OpenMS  3.0.0
FASTAFile.h
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31 // $Maintainer: Chris Bielow $
32 // $Authors: Chris Bielow, Nora Wild $
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34 
35 #pragma once
36 
40 
41 #include <fstream>
42 #include <utility>
43 #include <vector>
44 
45 namespace OpenMS
46 {
60  class OPENMS_DLLAPI FASTAFile : public ProgressLogger
61  {
62  public:
71  struct FASTAEntry
72  {
76 
77  FASTAEntry() = default;
78 
79  FASTAEntry(const String& id, const String& desc, const String& seq) :
80  identifier(id),
81  description(desc),
82  sequence(seq)
83  {
84  }
85 
86  FASTAEntry(const FASTAEntry& rhs) = default;
87 
88  FASTAEntry(FASTAEntry&& rhs) noexcept
89  :
90  identifier(::std::move(rhs.identifier)),
91  description(::std::move(rhs.description)),
92  sequence(::std::move(rhs.sequence))
93  {
94  }
95 
96 
97  FASTAEntry& operator=(const FASTAEntry& rhs) = default;
98 
99  bool operator==(const FASTAEntry& rhs) const
100  {
101  return identifier == rhs.identifier
102  && description == rhs.description
103  && sequence == rhs.sequence;
104  }
105 
106  bool headerMatches(const FASTAEntry& rhs) const
107  {
108  return identifier == rhs.identifier &&
109  description == rhs.description;
110  }
111 
112  bool sequenceMatches(const FASTAEntry& rhs) const
113  {
114  return sequence == rhs.sequence;
115  }
116  };
117 
119  FASTAFile() = default;
120 
122  ~FASTAFile() override = default;
123 
129  void readStart(const String& filename);
130 
138  bool readNext(FASTAEntry& protein);
139 
141  std::streampos position();
142 
144  bool atEnd();
145 
147  bool setPosition(const std::streampos& pos);
148 
153  void writeStart(const String& filename);
154 
160  void writeNext(const FASTAEntry& protein);
161 
165  void writeEnd();
166 
167 
174  void load(const String& filename, std::vector<FASTAEntry>& data) const;
175 
182  void store(const String& filename, const std::vector<FASTAEntry>& data) const;
183 
184  protected:
189  bool readEntry_(std::string& id, std::string& description, std::string& seq);
190 
191  std::fstream infile_;
192  std::ofstream outfile_;
193  Size entries_read_{0};
194  std::streampos fileSize_{};
195  std::string seq_;
196  std::string id_;
197  std::string description_;
198  };
199 
200 } // namespace OpenMS
OpenMS::FASTAFile::seq_
std::string seq_
sequence of currently read protein
Definition: FASTAFile.h:195
OpenMS::FASTAFile::FASTAEntry::identifier
String identifier
Definition: FASTAFile.h:73
OpenMS::FASTAFile
This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusua...
Definition: FASTAFile.h:60
OpenMS::FASTAFile::FASTAEntry::sequence
String sequence
Definition: FASTAFile.h:75
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::FASTAFile::FASTAEntry::description
String description
Definition: FASTAFile.h:74
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::FASTAFile::FASTAEntry
FASTA entry type (identifier, description and sequence) The first String corresponds to the identifie...
Definition: FASTAFile.h:71
OpenMS::FASTAFile::id_
std::string id_
identifier of currently read protein
Definition: FASTAFile.h:196
OpenMS::FASTAFile::FASTAEntry::FASTAEntry
FASTAEntry(const String &id, const String &desc, const String &seq)
Definition: FASTAFile.h:79
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Exception.h
OpenMS::FASTAFile::FASTAEntry::operator==
bool operator==(const FASTAEntry &rhs) const
Definition: FASTAFile.h:99
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::FASTAFile::FASTAEntry::sequenceMatches
bool sequenceMatches(const FASTAEntry &rhs) const
Definition: FASTAFile.h:112
OpenMS::FASTAFile::FASTAEntry::FASTAEntry
FASTAEntry(FASTAEntry &&rhs) noexcept
Definition: FASTAFile.h:88
OpenMS::FASTAFile::infile_
std::fstream infile_
filestream for reading; init using FastaFile::readStart()
Definition: FASTAFile.h:191
OpenMS::FASTAFile::FASTAEntry::headerMatches
bool headerMatches(const FASTAEntry &rhs) const
Definition: FASTAFile.h:106
String.h
OpenMS::FASTAFile::outfile_
std::ofstream outfile_
filestream for writing; init using FastaFile::writeStart()
Definition: FASTAFile.h:192
OpenMS::FASTAFile::description_
std::string description_
description of currently read protein
Definition: FASTAFile.h:197