Release notes
Modification display text can be arbitrary Unicode characters
This isn't really a new feature; it was always the case. But it's worth pointing out that it is useful since Unicode has such a variety of symbols. For instance, here's unicode characters for a [glowing star](https://unicode-table.com/en/1F31F/) and [medium black circle](https://unicode-table.com/en/26AB/) to represent a fluorophore and quencher:
<img width=300 src="https://user-images.githubusercontent.com/19274365/154812623-9f8b2443-998e-4a63-8616-527f26167705.png"> <img width=300 src="https://user-images.githubusercontent.com/19274365/154812651-c0f4f425-e5a6-4036-adb2-d6e7fded627d.png">
Change modification connector length
You can now change the length of the modification connector. The connector is drawn like a hydrocarbon chain with a default of 4 links:
You can now edit the length:
<img width=300 src="https://user-images.githubusercontent.com/19274365/151944581-5a8d5988-bd2a-406d-b4d1-8434f40cd887.png">
This is especially helpful to display modifications close to each other on a helix without their text overlapping:
Autofit added to View menu
The View→Autofit submenu now has an "Autofit" option, which can center the design. Starting with a design like this:
Clicking "View→Autofit→Autofit current design" changes the zoom and translation to fit it just in the window:
Disable display of helices in main view
Go to View→Helices→Show main view helices:
<img width=500 src="https://user-images.githubusercontent.com/19274365/152549923-f1eb3d43-69c7-432a-972b-cbe388621596.png">
Toggling it will turn off all view elements associated with helices, such as tick marks, helix circles with indices, major tick numbers, etc:
Before:
After:
Reset local settings
The File menu now has an option "Reset local settings". This will delete all settings stored in the browser, including the stored design, and reset scadnano to its original settings:
**NOTE:** If you need to reset local settings due to some design that is causing a bug, but the bug is preventing scadnano from loading and displaying the menu, here is how you can manually delete the local settings:
In your browser, open Developer Tools. This is Ctrl+Shift+I in Chrome and Firefox. It should also be accessible from your browser's menu, in Chrome:
<img width=500 src="https://user-images.githubusercontent.com/19274365/154977295-4f509ea0-cd61-4343-ac17-f7af2f757be9.png">
In Firefox:
<img width=300 src="https://user-images.githubusercontent.com/19274365/154977550-9ab8c0b9-074c-4f83-ad1a-2328df0b7f74.png">
In Chrome, click on Application→Local Storage→`https://scadnano.org`
<img width=400 src="https://user-images.githubusercontent.com/19274365/154977942-e0668f7f-455e-450d-9fdf-92c62af75efa.png">
In Firefox, click on Storage→Local Storage→`https://scadnano.org`
<img width=400 src="https://user-images.githubusercontent.com/19274365/154978395-cfc53f6c-b7b1-40ba-ac2e-044b83392415.png">
Delete the key `scadnano:design` to remove the stored design. Delete the key `scadnano:app_ui_state_storables` to reset other local settings.
Commits
- d934bc2: fixes 681: merging strands should keep at least one existing name (Cesar Alonso Guzman Avina) [741](https://github.com/UC-Davis-molecular-computing/scadnano/pull/741)
- 46398ac: changed variable names strand_from and strand_to to strand_3p and strand_5p to be consistent with naming convention in ligate reducer (and be more unambiguous about what it means) (David Doty) [741](https://github.com/UC-Davis-molecular-computing/scadnano/pull/741)
- dc6fc13: Update nick_ligate_join_by_crossover_reducers.dart (David Doty) [741](https://github.com/UC-Davis-molecular-computing/scadnano/pull/741)
- 3bc9561: renamed more strand variables in ligate and crossover join reducer to match convention, and changed convention of order of strand parameters to `join_two_strands_with_substrands` (David Doty) [741](https://github.com/UC-Davis-molecular-computing/scadnano/pull/741)
- 1b6d613: added naming behavior for nicked/deleted crossover/deleted domain as well as added naming behavior for ligate/crossovers (Cesar Alonso Guzman Avina) [741](https://github.com/UC-Davis-molecular-computing/scadnano/pull/741)
- 5ac76ef: Fixes 697; fix JSON encoding warning on startup (Benjamin Lee) [704](https://github.com/UC-Davis-molecular-computing/scadnano/pull/704)
