Ahhh, MCView... This was the prototype Jalview started in 1996 in Oxford (yes,
MC is Michele Clamp (note one 'l')). It had been renamed Jalview by 1998 but
neither Michele nor I can remember exactly when the change happened.
G.
On 28/11/2016 09:37, Mungo Carstairs (Staff) 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
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--
Geoff Barton | Professor of Bioinformatics | Head of Division of Computational
Biology
School of Life Sciences | University of Dundee, Scotland, UK |
[email protected]<mailto:[email protected]>
Tel: +44 1382 385860 |
www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> | twitter: @gjbarton
The University of Dundee is registered Scottish charity: No.SC015096
The University of Dundee is a registered Scottish Charity, No: SC015096
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