The StructureFileType enum is used by the method StructureFile.isStructureFile(fileType) to determine if a given file format is a structure file or not. It was introduced after 2.10.0 to replace explicit checks for ‘PDB', ‘mmCIF', or other structure file formats is some parts of the src code. See JAL-2280 for more history on this.
I can confirm that StructureFile.dbRefType is currently not used - that shouldn’t be the case though. I’d have to check the commit history to figure out what has gone wrong. We currently don’t utilise the MMTF format. However, the StructureFileType enum should Ideally contain structure file formats that is/could be supported by Jalview. The MCView parser is now kind of obsolete, however it was left for legacy purposes (i.e. importing older project files). IMHO, I think we could move the data model classes as suggested, but hold-up getting rid of the old parser for now. Charles Ofoegbu Tochukwu Charles Jalview Visual Analytics Developer/Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. Skype: cofoegbu www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> On 28 Nov 2016, at 09:37, Mungo Carstairs (Staff) <[email protected]<mailto:[email protected]>> wrote: I'm looking at my FileFormatI branch and wanting to minimise, and ideally remove, 'special case' treatment of structure files (PDB/mmCIF) as a format. Questions arising: * enum StructureFileType doesn't seem to get used - can it be removed? * corollary: we don't do anything with MMTF format? * StructureFile.dbRefType doesn't seem to get used - can it be removed? * StructureFile.structureFileType (this is PDB or mmCIF) * looks like it could be passed as a method parameter (to postProcessChain()) rather than saved in a field * the value gets copied to PDBEntry.type - which is therefore PDB or mmCIF after parsing a structure file * however a Uniprot fetch (uniprot_mapping.xml) binds 'dbReference' to PDBEntry * so in this context, PDBEntry.type is "PDB" or "EMBL" or "Ensembl" etc (see Uniprot.uniprotEntryToSequenceI()) * would it make more sense to bind Uniprot dbrefs to DBRefEntry instead? * should PDBEntry.type get set to PDB (as the database source) also for mmCIF format? * is the MCView parser now obsolete? in which case can we get rid of it? * perhaps move remaining datamodel classes used in the package to a datamodel.structure package? * with a suitable ceremony (MC is Michelle Clamp?) thanks, Mungo Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________ Jalview-dev mailing list [email protected]<mailto:[email protected]> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev The University of Dundee is a registered Scottish Charity, No: SC015096
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