# D3.js Tree Layout Implementation

**Date**: December 9, 2025
**Status**: ✅ Complete
**Files Modified**: `src/mcp_vector_search/cli/commands/visualize/templates/scripts.py`

## Overview

Replaced the incremental vertical positioning system with a proper D3.js hierarchical tree layout, matching the reference implementation at https://d3js.org/d3-hierarchy/tree.

## Changes Made

### 1. **New `buildHierarchyTree()` Function** (Lines 2733-2784)

Builds a complete D3.js hierarchy tree structure from flat node/link data.

**Key Features**:
- Recursively constructs tree from containment relationships
- Respects visibility state (expanded/collapsed nodes)
- Sorts children (directories first, then alphabetical)
- Returns proper D3 hierarchy format with children array

**Complexity**: O(n) where n = number of visible nodes

### 2. **Rewritten `calculateD3TreeLayout()` Function** (Lines 2786-2880)

Completely replaced the incremental positioning approach with a single-pass tree layout.

**Old Approach** (Removed):
- Called separately for each parent-child relationship
- Built tree incrementally with BFS queue
- Positioned children one level at a time
- Used parameters: `(parentNode, children, canvasWidth, canvasHeight)`

**New Approach** (Implemented):
- Builds complete hierarchy tree first
- Applies D3.js tree layout to entire structure at once
- Consistent spacing across all levels
- Uses parameters: `(visibleNodeIds, rootNode, canvasWidth, canvasHeight)`

**Algorithm**:
```javascript
1. Build hierarchy: buildHierarchyTree(visibleNodeIds, rootNode)
2. Create D3 tree layout: d3.tree().size([height, width])
3. Apply layout: treeLayout(d3.hierarchy(data))
4. Transform coordinates: Convert D3 tree coords to canvas positions
```

**Layout Dimensions**:
- Horizontal: `startX = 100px` (left margin) + depth-based expansion
- Vertical: Centered at `canvasHeight / 2`, spreading `±treeHeight/2`
- Node spacing: 50px vertical per node (adaptive)
- Level width: Full canvas width minus 200px margin

### 3. **Updated Rendering Logic** (Lines 3553-3585)

Simplified the tree_expanded mode rendering by removing BFS loop.

**Old Code** (~60 lines):
- Positioned root node manually
- BFS queue to process children level by level
- Called `calculateD3TreeLayout()` for each parent
- Incremental position map building

**New Code** (~15 lines):
- Single call to `calculateD3TreeLayout()` with visible nodes
- Positions calculated for entire tree at once
- Clean, declarative approach

### 4. **Curved Connector Lines with d3.linkHorizontal()** (Lines 3594-3662)

Replaced straight `<line>` elements with curved `<path>` elements using D3's link generator.

**Changed**:
- ❌ `<line x1="" y1="" x2="" y2="">` (straight lines)
- ✅ `<path d="">` with `d3.linkHorizontal()` (curved connectors)

**Implementation**:
```javascript
const linkGenerator = d3.linkHorizontal()
    .x(d => d.x)
    .y(d => d.y);

// Generate curved path
linkGenerator({
    source: { x: sourcePos.x, y: sourcePos.y },
    target: { x: targetPos.x, y: targetPos.y }
})
```

**Visual Result**: Smooth Bézier curves connecting parent → child nodes horizontally

**Styling**:
- Stroke: `#4a5568` (gray)
- Width: `2px`
- Opacity: `0.6`
- Fill: `none` (critical for path rendering)

## Design Decisions

### Why Full Hierarchy Build?

**Rationale**:
- D3.js tree algorithm works best on complete tree structure
- Consistent spacing across all hierarchy levels
- Proper parent-child relationships for curved links
- Standard D3 pattern matching official documentation

**Trade-offs**:
- ✅ Better visual quality (professional tree layout)
- ✅ Proper D3 link generation support
- ✅ Easier to maintain (follows D3 conventions)
- ⚠️ Slightly higher memory (full tree in memory vs. incremental)
- ⚠️ Performance: O(n log n) vs. O(k) per level (negligible for typical trees)

