Revise GUI inputs and result controls from #299 review

ChangeLog

@@ -14,6 +14,9 @@
 
 ## Interface and handling
 
+- reorganize GUI parameters, add conditional seed/accessibility controls and
+  grouped CSV defaults, expand FASTA limits and refine result headers (PR #299)
+
 - retain computed GUI runs as named, foldable sessions with JSON input restoration,
   independent outputs, per-session ZIP export and deletion (PR #297 review)
 
@@ -282,6 +285,27 @@ energies, restricted partition sums, and trackers.
 ################################################################################  
 ################################################################################
 
+261024 Alexander Mitrofanov
+ * gui/{app,options,columns}.js, gui/{index.html,styles.css}
+   * organize tabs/rows as Sequences, Seed, Output, Model & Energy, Query,
+     Target and CLI-only; align wrapped labels and place Compute first
+   + add a three-way seed selector, synchronized accessibility flags and
+     mode-dependent input availability; place SHAPE beside accessibility
+   * group compact CSV choices with descriptions and group selection actions;
+     default to 10 predictions and expanded task-specific energy columns,
+     explicitly preserving browser defaults in native-compatible JSON
+ * gui/{protocol,uploads,parameter-file}.js, gui/examples/
+   * accept 50 FASTA records per strand of 2-5,000 nt each, with longest
+     selected query x longest selected target <= 1,000,000; allow 1 MB FASTA
+   + warn about ignored FASTA header descriptions while using first-token IDs
+ * gui/{sessions,results}.js
+   * select results from the header/name, order Show/Hide before the name and
+     ZIP/delete actions, compact table headings and distinguish selected rows
+ * gui/tests/, scripts/wasm/test-browser.py, README.md, gui/docs/
+   + cover limits, native JSON replay/defaults, dependent controls, grouped CSV
+     choices, desktop/mobile alignment and result header selection
+   * address https://github.com/BackofenLab/IntaRNA/pull/299#issuecomment-6375752155
+
 261023 Alexander Mitrofanov
  * gui/{app,sessions,results,visualization}.js, gui/{index.html,styles.css}
    + retain successful runs in browser memory with unique IDs, editable names,

README.md

@@ -6,7 +6,8 @@
 seeding of interaction sites**
 
 Predict short RNA pairs or evaluate supplied structures locally with the [browser interface](https://backofenlab.github.io/IntaRNA/gui/).
-Computed runs stay in separate, foldable sessions in the current tab. Name and select sessions to restore their inputs and compare results; editing or resetting parameters keeps earlier runs.
+The browser accepts up to 50 records per strand, 2–5,000 nucleotides each, with longest selected query × longest selected target at most 1,000,000. Prediction defaults to 10 interactions per pair and includes opening and seed energies; evaluation selects all energy columns.
+Computed runs stay in separate, foldable sessions under Results in the current tab. Name and select sessions to restore their inputs and compare results; editing or resetting parameters keeps earlier runs.
 Select an interaction to view it in vaRRI, or download a session’s ZIP with inputs, compiled versions, reproducible parameters and all outputs. Sessions are temporary and are cleared when the page is reloaded.
 See the [WebAssembly build instructions](gui/docs/step1-wasm-compilation.md) and
 [interface/deployment notes](gui/docs/step4-results-and-deployment.md).

