OpenMS  2.5.0
FASTAFile.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Nico Pfeifer, Chris Bielow $
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34 
35 #pragma once
36 
39 
40 #include <functional>
41 #include <fstream>
42 #include <memory>
43 #include <utility>
44 #include <vector>
45 
46 namespace OpenMS
47 {
64  class OPENMS_DLLAPI FASTAFile
65  {
66 public:
76  struct FASTAEntry
77  {
81 
83  identifier(),
84  description(),
85  sequence()
86  {
87  }
88 
89  FASTAEntry(String id, String desc, String seq) :
90  identifier(id),
91  description(desc),
92  sequence(seq)
93  {
94  }
95 
96  FASTAEntry(const FASTAEntry& rhs)
97  :
98  identifier(rhs.identifier),
99  description(rhs.description),
100  sequence(rhs.sequence)
101  {
102  }
103 
104  FASTAEntry(FASTAEntry&& rhs) noexcept
105  :
106  identifier(::std::move(rhs.identifier)),
107  description(::std::move(rhs.description)),
108  sequence(::std::move(rhs.sequence))
109  {
110  }
111 
113  {
114  if (*this == rhs) return *this;
115  identifier = rhs.identifier;
116  description = rhs.description;
117  sequence = rhs.sequence;
118  return *this;
119  }
120 
121  bool operator==(const FASTAEntry& rhs) const
122  {
123  return identifier == rhs.identifier
124  && description == rhs.description
125  && sequence == rhs.sequence;
126  }
127 
128  bool headerMatches(const FASTAEntry& rhs) const
129  {
130  return identifier == rhs.identifier &&
131  description == rhs.description;
132  }
133 
134  bool sequenceMatches(const FASTAEntry& rhs) const
135  {
136  return sequence == rhs.sequence;
137  }
138  };
139 
141  FASTAFile();
142 
144  virtual ~FASTAFile();
145 
152  void readStart(const String& filename);
153 
163  bool readNext(FASTAEntry& protein);
164 
166  std::streampos position() const;
167 
169  bool atEnd() const;
170 
172  bool setPosition(const std::streampos& pos);
173 
179  void writeStart(const String& filename);
180 
188  void writeNext(const FASTAEntry& protein);
189 
194  void writeEnd();
195 
196 
205  void static load(const String& filename, std::vector<FASTAEntry>& data);
206 
214  void static store(const String& filename, const std::vector<FASTAEntry>& data);
215 
216 protected:
217  std::fstream infile_;
218  std::ofstream outfile_;
219  std::unique_ptr<void, std::function<void(void*) > > reader_;
221  };
222 
223 } // namespace OpenMS
224 
OpenMS::FASTAFile::FASTAEntry::identifier
String identifier
Definition: FASTAFile.h:78
OpenMS::FASTAFile
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
OpenMS::FASTAFile::FASTAEntry::sequence
String sequence
Definition: FASTAFile.h:80
OpenMS::FASTAFile::FASTAEntry::operator=
FASTAEntry & operator=(const FASTAEntry &rhs)
Definition: FASTAFile.h:112
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::FASTAFile::FASTAEntry::description
String description
Definition: FASTAFile.h:79
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)
Definition: FASTAFile.h:76
OpenMS::FASTAFile::reader_
std::unique_ptr< void, std::function< void(void *) > > reader_
filestream for reading; init using FastaFile::readStart(); needs to be a pointer, since its not copy-...
Definition: FASTAFile.h:219
OpenMS::FASTAFile::FASTAEntry::FASTAEntry
FASTAEntry(String id, String desc, String seq)
Definition: FASTAFile.h:89
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Exception.h
OpenMS::FASTAFile::FASTAEntry::operator==
bool operator==(const FASTAEntry &rhs) const
Definition: FASTAFile.h:121
OpenMS::FASTAFile::FASTAEntry::sequenceMatches
bool sequenceMatches(const FASTAEntry &rhs) const
Definition: FASTAFile.h:134
OpenMS::FASTAFile::FASTAEntry::FASTAEntry
FASTAEntry(FASTAEntry &&rhs) noexcept
Definition: FASTAFile.h:104
OpenMS::FASTAFile::infile_
std::fstream infile_
filestream for reading; init using FastaFile::readStart()
Definition: FASTAFile.h:217
OpenMS::FASTAFile::FASTAEntry::FASTAEntry
FASTAEntry(const FASTAEntry &rhs)
Definition: FASTAFile.h:96
OpenMS::FASTAFile::FASTAEntry::headerMatches
bool headerMatches(const FASTAEntry &rhs) const
Definition: FASTAFile.h:128
String.h
OpenMS::FASTAFile::outfile_
std::ofstream outfile_
filestream for writing; init using FastaFile::writeStart()
Definition: FASTAFile.h:218
OpenMS::FASTAFile::FASTAEntry::FASTAEntry
FASTAEntry()
Definition: FASTAFile.h:82
seqan::position
Size< TNeedle >::Type position(const PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:561
OpenMS::FASTAFile::entries_read_
Size entries_read_
some internal book-keeping during reading
Definition: FASTAFile.h:220