Class for reading Percolator tab-delimited output files. More...
#include <OpenMS/FORMAT/PercolatorOutfile.h>
Classes | |
struct | PSMInfoExtractor |
Description of how to extract information from PSM IDs. More... | |
struct | ScanInfo |
Information about a single fragment spectrum. More... | |
Public Types | |
enum | ScoreType { QVALUE, POSTERRPROB, SCORE, SIZE_OF_SCORETYPE } |
Types of Percolator scores. More... | |
Public Member Functions | |
PercolatorOutfile () | |
Constructor. More... | |
void | load (const String &filename, ProteinIdentification &proteins, std::vector< PeptideIdentification > &peptides, enum ScoreType output_score=QVALUE, const String &psm_regex="", bool count_from_zero=false, const MSExperiment<> *experiment_p=0) |
Loads a Percolator output file. More... | |
Static Public Member Functions | |
static enum ScoreType | getScoreType (String score_type_name) |
Return a score type given its name. More... | |
Static Public Attributes | |
static const std::string | score_type_names [SIZE_OF_SCORETYPE] |
Names of Percolator scores (to match ScoreType) More... | |
Private Types | |
typedef std::map< Size, struct ScanInfo > | ScanInfoMap |
Mapping: spectrum index -> fragment spectrum details. More... | |
Private Member Functions | |
bool | getPSMInfo_ (const String &PSM_ID, const std::vector< struct PSMInfoExtractor > &extractors, Int &scan_number, Int &charge, double &rt, double &mz) |
Extract information from a Percolator PSM ID. More... | |
void | getPeptideSequence_ (String peptide, AASequence &seq) const |
Converts the peptide string to an 'AASequence' instance. More... | |
void | preprocessExperiment_ (const MSExperiment<> &experiment, ScanInfoMap &scan_map) |
Extracts information from the raw data. More... | |
Private Attributes | |
std::vector< struct PSMInfoExtractor > | extractors_ |
List of data extractors to try by default. More... | |
Class for reading Percolator tab-delimited output files.
For PSM-level output, the file extension should be ".psms".
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private |
Mapping: spectrum index -> fragment spectrum details.
enum ScoreType |
Constructor.
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Converts the peptide string to an 'AASequence' instance.
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Extract information from a Percolator PSM ID.
Return a score type given its name.
void load | ( | const String & | filename, |
ProteinIdentification & | proteins, | ||
std::vector< PeptideIdentification > & | peptides, | ||
enum ScoreType | output_score = QVALUE , |
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const String & | psm_regex = "" , |
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bool | count_from_zero = false , |
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const MSExperiment<> * | experiment_p = 0 |
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) |
Loads a Percolator output file.
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private |
Extracts information from the raw data.
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private |
List of data extractors to try by default.
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static |
Names of Percolator scores (to match ScoreType)
OpenMS / TOPP release 2.0.0 | Documentation generated on Thu Aug 20 2015 01:44:39 using doxygen 1.8.9.1 |