OpenMS  3.0.0
InspectOutfile.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Martin Langwisch $
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34 
35 #pragma once
36 
44 
45 
46 namespace OpenMS
47 {
57  class OPENMS_DLLAPI InspectOutfile
58  {
59 public:
62 
64  InspectOutfile(const InspectOutfile & inspect_outfile);
65 
67  virtual ~InspectOutfile();
68 
70  InspectOutfile & operator=(const InspectOutfile & inspect_outfile);
71 
73  bool operator==(const InspectOutfile & inspect_outfile) const;
74 
86  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 = "");
87 
95  std::vector<Size> getWantedRecords(const String & result_filename, double p_value_threshold);
96 
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);
105 
110  void generateTrieDB(const String & source_database_filename, const String & database_filename, const String & index_filename, bool append = false, const String species = "");
111 
112 
115  void getACAndACType(String line, String & accession, String & accession_type);
116 
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);
122 
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);
129 
134  std::vector<Size> getSequences(const String & database_filename, const std::map<Size, Size> & wanted_records, std::vector<String> & sequences);
135 
141  void getExperiment(PeakMap & exp, String & type, const String & in_filename)
142  {
143  type.clear();
144  exp.reset();
145  //input file type
146  FileHandler fh;
147  FileTypes::Type in_type = fh.getTypeByContent(in_filename);
148  if (in_type == FileTypes::UNKNOWN)
149  {
150  throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Could not determine type of the file. Aborting!", in_filename);
151  }
152  type = FileTypes::typeToName(in_type);
153  fh.loadExperiment(in_filename, exp, in_type, ProgressLogger::NONE, false, false);
154  }
155 
161  bool getSearchEngineAndVersion(const String & cmd_output, ProteinIdentification & protein_identification);
162 
166  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);
167 
168 protected:
173  static const Size db_pos_length_;
174  static const Size trie_db_pos_length_;
175  static const Size protein_name_length_;
176  static const Size record_length_;
177  static const char trie_delimiter_;
178  static const String score_type_;
179  };
180 
181 } //namespace OpenMS
182 
FileHandler.h
FileTypes.h
OpenMS::MSExperiment::reset
void reset()
Clear all internal data (spectra, ranges, metadata)
OpenMS::InspectOutfile::trie_delimiter_
static const char trie_delimiter_
the sequences in the trie database are delimited by this character
Definition: InspectOutfile.h:177
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::InspectOutfile::getExperiment
void getExperiment(PeakMap &exp, String &type, const String &in_filename)
Definition: InspectOutfile.h:141
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::FileHandler::getTypeByContent
static FileTypes::Type getTypeByContent(const String &filename)
Determines the file type of a file by parsing the first few lines.
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:58
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::InspectOutfile::protein_name_length_
static const Size protein_name_length_
length of 3)
Definition: InspectOutfile.h:175
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Exception.h
OpenMS::InspectOutfile
Representation of an Inspect outfile.
Definition: InspectOutfile.h:57
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:66
OpenMS::FileHandler::loadExperiment
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.
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::InspectOutfile::record_length_
static const Size record_length_
length of the whole record
Definition: InspectOutfile.h:176
OpenMS::StringConversions::append
void append(const T &i, String &target)
Definition: StringConversions.h:118
OpenMS::InspectOutfile::db_pos_length_
static const Size db_pos_length_
length of 1)
Definition: InspectOutfile.h:173
OpenMS::InspectOutfile::score_type_
static const String score_type_
type of score
Definition: InspectOutfile.h:178
MSExperiment.h
OpenMS::Exception::ParseError
Parse Error exception.
Definition: Exception.h:622
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::InspectOutfile::trie_db_pos_length_
static const Size trie_db_pos_length_
length of 2)
Definition: InspectOutfile.h:174
String.h
OpenMS::ProgressLogger::NONE
No progress logging.
Definition: ProgressLogger.h:72
PeptideIdentification.h
StandardTypes.h
OpenMS::FileTypes::typeToName
static String typeToName(Type type)
Returns the name/extension of the type.