justify cannot be undone - commented out menu items for moment
3 lines of code changed in:
experimental: sort by feature UI in feature settings and variable height rendering of features by score
219 lines of code changed in:
new sort by length method, justify edit menu entries and experimental support for variable height sequence feature rendering
145 lines of code changed in:
catch null pointer exception when no colourscheme is active
8 lines of code changed in:
simple transformation of feature types like dbref and dbxref into database references
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todo
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wsdbfetch parameter change again (uniprotkb is dbname for uniprot)
3 lines of code changed in:
avoid null pointer exception when no features visible
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avoid null pointer exception when groupName is not set
5 lines of code changed in:
left and right justify method
98 lines of code changed in:
sort by length
34 lines of code changed in:
added (and enabled) switch to store gff source string as sequencefeature.group rather than add it to description
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temporary fix and note about null feature group mucking up selection of features to be sorted on
4 lines of code changed in:
warning for failed parsing of newick strings
6 lines of code changed in:
new callback handler allowing threads that request a progress bar to be cancelled (this is untested!)
61 lines of code changed in:
structureState element to structure view Id is a many to one relationship - so viewId cannot be an XML element ID.
37 lines of code changed in:
DAS feature scores are parsed into floats on sequence features
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output average score to stdout
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display feature score in tooltip
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order by feature documentation
42 lines of code changed in:
experimental buttons for sort on score/density and popup menu to sort by score/density for a specific feature type
164 lines of code changed in:
new sort functions for ordering sequence by annotated features (probably still buggy) - sorts on distribution and score
231 lines of code changed in:
added location of menu option and keystroke
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support for multiple accession retrieval from a database source
175 lines of code changed in:
added local das sequence source CLI and documentation
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fetch database references for all EBI db + selected das sequence sources or a specific list of named sources
82 lines of code changed in:
sequence fetchers generated for local das sequence sources
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das source browser uses local source method from jalview.bin.Cache and methods refactored to allow headless access to list of selected das sources
26 lines of code changed in:
allow sequence source to be specified as sequence:http://mydasserver/das/source
4 lines of code changed in:
local das source properties string constants and routine for generating sequence and feature sources from local source property
41 lines of code changed in:
properly catch exceptions from querying server with sequence command
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minimise exceptions for bad uniprot ids
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select source by implementation class
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fix null pointer exception for sources which don't have any additional properties
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clarity of tree menu calculation widget name
7 lines of code changed in:
match case switch should work for both sequence ID matches and sequence matches, and be case insensitive for both searched text and query text!
2 lines of code changed in: