Scadnano

new feature: "assign DNA complement from bound strands"

I couldn't think of a less awkward phrase, but what this feature allows you to do (see here: https://github.com/UC-Davis-molecular-computing/scadnano/issues/518) is to assign a DNA sequence to a strand based on existing strands bound to it that already have DNA assigned. This is under the context menu when right-clicking on a strand or a group of selected strands:


The "normal" way, particular for DNA origami with a single scaffold strand that is bound to every staple strand, is to assign a DNA sequnce to the scaffold and allow the complementary DNA sequence to be computed for every staple strand bound to it.

But in some circumstances, you might have some strand(s) that already have DNA sequences assigned, and through some modification of the design, new strand(s) come to be bound to them that were not present in the design at the time the DNA sequence was assigned. This feature allows you to select that new strand (or many strands if you like), and tell it to receive the appropriate complementary DNA sequence. It is equivalent to iterating over each strand bound to the selected strand(s), selecting "Assign DNA" from the context menu, and selecting the option "assign complement to bound strands", re-assigning the DNA sequence already assigned to that strand.

bug fix: exporting modifications to IDT files

This is technically classified as a bug fix, but really it's a feature I simply forgot to implement until now. The scadnano web interface supports displaying modifications on the 5' and 3' ends, and internal modifications, together with a "IDT text" field indicating what to output in exported files for ordering DNA strands from the synthesis company IDT. But until this version, the IDT text field was omitted from the exported DNA sequences. For instance, if you add a 5' biotin modification using IDT code `/5Biosg/`:


then it will show up in exported IDT files using the same text `/5Biosg/`.


Commits
- [[76ba84c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/76ba84c02f2c61c97a4fc162efc0d098ae7e2392)]: closes #518: add "assign DNA complement from bound strands" option (David Doty) [523](https://github.com/UC-Davis-molecular-computing/scadnano/pull/523)
- [[9b80745](https://github.com/UC-Davis-molecular-computing/scadnano/commit/9b8074556b9e450866750e4c8413cf6aeffaef3b)]: fixes #524: DNA ends not selectable by scaffold/staple after changing strand type (David Doty) [527](https://github.com/UC-Davis-molecular-computing/scadnano/pull/527)
- [[60ef6b8](https://github.com/UC-Davis-molecular-computing/scadnano/commit/60ef6b8daeb2392c1f2139300983c2a639666784)]: beefed up error-handling when catching errors with no cause or message field (David Doty) [#527](https://github.com/UC-Davis-molecular-computing/scadnano/pull/527)
- [[0fc270b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/0fc270bb6e127a855c4eeb9c670351de0e07719d)]: fixes #525: export sequences to IDT should put modifications in sequence (David Doty) [527](https://github.com/UC-Davis-molecular-computing/scadnano/pull/527)
- [[92035e9](https://github.com/UC-Davis-molecular-computing/scadnano/commit/92035e956713b8c07b7df7d1e67950b1a593e463)]: fixed unit test to properly test is_scaffold property on domains after Strand is_scaffold property is set by calling initialize(), which sets Domain.is_scaffold field (David Doty) [#527](https://github.com/UC-Davis-molecular-computing/scadnano/pull/527)
- [[981081a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/981081a3e9e49482ca2ed203c6ca5bf75cbe68fa)]: bumped version (David Doty) [#527](https://github.com/UC-Davis-molecular-computing/scadnano/pull/527)
- [[5bd9ba2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/5bd9ba2cec89fd3ca5b4136db6ae426ea2e6ead8)]: Merge branch 'master' into dev (David Doty) [#527](https://github.com/UC-Davis-molecular-computing/scadnano/pull/527)

No changes to software itself so web application is identical to [v0.13.0](https://github.com/UC-Davis-molecular-computing/scadnano/releases/tag/v0.13.0).

Fixes Github Action for deploying website.

