v0.13.0

Improved Batch Editing

can select many objects and edit/delete them at once, when objects are:

• deletions/insertions: deleting in batch, editing insertion length in batch, and adding many deletions/insertions to many helices by pressing Ctrl when adding to one Helix. The last is especially useful for doing twist-correction (see https://doi.org/10.1038/nchem.1070, https://www.dna.caltech.edu/Papers/stacking-bonds2011.pdf, Fig. 1) on DNA origami, which involves adding a "column" of deletions to every helix at the same offset.

• loopouts/crossovers (could delete before, now can convert between them, or change loopout lengths, in batch)
  

• modifications
  

• 5'/3' ends and add same modification to all of them at once
  

Rope Select Mode

Users can now draw an arbitrary non-self-intersecting polygon to select many items at once

Right click to edit insertion length

Previously this would be done by using (s)elect mode and clicking on the insertion. Now, users must right click on the insertion.

Links to older versions

Starting with v0.12.1, older versions of scadnano will hosted at scadnano.org/{version number}. This might be useful in case an update breaks some functionality.

Swap x and z coordinates

This change should not affect any users using only the web interface, but may be a breaking change for anyone using the Python scripting library. Python scripts using the "none" grid and specifying 3D coordinates will need to be rewritten so that x and z coordinates are swapped.

Previously, positive x moved right in the main view and into the screen in the side view, and positive z moved right in the side view and out of the screen in the main view. Now these are swapped.

