v0.17.6

Release notes

Single-stranded extensions

Single-stranded extensions on the end of a strand can now be specified. See related notes in the Python package.

Like a Loopout, it is single-stranded, so does not occupy a Helix. However, Loopouts always reside between two Domains (which are on a Helix and in general intended to be double-stranded), whereas an Extension is always at the 5' or 3' end of a strand. This is useful for describing toeholds and other single-stranded extensions on the end of a strand, particularly when there is not available space adjacent on the helix to represent it with an unbound Domain, such as the green strand below:

(If there is available space on the Helix, single-stranded extensions can also be represented as Domains on a Helix, such as the left-most Domain of the red strand above.)

Like a Loopout, an Extension has a number of bases that must be specified when creating it.

The displayed length and angle relative to the nearest domain are also configurable:

They can either be typed in the dialog as shown, or by clicking and dragging the free end of the extension; see #799.

Commits

• 5d905fc: Added view component to adjust helix indices (Venkat Bollapragada) #784
• 26dd6a0: closes #36 allow helix index changing in batch (Venkat Bollapragada) #784
• 9966f4a: move warning stars from behind insertions (sarahayu) #785
• ad730be: replace width with height (sarahayu) #785
• 503cd73: add scroll bars and show which index is duplicated (Ho-Chih) #784
• 52db830: Add dialog type storage (Edwin Chang) #805
• ca0ef7e: added new type of Substrand called Extension (David Doty) #800
• 099e3fc: added StrandMaker chained methods for Extension's (David Doty) #800
• c849679: got first unit test working for extensions (David Doty) #800
• ca94d87: got saved dialog to work with hash key (sarahayu) #805
• 1d6c63f: update warning for helix idxs change (sarahayu) #784
• 715b902: remove commented code (sarahayu) #784
• dbe8b40: implemented all unit tests for extensions (David Doty) #800
• e784084: Update extension.dart (David Doty) #800
• 4455305: added unit test for reading Extensions in JSON, and changed loopout.length to loopout.num_bases (David Doty) #800
• fba16fb: Update extensions_test.dart (David Doty) #800
• 041e4c3: got first rendering code working for extensions, and altered select mode to include it (David Doty) #800
• 494e97c: got preliminary view of extensions working with correct display length and display angle; no DNAEnds yet (David Doty) #800
• 3c96cd2: Update util.dart (David Doty) #800
• 279a7bf: added tooltip for extension select mode (David Doty) #800
• 88dc2ef: Merge branch 'dev' into 2-extensions-on-end-of-strand (David Doty) #800
• 39efde2: Update constants.dart (David Doty) #800
• 0141778: Update .gitignore (David Doty) #800
• ca9d233: some changes in support of extensions (David Doty) #800
• 0fa0c2b: Indicate all source indexes for duplicate helixes. (Venkat Bollapragada) #784
• e949fb1: closes #793 remove Loading... message when program crashes (sarahayu) #797
• 515d734: added return type to create_hash (David Doty) #805
• 430a43b: Merge branch 'dev' into 789-saved-dialog-for-future (sarahayu) #805
• afd45f0: Switch from hashing to enum (still broken) (Edwin Chang) #805
• 2aa6fd6: saved dialogtype now works (sarahayu) #805
• 817a469: updating DialogType (rishabhmudradi) #805
• de014f0: Update design_dialog_form.dart (Ho-Chih) #805
• 6794f0c: updated DialogTypes (Venkat Bollapragada) #805
• 88f120f: changed some names in Dialog to be more precise (David Doty) #805
• b18c74e: Update design_dialog_form.dart (David Doty) #805
• 5ac033f: Update design_dialog_form.dart (David Doty) #805
• 0f6c1d5: Update design_dialog_form.dart (David Doty) #805
• 62ba6b2: Update design_dialog_form.dart (David Doty) #805
• 2890b4e: Update design_dialog_form.dart (David Doty) #805
• 839c9d1: Update design_dialog_form.dart (David Doty) #805
• 26ca58d: Update menu_side.dart (David Doty) #805
• 6ed6bb3: Update menu_side.dart (David Doty) #805
• ec6f3a3: remove saved dialog (sarahayu) #805
• 478df80: put DNA end on end of Extension. still need to apply correct rotation (David Doty) #800
• d1adb04: got rotations of extension DNAEnds working (David Doty) #800
• 8b6d915: Create todo extensions.txt (David Doty) #800
• e7a8cff: got extension domain names to display; still need to ensure they are upright depending on display_angle (David Doty) #800
• c2bb5e4: fixed extension name display to be right-side up by always drawing extension path from left to right (David Doty) #800
• 1d72b50: implemented display of extension lengths (David Doty) #800
• c21c592: implemented display DNA sequence on extension (David Doty) #800
• d4c7ca5: changed zoom threshold for caching DNA as PNG image from 1 to 0.5 (David Doty) #800
• a5bbcf1: updated deletion of domain and end so that it removes adjacent extension as well (David Doty) #800
• 1a2ac16: delete selected extensions (David Doty) #800
• ba08c8b: select all selects extensions, and selection box and rope select extensions (David Doty) #800
• ccaf7cc: implemented context menu for extensions to change name, display length, display angle, and number of bases (David Doty) #800
• e07431c: fixed accidental rename of field (David Doty) #800
• 246d3bd: implemented displaying 5' and 3' modifications on extensions (David Doty) #800
• 66fe619: enable right-click context menu on 5' and 3' end (David Doty) #800
• adc6f5e: added "add extension" to strand context menu (David Doty) #800
• acab47c: Merge branch 'dev' into 2-extensions-on-end-of-strand (David Doty) #800
• 729b25c: fixed unit tests (David Doty) #800
• da4dff2: Merge branch '2-extensions-on-end-of-strand' of https://github.com/UC-Davis-molecular-computing/scadnano into 2-extensions-on-end-of-strand (David Doty) #800
• 0ac7d29: fixes #801: fix bug in assigning DNA sequence to strand bound to another strand with an extension (David Doty) #802
• 0766ad0: fixes 803: support extensions in oxDNA export (David Doty) #804
• 979e64c: Merge branch 'dev' into 789-saved-dialog-for-future (Ho-Chih) #805
• 7933fd2: updated new dialog types (Ho-Chih) #805
• 0d1f161: Add more dialog types (Edwin Chang) #805
• c3ccea8: closes #789 save dialog for future (Ho-Chih) #805
• 0693bdb: add callback to check add extension dialog items (sarahayu) #805
• 068029a: Add use_saved_response for dialogs (Edwin Chang) #805
• 706ea28: closes #807: Add option to disable PNG caching for DNA sequences (Edwin Chang) #808
• 61de27e: added more detailed tooltip explanation of option to disable PNG caching (David Doty) #808
• 248587b: changed name of ui_state.disable_png_cache_until_action_completes to export_svg_action_delayed_for_png_cache, and changed its type from generic Action to ExportSvg, and same with associated variables and props (David Doty) #808
• 9e733f9: Update app.dart (David Doty) #813
• c019c24: Changed names and fixed compilation error (Ho-Chih) #808
• 4200ada: Update reducer_test.dart (Ho-Chih) #808
• b12203b: fixed incorrect helix coordinates (Ho-Chih) #812
• acbd544: fixes #811 fix oxDNA export bug with incorrect helix coordinates in 3D (Ho-Chih) #812
• 7d98b3c: bumped version (David Doty) #813