Commits
- [[5d9a910](https://github.com/UC-Davis-molecular-computing/scadnano/commit/5d9a91048f54f441c612cf0840d667da3f6bfa36)]: Fixes #522; Fix build error in gh-pages action (Benjamin Lee) [526](https://github.com/UC-Davis-molecular-computing/scadnano/pull/526)
- [[630ec30](https://github.com/UC-Davis-molecular-computing/scadnano/commit/630ec301ea34642a8ff445913f3c8ea30f4f4790)]: Update version to v0.13.1 (Benjamin Lee) [#526](https://github.com/UC-Davis-molecular-computing/scadnano/pull/526)

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](https://github.com/UC-Davis-molecular-computing/scadnano/releases/tag/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: https://github.com/UC-Davis-molecular-computing/scadnano/issues/488


Commits
- [[a3c6b33](https://github.com/UC-Davis-molecular-computing/scadnano/commit/a3c6b332ddfa035525d774d513f708608f9f027f)]: added whitespace between IDT name displayed in footer and Strand name (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[4f9121f](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4f9121fb8e73f9d1b8828f5710ad6079b66821fc)]: Update dart.yml (Benjamin Lee) [#485](https://github.com/UC-Davis-molecular-computing/scadnano/pull/485)
- [[b7731f5](https://github.com/UC-Davis-molecular-computing/scadnano/commit/b7731f58902b3a548a63aca3593a489ea0812b0f)]: Update CONTRIBUTING.md (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[6454166](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6454166714685d50471c72a4c67d2be3500fc04a)]: Fixes #473; side cursor title use yz instead of xy (Benjamin Lee) [486](https://github.com/UC-Davis-molecular-computing/scadnano/pull/486)
- [[028162c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/028162cea896651aff4e864539297a0d7a3f8be9)]: Fixes #473; side cursor title use zy instead of xy (Benjamin Lee) [486](https://github.com/UC-Davis-molecular-computing/scadnano/pull/486)
- [[d75a989](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d75a98949427d194a8adb119f01cd0071a505f3c)]: Performance improvement for strand selection (Benjamin Lee) [#487](https://github.com/UC-Davis-molecular-computing/scadnano/pull/487)
- [[4c50667](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4c5066732abae278e190ace9d1f54d5c37424ff7)]: fixed bug with setting HTML id of modification that disabled right-click context menu for some of them (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[cc44388](https://github.com/UC-Davis-molecular-computing/scadnano/commit/cc44388aa38c90befdeebfb878d90ef655df98d7)]: fixed bug in converting from gridless 3D positions to square grid positions (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[cc9e10b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/cc9e10b4ea7f1db096238b48c92f5ebfd93f893b)]: added unit test for util.position3d_to_grid_position (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[36d27dd](https://github.com/UC-Davis-molecular-computing/scadnano/commit/36d27dd00b048fb63105951b4afad5c4a4e491a1)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[cf4ab54](https://github.com/UC-Davis-molecular-computing/scadnano/commit/cf4ab54871b0be8bf5c3cede32da0d3304d13ec2)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[9d681a1](https://github.com/UC-Davis-molecular-computing/scadnano/commit/9d681a1a8d5096cb1b83f47b25d1e61a4c5423ec)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[c5625b2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/c5625b294b579ff4a63d9ffe9c9bea2541b15103)]: Fixes #488; swap position x z coordinate (Benjamin Lee) [499](https://github.com/UC-Davis-molecular-computing/scadnano/pull/499)
- [[8e5bf03](https://github.com/UC-Davis-molecular-computing/scadnano/commit/8e5bf03d977df2724865157a38593b5ad7ac1999)]: fixed bug allowing null ModificationInternal.allowed_bases in constructor (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[421b66f](https://github.com/UC-Davis-molecular-computing/scadnano/commit/421b66f50ee1c9ec96bdafd5264996cebbc5f30e)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[0191ce1](https://github.com/UC-Davis-molecular-computing/scadnano/commit/0191ce142a8b5197f629c6000e7b2d6b490a6844)]: can select many loopouts and change all of their lengths at once (or convert all to crossovers by setting length 0) (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[2eb1bc4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2eb1bc4ffc3b67d8014971d791bb9bef062c3d96)]: updated pubspec.yamp to fix analyzer error after upgrading to Dart 2.10 (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[8b9a2b7](https://github.com/UC-Davis-molecular-computing/scadnano/commit/8b9a2b71e4c6cf9c3982c4a38100c1b671005b4a)]: fixed bug where helix groups were not properly updated after changing a helix's index (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[5aff64c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/5aff64c9e7b833869f2a1c2f6a70f4da56b8f3a4)]: Update helices_reducer.dart (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[6201886](https://github.com/UC-Davis-molecular-computing/scadnano/commit/620188600c1f385428b2a2a7a7b3c75454c011fc)]: