FileInfo Class Reference

Library-level equivalent of the FileInfo tool. More...

#include <OpenMS/FORMAT/FileInfo.h>

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

Public Member Functions
	FileInfo ()=default
	~FileInfo ()=default
Result	run (const std::string &filename, const Options &options)
	Load filename (type auto-detected unless Options::forced_type set) and compute everything requested.
Result	run (const std::string &filename)
	Load filename with default options (no extra flags).
Result	runAll (const std::string &filename)
	Convenience: compute all content metrics (meta/processing/statistics on; no v/i/d/c).

Static Public Member Functions
static std::string	toText (const Result &r, const Options &options)
static std::string	toText (const Result &r)
	Return the human-readable rendering produced by run() (== the FileInfo CLI -out output, cached in r).
static std::string	toTSV (const Result &r, const Options &options)
static std::string	toTSV (const Result &r)
	Return the TSV rendering produced by run() (== the FileInfo CLI -out_tsv output, cached in r).

Private Member Functions
void	report_ (const std::string &in, FileTypes::Type in_type, const Options &o, std::ostream &os, std::ostream &os_tsv, Result &r)

Detailed Description

Library-level equivalent of the FileInfo tool.

Loads a mass-spectrometry-related file (type auto-detected unless forced via Options::forced_type), extracts all file-level information into a structured FileInfo::Result, and can render that result as the exact human-readable text / TSV that the FileInfo command line tool emits.

Computation (run()) is fully separated from formatting (toText()/toTSV()), so the result is consumable directly from C++ and pyOpenMS without any stream.

FileInfo fi;
FileInfo::Result r = fi.runAll("data.consensusXML");
std::cout << r.feature->num_features << "\n";
std::cout << FileInfo::toText(r);     // == the FileInfo CLI output

---

Class Documentation

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::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::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::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::FileMeta

struct OpenMS::FileInfo::FileMeta

general header block (always populated)

Collaboration diagram for FileInfo::FileMeta:

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

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::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::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::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

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::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::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::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::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::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

Constructor & Destructor Documentation

FileInfo()

FileInfo ( )

default

~FileInfo()

~FileInfo ( )

default

Member Function Documentation

report_()

void report_ ( const std::string &  in, FileTypes::Type  in_type, const Options &  o, std::ostream &  os, std::ostream &  os_tsv, Result &  r  )

private

Single computation+rendering core: loads in (already type-detected as in_type), writes the human-readable / TSV report to os / os_tsv, and populates r. Mirrors the historical TOPPFileInfo::outputTo_ so CLI output stays byte-identical.

run() [1/2]

Result run ( const std::string &  filename )

inline

Load filename with default options (no extra flags).

See also

run(filename, options) for the exception contract.

References FileInfo::run().

Referenced by FileInfo::run().

run() [2/2]

Result run	(	const std::string &	filename,
		const Options &	options
	)

Load filename (type auto-detected unless Options::forced_type set) and compute everything requested.

Exceptions

Exception::FileNotFound	if filename does not exist
Exception::ParseError	/ format-specific exceptions if the file cannot be read (the loaders are not caught here; the CLI wrapper relies on TOPPBase to convert these to exit codes).

runAll()

Result runAll

(

const std::string &

filename

)

Convenience: compute all content metrics (meta/processing/statistics on; no v/i/d/c).

See also

run for throws.

toText() [1/2]

static std::string toText ( const Result &  r )

inlinestatic

Return the human-readable rendering produced by run() (== the FileInfo CLI -out output, cached in r).

References FileInfo::toText().

Referenced by FileInfo::toText().

toText() [2/2]

static std::string toText ( const Result &  r, const Options &  options  )

static

Return the human-readable rendering produced by run() (== the FileInfo CLI -out output, cached in r).

Note

options is accepted for API symmetry only; the rendering reflects the Options passed to run().

toTSV() [1/2]

static std::string toTSV ( const Result &  r )

inlinestatic

Return the TSV rendering produced by run() (== the FileInfo CLI -out_tsv output, cached in r).

References FileInfo::toTSV().

Referenced by FileInfo::toTSV().

toTSV() [2/2]

static std::string toTSV ( const Result &  r, const Options &  options  )

static

Return the TSV rendering produced by run() (== the FileInfo CLI -out_tsv output, cached in r).

Note

options is accepted for API symmetry only; the rendering reflects the Options passed to run().