gui/columns.js

@@ -313,3 +313,23 @@ export const CSV_CATALOG = [
     "numeric": true
   }
 ];
+
+// Every native column appears once. Ensemble energies and their components are
+// grouped with probabilities so users can see the cost/meaning of those outputs.
+export const CSV_GROUPS = [
+  { label: 'Energy', keys: ['E', 'ED1', 'ED2', 'E_init', 'E_loops', 'E_dangleL', 'E_dangleR', 'E_endL', 'E_endR', 'E_hybrid', 'E_norm', 'E_hybridNorm', 'E_add', 'seedE', 'seedED1', 'seedED2'] },
+  { label: 'Output', keys: ['subseqDP', 'subseqDB', 'hybridDP', 'hybridDB', 'hybridDPfull', 'hybridDBfull', 'bpList'] },
+  { label: 'Sequence', keys: ['id1', 'id2', 'seq1', 'seq2', 'subseq1', 'subseq2'] },
+  { label: 'Interaction', keys: ['start1', 'end1', 'start2', 'end2', 'seedStart1', 'seedEnd1', 'seedStart2', 'seedEnd2'] },
+  { label: 'Partition Function', keys: ['Pu1', 'Pu2', 'seedPu1', 'seedPu2', 'w', 'Etotal', 'Eall', 'Eall1', 'Eall2', 'Zall', 'Zall1', 'Zall2', 'EallTotal', 'P_E', 'RT'] },
+];
+
+export function defaultColumns(task) {
+  const context = ['id1', 'start1', 'end1', 'id2', 'start2', 'end2', 'subseqDP', 'hybridDP', 'E'];
+  // Seed energies remain available in evaluation, where native output is NAN.
+  // List them explicitly: seedEnd1/2 are coordinates, not energy columns.
+  const extra = task === 'evaluation'
+    ? [...CSV_CATALOG.filter(({ key }) => key.startsWith('E')).map(({ key }) => key), 'seedE', 'seedED1', 'seedED2']
+    : ['ED1', 'ED2', 'seedE', 'seedStart1', 'seedStart2'];
+  return [...new Set([...context, ...extra])];
+}

gui/docs/json-workflow.md

@@ -1,6 +1,7 @@
 # JSON settings and reproducible runs
 
-Load and Store sit to the right of Reset parameters. Store downloads
+The action bar starts with Compute/Evaluate, followed by Input Parameters:
+Examples, Store, Load and Reset. Store downloads
 `parameter.json` containing non-default settings and embedded input text in the
 [native JSON format](../../doc/json-parameters.md). `_comment` records compiled
 tool/library versions and executable reproduction commands. It is JSON metadata,
@@ -35,11 +36,11 @@ CSV output, additional files and diagnostics. Editing parameters, Load, examples
 Reset, invalid inputs, failed computations and cancellation preserve prior
 sessions. Failed or aborted computations do not create a session.
 
-The newest session opens automatically. Use **Show results** (or **Restore
-inputs** after editing), or select its output area, to restore that session’s
+The newest session opens automatically under **Results**. Use **Show**, select
+its header/name, or select its output area to restore that session’s
 computed inputs and fold the other sessions. The task, sequence text, signed
 indices, SHAPE/accessibility text, CSV selection/order and additional output
-selection are restored together. **Hide results** folds the output. Each session
+selection are restored together. **Hide** folds the output. Each session
 keeps its own filter, sorting and visible columns; folded vaRRI frames are unloaded
 and restored when their session is reopened.
 
@@ -60,8 +61,14 @@ JSON explicitly records that version information is unavailable.
 ## Reset and examples
 
 Reset clears the editable sequences, interactions and uploaded files and restores
-prediction defaults. Previously computed sessions remain available. Empty FASTA
-fields show the short demonstration sequences as placeholders only. The Example disclosure menu sits to the left of Reset.
+prediction defaults (10 interactions per pair, expanded energy/seed columns).
+Evaluation defaults select all energy columns. These GUI defaults are written
+explicitly in JSON when they differ from the CLI; importing existing JSON still
+uses native defaults for omitted parameters. Inactive controls keep their edits
+in the form for switching modes, but their values are omitted from executed and
+stored settings. Previously computed sessions remain available. Empty FASTA
+fields show the short demonstration sequences as placeholders only. The Examples
+disclosure menu follows the Input Parameters label.
 
 Maintainers edit `gui/examples/index.json` (an array of local JSON filenames).
 Each listed file contains `name`, `description`, and `configuration`, where the
@@ -73,9 +80,13 @@ examples show an error in the menu; they never overwrite the form.
 ## Local FASTA files
 
 Each strand has an Upload button and accepts a text-file drop into its textarea.
-Files are read locally (at most 60 KB), validated with the same FASTA checks as
+Files are read locally (at most 1 MB), validated with the same FASTA checks as
 manual entry, and replace only that strand after successful validation. Prediction
-accepts multi-FASTA; evaluation requires one record. Invalid files leave the
+accepts up to 50 FASTA records per strand, each 2–5,000 nt; evaluation requires
+one record. The longest selected query × longest selected target must be at most
+1,000,000. Names end at the first whitespace; ignored header descriptions produce
+a warning below the corresponding field. Both FASTA fields scroll horizontally
+and vertically. Invalid files leave the
 previous input intact. A later edit, reset, import or computation discards any
 pending file read, so delayed reads cannot replace newer input.
 