Update pubspec.yaml (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[4879318](https://github.com/UC-Davis-molecular-computing/scadnano/commit/487931868d8a35818bdd1ece390660d0b3678c8a)]: Update pubspec.yaml (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[ed98954](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ed989541811eabd68b42e118c91bdea7eb1677c0)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[758ec7d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/758ec7d4edef15677c5ab39ae48831334e98f630)]: fixed bug where deletions/insertions not updated properly when reflecting strands horizontally. (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[b68b9f4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/b68b9f4677c6e82a22aae7524ebcea2fdc1e28ad)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[2a6e225](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2a6e225c565881483f0651fa457f3fdde6a0c900)]: fixed unit tests to account for new "all_helices" field in DeletionAdd and InsertionAdd (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[8112c43](https://github.com/UC-Davis-molecular-computing/scadnano/commit/8112c43d33e1197e0695ec2b32df41390cbba9e5)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[70e6468](https://github.com/UC-Davis-molecular-computing/scadnano/commit/70e6468469096f947af95fa692563af88101aa8f)]: fixed bug when removing only deletions or only insertions (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[1bfb660](https://github.com/UC-Davis-molecular-computing/scadnano/commit/1bfb6601aec9d61f244c72b91955e3e4e29d5c87)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[113355f](https://github.com/UC-Davis-molecular-computing/scadnano/commit/113355fa9b0fc366f6ce3492a421ee5d34f0f48d)]: added discussion of new select/remove capability for insertions/deletions (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[bc5bc99](https://github.com/UC-Davis-molecular-computing/scadnano/commit/bc5bc99fa6752313ae58da33cc9ea0acc9471625)]: Fix helix position set on crossover for #488 (Benjamin Lee) [499](https://github.com/UC-Davis-molecular-computing/scadnano/pull/499)
- [[2066621](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2066621e05d5b2169d7b3ec82e468f2a3d6e4a35)]: Merge branch 'dev' into dev-issue-488 (Benjamin Lee) [#499](https://github.com/UC-Davis-molecular-computing/scadnano/pull/499)
- [[e3050a5](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e3050a5f42975d244d8008edd56f15f0638cc1a3)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[73cc42d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/73cc42dd67566f8791bb9d812455c2e56934a4ea)]: closes #502; can select many 3' ends or 5' ends and add same modification to all of them (David Doty) [507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[8c9a614](https://github.com/UC-Davis-molecular-computing/scadnano/commit/8c9a614f6e249e5507c75d174332339690e53a26)]: Fixes #500; freeze versions in all GitHub actions (Benjamin Lee) [506](https://github.com/UC-Davis-molecular-computing/scadnano/pull/506)
- [[e30040a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e30040a7eb9ba01e28304eca0d6aede426730d9c)]: Merge branch 'dev' into dev-issue-488 (Benjamin Lee) [#499](https://github.com/UC-Davis-molecular-computing/scadnano/pull/499)
- [[da634a0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/da634a00c5c57588317ec5b28840a6a012620ae9)]: Revert pubspec version to 2.9 for #500 (Benjamin Lee) [506](https://github.com/UC-Davis-molecular-computing/scadnano/pull/506)
- [[3802a5d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/3802a5dcd9c3ec2aa64bfaabc27833611915219e)]: Update web examples (Benjamin Lee) [#499](https://github.com/UC-Davis-molecular-computing/scadnano/pull/499)
- [[d8af1fc](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d8af1fc80340f8ed3704dffa2e3c02169382430d)]: Fix analyzer issue (Benjamin Lee) [#506](https://github.com/UC-Davis-molecular-computing/scadnano/pull/506)
- [[8bc218e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/8bc218e2a996a19dba65d25a0ed2c33ce99569f3)]: Set build_runner to ^1.10.1 (Benjamin Lee) [#506](https://github.com/UC-Davis-molecular-computing/scadnano/pull/506)
- [[1e77fe2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/1e77fe2996d846c2159ec551657e97c7c232e697)]: updated README with instructions on batch editing/adding/deleting modifications/insertions/deletions as in issues #502, 502, 504, 505 (David Doty) [507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[8039cc0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/8039cc03e0d9e5f9c464ae9b3a6f0dee09814031)]: Fixes #490; store old versions of scadnano at version-specific URLs (Benjamin Lee) [508](https://github.com/UC-Davis-molecular-computing/scadnano/pull/508)
