SMS3 v0.4.45

SMS3 v0.4.45

Added space between the output header and sequence navigation controls in PCR
Primer Design and the other sequence and alignment viewers. The gap matches
the side spacing and also appears in newly downloaded standalone HTML viewers.

Sequence Manipulation Suite v0.4.44

SMS3 v0.4.44

Revised descriptions for 43 tools to state their supported actions, inputs and
outputs directly. Removed filler such as "readable", "publication-ready" and
"quick", and replaced vague phrases with specific operations.

The wording is shared by featured cards, search, catalogs and tool help.
Tool behavior is unchanged.

Sequence Manipulation Suite v0.4.43

SMS3 v0.4.43

This release refines image editing, Showcase examples and featured-tool descriptions.

• Table to Image now applies column fonts and sizes to values by default.
  A checkbox also applies them to the column header when wanted. Existing saved
  documents preserve their previous styling.
• All four image editors show temporary circle crosshairs and a square diagonal
  guide while drawing or resizing equal-sided shapes. The guides match the
  alignment guides and disappear when the interaction ends.
• Color-picker swatches have cleaner edges, and Text to Image and Table to Image
  source actions use consistent button sizes.
• Showcase examples have improved typography: a sharper Image Annotator plot,
  proportional table headers with fixed-width sequence values, and a sequence
  legend that matches the sequence font. The primer table now highlights an
  entire row with an editable annotation.
• Sixteen featured-tool descriptions now more clearly explain their tools'
  capabilities, accepted formats and scope, including pooled sequence sampling
  and the option to sample each record separately.

Sequence Manipulation Suite v0.4.42

SMS3 v0.4.42

Text to Image and Table to Image are now separate tools in Text, Notes & Images,
bringing SMS3 to 156 tools.

• Text to Image preserves formatted text and sequence spacing, with font
  choices, editable annotations, and SVG/PNG exports.
• Table to Image accepts CSV, TSV, Excel workbooks and delimited plain text.
  Individual columns can use different fonts and sizes, including bundled
  fixed-width fonts for sequences. Existing saved image documents still open in
  the appropriate editor.
• All four image editors have compact icon toolbars with hover/focus tooltips,
  a compact color chooser with opacity, recent colors and an image eyedropper,
  and simpler contextual controls. Filled boxes replace the separate Highlight
  tool; existing highlights retain their appearance.
• SVG dragging stays stable during repeated moves and resizing. Alignment and
  proportional-resize guides are graphical, pointer end controls show dots,
  and copied text/table annotations appear separately from the original.
• Text/table source settings survive other edits, blank labels stay blank, and
  color opacity matches exported fills. Each image tool has an annotated,
  editable example in the Showcase.

Sequence Manipulation Suite v0.4.41

SMS3 v0.4.41

SMS3 adds three image tools and a rotating Featured tool card on Home, bringing
the public toolkit to 155 tools.

• SVG Editor lets you adjust SVG objects and add editable annotations.
• Image Annotator adds drawings, labels, arrows, boxes, and highlights to PNG
  images.
• Text & Table to Image turns formatted text and tables into editable images,
  with font controls and optional annotations.
• Image editing includes selection and resize handles, alignment snapping,
  editable labels, color swatches, opacity, an eyedropper, and recent colors.
  The editors support touch and trackpad navigation, portable editable documents,
  and image exports. Bundled fonts remain available in supported exports.
• The Showcase includes working examples of the three image tools.
• The Featured tool card below the Home showcase link draws from the entire
  visible tool registry. It changes on a later day's visit and offers Show
  another, avoiding repeats until all tools have appeared. Progress is stored
  in the browser, and newly registered tools join automatically.

Sequence Manipulation Suite v0.4.40

SMS3 v0.4.40

GenBank and GFF3 inputs retain their correct record identities, sequence bases,
and annotations across conversion, extraction, PCR, editor, and workflow tools.

• Blank GenBank headers no longer consume the following header, and Windows
  line endings preserve feature tables. NCBI download validation checks fields
  within the correct line and record.
• GFF3 imports recognize embedded FASTA with or without an explicit separator,
  match percent-escaped contig IDs correctly, and report malformed annotation
  rows. Paired sequences remain available when conversion skips invalid features.
• GFF/GTF Feature Extractor passes matching IDs to gffread and reports native
  extraction errors clearly. Interval Operations matches escaped GFF3 contig IDs
  to corresponding BED intervals.
• Sanger Viewer help stays dismissed after Escape, including when closing the
  tooltip triggers a delayed pointer event.

Regression coverage includes 22 parser checks and eight production browser
journeys using the bundled gffread and bedtools engines.

Sequence Manipulation Suite v0.4.39

SMS3 v0.4.39

Feature mouseovers stay inside the visible viewer panel, including smaller
scrolling containers, instead of extending below it and introducing scrollbars
that make the view jump. Long annotation cards scroll internally and open inward
when close to an edge.

