Implement trajectory indicator#4
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Roy-Kid merged 4 commits intoJun 11, 2025
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* [feat] add edite mode * Add edit mode and tests * Refine edit mode and rename manager * Add magnetic bond snapping in edit mode * Refine view mode menu (#3) * Implement trajectory indicator (#4) * Add trajectory view and frame indicator * Use Tweakpane slider for frame indicator * Refine frame indicator * Refine frame indicator layout * Implement edit mode menu (#5) * Add edit mode menu with periodic table plugin * Show menu only when no mesh is picked * Fix periodic table plugin registration and set menu title * Fix tweakpane plugin registration * fix plugin compatibility * Remove periodic table plugin and use list * Implement multi-order bonds * Fix multi-bond offsets and click behavior * feat: enable select mode (#7)
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…FrameDataSource Phase 1, task #1 of multi-data-source-pipeline spec. DataSourceModifier becomes an abstract base. Two concrete subclasses: - TrajectoryDataSource(trajectory): owns a multi-frame Trajectory. frameCount = trajectory.length; getFrame(i) = trajectory.frame(i) (async). preload(i) caches the i-th frame for sync access during pipeline phase A. dispose() forwards to trajectory.dispose(). - FrameDataSource(frame): owns a single Frame. frameCount = 1; getFrame(_) returns the same frame regardless of index — this is the static-topology broadcast mechanism. preload() is a no-op; cachedFrame is always available. dispose() calls frame.free(). Both retain the existing identity apply() semantics (block injection will move to ModifierPipeline.compute phase A in task #2). Visibility flags showAtoms/showBonds/showBox are kept on the abstract base @deprecated for the existing UI panel — will be removed in phase 3 when per-DS Draw modifier toggles take over. DataSourceModifier no longer registers itself in ModifierRegistry — DSs enter the pipeline only via file ingress (`io/loadFileContent`, `io/loadFileStream`) or RPC. Users cannot add a bare DS from the modifier picker. Existing call sites that constructed `new DataSourceModifier()` now construct `new FrameDataSource(...)` as a transitionary placeholder; tasks #4–#5 replace those with proper addDataSource flows. All 445 core tests pass. Core typecheck clean.
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Phase 1, task #2 of multi-data-source-pipeline spec. ModifierPipeline.compute() drops its FrameSource argument and now runs in two phases: Phase A — DS merge: walk every enabled DataSourceModifier in array order, await preload(frameIndex) in parallel, then insertBlock each DS's contributedBlocks (or the default {atoms, bonds} fallback) into a fresh working Frame. Last-wins on block-name and simbox conflict. molrs Block::clone is an Arc::clone (refcount bump), so this merge is O(num_columns) per DS. Phase B — modifier apply: walk every enabled non-DS modifier, preserving the existing parent/selection-resolution and validation logic. DSs are skipped (their identity apply() is a no-op). The new signature accepts an optional `overrideFrame` that short-circuits phase A, used as a transitional bridge by `MolvisApp.applyPipeline({ sourceFrame })` until tasks #3–#4 retire the legacy "pass a frame to the pipeline" path. Removed: - `FrameSource` interface (pipeline.ts) - `ArrayFrameSource` / `SingleFrameSource` / `AsyncFrameSource` / `ZarrFrameSource` classes (commands/sources.ts deleted) - `ZarrReaderLike` type (no consumer left) - Dead `MolvisApp.computeFrame` method (no callers) - Re-exports through commands/index.ts and core/src/index.ts Updated: - `dag_pipeline.test.ts` switched its inline FrameSource helper to the override-bridge form. State-transition tests for phase A live in task #7. All 445 core tests pass. Core typecheck clean.
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Phase 1, task #6 of multi-data-source-pipeline spec. `loadFileContent` and `loadFileStream` gain an optional `mode` parameter (`"replace" | "append"`, default `"replace"` to preserve existing UX). In append mode they apply the spec's load decision tree: - Single-frame file (`N_file === 1`) → wrap as `FrameDataSource` and broadcast across whatever trajectory length the pipeline already has (or stay at 1 if there's no trajectory yet). - Multi-frame file matching the existing trajectory length (or no existing trajectory) → wrap as `TrajectoryDataSource` so phase A index-aligns frame-by-frame. - Frame-count mismatch → throw `Cannot append "<filename>": file has N frame(s); existing trajectory has M. File must be single-frame (topology) or match existing frame count.` A new internal helper `appendTrajectoryAsDataSource` runs the decision tree and adds an atom-count consistency check: if both the existing system and the new file contribute an `atoms` block, their atom counts must match (otherwise downstream bonds/selection indices would dangle). Then forwards to `MolvisApp.addDataSource`, which performs the redundant frame-count check and runs auto-attach. Trajectory disposal on error stays correct: append mode disposes the trajectory if validation throws, so failed loads don't leak WASM. Replace mode is unchanged — keeps using `ensureDataSource` + `setTrajectory`, which after task #3+#4 also routes through a TrajectoryDataSource transparently. Page UI stays single-DS until the phase-3 "Add Data Source" button passes `mode: "append"`. All 445 core tests pass.
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Summary
Testing
npm run testhttps://chatgpt.com/codex/tasks/task_e_6849653e8ce08324a430cb3b6ea6f7be