- [[6a12f7d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6a12f7d78513ae5b638abf326f8be16cf76c8b19)]: Update README.md (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[6aa32c9](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6aa32c9b9dcd0b183cafd35308539ecd30060491)]: added note to README explaining how to simulate loopouts on end of a strand using 5'/3' modifications (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[4f69b72](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4f69b725af1e3c353e70f8359ada8f5cbb75ad38)]: Add links to older version (Benjamin Lee) [#510](https://github.com/UC-Davis-molecular-computing/scadnano/pull/510)
- [[7b959f4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7b959f41fa9b6cdcf1b5c3dc34d72a21fa366a30)]: closes #364; add "rope select" mode to select items by drawing an arbitrary polygon (David Doty) [511](https://github.com/UC-Davis-molecular-computing/scadnano/pull/511)
- [[0834bcd](https://github.com/UC-Davis-molecular-computing/scadnano/commit/0834bcd18cfd0ed726be7804eb52c1fd1c3658ad)]: Update README.md (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[15cfaf3](https://github.com/UC-Davis-molecular-computing/scadnano/commit/15cfaf3476e051c55551d7605ecf27fa2fa97c7f)]: Ctrl+A now selects all selectable items while in rope select mode (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[3c13379](https://github.com/UC-Davis-molecular-computing/scadnano/commit/3c1337938d6c52eac934dec1f98e23a0496600be)]: closes #513; unselect selected objects when switching from non-end select mode to "all ends" select mode (David Doty) [507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[fa2c3d8](https://github.com/UC-Davis-molecular-computing/scadnano/commit/fa2c3d8de86d4b9776cde5d51fb0c2fee3acfab3)]: Update README.md (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[d19ac32](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d19ac32b88656de64e26a42c8e96e27cd0ef15ee)]: Add dropdown right component for making sub menus (Benjamin Lee) [#510](https://github.com/UC-Davis-molecular-computing/scadnano/pull/510)
- [[6c13377](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6c133774a142052c36dbf71fe536c010bbb39ab5)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[2879ffc](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2879ffc1fba4602c4a031df93da650ce46405507)]: Update README.md (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[22b1065](https://github.com/UC-Davis-molecular-computing/scadnano/commit/22b1065e4ec35032bec13acfdf0e3db699d110c6)]: Update README.md (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[ee8301e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ee8301e7a3e893d1d9e0ab8ee588e2cd0b543372)]: Update README.md (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[889bdc8](https://github.com/UC-Davis-molecular-computing/scadnano/commit/889bdc8f8029e0330a42b9697acadd4a99b4595c)]: rearranged other versions in dropdown menu (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[7880ad8](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7880ad8a5a3e542757147a8c933633b271ffddbe)]: Merge branch 'master' into dev (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[4ae14c6](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4ae14c6e70e38eef3c16cd910f9981dd82346608)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[319524c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/319524c11d4871cc38e9be8f75936bb8bc56ed08)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[dc4ada7](https://github.com/UC-Davis-molecular-computing/scadnano/commit/dc4ada73a1ac1a8dc82d18ac55900684858b5852)]: fixes #509; display hairpins properly when 5' end is on reverse domain (David Doty) [507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[c207995](https://github.com/UC-Davis-molecular-computing/scadnano/commit/c207995e9980abefed75c13be39a2f0bf8aa194b)]: fixed bug in menu not having unique React key for link to dev site (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[3b55689](https://github.com/UC-Davis-molecular-computing/scadnano/commit/3b55689d7d485303d919c2146e7fca408b38c68e)]: fixed bug in loading null design (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[c1180d1](https://github.com/UC-Davis-molecular-computing/scadnano/commit/c1180d15253d96471d3919de613933c809ba41aa)]: modified export to use Strand.idt.name or Strand.name if they exist, before going with default (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[59a2638](https://github.com/UC-Davis-molecular-computing/scadnano/commit/59a2638f492c34efce2ad8c4712b96a9c6b3d4ed)]: fixes #519; don't use IDT text as key for modifications if two types of modifications have the same IDT text (David Doty) [507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[8484ca0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/8484ca07626a6cd592f5c5998318df0a801b0834)]: added v0.12.2 to list of older versions to link to in Help menu (David Doty) [#507](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)
- [[62fb2c7](https://github.com/UC-Davis-molecular-computing/scadnano/commit/62fb2c78537cf711c6763359c8c9df8b25c4a2ed)]: 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](https://github.com/UC-Davis-molecular-computing/scadnano/pull/507)