@@ -117,3 +128,22 @@ pending file read, so delayed reads cannot replace newer input.
   `tests/data` directory for the existing CLI harness.
 - Static staging (including the new session module and engine digest checks),
   shell syntax and `git diff --check` passed.
+
+## PR #299 review validation (2026-10-24)
+
+- `npm test --prefix gui`: all 20 tests passed, including FASTA limits, header
+  warnings, complete column grouping and explicit browser-default JSON replay.
+- `scripts/wasm/test-browser.py` passed with real WASM in Chromium and Firefox.
+  It covers the reordered panels, aligned controls, shared accessibility flags,
+  seed/accessibility/helix modes, inactive values, explicit-seed Load/Store,
+  group selection, FASTA scrolling/warnings and result header/name selection,
+  plus the existing prediction/evaluation, ZIP, abort and session checks.
+- Desktop and 390 px mobile screenshots were inspected. All seven panels have
+  no document overflow; table contents retain their own horizontal scrolling.
+- `node scripts/wasm/smoke-protocol.mjs <staged-engine>` passed native-reference
+  checks and byte-identical JSON archive replay. The unchanged engine uses the
+  parent branch's Emscripten 4.0.23 / ViennaRNA 2.7.2 assets and original metadata.
+- A fresh GCC 14 release build passed `make tests -j2`: all nine API/CLI groups.
+  Existing CLI fixtures were linked into the out-of-tree `tests/data` directory.
+- Static staging with engine digest validation, JavaScript/Python syntax checks,
+  shell syntax and `git diff --check` passed.

gui/docs/step3-frontend-ui.md

@@ -21,25 +21,26 @@ the group website. Footer and table notes use the available width, wrapping only
 when the viewport requires it.
 
 ```text
-Group logo       IntaRNA / RNA–RNA interaction analysis        University logo
+Group logo       IntaRNA package / RNA–RNA interaction analysis        University logo
 RNA–RNA interactions                             Computations stay on your device
-Task: Prediction / Evaluation                                Load example
-[ Sequence input | Query | Target | Seed | Helix | SHAPE | Energy | Output | General ]
+Task: Prediction / Evaluation
+[ Sequences | Seed | Output | Model & Energy | Query | Target | CLI-only ]
 [ Active panel: e.g. query + target, start indices, evaluation structures      ]
-Reset parameters                                                Compute
-Interactions / search / show-hide columns / CSV + ZIP download
+Compute     Input Parameters: Examples / Store / Load / Reset
+Results / Show-Hide / name / ZIP download / delete
+Interactions / search / show-hide columns / CSV download
 Selected interaction / embedded vaRRI
 Additional output files / diagnostics / compiled versions
 ```
 
-Every CLI group has a tab with one visible panel. Sequence input is selected
+Every CLI group has a tab with one visible panel. Sequences is selected
 initially. Tabs expose `aria-selected`, `aria-controls` and roving focus; Left/Right
 move between available tabs, and Home/End select the first/last. Tab names wrap
 on narrow screens. Prediction-only tabs and controls are disabled/hidden during
-evaluation; if the selected tab becomes unavailable, Sequence input is selected.
-Changing task resets parameters to their CLI defaults while preserving sequence text; Load example also restores the
-complementary pair. The native default output count is one; browser users can
-request 0–100 interactions per pair. Zero enables accessibility-only output.
+evaluation; if the selected tab becomes unavailable, Sequences is selected.
+Changing task resets parameters to their task defaults while preserving sequence text; Load example also restores the
+complementary pair. The browser defaults to 10 interactions per pair (the native default remains
+one), and accepts 0–100. Zero enables accessibility-only output.
 
