v2.3.0

PDV 2.3.0

This release adds a command-line launch mode for PDV's De Novo viewer, enabling one-click visualization of de novo sequencing results from external tools — in particular the new CasanovoGUI "Open in PDV" integration — plus a fix to the batch command-line module.

✨ New: launch the De Novo viewer from the command line

PDV can now open its De Novo result viewer directly from the command line, preloaded with a Casanovo mzTab result and the corresponding spectrum file(s) — no manual import steps:

java -jar PDV-2.3.0.jar denovo-gui \
  --mztab result.mztab \
  --spectrum run1.mzML,run2.mzML \
  --tol 0.05 \
  --tol-unit Da

Option	Description
--mztab <file>	Casanovo mzTab result to visualize (required)
--spectrum <f1[,f2,…]>	One or more spectrum files (mzML / MGF), comma-separated (required)
--tol <value>	Fragment-ion tolerance for spectrum annotation (default 0.05)
--tol-unit Da|ppm	Unit for the fragment tolerance (default Da)

This is the version required by CasanovoGUI — its Open in PDV feature passes exactly these arguments (including --tol-unit), so the GUI's spectrum-annotation tolerance and unit are now honored.

🐛 Fixes

• Fixed a bug in the batch command-line module (PDVCLIMainClass).

🔄 Compatibility

• Works with CasanovoGUI's Open in PDV integration out of the box.
• Earlier PDV releases (≤ 2.2.3) do not include the denovo-gui command; CasanovoGUI users should upgrade to 2.3.0.

📦 Full changelog

• denovo-gui: support launching the De Novo GUI through the command line (f2de55c)
• denovo-gui: add --tol-unit (Da/ppm) for fragment tolerance (73b493c)
• Fix a command-line bug (1e9ea22)
• Bump version to 2.3.0

Full diff: v2.2.3...v2.3.0