35 #ifndef OPENMS_FORMAT_INSPECTOUTFILE_H 
   36 #define OPENMS_FORMAT_INSPECTOUTFILE_H 
   86     std::vector<Size> load(
const String & result_filename, std::vector<PeptideIdentification> & peptide_identifications, 
ProteinIdentification & protein_identification, 
const DoubleReal p_value_threshold, 
const String & database_filename = 
"");
 
   95     std::vector<Size> getWantedRecords(
const String & result_filename, 
DoubleReal p_value_threshold);
 
  104     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);
 
  110     void generateTrieDB(
const String & source_database_filename, 
const String & database_filename, 
const String & index_filename, 
bool append = 
false, 
const String species = 
"");
 
  121     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);
 
  128     void getLabels(
const String & source_database_filename, 
String & ac_label, 
String & sequence_start_label, 
String & sequence_end_label, 
String & comment_label, 
String & species_label);
 
  134     std::vector<Size> getSequences(
const String & database_filename, 
const std::map<Size, Size> & wanted_records, std::vector<String> & sequences);
 
  141     template <
typename PeakT>
 
  151         throw Exception::ParseError(__FILE__, __LINE__, __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:61
A more convenient string class. 
Definition: String.h:56
static const Size db_pos_length_
length of 1) 
Definition: InspectOutfile.h:174
void reset()
Resets all internal values. 
Definition: MSExperiment.h:635
static const String score_type_
type of score 
Definition: InspectOutfile.h:179
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. 
static const Size record_length_
length of the whole record 
Definition: InspectOutfile.h:177
Unknown file extension. 
Definition: FileTypes.h:61
Representation of a mass spectrometry experiment. 
Definition: MSExperiment.h:68
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:57
size_t Size
Size type e.g. used as variable which can hold result of size() 
Definition: Types.h:144
bool loadExperiment(const String &filename, MSExperiment< PeakType > &exp, FileTypes::Type force_type=FileTypes::UNKNOWN, ProgressLogger::LogType log=ProgressLogger::NONE, const bool compute_hash=true)
Loads a file into an MSExperiment. 
Definition: FileHandler.h:121
static String typeToName(Type type)
Returns the name/extension of the type. 
void getExperiment(MSExperiment< PeakT > &exp, String &type, const String &in_filename)
Definition: InspectOutfile.h:142
int Int
Signed integer type. 
Definition: Types.h:100
Facilitates file handling by file type recognition. 
Definition: FileHandler.h:73
Parse Error exception. 
Definition: Exception.h:608