The shared positioning fix covers Canvas and SVG inspection, including linear
DNA, circular DNA and protein viewers and their standalone HTML exports.
Annotation text, feature colours and scientific coordinates are preserved.

Release tests, local browser gates and live browser smoke tests are intentionally
skipped at the maintainer's request. The tooltip fix was verified before this
release request; no tests were rerun for publication.

Sequence Manipulation Suite v0.4.38

SMS3 v0.4.38

Feature hover and selection use a warm amber glow matching the viewer's DNA
selection colour. The glow follows the visible rectangle, arrow or circular
arc and stays outside the feature, preserving labels and CDS amino-acid letters.
CDS translation shading is clipped to the actual arrow shape.

The shared linear DNA, protein and circular DNA viewers, including portable
HTML exports, use this treatment. Scientific data and coordinates are unchanged.

Tests are intentionally skipped at the maintainer's request. Browser review
covers the affected feature and CDS rendering; this is not a full release test.

Sequence Manipulation Suite v0.4.37

SMS3 v0.4.37

Improve annotation inspection, navigation stability, and image exports in the
linear DNA, circular DNA, and protein sequence viewers.

• Show full feature notes, products, identifiers, and repeated annotation values
  in inspection cards. Cards support text selection, scrolling, and keyboard
  access, and stay within the viewport.
• Preserve feature category colours during hover and selection, with a neutral
  outline to identify the inspected feature.
• Keep linear viewer page space stable while zooming, panning, and fitting the
  sequence, even when dense annotations change the number of visible rows.
• Keep linear ruler labels, codon graphics, and their inspection targets within
  the plot boundaries.
• Preserve the displayed viewer theme and colours in PNG downloads.
• Include the viewer fixes in downloaded standalone HTML files.

Open SMS3.

Validation

The core suite passed 2,713 tests with 11 existing skips. All 1,019 Chromium
journeys passed across the full generated-site gate and focused repeats.
The full gate identified two test assertions that needed to follow the updated
viewer behaviour: pointer coordinates after selection-related scrolling, and
neutral selection outlines. Both were corrected and passed twice in Chromium
and twice in WebKit without changing application files.

The full WebKit gate passed 1,009 journeys with ten expected native-input skips
and no failures, using 26 fresh-browser batches and zero retries. The portable
viewer runtime check passed. All 797 generated release files remained identical
through verification and publication preparation.

GitHub Pages deployment succeeded. The live app version and entry-page hash
matched the verified release before Chromium and WebKit smoke checks passed
with all 152 tools available.

Sequence Manipulation Suite v0.4.36

SMS3 v0.4.36

Improve sequence inputs, design against annotated features, and retain
annotations through supported workflows.

• Enter multiple primers or oligos as one sequence per line, or use FASTA for
  named records, in In Silico PCR and Primer / Oligo Basic Properties. Shared
  guidance and live counts make the input boundaries explicit.
• Use consistent sequence, annotated-record, and annotation-plus-FASTA input
  tabs where supported, including PCR Primer Design, restriction tools,
  CRISPR Guide Design, and TALEN Target Finder.
• Correct annotated-file uploads and prevent inactive uploaded files from
  overriding the selected input. Sequence-only tools reject unsupported
  annotated formats instead of interpreting their metadata as sequence.
• Select parsed features as targets for PCR primer design, CRISPR guides, and
  TALEN candidates. PCR supports flanking a feature or designing within it;
  CRISPR targets cut positions and TALEN targets the complete spacer. Changed
  or unavailable targets are reported explicitly.
• Show source annotations alongside primers, products, restriction sites, and
  design candidates in compatible sequence viewers.
• Preserve annotations and source identity through supported typed workflow
  handoffs, whole-record extraction, filtering, sorting, and mapping. Keep
  feature choices synchronized with active workflow input, and use remapped
  annotations for annotated pseudomolecule output.
• Correct workflow imports, source switching, and recipe-only exports so
  hidden structured input cannot override edited text or leak into a recipe.

Sequence-only transformations and exports retain their existing annotation
limits. Workspace feature layers remain separate visual attachments; design
targets require annotated input or structured sequence records.

Open SMS3.

Validation

The core suite passed with 2,710 tests and 11 existing skips. All 1,011 Chromium
journeys and 1,001 WebKit-compatible journeys passed across the full generated-site
gate and focused checks, with ten expected WebKit native-input skips. The gate
identified four assertions for superseded input controls and one rendering-timing
assertion; these tests were corrected and verified without changing application
code or the generated release files. Focused coverage includes uploads, feature
targeting, workflow annotation handoffs, viewers, and portable exports.

GitHub Pages deployment succeeded. The live version and entry-page hash matched
the tested release before Chromium and WebKit smoke checks passed with all 152
tools available.