35 #ifndef OPENMS_FORMAT_INSPECTOUTFILE_H 36 #define OPENMS_FORMAT_INSPECTOUTFILE_H 87 std::vector<Size> load(
const String & result_filename, std::vector<PeptideIdentification> & peptide_identifications,
ProteinIdentification & protein_identification,
const double p_value_threshold,
const String & database_filename =
"");
96 std::vector<Size> getWantedRecords(
const String & result_filename,
double p_value_threshold);
105 void compressTrieDB(
const String & database_filename,
const String & index_filename, std::vector<Size> & wanted_records,
const String & snd_database_filename,
const String & snd_index_filename,
bool append =
false);
111 void generateTrieDB(
const String & source_database_filename,
const String & database_filename,
const String & index_filename,
bool append =
false,
const String species =
"");
122 void getPrecursorRTandMZ(
const std::vector<std::pair<
String, std::vector<std::pair<Size, Size> > > > & files_and_peptide_identification_with_scan_number, std::vector<PeptideIdentification> & ids);
129 void getLabels(
const String & source_database_filename,
String & ac_label,
String & sequence_start_label,
String & sequence_end_label,
String & comment_label,
String & species_label);
135 std::vector<Size> getSequences(
const String & database_filename,
const std::map<Size, Size> & wanted_records, std::vector<String> & sequences);
151 throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"Could not determine type of the file. Aborting!", in_filename);
167 void readOutHeader(
const String & filename,
const String & header_line,
Int & spectrum_file_column,
Int & scan_column,
Int & peptide_column,
Int & protein_column,
Int & charge_column,
Int & MQ_score_column,
Int & p_value_column,
Int & record_number_column,
Int & DB_file_pos_column,
Int & spec_file_pos_column,
Size & number_of_columns);
184 #endif // OPENMS_FORMAT_INSPECTOUTFILE_H Type
Actual file types enum.
Definition: FileTypes.h:59
Representation of a protein identification run.
Definition: ProteinIdentification.h:62
A more convenient string class.
Definition: String.h:57
static const Size db_pos_length_
length of 1)
Definition: InspectOutfile.h:174
void reset()
Resets all internal values.
Definition: MSExperiment.h:709
static const String score_type_
type of score
Definition: InspectOutfile.h:179
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
static const Size protein_name_length_
length of 3)
Definition: InspectOutfile.h:176
static FileTypes::Type getTypeByContent(const String &filename)
Determines the file type of a file by parsing the first few lines.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
static const Size record_length_
length of the whole record
Definition: InspectOutfile.h:177
bool loadExperiment(const String &filename, MSExperiment &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE, const bool rewrite_source_file=true, const bool compute_hash=true)
Loads a file into an MSExperiment.
Unknown file extension.
Definition: FileTypes.h:61
No progress logging.
Definition: ProgressLogger.h:75
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
static const Size trie_db_pos_length_
length of 2)
Definition: InspectOutfile.h:175
static const char trie_delimiter_
the sequences in the trie database are delimited by this character
Definition: InspectOutfile.h:178
Representation of an Inspect outfile.
Definition: InspectOutfile.h:58
void getExperiment(PeakMap &exp, String &type, const String &in_filename)
Definition: InspectOutfile.h:142
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
static String typeToName(Type type)
Returns the name/extension of the type.
int Int
Signed integer type.
Definition: Types.h:103
Facilitates file handling by file type recognition.
Definition: FileHandler.h:63
Parse Error exception.
Definition: Exception.h:623