- d4f5244: closes 709; in DNA sequence assignment, disable "warn if assigning different sequence to bound strand" checkbox when "assign complement to bound strands" is unchecked (David Doty) [710](https://github.com/UC-Davis-molecular-computing/scadnano/pull/710)
- dd318c8: closes 711: remember previously chosen M13 rotation in Assign DNA sequence dialog (David Doty) [713](https://github.com/UC-Davis-molecular-computing/scadnano/pull/713)
- 5f44b9c: Added new unit test file for strand naming behavior when ligating and nicking (Cesar Alonso Guzman Avina) [741](https://github.com/UC-Davis-molecular-computing/scadnano/pull/741)
- 1b2e320: Added autofit submenu, with the new 'autofit current design' option and fixed autofit behavior (Cesar Alonso Guzman Avina) [742](https://github.com/UC-Davis-molecular-computing/scadnano/pull/742)
- 929be7f: closes 715: assign DNA sequence dialog should state p7249 instead of p7429 (David Doty)
- 3460729: Fixes 650; move svg position of helices out of design and into app state (703) (Benjamin Lee) [703](https://github.com/UC-Davis-molecular-computing/scadnano/pull/703)
- 3651532: changed tooltip for View --> Invert y-axis (David Doty)
- c5077c1: Fixes 668; fix crash error when deselecting strand while strands from multiple helix groups are selected (720) (Benjamin Lee) [720](https://github.com/UC-Davis-molecular-computing/scadnano/pull/720)
- 155dfa2: changed "Set helix coordinates based on crossovers" tooltip to explain why it is disabled if it is. (David Doty)
- 7587bc7: basic ligate unit tests with scaffolds (Cesar Alonso Guzman Avina) [741](https://github.com/UC-Davis-molecular-computing/scadnano/pull/741)
- 16a36ee: closes 719: add "reset local settings" button (rishabhmudradi) [723](https://github.com/UC-Davis-molecular-computing/scadnano/pull/723)
- 1104584: add tests for checking name property after ligating and adding crossovers to same type strands (sarahayu) [741](https://github.com/UC-Davis-molecular-computing/scadnano/pull/741)
- feffe7b: crossover and ligate unit tests for nullable strands (rishabhmudradi) [741](https://github.com/UC-Davis-molecular-computing/scadnano/pull/741)
- cf86bda: refactored const containing message displayed when there's no design (David Doty) [749](https://github.com/UC-Davis-molecular-computing/scadnano/pull/749)
- 81b49fd: Update design_main_domain_moving.dart (David Doty) [726](https://github.com/UC-Davis-molecular-computing/scadnano/pull/726)
- f3477d8: turned off Redux Devtools (David Doty) [726](https://github.com/UC-Davis-molecular-computing/scadnano/pull/726)
- 427dfd7: added comments clarifying difference between in_bounds and is_allowable for moving strands and domains (David Doty) [726](https://github.com/UC-Davis-molecular-computing/scadnano/pull/726)
- 2f2c2d0: fixes 722: moving domain should be disallowed if overlapping another domain (David Doty) [726](https://github.com/UC-Davis-molecular-computing/scadnano/pull/726)
- d2d2fbe: fixes 717: Disable drawing of strands when connecting a crossover (David Doty) [727](https://github.com/UC-Davis-molecular-computing/scadnano/pull/727)
- 17991c1: fixes 725: moved domains should be reselected after move (David Doty) [728](https://github.com/UC-Davis-molecular-computing/scadnano/pull/728)
- d6f4c39: refactored PotentialCrossover to use Address field (David Doty) [749](https://github.com/UC-Davis-molecular-computing/scadnano/pull/749)
- 105fb9d: closes 716: drag crossover/loopout from end of one domain to another (David Doty) [729](https://github.com/UC-Davis-molecular-computing/scadnano/pull/729)
- 17cb96a: fixing generic type error in Strand.loopouts getter (David Doty) [729](https://github.com/UC-Davis-molecular-computing/scadnano/pull/729)
- 3a54fee: fixed generic type error in Strand.crossovers getter (David Doty) [729](https://github.com/UC-Davis-molecular-computing/scadnano/pull/729)
- 93fa987: fixed bug in displaying moving domains, where they were only be displayed on the original helix even if the cursor moved to a new helix (David Doty) [749](https://github.com/UC-Davis-molecular-computing/scadnano/pull/749)
