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@wenbostar wenbostar released this 18 Jun 22:12
· 48 commits to master since this release
v2.4.0
9e5fb4a

PDV 2.4.0

This release adds support for InstaNovo de novo sequencing results and ships a modernized user interface built on the FlatLaf light theme with a consistent, centralized font and table style across every PDV window.

✨ New: visualize InstaNovo de novo results

PDV can now import and visualize the CSV prediction output from InstaNovo (tested with v1.0.0+), alongside the existing Casanovo, Novor, DeepNovo, PepNovo+, pNovo, and DirecTag de novo formats.

  • Open the De Novo import dialog and choose an InstaNovo .csv file together with the corresponding spectrum file(s) (mzML / MGF).
Tool Accepted input
InstaNovo CSV prediction output (tested with InstaNovo v1.0.0+)

🎨 Modernized user interface

The entire PDV interface has been refreshed for a cleaner, more consistent look:

  • FlatLaf light theme is now the default Look and Feel across all PDV windows.
  • Centralized fonts (PDVFonts) — PDV's dialogs and windows now derive their fonts from one consistent, modern font family, replacing much of the previous mix of hardcoded Console, Lucida, simsun, and Arial fonts (several of which were not installed on most systems and silently fell back anyway). Spectrum and chart visualization fonts are intentionally left unchanged.
  • Centralized table styling (PDVTableStyle) and consistent row foreground colors across all result tables.
  • Rounded buttons, components, progress bars, and scroll bars; refined tabbed-pane spacing and tooltips.

These changes are purely cosmetic — no result data, import behavior, or file formats are affected.

⬆️ Dependencies

  • Added FlatLaf 3.4 (com.formdev:flatlaf) for the new Look and Feel.
  • Updated commons-lang3 from 3.5 to 3.18.0.

🔄 Compatibility

  • Existing projects, import formats, and command-line modes (including denovo-gui from 2.3.0) continue to work unchanged.
  • InstaNovo import expects the CSV format produced by InstaNovo (tested with v1.0.0+).

🙌 Contributors

  • Jeroen Van Goey (@BioGeek, InstaDeep) — InstaNovo CSV import support (#107)
  • Bo Wen (@wenbostar) — UI modernization, font/table refactor, and dependency updates

📦 Full changelog

  • Add InstaNovo CSV import support (eb21e41)
  • Document InstaNovo de novo support (89bc03a)
  • Refactor font settings and table styles across dialogs to use PDVFonts and PDVTableStyle for consistency (1cf05bd)
  • Enhance row rendering in tables with consistent foreground colors (2b651d5)
  • Set font for loading button to use PDVFonts for consistency (9e5fb4a)
  • Update commons-lang3 to 3.18.0 and remove an unused import (cde1149)
  • Bump version to 2.4.0 (included in 1cf05bd)

Full diff: v2.3.0...v2.4.0

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