| OpenMS 2.5.0

FASTAFile.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Nico Pfeifer, Chris Bielow $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/Exception.h>
38 #include <OpenMS/DATASTRUCTURES/String.h>
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 {
78 String identifier;
79 String description;
80 String sequence;
81
82 FASTAEntry() :
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
112 FASTAEntry& operator=(const FASTAEntry& rhs)
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_;
220 Size entries_read_;
221 };
222
223 } // namespace OpenMS
224
OpenMS::FASTAFile::FASTAEntry::FASTAEntry
FASTAEntry(String id, String desc, String seq)
Definition: FASTAFile.h:89
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::FASTAFile::FASTAEntry::sequence
String sequence
Definition: FASTAFile.h:80
seqan::position
Size< TNeedle >::Type position(const PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:561
Exception.h
OpenMS::FASTAFile::FASTAEntry::FASTAEntry
FASTAEntry()
Definition: FASTAFile.h:82
OpenMS::FASTAFile::FASTAEntry::FASTAEntry
FASTAEntry(FASTAEntry &&rhs) noexcept
Definition: FASTAFile.h:104
OpenMS::FASTAFile
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
OpenMS::FASTAFile::entries_read_
Size entries_read_
some internal book-keeping during reading
Definition: FASTAFile.h:220
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
String.h
OpenMS::FASTAFile::outfile_
std::ofstream outfile_
filestream for writing; init using FastaFile::writeStart()
Definition: FASTAFile.h:218
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::description
String description
Definition: FASTAFile.h:79
OpenMS::FASTAFile::infile_
std::fstream infile_
filestream for reading; init using FastaFile::readStart()
Definition: FASTAFile.h:217
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::FASTAFile::FASTAEntry
FASTA entry type (identifier, description and sequence)
Definition: FASTAFile.h:76
OpenMS::FASTAFile::FASTAEntry::headerMatches
bool headerMatches(const FASTAEntry &rhs) const
Definition: FASTAFile.h:128
OpenMS::FASTAFile::FASTAEntry::identifier
String identifier
Definition: FASTAFile.h:78
OpenMS::FASTAFile::FASTAEntry::FASTAEntry
FASTAEntry(const FASTAEntry &rhs)
Definition: FASTAFile.h:96
OpenMS::FASTAFile::FASTAEntry::operator=
FASTAEntry & operator=(const FASTAEntry &rhs)
Definition: FASTAFile.h:112
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127