Intensity Less Than and Greater Than actually working#254
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Intensity Less Than and Greater Than actually working#254
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Pull request overview
This PR aims to make MassQL intensity qualifiers respect comparator operators (>, <, =) end-to-end by parsing the operator in the parser and applying it consistently in the engine’s intensity filtering.
Changes:
- Extend the parser to capture the qualifier comparator operator (
equal,greaterthan,lessthan). - Introduce
_get_intensity_mask()and replace legacy “minimum intensity” filtering with comparator-aware masking across MS1/MS2 filtering paths. - Add a development-oriented test that exercises
>,<, and=intensity queries on an MGF fixture.
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 4 comments.
| File | Description |
|---|---|
tests/test_agent_dev.py |
Adds a development test for GT/LT/EQ intensity comparator behavior on MGF data. |
massql/msql_parser.py |
Captures the comparator operator for qualifier leaves into the parsed JSON. |
massql/msql_engine_filters.py |
Adds comparator-aware intensity masking and applies it to MS1/MS2 filtering paths. |
massql/msql_engine.py |
Switches variable-query filtering and MS2 execution filtering to use _get_intensity_mask(). |
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| # Equality should usually be narrower than broad threshold matching. | ||
| assert scans_eq != scans_gt or scans_eq != scans_lt |
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| else: | ||
| qualifier_dict[qualifier_type]["comparator"] = "equal" |
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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