If you are curious why this was done, read here: #488

Commits

• [a3c6b33]: added whitespace between IDT name displayed in footer and Strand name (David Doty) #507
• [4f9121f]: Update dart.yml (Benjamin Lee) #485
• [b7731f5]: Update CONTRIBUTING.md (David Doty) #507
• [6454166]: Fixes #473; side cursor title use yz instead of xy (Benjamin Lee) #486
• [028162c]: Fixes #473; side cursor title use zy instead of xy (Benjamin Lee) #486
• [d75a989]: Performance improvement for strand selection (Benjamin Lee) #487
• [4c50667]: fixed bug with setting HTML id of modification that disabled right-click context menu for some of them (David Doty) #507
• [cc44388]: fixed bug in converting from gridless 3D positions to square grid positions (David Doty) #507
• [cc9e10b]: added unit test for util.position3d_to_grid_position (David Doty) #507
• [36d27dd]: when adding modification, dialog remembers choice of modification display text, id, and idt text (depending on type of mod: 5', 3', or internal), so that it does not need to be typed in the next dialog. (useful for adding several copies of the same modification to several places in the design) (David Doty) #507
• [cf4ab54]: removed string id as option to set when adding or editing modification; now it automatically uses the IDT text field as the ID. (David Doty) #507
• [9d681a1]: added ability to convert all selected crossovers to loopouts via right-click context menu (haven't yet implemented changing all loopout lengths at once, including setting length to 0 to convert back to crossover) (David Doty) #507
• [c5625b2]: Fixes #488; swap position x z coordinate (Benjamin Lee) #499
• [8e5bf03]: fixed bug allowing null ModificationInternal.allowed_bases in constructor (David Doty) #507
• [421b66f]: closes #493 ; displays more nicely loopouts on a single helix between two domains in the same direction, so it looks more like an insertion (David Doty) #507
• [0191ce1]: can select many loopouts and change all of their lengths at once (or convert all to crossovers by setting length 0) (David Doty) #507
• [2eb1bc4]: updated pubspec.yamp to fix analyzer error after upgrading to Dart 2.10 (David Doty) #507
• [8b9a2b7]: fixed bug where helix groups were not properly updated after changing a helix's index (David Doty) #507
• [5aff64c]: Update helices_reducer.dart (David Doty) #507
• [6201886]: Update pubspec.yaml (David Doty) #507
• [4879318]: Update pubspec.yaml (David Doty) #507
• [ed98954]: changed IDT export plates code to put last 24 strands on last 96-well plate if necessary (since minimum per plate is 24), and similarly for 96 strands per 384-well plate. (David Doty) #507
• [758ec7d]: fixed bug where deletions/insertions not updated properly when reflecting strands horizontally. (David Doty) #507
• [b68b9f4]: closes #494; allow deletions/insertions to be added to all domains in a HelixGroup occupying the clicked offset, which helps with implementing twist correcting-deletions for flat square-lattice origami, for instance (David Doty) #507
• [2a6e225]: fixed unit tests to account for new "all_helices" field in DeletionAdd and InsertionAdd (David Doty) #507
• [8112c43]: closes #501; make deletions/insertions selectable/deletable; this makes it easier to select large groups of deletions or insertions and delete them, instead of clicking one at a time (David Doty) #507
• [70e6468]: fixed bug when removing only deletions or only insertions (David Doty) #507
• [1bfb660]: closes #504; add right-click context menu to insertion to allow editing insertion length; When multiple insertions are selected, this adjusts all of their lengths. (David Doty) #507
• [113355f]: added discussion of new select/remove capability for insertions/deletions (David Doty) #507
• [bc5bc99]: Fix helix position set on crossover for #488 (Benjamin Lee) #499
• [2066621]: Merge branch 'dev' into dev-issue-488 (Benjamin Lee) #499
• [e3050a5]: closes #505; can select many modifications and edit/delete them in batch. Deleting can either be done by pressing the delete key, or by right-clicking and selecting "Remove modification" (both will delete everything that is selected, which is only modifications, since nothing else is selectable when modifications are selectable) (David Doty) #507
• [73cc42d]: closes #502; can select many 3' ends or 5' ends and add same modification to all of them (David Doty) #507
• [8c9a614]: Fixes #500; freeze versions in all GitHub actions (Benjamin Lee) #506
• [e30040a]: Merge branch 'dev' into dev-issue-488 (Benjamin Lee) #499
• [da634a0]: Revert pubspec version to 2.9 for #500 (Benjamin Lee) #506
• [3802a5d]: Update web examples (Benjamin Lee) #499
• [d8af1fc]: Fix analyzer issue (Benjamin Lee) #506
• [8bc218e]: Set build_runner to ^1.10.1 (Benjamin Lee) #506
• [1e77fe2]: updated README with instructions on batch editing/adding/deleting modifications/insertions/deletions as in issues #502, #502, #504, #505 (David Doty) #507
• [8039cc0]: Fixes #490; store old versions of scadnano at version-specific URLs (Benjamin Lee) #508
• [6a12f7d]: Update README.md (David Doty) #507
• [6aa32c9]: added note to README explaining how to simulate loopouts on end of a strand using 5'/3' modifications (David Doty) #507
• [4f69b72]: Add links to older version (Benjamin Lee) #510
• [7b959f4]: closes #364; add "rope select" mode to select items by drawing an arbitrary polygon (David Doty) #511
• [0834bcd]: Update README.md (David Doty) #507
• [15cfaf3]: Ctrl+A now selects all selectable items while in rope select mode (David Doty) #507
• [3c13379]: closes #513; unselect selected objects when switching from non-end select mode to "all ends" select mode (David Doty) #507
• [fa2c3d8]: Update README.md (David Doty) #507
• [d19ac32]: Add dropdown right component for making sub menus (Benjamin Lee) #510
• [6c13377]: removed statement from README recommending single-stranded Domains for extensions on the end of a strand, since 5'/3' modifications are now the recommended way to do that (David Doty) #507
• [2879ffc]: Update README.md (David Doty) #507
• [22b1065]: Update README.md (David Doty) #507
• [ee8301e]: Update README.md (David Doty) #507
• [889bdc8]: rearranged other versions in dropdown menu (David Doty) #507
• [7880ad8]: Merge branch 'master' into dev (David Doty) #507
• [4ae14c6]: re-arranged list of versions in constants.dart to make an explicit list of older versions and add CURRENT_VERSION to it (more DRY not to write the same current version twice) (David Doty) #507
• [319524c]: fixed bug where rope selections were made even if rope polygon did not have >= 3 points ; now it must have >= 3 points for anything to get selected (David Doty) #507
• [dc4ada7]: fixes #509; display hairpins properly when 5' end is on reverse domain (David Doty) #507
• [c207995]: fixed bug in menu not having unique React key for link to dev site (David Doty) #507
• [3b55689]: fixed bug in loading null design (David Doty) #507
• [c1180d1]: modified export to use Strand.idt.name or Strand.name if they exist, before going with default (David Doty) #507
• [59a2638]: fixes #519; don't use IDT text as key for modifications if two types of modifications have the same IDT text (David Doty) #507
• [8484ca0]: added v0.12.2 to list of older versions to link to in Help menu (David Doty) #507
• [62fb2c7]: added note in menu on link to current version (e..g, https://scadnano.org/v0.13.0) that it is the current version (David Doty) #507