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Interface

Global toolbar

The top row contains project-wide actions:

  • the current AGP name and Auto-save setting;
  • Add Data for project folders and individual evidence files;
  • the global Homolog regex used to arrange GFA homolog groups;
  • the Chromosomes display filter shared by the heatmap, synteny, coverage, and GFA views without modifying the AGP;
  • undo, redo, AGP save/Save As, inspector visibility, and application information.

Saving writes both the edited AGP and its same-prefix operation-history sidecar.

The information menu also lists the active keyboard shortcuts and the core's coordinate convention.

Heatmap toolbar

The second row controls the contact-map view:

  • resolution slider and resolution lock;
  • color minimum, maximum, and Auto range;
  • contact-map normalization;
  • chromosome, block, and contig annotation visibility;
  • whole-genome Fit and X/Y region Jump.

For .mcool, the resolution slider uses the pyramid levels physically present in the file. Other views are constrained by the current viewport and supported display levels.

Central workspace

The heatmap is the primary workspace. It can show:

  • contact tiles projected through the current AGP layout;
  • chromosome, composite-block, and contig overlays;
  • synchronized selection bands on both matrix axes;
  • the coverage track below the matrix;
  • an optional side-by-side synteny pane;
  • an optional resizable GFA graph panel.

The heatmap and evidence windows can be closed or expanded. Closing one does not unload its source data.

Inspector

The right inspector is resizable and can be shown or hidden from the toolbar. It contains:

  • Overview: whole-assembly contact overview;
  • Synteny: compact PAF view; double-click opens the interactive split pane;
  • GFA: compact assembly-graph preview; double-click opens the graph panel;
  • Selection: selected chromosome, block, contig, and copy information;
  • History: applied and undone operations;
  • Project Info and export readiness.

Hovering or focusing a history entry previews the affected area. Clicking it focuses the view. Right-clicking an applied history entry offers Undo to here.

Status bar

The bottom status bar reports resolution, normalization, matrix, assembly, selected tool, X/Y centers, and the latest status message. Diagnostic timing text appears only when performance logging is explicitly enabled.