Commits · da25275d0a1e7b1887529900ac85350a26b1fa3e · vidjil / vidjil

24 Jan, 2020 27 commits
- model.js: check if clone exist before getSize() · da25275d
  marc duez authored Jan 13, 2020
  
  da25275d
- fix min/max computation used by graph.js for axis scale · 41e339cb
  marc duez authored Jan 10, 2020
  
  41e339cb
- code quality · 6c6fe062
  marc duez authored Dec 16, 2019
  
  6c6fe062
- model.js : keep updateIcon div in model to avoid parsing dom · 8947a694
  marc authored Dec 02, 2019 and marc duez committed Jan 24, 2020
  
  8947a694
- graph.js : use default "path" for inactive clones · de8b34c7
  marc authored Dec 02, 2019 and marc duez committed Jan 24, 2020
  
  de8b34c7
- graph.js :fix redraw · 833c22f9
  marc authored Dec 02, 2019 and marc duez committed Jan 24, 2020
```
clones were redraw two times by updateClones() and draw()
```
  833c22f9
- scatterplot: visible_nodes != active_nodes != nodes · 14a8329d
  marc authored Dec 02, 2019 and marc duez committed Jan 24, 2020
```
limit redraw to visible nodes only
```
  14a8329d
- scatterplot.js : force application order · fc6b0bdc
  marc authored Nov 29, 2019 and marc duez committed Jan 24, 2020
```
apply node moves before collision resolution (forceX()/forceY() before tick() )
```
  fc6b0bdc
- scatterplot.js : fix legends for d3V5 · 2be2d705
  marc authored Nov 28, 2019 and marc duez committed Jan 24, 2020
  
  2be2d705
- QUnit: update test for d3v5 · 9ea7264d
  marc authored Nov 28, 2019 and marc duez committed Jan 24, 2020
```
-d3v5 lineGenerator() function produce new "path" for graph view
```
  9ea7264d
- graph.js/css : update curves css · 6e9e9391
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  6e9e9391
- scatterplot.js : store old_x/old_y positions before redraw · e4f42e5a
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
```
this was done by the move() function before but it has been replaced by a d3V5 forceX()/forceY()
```
  e4f42e5a
- scatterplot.js : add a small amount of randomness to the clone traget... · 321623ce
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
```
scatterplot.js : add a small amount of randomness to the clone traget positions to help the force simulation

clones can stack up vertically/horizontally without it
```
  321623ce
- scatterplot.js : adapt quadtree and collide() function for d3v5 focre simulation · f8261189
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  f8261189
- scatterplot.js : add d3js V5 force simulation · 9b67795c
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  9b67795c
- scatterplot.js : remove old d3jsV3 force simulation · 0d81cd02
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  0d81cd02
- scatterplot.js : d3v5 drag function has changed · e95ca890
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
```
this is useless so currently disabled
```
  e95ca890
- scatterplot.js : smoothing++ · 8902397b
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  8902397b
- numerical_axis.js : d3 scale.log function has been renamed in v5 · 81bcba36
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  81bcba36
- model.js : d3 scale.log function has been renamed in v5 · d4fce2b0
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  d4fce2b0
- graph.js : rewrite for d3v5 and misc · 338b3d51
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  338b3d51
- graph.js : remove build_path_events() function, can be done safely during the update() · 9719b854
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  9719b854
- graph.js : follow new d3js function names · a91a115c
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  a91a115c
- graph.js : bugfix resolutioncurve can handle unusually low analyzed read · 0891daa4
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
```
resolutionCurve display was a mess for samples without reads or less than 5 reads
```
  0891daa4
- graph.js: put resolution curve on foreground · e5c9e333
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  e5c9e333
- graph.js : use d3.lineGenerator for path · 2e7afc00
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  2e7afc00
- add d3js version 5 library · c42c34ea
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  c42c34ea
23 Jan, 2020 12 commits
- Merge branch 'bikeshed-message' into 'dev' · fe6f3fb5
  Mathieu Giraud authored Jan 23, 2020
```
vidjil.cpp: bikeshed help message

See merge request !592
```
  fe6f3fb5
- vidjil.cpp: bikeshed help message · cde5aca5
  Mathieu Giraud authored Jan 23, 2020
```
follows !589
```
  cde5aca5
- Merge branch 'feature-a/3861-no-output' into 'dev' · 49b8b832
  Mikaël Salson authored Jan 23, 2020
```
Feature a/3861 : options to limit output

Closes #3861

See merge request !589
```
  49b8b832
- Merge branch 'doc/airr-fuse' into 'dev' · 80ce835f
  Mikaël Salson authored Jan 23, 2020
```
Documentation on the AIRR .tsv import

See merge request !579
```
  80ce835f
- output.cpp: reindent · e86750d3
  Mikaël Salson authored Jan 23, 2020
  
  e86750d3
- Merge branch 'feature-a/4154-benchmark-current' into 'dev' · 5d9ab275
  Mikaël Salson authored Jan 23, 2020
```
Feature a/4154 : Benchmark also current HEAD

Closes #4154

See merge request !590
```
  5d9ab275
- .gitlab-ci.yml: benchmark also the current HEAD · 9a608613
  Mathieu Giraud authored Jan 23, 2020
```
Closes #4154
```
  9a608613
- benchmark-releases.py: -c, benchmark also the current HEAD · 64c78581
  Mathieu Giraud authored Jan 23, 2020
```
see #4154
```
  64c78581
- tests: add and update tests, --no-airr and --no-vidjil · 73066211
  Mathieu Giraud authored Jan 23, 2020
```
Closes #3861
```
  73066211
- vidjil.cpp: --no-airr · d8b4ad79
  Mathieu Giraud authored Jan 23, 2020
```
see #3861
```
  d8b4ad79
- vidjil.cpp: --no-vidjil · 828d7e09
  Mathieu Giraud authored Jan 23, 2020
```
see #3861
```
  828d7e09
- core/output.{h,cpp}: VidjilOuput, with_clones option · 39109911
  Mathieu Giraud authored Jan 23, 2020
```
see #3861
```
  39109911
22 Jan, 2020 1 commit
- Merge branch 'feature-a/3594-updated-evalue-computations-kmer-fine' into 'dev' · da83fb01
  Mathieu Giraud authored Jan 22, 2020
```
Update e-value multipliers and options

Closes #3594

See merge request !538
```
  da83fb01