### Why d3.linkHorizontal()?

**Rationale**:
- Standard D3.js pattern for tree connectors
- Automatic Bézier curve generation
- Horizontal orientation (left → right tree)
- Professional appearance matching reference examples

**Alternatives Considered**:
1. Straight lines: ❌ Rejected - looks amateur
2. Custom curves: ❌ Rejected - reinventing D3's proven algorithm
3. d3.linkVertical(): ❌ Rejected - wrong orientation (top → down)

## Performance Analysis

### Time Complexity

| Operation | Old | New |
|-----------|-----|-----|
| Build hierarchy | N/A | O(n) |
| Tree layout | O(k) per level × depth | O(n log n) single pass |
| Link rendering | O(e) | O(e) |
| **Total** | **O(k × d + e)** | **O(n log n + e)** |

Where:
- n = total visible nodes
- k = average children per node
- d = tree depth
- e = number of edges

**Expected Performance**:
- Typical tree (100-500 nodes): <10ms layout calculation
- Large tree (1000+ nodes): <50ms layout calculation
- Negligible difference from old approach for practical use cases

### Space Complexity

| Structure | Old | New |
|-----------|-----|-----|
| Position map | O(n) | O(n) |
| Hierarchy tree | Incremental | O(n) |
| D3 hierarchy | N/A | O(n) |
| **Total** | **O(n)** | **O(n)** |

No significant memory increase.

## Visual Changes

### Before (Incremental Positioning)
- Vertical stacking of children
- Straight lines connecting nodes
- Spacing calculated per-level
- Possible alignment inconsistencies across levels

### After (D3 Tree Layout)
- ✅ Professional hierarchical tree structure
- ✅ Curved connector lines (Bézier curves)
- ✅ Consistent spacing across all levels
- ✅ Proper parent-child visual hierarchy
- ✅ Horizontal layout: root left → children right

## Testing Recommendations

1. **Basic Tree Expansion**:
   - Click root folder → should show tree layout
   - Children positioned to right of parent
   - Curved lines connecting parent → child

2. **Multi-level Expansion**:
   - Expand folder → expand subfolder → expand file
   - Tree should grow horizontally to the right
   - All levels properly aligned vertically

3. **Large Trees**:
   - Expand folder with 20+ children
   - Should see vertical spreading with proper spacing
   - No overlapping nodes or labels

4. **Edge Cases**:
   - Single child: Should still render with curve
   - Leaf nodes: No children, no expand indicator
   - Deep nesting: Should scroll horizontally if needed

## Migration Notes

### Breaking Changes
None. The new implementation maintains the same public API.

### Deprecated Functions
- `calculateD3TreeLayout(parentNode, children, width, height)` - signature changed

### New Functions
- `buildHierarchyTree(visibleNodeIds, rootNode)` - hierarchy builder

## Related Files

- `scripts.py` - Main implementation
- `styles.py` - Link styling (already supports path elements)
- `server.py` - No changes needed (serves same HTML/JSON)

## Future Enhancements

1. **Collapsible Subtrees**: Click to collapse branches
2. **Zoom to Subtree**: Focus on specific branch
3. **Tree Orientation Toggle**: Vertical vs. horizontal
4. **Link Styling by Type**: Different colors for different relationships
5. **Animation**: Smooth transitions when expanding/collapsing

## References

- D3.js Tree Layout: https://d3js.org/d3-hierarchy/tree
- D3.js Links: https://d3js.org/d3-shape/link
- D3.js Hierarchy: https://d3js.org/d3-hierarchy

## Summary

Successfully implemented professional D3.js tree layout matching industry-standard patterns. The visualization now displays a proper hierarchical tree with:

- ✅ Complete hierarchy built at once
- ✅ D3.js tree algorithm for optimal spacing
- ✅ Curved connector lines via d3.linkHorizontal()
- ✅ Horizontal layout (root left, children right)
- ✅ Clean, maintainable code following D3 conventions

**Net Impact**: -45 lines of code, +professional tree visualization

---

*Implementation complete. Ready for testing via `mcp-vector-search visualize serve`.*
