FileInfo.h File Reference

#include <OpenMS/config.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/MATH/StatisticFunctions.h>
#include <cstdint>
#include <iosfwd>
#include <map>
#include <optional>
#include <string>
#include <tuple>
#include <utility>
#include <vector>

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Classes
class	FileInfo
	Library-level equivalent of the FileInfo tool. More...
struct	FileInfo::Range
	one [min,max] interval for a single dimension; present==false => "<none>" More...
struct	FileInfo::RangeSet
	the four range dimensions FileInfo reports for a map / spectrum group More...
struct	FileInfo::Ranges
	MSExperiment carries four range categories; non-MSExperiment maps fill only combined. More...
struct	FileInfo::FileMeta
	general header block (always populated) More...
struct	FileInfo::ExperimentMeta
	experiment / instrument / sample / contact metadata (the -m block, peak files) More...
struct	FileInfo::ExperimentMeta::Contact
struct	FileInfo::ProcessingStep
	one data-processing step (the -p block) More...
struct	FileInfo::NamedStats
	one named SummaryStatistics block; title is the label used in both renderers More...
struct	FileInfo::PeakInfo
	peak-file (MSExperiment) specifics More...
struct	FileInfo::FeatureInfo
	feature / consensus specifics More...
struct	FileInfo::FeatureInfo::MapColumn
struct	FileInfo::IdentInfo
	identification specifics (idXML / mzIdentML) More...
struct	FileInfo::FastaInfo
	FASTA specifics. More...
struct	FileInfo::MzTabInfo
	mzTab specifics More...
struct	FileInfo::ValidationInfo
	the -v (schema/semantic validation) and -i (indexed mzML) blocks More...
struct	FileInfo::CorruptionInfo
	the -c (corrupt data) block More...
struct	FileInfo::DetailInfo
	detailed per-spectrum listing (the -d block); kept as pre-rendered lines More...
struct	FileInfo::Result
	the master result aggregate More...
struct	FileInfo::Options
	what to compute (mirrors the CLI flags; lets callers opt into expensive work) More...

Namespaces
namespace	OpenMS
	Main OpenMS namespace.

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Class Documentation

OpenMS::FileInfo::Range

struct OpenMS::FileInfo::Range

one [min,max] interval for a single dimension; present==false => "<none>"

Collaboration diagram for FileInfo::Range:

Class Members
double	max = 0.0
double	min = 0.0
bool	present = false

OpenMS::FileInfo::RangeSet

struct OpenMS::FileInfo::RangeSet

the four range dimensions FileInfo reports for a map / spectrum group

Collaboration diagram for FileInfo::RangeSet:

Class Members
bool	has_mobility = false	whether the mobility dimension applies at all
Range	intensity
Range	mobility	ion mobility (only filled when the source carries it)
Range	mz	mass-to-charge
Range	rt	retention time (seconds)

OpenMS::FileInfo::Ranges

struct OpenMS::FileInfo::Ranges

MSExperiment carries four range categories; non-MSExperiment maps fill only combined.

Collaboration diagram for FileInfo::Ranges:

Class Members
RangeSet	chromatograms	MSExperiment only.
RangeSet	combined	spectra + chromatograms (or the whole map)
bool	is_experiment = false	true => the per-level / chrom sections apply
map< UInt, RangeSet >	per_ms_level	MSExperiment only, keyed by MS level.
RangeSet	spectra_overall	MSExperiment only.

OpenMS::FileInfo::FileMeta

struct OpenMS::FileInfo::FileMeta

general header block (always populated)

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Class Members
string	file_name
Type	file_type = FileTypes::UNKNOWN
string	file_type_name	FileTypes::typeToName(file_type)

OpenMS::FileInfo::ExperimentMeta

struct OpenMS::FileInfo::ExperimentMeta

experiment / instrument / sample / contact metadata (the -m block, peak files)

Collaboration diagram for FileInfo::ExperimentMeta:

Class Members
vector< Contact >	contacts
string	date
vector< string >	detectors
string	document_id
string	instrument_model
string	instrument_name
string	instrument_vendor
vector< string >	ion_sources
vector< string >	mass_analyzers
bool	present = false
string	sample_comment
string	sample_name
string	sample_organism

OpenMS::FileInfo::ExperimentMeta::Contact

struct OpenMS::FileInfo::ExperimentMeta::Contact

Collaboration diagram for FileInfo::ExperimentMeta::Contact:

Class Members
string	email
string	first_name
string	last_name

OpenMS::FileInfo::ProcessingStep

struct OpenMS::FileInfo::ProcessingStep

one data-processing step (the -p block)

Collaboration diagram for FileInfo::ProcessingStep:

Class Members
vector< string >	actions
string	completion_time
string	software_name
string	software_version

OpenMS::FileInfo::NamedStats

struct OpenMS::FileInfo::NamedStats

one named SummaryStatistics block; title is the label used in both renderers

Collaboration diagram for FileInfo::NamedStats:

Class Members
SummaryStatistics< vector< double > >	stats
string	title

OpenMS::FileInfo::FeatureInfo

struct OpenMS::FileInfo::FeatureInfo

feature / consensus specifics

Collaboration diagram for FileInfo::FeatureInfo:

Class Members
UInt64	assigned_ids = 0
map< Int, UInt64 >	charges	charge -> count
map< UInt64, UInt64 >	ids_per_element	number of IDs -> number of elements
bool	is_consensus = false
vector< MapColumn >	map_columns
UInt64	num_features = 0	number of (consensus) features
map< UInt64, UInt64 >	size_distribution	consensus-feature size -> count
double	tic = 0.0	total ion current (featureXML)
UInt64	unassigned_ids = 0

OpenMS::FileInfo::FeatureInfo::MapColumn

struct OpenMS::FileInfo::FeatureInfo::MapColumn

Collaboration diagram for FileInfo::FeatureInfo::MapColumn:

Class Members
string	filename
string	identifier
string	label
UInt64	size = 0

OpenMS::FileInfo::IdentInfo

struct OpenMS::FileInfo::IdentInfo

identification specifics (idXML / mzIdentML)

Collaboration diagram for FileInfo::IdentInfo:

Class Members
double	avg_peptide_length = 0.0
string	db_name
string	db_version
UInt64	matched_spectra = 0
map< string, UInt64 >	modification_counts
UInt64	modified_tophits = 0
UInt64	non_redundant_peptides = 0
UInt64	non_redundant_protein_hits = 0
UInt64	num_runs = 0
UInt64	peptide_hits = 0
UInt64	protein_hits = 0
double	psms_per_spectrum = 0.0
vector< string >	search_engines	"engine (version)"
string	taxonomy

OpenMS::FileInfo::FastaInfo

struct OpenMS::FileInfo::FastaInfo

FASTA specifics.

Collaboration diagram for FileInfo::FastaInfo:

Class Members
map< string, UInt64 >	ambiguity_counts	buckets depend on is_nucleic_acid
UInt64	dup_headers = 0
UInt64	dup_sequences = 0
bool	is_nucleic_acid = false
SummaryStatistics< vector< double > >	length_stats
UInt64	num_sequences = 0
map< char, UInt64 >	residue_counts
UInt64	seq_with_ambiguous = 0
UInt64	total_residues = 0

OpenMS::FileInfo::MzTabInfo

struct OpenMS::FileInfo::MzTabInfo

mzTab specifics

Collaboration diagram for FileInfo::MzTabInfo:

Class Members
string	mode
UInt64	nucleic_acids = 0
UInt64	oligonucleotides = 0
UInt64	osms = 0
UInt64	peptides = 0
UInt64	proteins = 0
UInt64	psms = 0
UInt64	small_molecules = 0
string	type
string	version

OpenMS::FileInfo::ValidationInfo

struct OpenMS::FileInfo::ValidationInfo

the -v (schema/semantic validation) and -i (indexed mzML) blocks

Collaboration diagram for FileInfo::ValidationInfo:

Class Members
string	detail	captured validator output (re-emitted verbatim)
vector< string >	errors	semantic validation
bool	index_checked = false
bool	index_valid = false
UInt64	indexed_chromatograms = 0
UInt64	indexed_spectra = 0
bool	performed = false
string	schema_version
bool	supported = true
bool	valid = false
vector< string >	warnings

OpenMS::FileInfo::CorruptionInfo

struct OpenMS::FileInfo::CorruptionInfo

the -c (corrupt data) block

Collaboration diagram for FileInfo::CorruptionInfo:

Class Members
vector< string >	errors
bool	performed = false
vector< string >	warnings	already-formatted message lines

OpenMS::FileInfo::DetailInfo

struct OpenMS::FileInfo::DetailInfo

detailed per-spectrum listing (the -d block); kept as pre-rendered lines

Collaboration diagram for FileInfo::DetailInfo:

Class Members
vector< string >	lines
bool	performed = false

OpenMS::FileInfo::Result

struct OpenMS::FileInfo::Result

the master result aggregate

Collaboration diagram for FileInfo::Result:

Class Members
CorruptionInfo	corruption
DetailInfo	detail
optional< ExperimentMeta >	experiment_meta
optional< FastaInfo >	fasta
optional< FeatureInfo >	feature
optional< IdentInfo >	ident
FileMeta	meta
optional< MzTabInfo >	mztab
optional< PeakInfo >	peak
vector< ProcessingStep >	processing
Ranges	ranges	filled for peak / feature / consensus
vector< NamedStats >	statistics
string	targeted_summary	PQP: getSummary()
string	text	Human-readable rendering, identical to the FileInfo CLI -out output (filled by run()).
string	transformation_summary	trafoXML: model + printSummary
string	tsv	TSV rendering, identical to the FileInfo CLI -out_tsv output (filled by run()).
ValidationInfo	validation

OpenMS::FileInfo::Options

struct OpenMS::FileInfo::Options

what to compute (mirrors the CLI flags; lets callers opt into expensive work)

Collaboration diagram for FileInfo::Options:

Class Members
bool	check_corrupt = false	-c
bool	check_index = false	-i
bool	detailed = false	-d
Type	forced_type = FileTypes::UNKNOWN	== CLI -in_type
bool	meta = false	-m
bool	processing = false	-p
bool	statistics = false	-s
bool	validate = false	-v