I broke (briefly) the display of mmCIF files in Chimera.
For this to work, the structure file fetched by Jalview and passed to Chimera has to have extension “.cif”.
This got broken in the merge, but is now fixed by a change to enum
PDBEntry.Type.MMCIF(“mmcif”, “cif”)
where “mmcif” is the format specifier for the DBFetch service, and “cif” is the cached file extension (if you care).
For me to discuss with Tochukwu: can I replace Type with FileFormat?
Just need to figure out places where Type.FILE is currently set.
Mungo
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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
www.compbio.dundee.ac.uk
From: jalview-dev-bounces@jalview.org jalview-dev-bounces@jalview.org on behalf of Mungo Carstairs (Staff) g.m.carstairs@dundee.ac.uk
Sent: 29 November 2016 13:29:01
To: Jalview Development List
Subject: [Jalview-dev] FileFormatI merged to develop
I’ve merged in features/JAL-2344 to develop.
This adds an interface FileFormatI and enums FileFormat (Fasta, …etc) and DataSourceType(File, URL, Paste, Classloader).
With corresponding changes to all methods that are parameterised by either of these.
Functional tests all pass as before.
Let me know if you come across any suspicious I/O behaviour (read/write/output/fetch/drag/drop/etc…)!
Thanks
Mungo
The University of Dundee is a registered Scottish Charity, No: SC015096
The University of Dundee is a registered Scottish Charity, No: SC015096
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
www.compbio.dundee.ac.uk