TODO

Normalize bit scores relative to highest score in filtered results, not all results
Include query sequences with no hits in count of hits

Ivan's suggestions:
  Display blown-up SVG for particular hit of interest
  Fix axis labels -- don't necessarily label with "b", given that some sequences may be for AAs

  Allow user to export table with data -- format:
    Query ID
    Subject ID
    Bit score
    E value
    Query start/end
    Subject start/end

Verify that results are valid based on strandedness, etc.
Add loading animation
Display scale demonstrating what gradient means

Add means of setting resolution of PNG export
Support drag/drop file uploads
Make long query/subject names render better

Write bookmarklet to allow direct loading of Kablammo from NCBI BLast
Refactor -- replace jQuery XML parsing with native to speed up this step
Enable pinch-to-zoom on touch devices

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Before submitting manuscript
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Change terminology: "subject" -> "hit"
Prepend hit name to exported filename so that files will sort in same order as graphs were displayed
Add option to display sequence names in place of generic "Query"/"Subject" labels on graph

When scale zoomed in, display decimal points on labels -- don't have "39 kb, 39 kb, 39 kb, ..."
Move count of "hidden" queries/subjects from headers to better place in interface
Produce error on XML file that's not BLAST XML
Show tooltips on first load -- "can use mousewheel to scroll!"
Write help section
  Show how to get BLAST XML file (via NCBI BLAST or CLI) in README and in help section
Have "tour" on homepage

Improve alignment viewing
  Show summation of alignment instead of simple scrollbar, a la Benchling
  Enable exporting the subject or query sequence corresponding to that portion of the alignment
Provide script for augmenting JSON file listing XML
  Be sure to lock file when operating

Implement "choose optimal HSP set" algorithm
Visualize coverage of all hits across sequence
  Considering all hits, which parts of query sequence have no hits?
For given set of queries/subjects, generate Circos diagram showing HSPs between them
"Only show subjects that align to at least x% of the query" (i.e., length of HSP union)

James' requests:
  Make alignment viewing more simialr to NCBI version

Make scrollbars in alignment viewer appear for OS X users
Fix bug with SVG export -- polygons aren't clipped according to view
  I can probably fix this by clipping to the SVG's document size, but I'm not sure of algorithm that does this