Bugfixes

[t0mdavid-m]

Bidirectional Mass Selection for Fragment Table
Filtering stays applied if table content is changed
Add selenocystein

Summary by CodeRabbit

• New Features

  • Added support for selenocysteine (U) in sequence handling, delivering accurate mass calculations and fragment analysis for peptides containing U. Improves result fidelity and prevents errors when working with sequences that include this residue.

• Chores

  • Updated the embedded UI component to the latest revision to stay current with upstream changes. No functional or behavioral changes for end-users.

[coderabbitai]

Walkthrough

Updated the openms-streamlit-vue-component submodule reference to a new commit and added selenocysteine ('U') with mass 150.953633405 to the amino acid mass table in src/render/sequence.py. No changes to functions, control flow, or public APIs.

Changes

Cohort / File(s)	Summary
Submodule bump: openms-streamlit-vue-component openms-streamlit-vue-component	Updated submodule pointer from 1a1b43b to 427dac2. No code changes in this repo.
Amino acid mass table update src/render/sequence.py	Added 'U': 150.953633405 to aa_masses for selenocysteine support. No functional logic changes.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• update vue #22 — Also updates the openms-streamlit-vue-component submodule pointer, indicating alignment across projects.

Poem

I hop through code, ears tuned to cues,
A ‘U’ now joins the massy news.
Submodules shift, the hashes gleam,
Proteins hum a richer theme.
With whiskers twitch and tiny cheer,
Seleno-songs are crystal clear. 🐇✨

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[coderabbitai]

Actionable comments posted: 0

🔭 Outside diff range comments (1)

src/render/sequence.py (1)

266-273: Fix: 'cy' → 'cz' (ion-type mismatch in internal fragment code)

Short: Verified — the codebase uses 'cz' elsewhere but the loop at src/render/sequence.py iterates ['by','bz','cy']. getInternalFragmentMassesWithSeq and other places explicitly check/expect 'cz', so the current 'cy' will take the wrong branch and produce incorrect shifts/fragment masses.

Locations to fix (found via repo search):

• src/render/sequence.py:40-42 — branch checks res_type == 'cz'
• src/render/sequence.py:108-110 — earlier loop uses ['ax', 'by', 'cz']
• src/render/sequence.py:203-206 — getInternalFragmentMassesWithSeq: shift = ... res_type == 'cz'
• src/render/sequence.py:211-214 — tmp code: czp, czs = getFragmentMassesWithSeq(..., 'cz')
• src/render/sequence.py:266-273 — current loop (the problematic snippet):
  • • for ion_type in ['by', 'bz', 'cy']: # by cz are the same.

Suggested fixes (choose one):

• Non-breaking (recommended if consumers rely on 'cy' keys in output):
  Replace the call with an internal mapping so output keys remain "cy" but computation uses "cz":

  for ion_type in ['by', 'bz', 'cy']:
      internal_type = 'cz' if ion_type == 'cy' else ion_type
      ions, start_indices, end_indices = getInternalFragmentMassesWithSeq(
          sequence, internal_type, modifications
      )
      out_object[f'fragment_masses_{ion_type}'] = ions
      ...
  

• Simple/safe fix (if you can change output keys):

  - for ion_type in ['by', 'bz', 'cy']:
  + for ion_type in ['by', 'bz', 'cz']:
  

This is a functional bug — please apply one of the fixes above.

🧹 Nitpick comments (3)

src/render/sequence.py (3)

215-216: Nit: typos and naming (“termianl” → “terminal”, comments spelling)

Renaming improves readability, and comment spelling fixes reduce friction for future maintenance. No behavioral changes.

-    termianl_masses = byp + bys + czp + czs#tmp code
-    termianl_masses.sort()#tmp code
+    terminal_masses = byp + bys + czp + czs  # tmp code
+    terminal_masses.sort()  # tmp code

-            # Only conside fragments of at least length 5
+            # Only consider fragments of at least length 5

-                # TODO: Should be adressed in component
-                if isMatchWithTolerance(termianl_masses, mass, 10.0): #tmp code
+                # TODO: Should be addressed in component
+                if isMatchWithTolerance(terminal_masses, mass, 10.0):  # tmp code

Also applies to: 233-233, 248-249

---

253-253: Nit: use the H20 constant instead of a hardcoded literal

Keeps constants centralized and avoids magic numbers.

-                masses.append(mass + 18.010564683 + shift)
+                masses.append(mass + H20 + shift)

---

165-167: Align selenocysteine mass precision and document source

To keep all entries at six-decimal precision and cite the upstream definition, update in src/render/sequence.py:

• Line 166:

-    'U': 150.953633405,
+    'U': 150.953633,  # source: Unimod (mod 162)/OpenMS monoisotopic mass 150.9536334 Da

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📥 Commits

Reviewing files that changed from the base of the PR and between 5c3f5c8 and 334e4b7.

⛔ Files ignored due to path filters (3)

• js-component/dist/assets/index-7cc3fbf2.css is excluded by !**/dist/**
• js-component/dist/assets/index-871c0fa8.js is excluded by !**/dist/**
• js-component/dist/index.html is excluded by !**/dist/**

📒 Files selected for processing (2)

• openms-streamlit-vue-component (1 hunks)
• src/render/sequence.py (1 hunks)

🔇 Additional comments (1)

openms-streamlit-vue-component (1)

1-1: Ensure CI Can Fetch the Submodule and Verify Host-App Contracts

I ran the recommended submodule-init script and saw clone failures due to SSH not being available in this environment. Please:

• Update the submodule remote in .gitmodules to use an HTTPS URL (or ensure your CI agents have SSH set up and keys loaded).
• Add a step in your CI config to run:

  git submodule update --init --recursive
  

  before any build or test commands.
• Double-check that the bumped commit in openms-streamlit-vue-component doesn’t introduce breaking UI prop or event name changes in the host Streamlit integration.