Resolve the precursor hierarchy from bridge metadata without fetching peaks. Keeps isolation targets distinct from selected ions, and retains SPS selections and supplemental reactions. The filter fallback follows ThermoRawFileParser.
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#include <OpenMS/FORMAT/HANDLERS/ThermoRawFileMetadata.h>
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| struct | State |
| | What is retained per seen scan to resolve later scans' parents. More...
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| static std::string | trailer (const ThermoScan &scan, const std::string &label) |
| | Value of the trailer-extra entry with exactly this label, or "" if absent.
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| static std::optional< double > | number (std::string_view value) |
| | Parse a trailer value as a number (locale-independent).
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| static std::string | filterKey (const std::string &filter) |
| | Filter key of an MSn filter string: the text between "ms<N> " and the following " [".
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| static bool | isSRM (const std::string &filter) |
| | Whether a filter string describes a selected reaction monitoring (SRM) scan.
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| static double | selectedIon (double target, std::optional< double > mono, double width) |
| | Selected ion m/z of a precursor (ThermoRawFileParser rule).
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| static constexpr int | retentionWindow () |
| | Number of preceding scans whose state is always retained to resolve master scan references.
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| void | prune_ (int current) |
| | Forget scans that no later scan can reference (see precursors()).
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| int | parentFromFilter_ (const std::string &key) const |
| | Most recent scan whose filter key is the parent of key (0 if none).
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| std::vector< double > | spsMasses_ (const ThermoScan &scan) |
| | SPS target masses from the legacy ("SPS Mass N:") or modern ("SPS Masses:") trailer labels.
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| static bool | supplemental_ (const ThermoReaction &first, const ThermoReaction &second) |
| | True if second is the supplemental (HCD / CID) step of an ETD / ECD reaction first on the same target.
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| static std::size_t | lastReaction_ (const std::vector< ThermoReaction > &reactions) |
| | Index of the reaction that isolated this scan's precursor when no parent is known.
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| static bool | isLegacySpsLabel_ (const std::string &label) |
| | True if label is a legacy "SPS Mass <N>:" label.
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| static bool | isModernSpsLabel_ (const std::string &label) |
| | True if label is "SPS Masses:" or "SPS Masses Continued:".
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Resolve the precursor hierarchy from bridge metadata without fetching peaks. Keeps isolation targets distinct from selected ions, and retains SPS selections and supplemental reactions. The filter fallback follows ThermoRawFileParser.
◆ OpenMS::Internal::ThermoRawFileMetadata::State
| struct OpenMS::Internal::ThermoRawFileMetadata::State |
What is retained per seen scan to resolve later scans' parents.
| Class Members |
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int |
level = 1 |
MS order. |
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string |
native_id |
spectrum reference for descendants |
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vector< ThermoPrecursor > |
own |
this scan's own precursor descriptors |
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int |
parent = 0 |
scan this one descends from (0 if unknown) |
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size_t |
reactions = 0 |
reactions consumed up to and including this scan |
◆ ThermoRawFileMetadata()
◆ filterKey()
| static std::string filterKey |
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const std::string & |
filter | ) |
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static |
Filter key of an MSn filter string: the text between "ms<N> " and the following " [".
Used to find a scan's parent by filter when no master scan is known, e.g. "FTMS + c NSI Full ms2 500.00@hcd30.00 [100-1000]" yields "500.00@hcd30.00".
- Returns
- the key, or "" if the filter has no such part.
◆ isLegacySpsLabel_()
| static bool isLegacySpsLabel_ |
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const std::string & |
label | ) |
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staticprivate |
True if label is a legacy "SPS Mass <N>:" label.
◆ isModernSpsLabel_()
| static bool isModernSpsLabel_ |
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const std::string & |
label | ) |
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staticprivate |
True if label is "SPS Masses:" or "SPS Masses Continued:".
◆ isSRM()
| static bool isSRM |
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const std::string & |
filter | ) |
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static |
Whether a filter string describes a selected reaction monitoring (SRM) scan.
