- Fix zoom speed.
- Features
- Maypole vertical-aligner
- Ghost transcripts
- Focus locations
- Focus transcripts collapse to gene blocks
- Region labels flip when too close
- Code improvments:
- Overhaul and document 2D-canvas management code
- Overhaul and document box model code
- Remove reporting-metadata code, to fit with the shape code
- Start overhaul of "global" code
- Code documentaiton
- Features:
- New JS "in-browserbackend" support
- Reform backend protocol for track-api integration
- Handle integer/float positions coherently
- Add support for ensembl "+1" co-ordinates
- Add "too old" message for in-field version migration
- "Auto-encoding" data in data endpoints (allowing js to send uncompressed data)
- Supporting changes:
- Support multiple backends
- Reform handling/meaning of channels
- API and then separate crates for backends (both network/python and js)
- Move cbor handling out of main code into python backend
- New StructValue format for arbitrary json-like data
- Improvements:
- Fix retry handling
- Speed up puzzle by removing thread-safety (is single thread activity)
- Less data transferred due to track setting changes
- Code tidying
- Remove unused style-compiler program types
- Features:
- systematic handling of species for UUID support
- data-test script to look at payload contents
- consistent support for both versionad and unversioned IDs
- new "tangle" system to minimise boilerplate code in backend
- allow multiple data sources in backend based on protocol version
- "invariant" mechanism to reduce traffic
- New data pipeline run:
- misc zmenu fixes
- wheat contigs
- Improvements:
- fix track names
- unit test improvements
- tidy and reduce transmitted data
- simplify "anticipation" to reduce network traffic
- improved data-test script for error cases
- simplify data-compression code in BE/FE communitcation (size & speed)
- Bugfixes:
- better handling of webgl buffers (performance)
- problem with contig handling identified when handling new wheat tracks
- alignment of sticky gene labels
- focus transcript id fixes
- fix switch_null
- Update 3rd-party packages and tool versions
- Drop support for 0.3.x clients (all versions prior to 9)
- Features:
- Add blank 90px at bottom as requested by Andrea via Jyo
- Bugfixes:
- gene label was scrambled at most-zoomed-in display level
- flagtop offset was incorrect on LHS
- Don't send summary updates too frequently
- Force send empty metadata via boxes when none present
- Always retrieve focus data to force box reports even when very off-screen
- Features
- "Flagtop" track for showing focus region endpoints
- special, dark lhs chevrons
- Feature-enabling functionality
- text alignable against right edge (for flagtop)
- Bug-fixes:
- don't show any zmenus when over dotted lines
- variation track name per side panel
- Remove dashes from track names
- large gene truncation issue (seen in MAPK10)
- lhs white ground data showing through bug
- stop zmenus forcing full gene size when fewer transcripts shown
- Doubled letter rhs bug
- rhs frame layering bug
- remove hyphen from focus track.
- Build process
- fix handling of dpr-force parameter when dpr-forcing disabled
- Bug-fixes:
- Fix chevron tangle bug
- Fix gene labels drawn on wrong transcripts
- Fix zmenus not including type payload
- Don't report trivial changes and rounding errors as location events on click
- New track names
- Use item object as focus track name
- Fix track ordering
- Fix dotted line height bug
- Fix dotted line device-pixel-ratio bug
- Build process
- Allow dockerised integration to checkout ensembl-client on given branch
- Compile time ability to override device-pixel-ratio for testing
- Separate focus egs file to allow always shown in transcript view.
- Factoring egs stuff shared between tracks
- Impl of "don't know" state for eye icons
- Fix label spacing between gene and transcript labels
- Left-sticky labels
- Fix reporting of boxes from flanks (reported in 0.4.0)
- Multiple transcript update from genes
- Visual fixes
- move labels to bottom of genes
- vertical alignment between transcript and sequence.
- flip boxed and unboxed UTR/intron; fix split UTR rendering bug.
- fix utr box colour bug
- can't turn first tr off bug
- show tr labels on zoomed view
- make tr labels independent of gn labels
- dotted lines at zoomed scale
- Failed unload bug fix (again)
- Multiple transcript reporting
- Flexible data-types in reporting
- Unit testing
- Metadata report object
- Visual fixes
- make lozenges blue and round corners
- reduce overwhelming chevron opacity to a point people don't notice it in advance of design review
- Lato -> Plex
- Correct, ultra-fine line thickness
- Open out focus track somewhat
- Fix wonky blue lhs swatch so doesn't become too noticeable in advance of design review
- Pick off some inter-scale spacing-fix tasks: no bumping labelless view
- remove endcaps for focus genes
- em-dashes not dash-dash.
- unboxed letters for UTRs.
- grey sequence
- Don't show letters until more zoomed in.
- Failed unload bugfix
- Fix image size bug (chevrons)
- Multiple transcripts
- show transcript ids (incorrectly laid out)
- "several" flipping for lozenges (disabled in release)
- Speed improvements
- In-code documetnation
- Performance sampler to test speed issues
- Improved debugging of train transitions
- Improve anticipation algorithm
- Bugfixes (speed) in train code
- Refactor inout code (tidy and speed up)
- Flashes-of-white bugfix
- Refactor railway code
- Optimise style-compiler programs
- Fix unit tests
- Preload wgsl
- Fix resizer
- EachOrEvery fixes for indexed vectors
- Replace mask with alpha in 2d backing bitmaps
- Gene bumping
- Add "functional" puzzle systm for inter-carriage dependencies
- Full box model for vertical positioning
- Style model
- Accompanying style-compiler program changes
- Multiple transcripts on screen
- "Several" transcripts mode via
["track",X,"several"]flag - Support for on-screen buttons (not used this release)
- Accopanying style-compiler program changes
- "Several" transcripts mode via
- New "empty" shape which occupies space but has no content
- Support for scope flags in BE communication.