 ## Inputs, defaults and validation
 
@@ -53,15 +54,29 @@ CSV uses a fixed semicolon delimiter.
 Process settings (threads, file/log paths, parameter files, help/version commands)
 are replaced by the worker lifecycle, local data inputs, downloads and displayed
 compiled versions. The base-pair maximization energy model is intentionally
-excluded. The helix-block interaction model B is supported.
+excluded. The helix-block interaction model B is supported, with helix controls at the end
+of Model & Energy, enabled only for model B. Seed constraint offers Disable,
+Explicit seed and Identify seeds, enabling only the relevant controls. Query and
+Target include their own accessibility/SHAPE columns and synchronized copies of
+the two shared accessibility flags. Ignore disables accessibility controls;
+import modes disable window/span and enable the data input. Disabled settings
+remain editable when re-enabled but do not enter the request. Explicit row grids
+align inputs even when their labels wrap.
 
-Prediction accepts plain sequence or up to 20 FASTA records per strand.
+CSV columns are grouped as Energy, Output, Sequence, Interaction and Partition
+Function, with per-group selection actions and name-only labels with description
+tooltips. Prediction adds ED1, ED2, seedE, seedStart1 and seedStart2 to the native
+CSV columns; evaluation selects all energy outputs. JSON records these browser
+defaults explicitly so native replay retains the same output.
+
+Prediction accepts plain sequence or up to 50 FASTA records per strand.
 Evaluation requires one query and target and 1–100 predefined structures.
 Wrapped/lowercase sequence text and DNA T normalize to uppercase RNA U. A/C/G/U/N
-are accepted. Each record is 2–2,000 nt; seed predictions additionally require
+are accepted. Each record is 2–5,000 nt; seed predictions additionally require
 at least `seedBP` nucleotides. FASTA IDs end at the first whitespace, matching the CLI. Duplicate IDs (including collisions after
-native CSV semicolon replacement) are rejected. The total selected all-vs-all
-query length × target length, or sum of pairwise products, is capped at 1,000,000.
+native CSV semicolon replacement) are rejected. Ignored header descriptions are reported below the input. The longest selected
+query length × longest selected target length is capped at 1,000,000, including
+pairwise mode; the cap is not summed over records.
 The per-strand start index applies to all records and defaults to one. Negative
 indices skip zero, matching `RnaSequence`; output coordinates remain inclusive.
 

gui/examples/evaluation.json

@@ -5,9 +5,14 @@
     "schema": "IntaRNA-parameters-v1",
     "parameters": {
       "personality": "IntaRNAeval",
-      "query": {"text": ">query\nGGGAGGAGGG\n"},
-      "target": {"text": ">target\nCCCUCCUCCC\n"},
-      "rri": "1||||||||||&1||||||||||"
+      "query": {
+        "text": ">query\nGGGAGGAGGG\n"
+      },
+      "target": {
+        "text": ">target\nCCCUCCUCCC\n"
+      },
+      "rri": "1||||||||||&1||||||||||",
+      "outCsvCols": "id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E,Etotal,ED1,ED2,E_init,E_loops,E_dangleL,E_dangleR,E_endL,E_endR,E_hybrid,E_norm,E_hybridNorm,E_add,Eall,Eall1,Eall2,EallTotal,seedE,seedED1,seedED2"
     }
   }
 }

gui/examples/prediction.json

@@ -4,8 +4,14 @@
   "configuration": {
     "schema": "IntaRNA-parameters-v1",
     "parameters": {
-      "query": {"text": ">query\nGGGAGGAGGG\n"},
-      "target": {"text": ">target\nCCCUCCUCCC\n"}
+      "query": {
+        "text": ">query\nGGGAGGAGGG\n"
+      },
+      "target": {
+        "text": ">target\nCCCUCCUCCC\n"
+      },
+      "outNumber": 10,
+      "outCsvCols": "id1,start1,end1,id2,start2,end2,subseqDP,hybridDP,E,ED1,ED2,seedE,seedStart1,seedStart2"
     }
   }
 }