Release notes
Several bug fixes and a few new features:
Export to oxView format
The scadnano web interface can now export to the oxView format, which (like oxDNA files) can be read the tool oxView.
It has been possible for a while to export to the oxDNA format, but this is nicer just for visualizing scadnano structures in oxView, because
- The oxDNA format has two files, whereas oxView has only one.
- The oxView format includes some extra data such as which bases are paired, and what color strands are. This information is populated with the relevant scadnano data. Have the strands be the same color in each tool makes it easier to figure out which strand is which.
For example, this scadnano design:
exports like this in oxView:
In particular, this provides an immediate visual cue that the view angle in oxView is reversed in both horizontal and vertical directions from that of scadnano, since the purple staple in the bottom right of scadnano appears in the top left of oxView. Rotating it 180 degrees around the y (up-down) axis, and then rotating 180 degree around the z (left-right) axis, then the oxView orientation matches scadnano's:
This can also be checked with the axis arrows of oxView and scadnano, which match colors:
Sequences of selected strands are not exported
There was already a feature where only sequences of selected strands could be exported. Now it is possible to declare that exactly the unselected strands should be exported:
Commits
- a071097: bumped version (David Doty) #972
- 58cd26e: added css class for darker stroke on crossovers within the same helix (David Doty) #972
- e487457: fixed batch remove label, remove name, set name (Raybipse) #954
- abcecd2: fixes #953 (Raybipse) #954
- 22ae227: Fixed batch remove/set for extensions and loopouts (Raybipse) #954
- f72c32c: implemented logic for filtering connected base pairs (Raybipse) #955
- 8657d04: Fixed typo in action name for remove strand name (Raybipse) #954
- d291063: add menu option for retaining color on strand selection (Edwin Chang) #957
- 1471f3f: implemented logic for filtering connected base pairs (Raybipse) #955
- 17f944b: closes #895 selected base pair lines is exported (Raybipse) #955
- 34ff35c: Rebased branch onto dev and fixed minor bug (Raybipse) #955
- e438f97: Fixed copy image not displaying base lines (Raybipse) #955
- b3dd9c7: Changed to letterSpacing (Raybipse) #963
- 146a350: closes #870: Feature request: selection preserves color (Edwin Chang) #957
- d68babc: reformat code (Edwin Chang) #957
- 94c0b0f: Refractored code for readability and consistency (RayBipse) #955
- 1a66286: Setup separate export setting (RayBipse) #963
- 692e01d: moved set separate text menu (RayBipse) #963
- a0d3ac2: Added separate text support (RayBipse) #963
- 5d4cc56: Merge branch 'dev' of https://github.com/UC-Davis-molecular-computing/scadnano into dev (RayBipse) #955
- 760fb4a: fixes #959: display DNA sequence on extension in order 5' to 3' (David Doty) #960
- 1840933: fixes bug with setting extension name when no extensions are selected (David Doty) #960
- 35f4e9f: fixes bug with selecting strand "pieces" (domains/extensions/ends/etc) with new property
retain_strand_color_on_selection, which was not being properly prop-drilled into those view components (David Doty) #960 - da99847: fixed some variable/file names (David Doty) #972
- c9c2894: fixed problem with non-unique React key when a strand has a 5' and a 3' extension adjacent to the same domain (David Doty) #972
- 2cfac1f: Update README.md (David Doty) #972
- 1e78e1e: Fixed the frequent "cannot read undefined" error in console (RayBipse) #963
- 63b66af: Fixes #941 (RayBipse) #963
- b307a48: Changed names to snakes case and fixed outline bug (RayBipse) #963
- bf718f2: Fixed bug export SVG main view doesn't contain a viewbox (RayBipse) #963
- d0adc28: Merge branch 'dev' into 941-dna-sequences-justified (Ray Zhu) #963
- 3ce8c86: Fixed wrong merge resolve (RayBipse) #963
- 3850c48: Fixed bug where selected strands were pink (RayBipse) #963
- a6b06ac: re-ordered export menu (David Doty) #963
- 34ba098: added ability to exclude scaffolds from selection when using "select all with same..." (David Doty) #972
- 33a5630: closes #964: exclude selected strands from export DNA sequences (Dave Doty) #965
- 77e21ef: Added the button for base pair display (RayBipse) #966
- 7c5645a: Closes #897 (RayBipse) #966
- f842e25: Changed the layout for base pair display to checkboxes (RayBipse) #966
- 4e75ec2: closes #588: export to oxView format (David Doty) #971