Commits
- [[256ccfb](https://github.com/UC-Davis-molecular-computing/scadnano/commit/256ccfb4ae64f46ed07dbc9a0dac8d9083f68a7d)]: Fixes #512; fix strand color picker (Benjamin Lee) [516](https://github.com/UC-Davis-molecular-computing/scadnano/pull/516)
- [[470dfac](https://github.com/UC-Davis-molecular-computing/scadnano/commit/470dfacca889f812f2d565a260f227ec6dd8c54a)]: Rename event to _ (Benjamin Lee) [#516](https://github.com/UC-Davis-molecular-computing/scadnano/pull/516)

Better color picker

Before, one had to type a hex string such as `ff0000` to assign a color to a Strand. Now a more advanced tool is available:



Strand, Domain, and Loopout names
Strands, domains, and loopouts now have a `name` field. Unfortunately they cannot yet be set in the web interface. They can be set in the Python scripting library:

- https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Domain.name
- https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Domain.set_name
- https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Loopout.name
- https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Loopout.set_name
- https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Strand.name
- https://scadnano-python-package.readthedocs.io/en/latest/#scadnano.Strand.set_name

The Strand name is displayed in the tooltip on hover:


and in the footer when in "backbone" mode:


The domain and loopout names can be displayed through the option "Show domain names" in the View menu:


The convention is that two domain names are "complementary" if they are the same name, except that exactly one ends with a `*`.

The option "Show domain name mismatches" will show a red star warning to indicate if two domains both have names assigned, but

- the names are not complementary:


- or the domains do not have the same start and end offsets:



Commits
- [[eeb8ddc](https://github.com/UC-Davis-molecular-computing/scadnano/commit/eeb8ddca9738c71712fcbbaa1c5a93bcf3d8e96b)]: updated paper URL (David Doty) [#483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[16d5d66](https://github.com/UC-Davis-molecular-computing/scadnano/commit/16d5d66462de604a353adbfd6eb16e692dff8a9f)]: fixed loopout name centering (David Doty) [#483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[ec085fd](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ec085fd4dcb5b1c968495deb1658a1d01b9bee48)]: footer displays strand name (in addition to IDT strand name) in backbone mode (David Doty) [#483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[27a7f1d](https://github.com/UC-Davis-molecular-computing/scadnano/commit/27a7f1d8f5fe083a524d066a9bee4f7ca0ff7fa8)]: fixed typos in CONTRIBUTING and README (David Doty) [#483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[9a4d6c8](https://github.com/UC-Davis-molecular-computing/scadnano/commit/9a4d6c8f5633b723eb148be9511b476bec48040d)]: added check for null design when setting displayed group name in side view (David Doty) [#483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[4b75cee](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4b75cee34f75d1ce85f4208a3bdce4c1280db63d)]: fixed #472; When reading from a scadnano JSON file, duplicate deletions/insertions are removed. (David Doty) [483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[3f8f841](https://github.com/UC-Davis-molecular-computing/scadnano/commit/3f8f841e157c3201cab1f7a8405ddb785df5b111)]: added check for multiple inconsistent insertions, and unit tests for duplicate deletions/insertions, related to issue #472 (David Doty) [483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[4f12a66](https://github.com/UC-Davis-molecular-computing/scadnano/commit/4f12a667af4db935e09eeae14e5fb9067ffbc032)]: added some error-checking code to deletions/insertions JSON parsing (David Doty) [#483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[2dfc052](https://github.com/UC-Davis-molecular-computing/scadnano/commit/2dfc0525fca9021134955747df1c2afd5d2f4356)]: add option to show domain name mismatches; closes #471 (rishabhmudradi) [475](https://github.com/UC-Davis-molecular-computing/scadnano/pull/475)
- [[6bbea7b](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6bbea7b948a2bfc633d232fed714f003e3b2c4a5)]: Update CONTRIBUTING.md (David Doty) [#483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[5f8c80c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/5f8c80cc3c4173ee3f18c3ebdf5e5bffc06690ff)]: fixing error in spelling (rishabhmudradi) [#475](https://github.com/UC-Davis-molecular-computing/scadnano/pull/475)
- [[3896c0a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/3896c0ab74f562f30f856afea69053cd991f3c86)]: fixed bug causing crash when displaying domain name mismatches and some domain does not have a name (David Doty) [#483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[1800a95](https://github.com/UC-Davis-molecular-computing/scadnano/commit/1800a954e772c6190aab411cc98c5fb9b037abde)]: Fixes #199; add strand color picker (Benjamin Lee) [479](https://github.com/UC-Davis-molecular-computing/scadnano/pull/479)
- [[945c904](https://github.com/UC-Davis-molecular-computing/scadnano/commit/945c904a8cb7d00ccb8c90947f8de88bbd4b0164)]: Fixes #280; Enable helix selection clear on load (Benjamin Lee) [481](https://github.com/UC-Davis-molecular-computing/scadnano/pull/481)
- [[ce49bb6](https://github.com/UC-Davis-molecular-computing/scadnano/commit/ce49bb61db664863bfb528558211a0933375f1c4)]: fixed bug in adding modification through web interface; was improperly checking whether a DialogCheck was enabled, but that index was a DialogRadio; now supports disabling certain dialog items when a DialogRadio option(s) is selected (David Doty) [#483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[6879b82](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6879b82dcb7ab3aefc6242d4718d031005f72b55)]: fixed bug in displaying domain name mismatches (David Doty) [#483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[31061b0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/31061b0c379dba1b6c9ba88c774c2e8a30fe1620)]: fixed #482 (in last commit but forgot to add to commit message) (David Doty) [483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)
- [[eb2d670](https://github.com/UC-Davis-molecular-computing/scadnano/commit/eb2d6701db2c7e40123845dde807bddc45a730c2)]: bumped version (David Doty) [#483](https://github.com/UC-Davis-molecular-computing/scadnano/pull/483)

