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Merged
boopthesnoot merged 9 commits into from
Dec 4, 2025
Merged

NEW: annotating real spectra vs calculated one #314

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1ba2463
NEW: annotating real spectra vs calculated one
boopthesnoot Apr 9, 2025
a018f49
FIX: circular dependencies
boopthesnoot Apr 10, 2025
231c73d
FIX: 3.9 typing
boopthesnoot Apr 10, 2025
1baf584
new: annotating a library with seq and spec coverage
boopthesnoot Oct 9, 2025
d54af4f
fix: ruff
boopthesnoot Oct 9, 2025
c7bd689
enh: moved UNANNOTATED_TYPE to fragment.py
boopthesnoot Oct 9, 2025
2a3d8b1
fix: saving spec_idx
boopthesnoot Nov 28, 2025
d29634e
linting
boopthesnoot Dec 4, 2025
cee8362
fix: _mass_accuracy_metric on flat
boopthesnoot Dec 4, 2025
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6 changes: 6 additions & 0 deletions alphabase/constants/spectral_library.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
"""Constants for spectral library related functionality."""

# Loss type mappings - these map loss type numeric codes to their string representations
# Used in annotate.py and flat.py

LOSS_NUMBER_TO_TYPE = {0: "", 17: "_NH3", 18: "_H2O", 98: "_modloss"}

@GeorgWa GeorgWa Apr 10, 2025

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This is now covered in https://github.com/MannLabs/alphabase/blob/main/alphabase/peptide/fragment.py

@jalew188 jalew188 Apr 10, 2025

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How much redundency is there between these two modules?

@boopthesnoot boopthesnoot Apr 10, 2025

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i'll try to minimize redundancy, thank you for pointing it out

@GeorgWa GeorgWa Apr 11, 2025

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I think this can be removed as it's not needed by the new AB based implementation :).

2 changes: 2 additions & 0 deletions alphabase/peptide/fragment.py
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Expand Up @@ -83,6 +83,8 @@ class Series:

SERIES_MAPPING_INV = {v: k for k, v in SERIES_MAPPING.items()}

UNANNOTATED_TYPE = 255


@dataclass(frozen=True)
class FragmentType:
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