issue 28 refactor issue 59 linear layout

[martin-raden]

fix #28
fix #59

[martin-raden]

Hi @Alexander-Mitrofanov

looks nice! I reviewed all changes and agree with them. They nicely generalize redundant code parts, as I had hope for...

There are a few things to change, see review below.

I will play around with the UI to test a few border cases and to ensure the UI behaviour is still the same. Will report if I find anything, but given the changes I reviewed, I dont expect much to come.. most code was kept unchanged!

thanks a lot!
Best,
Martin

[martin-raden]

here the request for the RRI-linearization issue

[martin-raden]

• final todo: use linearization constraint in 2nd example in example.html

[martin-raden]

Issue #28 refactoring report

This report records behavior-preserving cleanup completed for Issue #28.

Removed code

Removed code	Reason
removeBPoutsideBounds() in src/vaRRI.js	It had no callers, was not exported, and duplicated cropping behavior handled by applyCropping().
sameLength() in src/vaRRI.js	It only wrapped one direct string-length comparison, adding indirection without domain meaning.
Dynamic inline library loader in index.html	It duplicated normal script loading and could race the deferred UI script. The source library is now loaded explicitly; integrations can still select dist/vaRRI.min.js.
Empty inline <script> block in index.html	It executed no code.
Commented-out example buttons in index.html	They were unreachable UI code; the example data remains available to JavaScript callers.
Inline event handlers and inline presentation styles	Behavior now lives in index.js and presentation in style.css, giving each concern one owner.
Duplicate #regionColor CSS declaration	It was identical to #subseqColor; both now share one rule.
Redundant and translated button-link CSS comments/declarations	They repeated declarations or described syntax rather than project behavior.
tests/ui.test.js and tests/ui-jsdom.test.js	All 744 lines were commented out and the files were explicitly ignored by Jest. Active UI coverage now lives in focused structure and bootstrap tests.
Diagnostic environment test	It printed process and global-state details without asserting behavior.
Unused CSS selectors	.row-3, .row-4, .label-dropdown-row, .region-color-picker, .swatch, .input-line, and the unused radio-input rule had no consumers in any source or generated UI state.
Manual parenthesis URL replacements in index.js and examples.js	Native URLSearchParams already percent-encodes parentheses; a regression test now protects that behavior.
Stale render() legend option documentation	The option was not implemented or accepted by render().
Duplicate profileData2 example property and obsolete form classes/attributes	They were redundant or invalid and had no runtime effect.

Structural changes

• Annotation registries share internal clear/find/list/register/remove helpers.
  Public registry functions, returned object shapes, ID behavior, and errors remain
  compatible.
• The public vaRRI object is grouped by semantic context and alphabetized within
  each group.
• UI actions are bound centrally by attachUiActionListeners(); HTML contains no
  executable event attributes.
• Annotation editors share reset, error-clearing, and counter helpers. Share-link
  serialization shares registry, style, and URL-list helpers and reuses one parsed
  URLSearchParams instance.
• CSS color conversion shares one canvas sampler; SVG polyline and polygon creation
  share one shape insertion helper; single-molecule examples share default data.
• The HTML passes html-validate, repeated landmarks have unique accessible names,
  profile controls have unambiguous labels, and invalid void/form markup was removed.
• Invalid HTML (class="checkbox-row"") and the incorrect list-counter CSS
  selector were corrected.
• src/README.md now inventories every exported API and documents current render
  options and annotation schemas.
• tests/ui-structure.test.js protects script order, unique IDs, accessibility names,
  standards-compliant form markup, and separation of HTML behavior/presentation.
• Repeated VM setup and background-highlight fixtures in the test suite use shared
  helpers. The URL tests cover native parenthesis encoding and malformed alpha values.

Remaining architectural candidates

The clone audit still identifies repeated static markup when HTML is included: parallel
annotation form controls in index.html, and shared header/footer fragments across
index.html, examples.html, and citation.html. Extracting these cleanly would require
a template or component build step. Adding that infrastructure would change the current
open-as-a-file deployment model, so it is intentionally left for a separate issue.

Compatibility and verification

The camel-case field IDs and URL parameter names finalized before this refactor
were preserved. The default Jest suite passes 140 tests across public library, URL,
UI bootstrap, and document-structure behavior. A full-size JavaScript clone scan reports
zero clones at the six-line/50-token threshold, and index.html passes html-validate.

[Alexander-Mitrofanov]

Review follow-up completed in ee72f3d. All inline requests are addressed and answered: local development loads src/vaRRI.js while the Pages artifact uses dist/vaRRI.min.js; the refactoring report lives in the PR discussion rather than the repository; the diagnostic now runs once before the complete test suite; and linear rail spacing uses the larger loop with documentation and regression coverage. The separate request for the second example is also implemented: wu-2024 enables both forceLayout and forceLayoutLinear, protected by a UI regression test. Verification: 4 suites and 283 tests passed, and the production Pages minification/path rewrite was reproduced successfully. No renderer behavior was removed in this follow-up.