Optional field `name` now supported in Strand, Domain, and Loopout.

The name is displayed (optionally) in the scadnano web interface.

All three are also used with the dsd DNA sequence designer (not public yet).

Many other minor features and bugfixes; see below.

Commits
- [[771f5b0](https://github.com/UC-Davis-molecular-computing/scadnano/commit/771f5b0df2eecefee866eba52fad2a02ecd1ba08)]: Fix #453; Fix svg-png-caching image translation (Benjamin Lee) [454](https://github.com/UC-Davis-molecular-computing/scadnano/pull/454)
- [[0165e55](https://github.com/UC-Davis-molecular-computing/scadnano/commit/0165e552eb4589fd8f52c7f9a37c1c5860c81327)]: changed poorly named "context_menu_strand" to "context_menu_crossover" (David Doty) [#470](https://github.com/UC-Davis-molecular-computing/scadnano/pull/470)
- [[dfefc6e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/dfefc6ee00b3d1c657b9472a8e743f4472c02781)]: adding editing/removing/adding modifications to designs; closes#208 (rishabhmudradi) [457](https://github.com/UC-Davis-molecular-computing/scadnano/pull/457)
- [[c60a34e](https://github.com/UC-Davis-molecular-computing/scadnano/commit/c60a34e18f770f07b14f3c99050445983051597d)]: Updating selected index for adding modifications; closes #208 (rishabhmudradi) [457](https://github.com/UC-Davis-molecular-computing/scadnano/pull/457)
- [[6a0bb13](https://github.com/UC-Davis-molecular-computing/scadnano/commit/6a0bb13b808619d258780d1d87200bbdbafcf309)]: Disabling index_of_dna_base_idx when necessary (rishabhmudradi) [#457](https://github.com/UC-Davis-molecular-computing/scadnano/pull/457)
- [[040dffa](https://github.com/UC-Davis-molecular-computing/scadnano/commit/040dffaec2e9450f6cf536ec629d7c612bc5ae15)]: Editing view options (rishabhmudradi) [#457](https://github.com/UC-Davis-molecular-computing/scadnano/pull/457)
- [[67c3715](https://github.com/UC-Davis-molecular-computing/scadnano/commit/67c37156f86e2af99e3c735e6918f484a5c295cd)]: fixes #407; when re-assigning helix idx, re-assign view order (David Doty) [470](https://github.com/UC-Davis-molecular-computing/scadnano/pull/470)
- [[b4377f7](https://github.com/UC-Davis-molecular-computing/scadnano/commit/b4377f7ad1814e53f6c7d8433ff4e32f811ded1b)]: fixes #460: Dialog form input elements should be enabled when conditions are met 460 (David Doty) [470](https://github.com/UC-Davis-molecular-computing/scadnano/pull/470)
- [[e23fe02](https://github.com/UC-Davis-molecular-computing/scadnano/commit/e23fe0201604e0981b6b610ba3562a7c313e258c)]: Update design_dialog_form.dart (David Doty) [#470](https://github.com/UC-Davis-molecular-computing/scadnano/pull/470)
- [[b6c8b20](https://github.com/UC-Davis-molecular-computing/scadnano/commit/b6c8b208ec8623fdbc3c2c45ffa5ab46130d785d)]: only selects DNA ends on left-click; closes #458 (rishabhmudradi) [463](https://github.com/UC-Davis-molecular-computing/scadnano/pull/463)