- a5a54a7: fixed bug with displaying strand and domain names where the React components were not being passed the helix svg positions causing a crash (David Doty) [749](https://github.com/UC-Davis-molecular-computing/scadnano/pull/749)
- 6be2d47: closes 733: right click on strand name or domain name brings up strand context menu (David Doty) [734](https://github.com/UC-Davis-molecular-computing/scadnano/pull/734)
- 2ae16a4: fixes 732: fix bug where copy/paste strands breaks when helix counts/indices are not sufficient in destination design (David Doty) [735](https://github.com/UC-Davis-molecular-computing/scadnano/pull/735)
- 967dba1: fixes 732: fix bug where copy/paste strands breaks when helix counts/indices are not sufficient in destination design (last commit only fixed some special cases)) (David Doty) [735](https://github.com/UC-Davis-molecular-computing/scadnano/pull/735)
- 902bea2: Fixes 706; Update dependencies and Dart SDK in workflows (730) (Benjamin Lee) [730](https://github.com/UC-Davis-molecular-computing/scadnano/pull/730)
- e0ec0af: added option to set max offset of every helices based on largest-offset domain on any helix, and fixed crash bug in setting this for helices with no domains (David Doty) [736](https://github.com/UC-Davis-molecular-computing/scadnano/pull/736)
- dbac38a: Closes 686; Don't run unit tests on draft/incomplete PRs (737) (Benjamin Lee) [737](https://github.com/UC-Davis-molecular-computing/scadnano/pull/737)
- c556814: Create pull_request_template.md (738) (Benjamin Lee) [738](https://github.com/UC-Davis-molecular-computing/scadnano/pull/738)
- ac26f5c: fixed case-sensitivity bug in checking file extension (David Doty) [749](https://github.com/UC-Davis-molecular-computing/scadnano/pull/749)
- 2f8fc6d: initial middleware implementation (rishabhmudradi) [723](https://github.com/UC-Davis-molecular-computing/scadnano/pull/723)
- 0be2ca1: removing '.g' import (rishabhmudradi) [723](https://github.com/UC-Davis-molecular-computing/scadnano/pull/723)
- 02936f2: fixes 707: autofit in View menu (rishabhmudradi) [742](https://github.com/UC-Davis-molecular-computing/scadnano/pull/742)
- 83d6c74: Update menu.dart (David Doty) [742](https://github.com/UC-Davis-molecular-computing/scadnano/pull/742)
- e496476: Merge branch 'dev' into 681-merging-strands-should-keep-at-least-one-existing-name (David Doty) [741](https://github.com/UC-Davis-molecular-computing/scadnano/pull/741)
- 8feabf4: fixes 743: change length of modification "connector" (David Doty) [744](https://github.com/UC-Davis-molecular-computing/scadnano/pull/744)
- 438ef0a: fix bug where 'stap_loop' key was used instead of 'stapLoop' in cadnano export (David Doty) [749](https://github.com/UC-Davis-molecular-computing/scadnano/pull/749)
- 696601c: Update load_dna_file_reducer.dart (David Doty) [749](https://github.com/UC-Davis-molecular-computing/scadnano/pull/749)
- 4172cd2: fixes bug in cadnano import when crossover connects two ends on same helix (David Doty) [749](https://github.com/UC-Davis-molecular-computing/scadnano/pull/749)
- 6aa0db1: closes 746: disable display of helices in main view (David Doty) [747](https://github.com/UC-Davis-molecular-computing/scadnano/pull/747)
- 1e2d52a: re-arranged show/hide options dealing with helices into their own submenu of the View menu (David Doty) [747](https://github.com/UC-Davis-molecular-computing/scadnano/pull/747)
- 9b82855: fixed crash bug in displaying only selected helices (David Doty) [747](https://github.com/UC-Davis-molecular-computing/scadnano/pull/747)
- 67414ad: Merge branch 'dev' into add-reset-local-settings-button-719 (Rishabh Mudradi) [723](https://github.com/UC-Davis-molecular-computing/scadnano/pull/723)
- 47d11f9: connector length in "add modification" is updated to be most recently used length instead of 4 (David Doty) [749](https://github.com/UC-Davis-molecular-computing/scadnano/pull/749)
- 13a35be: Merge branch 'dev' into 707-autofit-in-View-menu (Rishabh Mudradi) [742](https://github.com/UC-Davis-molecular-computing/scadnano/pull/742)
- 527d47c: changed comments around ResetLocalStorage action and added confirmation prompt for the user if they click "Reset local settings" (David Doty) [723](https://github.com/UC-Davis-molecular-computing/scadnano/pull/723)
- 50b95c7: bumped version (David Doty) [749](https://github.com/UC-Davis-molecular-computing/scadnano/pull/749)