| OpenMS 2.5.0

InspectOutfile.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Martin Langwisch $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/Exception.h>
38 #include <OpenMS/DATASTRUCTURES/String.h>
39 #include <OpenMS/KERNEL/MSExperiment.h>
40 #include <OpenMS/KERNEL/StandardTypes.h>
41 #include <OpenMS/METADATA/PeptideIdentification.h>
42 #include <OpenMS/FORMAT/FileHandler.h>
43 #include <OpenMS/FORMAT/FileTypes.h>
44
45
46 namespace OpenMS
47 {
57 class OPENMS_DLLAPI InspectOutfile
58 {
59 public:
61 InspectOutfile();
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
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::String
A more convenient string class.
Definition: String.h:58
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Exception.h
StandardTypes.h
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
FileTypes.h
OpenMS::InspectOutfile::score_type_
static const String score_type_
type of score
Definition: InspectOutfile.h:178
OpenMS::ProgressLogger::NONE
No progress logging.
Definition: ProgressLogger.h:74
OpenMS::InspectOutfile
Representation of an Inspect outfile.
Definition: InspectOutfile.h:57
String.h
OpenMS::StringConversions::append
void append(const T &i, String &target)
Definition: StringUtils.h:77
OpenMS::FileTypes::typeToName
static String typeToName(Type type)
Returns the name/extension of the type.
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Exception::ParseError
Parse Error exception.
Definition: Exception.h:622
MSExperiment.h
OpenMS::MSExperiment::reset
void reset()
Resets all internal values.
FileHandler.h
OpenMS::InspectOutfile::protein_name_length_
static const Size protein_name_length_
length of 3)
Definition: InspectOutfile.h:175
OpenMS::InspectOutfile::trie_db_pos_length_
static const Size trie_db_pos_length_
length of 2)
Definition: InspectOutfile.h:174
OpenMS::FileHandler::getTypeByContent
static FileTypes::Type getTypeByContent(const String &filename)
Determines the file type of a file by parsing the first few lines.
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:58
OpenMS::InspectOutfile::record_length_
static const Size record_length_
length of the whole record
Definition: InspectOutfile.h:176
OpenMS::InspectOutfile::getExperiment
void getExperiment(PeakMap &exp, String &type, const String &in_filename)
Definition: InspectOutfile.h:141
int
OpenMS::InspectOutfile::db_pos_length_
static const Size db_pos_length_
length of 1)
Definition: InspectOutfile.h:173
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:60
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
OpenMS::InspectOutfile::trie_delimiter_
static const char trie_delimiter_
the sequences in the trie database are delimited by this character
Definition: InspectOutfile.h:177