Various Java apps written at NCGR for a variety of purposes, mostly to handle data for InterMine loaders. Each directory is an org.ncgr Java package.
ncgr / lis_sequence_search Goto Github PK
View Code? Open in Web Editor NEWLIS sequence search
LIS sequence search
See the feature branch:
Add GBrowse linkouts for hits to proteomes using existing genome urls with slight modification.
clicking headers now seems to invalidate the rows (all cell values are undefined)
sometimes, you'd just like to group things this way.
for example, if I have a few protein sequences, and request a search with
blastp and tblastn (correct) and also blastx (incorrect-o!), the initial view is
partition only, no table. This is not corrected upon a refresh, but the table
does appear upon any interaction with the partition or filters.
not a big deal, but since you're a perfectionist...
It's in a feature branch if useful.
Enable sign on / sign out while using search interface.
The subject of whether the partition view or the tabular view should be presented as the default is contentious. On the other hand, strong arguments can be made that neither view by itself tells the complete story. Presenting the two together in a split pane (or similar) context, in which both were simultaneously updated with changes to the model effected by filter applications may be a way forward.
As per email discussions, often the initial view of a result set must be reloaded from the server before
it actually contains all the hits returned by a given algorithm.
e.g.: a hit to gene family consensus sequence 28707938 would lead to:
http://leggle.comparative-legumes.org/gene_families/name=28707938
Enable switching between dual view (table and partition - default), table view and partition view. Add "table", "partition" and "dual view" to view as drop down in search results menu. Highlight currently selected view.
Allow users to export search results as gff.
e-values are a good first filter, but once they get low enough to be reported as zero, there is no finer level filtering that can be done using that property of a set of hits. Adding bit score filtering would help.
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