The scan mode is one of the words before the mass ranges ("Full", "SIM", "SRM", "CRM", "Z", "Q1MS", "Q3MS"), e.g. "+ c NSI SRM ms2 549.272 [246.107-246.109, 529.776-529.778]" is an SRM scan.
◆ lastReaction_()
| static std::size_t lastReaction_ |
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const std::vector< ThermoReaction > & |
reactions | ) |
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staticprivate |
Index of the reaction that isolated this scan's precursor when no parent is known.
◆ number()
| static std::optional< double > number |
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std::string_view |
value | ) |
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static |
Parse a trailer value as a number (locale-independent).
- Returns
- the number, or an empty optional when the value is empty, not fully numeric (e.g. "2,5" or "12.3abc") or not finite. Surrounding whitespace and a leading '+' are accepted. A literal zero is a valid number, not "missing".
◆ parentFromFilter_()
| int parentFromFilter_ |
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const std::string & |
key | ) |
const |
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private |
Most recent scan whose filter key is the parent of key (0 if none).
◆ precursors()
Precursor descriptors of one scan; scans must be passed in acquisition order.
MS1 scans return an empty vector and are only recorded as potential parents. For MSn scans the vector holds the scan's own precursor (isolation target, selected ion, charge, window, parent scan / spectrum reference, activation and supplemental activation), followed by further SPS selections and then the precursors of every ancestor scan, so an MS3 scan lists its MS2 parent's precursor as well. Only each scan's own precursors are retained internally; ancestors are resolved through parent links on request.
Memory stays bounded: the state of scans more than retentionWindow() scans before the current one is forgotten, unless it is an ancestor of a retained scan, and so are filter keys last seen before that. A master scan reference to a forgotten scan is reported with a warning and resolved like an unknown parent. Real acquisitions reference parents within a duty cycle, far below the window.
◆ prune_()
| void prune_ |
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int |
current | ) |
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private |
Forget scans that no later scan can reference (see precursors()).
◆ retentionWindow()
| static constexpr int retentionWindow |
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inlinestaticconstexpr |
Number of preceding scans whose state is always retained to resolve master scan references.
◆ selectedIon()
| static double selectedIon |
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double |
target, |
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std::optional< double > |
mono, |
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double |
width |
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static |
Selected ion m/z of a precursor (ThermoRawFileParser rule).
- Parameters
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| target | isolation window target m/z of the reaction |
| mono | "Monoisotopic M/Z:" trailer value as returned by number() |
| width | isolation width (0 if unknown) |
- Returns
- the monoisotopic m/z when it is set and plausibly inside the isolation window (narrow windows accept -3.0 / +2.5 Th around the target), otherwise the target
◆ spsMasses_()
| std::vector< double > spsMasses_ |
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const ThermoScan & |
scan | ) |
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private |
SPS target masses from the legacy ("SPS Mass N:") or modern ("SPS Masses:") trailer labels.
◆ supplemental_()
True if second is the supplemental (HCD / CID) step of an ETD / ECD reaction first on the same target.
◆ trailer()
| static std::string trailer |
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const ThermoScan & |
scan, |
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const std::string & |
label |
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) |
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static |
Value of the trailer-extra entry with exactly this label, or "" if absent.
◆ charge_key_
◆ filters_
| std::map<std::string, int> filters_ |
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private |
most recent scan per filter key ("" for MS1), pruned with scans_
◆ first_seen_
◆ forgotten_below_
scans before this one may have been forgotten
◆ master_key_
◆ mono_key_
◆ scans_
| std::map<int, State> scans_ |
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private |
retained scans by scan number
◆ sps_masses_key_
◆ trailer_
per-file positions of the trailer labels read below
◆ warned_forgotten_
| bool warned_forgotten_ = false |
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private |
a forgotten master scan was reported
◆ width_keys_
"MS<level> Isolation Width:" by level
1.9.8 