- [[c4fdfbe](https://github.com/UC-Davis-molecular-computing/scadnano/commit/c4fdfbeefbc0d69e0efde1b14a48bd1782aabac4)]: using constants and adding Middle_Click (rishabhmudradi) [#463](https://github.com/UC-Davis-molecular-computing/scadnano/pull/463)
- [[a917fe2](https://github.com/UC-Davis-molecular-computing/scadnano/commit/a917fe2a50a7061a231f7ed85395dcb442688c24)]: closes #464; display domain/loopout labels (David Doty) [470](https://github.com/UC-Davis-molecular-computing/scadnano/pull/470)
- [[beb22aa](https://github.com/UC-Davis-molecular-computing/scadnano/commit/beb22aabcab88999316d47109cec833b4757eee1)]: Adding code for pointer_up (rishabhmudradi) [#466](https://github.com/UC-Davis-molecular-computing/scadnano/pull/466)
- [[56a936a](https://github.com/UC-Davis-molecular-computing/scadnano/commit/56a936a988b5198b5670905518f9e03d7e745055)]: Adding comments for event.button on a mac (rishabhmudradi) [#466](https://github.com/UC-Davis-molecular-computing/scadnano/pull/466)
- [[b26c339](https://github.com/UC-Davis-molecular-computing/scadnano/commit/b26c3399db76cb51554c6f2efae2a7ababa3f8ed)]: Adding comment (rishabhmudradi) [#466](https://github.com/UC-Davis-molecular-computing/scadnano/pull/466)
- [[cbed2e4](https://github.com/UC-Davis-molecular-computing/scadnano/commit/cbed2e44c036ca249fd56aba5fe18581da14ffb0)]: minor (David Doty) [#470](https://github.com/UC-Davis-molecular-computing/scadnano/pull/470)
- [[d52e414](https://github.com/UC-Davis-molecular-computing/scadnano/commit/d52e414c0382361dbdf03c6a0ce8acedf9abf836)]: uncapitalized menu items (David Doty) [#470](https://github.com/UC-Davis-molecular-computing/scadnano/pull/470)
- [[31a079c](https://github.com/UC-Davis-molecular-computing/scadnano/commit/31a079cc3fdc7be3b1eaaa87339db87f3e96c8ec)]: changed paper links in README to doi links (hopefully more permanent) (David Doty) [#470](https://github.com/UC-Davis-molecular-computing/scadnano/pull/470)
- [[dbd3476](https://github.com/UC-Davis-molecular-computing/scadnano/commit/dbd34762c57626e3834c2ce282936ae594ad9033)]: added instructions for voting on issues in GitHub (David Doty) [#470](https://github.com/UC-Davis-molecular-computing/scadnano/pull/470)
- [[7d19d63](https://github.com/UC-Davis-molecular-computing/scadnano/commit/7d19d63d9ccafa06fd358c6a48cc218176e0dfc9)]: added optional String name fields to Strand, Domain, and Loopout; these are used now instead of (the untyped) label to assign names to Strands, Domains, and Loopouts in the dsd DNA strand designer (though Strand labels are still used to assign Strand groups in the dsd sequence designer); also domain name is displayed (optionally) in the web interface now instead of label (David Doty) [#470](https://github.com/UC-Davis-molecular-computing/scadnano/pull/470)