming of other classes.

[Nicklas Nordborg]

(In [5219]) References #1448: Implement BFS exporter for spot data

Added possibility to export to a zip file.

[Nicklas Nordborg]

(In [5223]) References #1448: Implement BFS exporter for spot data

Corrected a problem with the exporter that caused the first position to be missing from the rdata file.

[Nicklas Nordborg]

The exporter seems to be working.

[Nicklas Nordborg]

(In [5269]) References #1448: Implement BFS exporter for spot data

Fixed an issue with progress report intervals not being consistent.

[Nicklas Nordborg]

(In [5309]) References #1444, #1448, #1451. Added methods for closing BFS parsers and an auto-close feature on the exporter and importer. This was needed since some temporary working files could not be deleted without closing the streams.