- Memcached backend flushing
- alwaysflush in dev mode
- take egs version into account in production mode
- Tidy & Refactor
- Carriage-positioning code
- Each/Every repetition code
- spacebase coordinate sytem
- spectres for marching-ants zoom
- Bug fixes
- Fix stall bug in scheduler when under load
- Fix screen resize bug
- Fix various styling bugs in sequence view
- NEW BUGS / REVERSIONS (to be removed in 0.3.1):
- some alignment bugs when transitioning scales make it look dodgy
- some flicker during scaling
- slow sequence views
- Build system improvements
- Document it
- Present previous options for confirmation to allow easy repeat builds
- Change DOckerfile in light of npm scope changes
- Reduce fuzziness
- Take devicepixelratio into account on both webgl and bitmap canvases
- Fix dotted lines in various minor ways
- Add scale option to pngs
- Fix scaling of canvas in integration (also bottom ruler reappears).
- Round sizes correctly in observer to avoid excessive CPU usage
- Don't crash if window size becomes zero
- New "variety" key to reduce zmenu ambiguity.
- Deduplicate varieties
- Update current style compiler programs to use "variety key" (BE version 6->7, code version 0.1.x->0.2.x)
- Allow an element to be passed in the config instead of an element id (if desired)
- Replace ad-hoc approaches to logging verbosity on console with single, unified and configurable approach
- Build system work:
- Use dockerignore to reduce build time of docekr builds
- Use docker buildkit for extra features
- Menuize build scripts
- Bust docker cacheing to pick up github changes, where requested
- Code quality work in callbacks:
- Simpler scheduler
- New, self-contained classes which manage unloading correctly for
- timer
- requestanimationframe
- custom events
- Remove annoying "double flash" on gene move
- Additional key in zmenu payload to link genes and transcripts
- Move data release on in standalone browser
- Fix accidentally-changed library hash
- Fix various scrolling bugs
- Bug-fixes in chromosome switching
- Enforce size/position limits in more places
- Use van Wijk and Nuij's hyperbolic space algorithm for moves and pans rather than pile of buggy heuistics
- Use fade not animate for very long moves even if on same stick.
- Misc draw speed bugfixes and instrumentation
- Fixed version strings so that they survive CI/CD
- Fix default tack order
- Cleanly handle possibility of 404s (and other unexpected status codes) from BE
- Cleanly fail on jump target not found
- Reduce unnecessary draw groups for efficiency and code cleanliness
- Milestone trains for smooth scrolling at speed
- Fix anticipation code to make "lo" more effective following metrics analysis
- Fix priority inversion stalling focus change instructions
- Remove accidentally-retained console.log()s
- Bugfixes
- Report "bad stick" immediately, don't retry
- Chromosome switch bug (wrong size used during switching)
- Reduce technical debt to allow speed improvements
- Rational use of depths: prevents layering bugs
- Start recording metrics for WebGL buffers
- Rewrite "railway" code, cleaner and more rational
- Priority fixes
- Rationalised and co-ordinated co-ordinate systems
- Code tidying and improvements for large chromosomes
- Less fuzzy display of very zoomed-out chromosomes
- Manage absence of wheat contig file gracefully
- Reduced reliance on spot colours
- Tweak number of levels requiring data fetch
- Shrink and rationalise buffer usage
- Allow async even in webgl code
- Increased protocol version to 6
- Verified 0.0.12 works with 0.1.0 backend
- REGRESSION: display juddery (already fixed in 0.1.1)
- Select correct designated transcript in backend
- (Hopefully) fix (at least reduce) jumping track bug.
- Remove lots of unnecessary key bindings interfering with browser chrome
- Reformat zmenu payloads
- Backend/frontend versioning support for multiple egs files, depending on FE capabilities.
- reliably show sequence letters at zoomed-in level
- show red-dotted line even at most zoomed-in level
- correct swatch colour
- corrext swatch size
- correct font size in track category
- Cleaner backand request/response API on frontend
- Backend errors no longer cause CORS knockon errors
- GC track fixes:
- wrong colour;
- horiz bar missing;
- incorrect spikiness;
- mini-blank bug;
- incorrect at most-zoomed-in level;
- missing data blanks.
- cleaner use of WebGL
- new target location mechanism.
- more intelligent handling of failed backends
- bugfix for vertical dotted lines (broken by 0.0.4)
- display dotted red lines
- don't show dotted lines when focus track is off.
- fix lhs track category track-on/off bug
- fix lhs swatch track-on/off bug
- fix tracks-drawn-in-wrong-place bug
- add track category letters
- add "bp" edges to ruler and correct overlapping on rhs
- blue swatch for focus track
- Bug: lhs doesn't interact well with turning tracks off (yet)
- bottom ruler in the correct place,
- white left and right sides. (blank)
- Bug: in some positions the tracks are sometimes drawn in the wrong place
- still a bit slow on wheat (at least on the s3 server)