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Fix distortion after rotation #102

Merged
merged 70 commits into from
Aug 4, 2018
Merged

Fix distortion after rotation #102

merged 70 commits into from
Aug 4, 2018

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eweitz
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@eweitz eweitz commented Aug 4, 2018

This fixes distortion in chromosomes and annotations seen after rotating a chromosome (#60).

Below is a short animation showing Ideogram before and after this change.
Ideogram rotation distortion and fix

eweitz added 30 commits January 17, 2018 08:18
@eweitz
Extract chromosome pixel and scaling into new method
40baa60
@eweitz
Refactor chromosome drawing methods
3e1f25d
@eweitz
Continue refactoring chromosome drawing methods
2ef6d5a
@eweitz
Extract code to append homolog into new method
999688b
@eweitz
Refactor drawing sex chromosomes
a1908ce
@eweitz
Simplify parameters and name of drawChromosomeSet, document appendHom…
5854c75 
…olog
@eweitz
Fix, crudely, basic cause of distortion
456ce9b
@eweitz
Account for narrow viewport in rotated chromosome height
2356b45
@eweitz
Move 'var' declarations to top of functions
d90a943
@eweitz
Preserve telocentric centromere upon rotate and redraw
921601e
@eweitz
Fix build configuration, 18s -> 1s
c6376a5
@eweitz
Update webpack dependencies, 'start' command
db965a6
@eweitz
Enable local development on non-stardard port without Internet
45e72be
@eweitz
Merge from upstream
d74b752
@eweitz
Remove unnecessary indirection in Range class
324e409
@eweitz
Refactor variables for consistency: *Number -> *Index
3bc1952
@eweitz
Keep pter band; enables redraw of telocentric chromosomes
1965149
@eweitz
Fix rotation in horizontal layout
ef9035a
@eweitz
Adjust rotated chromosome width; refactor bandsArray, chromosome argu…
27bd9cb 
…ment
@eweitz
Extract method for click handlers to rotate and toggle chromosomes
cf7209b
@eweitz
Begin restoration of rotateBack
17dca6e
@eweitz
Extract common code into new didRotate method
c8fd38a
@eweitz
Smoothen forward rotation in transit
c62d850
@eweitz
Remove scaling at end of transition
4d7ae6d
@eweitz
Extract scaling code into new method
06b2075
@eweitz
Smoothen back rotation
1b86c6c
@eweitz
Fix off-by-one chromosome position bug
466915f
@eweitz
Fix regression in top position in horizontal layout
d23ab38
@eweitz
Fix off-by-one regression affecting histograms
7916cbb
@eweitz
Fix misplaced annotations in rotate chromosome
0a74ba8
eweitz added 25 commits July 18, 2018 17:34
@eweitz
Update orientation for vertical chromosomes upon rotation
7dc0ab0
@eweitz
Hide unshown band labels after rotation
bb8a16c
@eweitz
Refresh bandsToShow upon each rotation
428bbf9
@eweitz
Refactor drawChromosome to use model, not name
aa50c23
@eweitz
Fix band index bug discovered via automated tests
8292143 
The first p-terminal (pter) band in telocentric chromosomes like those in mouse had been getting dropped from the data model to ease initial rendering.  Now, with bands being re-rendered upon rotation, pter bands are preserved.  To account for this, all client code referencing band indexes for mouse chromosomes needs to add 1 to the band index.
@eweitz
Tweak positioning values in tests
831edce
@eweitz
Fix inconsistent indentation and other whitespace
f383ea6
@eweitz
Fix rendering chromosomes without cytoband data
08ba447
@eweitz
Fix a failing test
385f34f
@eweitz
Merge from upstream, fix compilation
acaa34c
@eweitz
Update to revised chrIndex
b21649c
@eweitz
Add test for rotating labeled vertical chromosome
9c7387e
@eweitz
Test scaling of annotations after rotating
900f9e8
@eweitz
Add onDidRotate callback, fix invalid test
e8cae1a
@eweitz
Document new onDidRotate callback
a678a67
@eweitz
Fix documentation merge, build
8627696
@eweitz
Discard obsolete module; clean-up from merge
26b9a12
@eweitz
Fix regression in length issue in rotated histogram annotations
33e491a
@eweitz
Remove band labels from human example
c6ecac6
@eweitz
Refine expected test values
6f07b36
@eweitz
Permit wiggle in expected test value
7fbee39
@eweitz
Permit wiggle in expected test value
3468eec
@eweitz
Fix bar rendering in filtered, rotated, and filtered-and-rotated hist…
85cb299 
…ogram
@eweitz
Fix tooltip after redrawing ideogram with default container
283eecc
@eweitz
Thicken rotated chromosome
ce2d1e7
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Coverage Status

Coverage increased (+0.1%) to 92.166% when pulling ce2d1e7 on fix-rotation-distortion into 4a8e526 on master.

@eweitz eweitz merged commit 86dcea7 into master Aug 4, 2018
@eweitz eweitz mentioned this pull request Aug 4, 2018
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@eweitz eweitz deleted the fix-rotation-distortion branch August 19, 2018 11:04
@eweitz eweitz mentioned this pull request Nov 6, 2018
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