OpenMS
DigestionEnzyme.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 2002-2023.
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: Xiao Liang $
32 // $Authors: Xiao Liang $
33 // --------------------------------------------------------------------------
34 //
35 
36 #pragma once
37 
40 
41 #include <iosfwd>
42 #include <set>
43 #include <vector>
44 
45 namespace OpenMS
46 {
52  class OPENMS_DLLAPI DigestionEnzyme
53  {
54  public:
55 
60  DigestionEnzyme(const DigestionEnzyme&) = default;
61 
64 
66  explicit DigestionEnzyme(const String& name,
67  const String& cleavage_regex,
68  const std::set<String>& synonyms = std::set<String>(),
69  String regex_description = "");
70 
72  explicit DigestionEnzyme(const String& name,
73  String cut_before,
74  const String& nocut_after = "",
75  String sense = "C",
76  const std::set<String>& synonyms = std::set<String>(),
77  String regex_description = "");
78 
80  virtual ~DigestionEnzyme();
82 
88 
92 
97  void setName(const String& name);
98 
100  const String& getName() const;
101 
103  void setSynonyms(const std::set<String>& synonyms);
104 
106  void addSynonym(const String& synonym);
107 
109  const std::set<String>& getSynonyms() const;
110 
112  void setRegEx(const String& cleavage_regex);
113 
115  const String& getRegEx() const;
116 
118  void setRegExDescription(const String& value);
119 
121  const String& getRegExDescription() const;
123 
128  bool operator==(const DigestionEnzyme& enzyme) const;
129 
131  bool operator!=(const DigestionEnzyme& enzyme) const;
132 
134  bool operator==(const String& cleavage_regex) const;
135 
137  bool operator!=(const String& cleavage_regex) const;
138 
140  bool operator<(const DigestionEnzyme& enzyme) const;
142 
148  virtual bool setValueFromFile(const String& key, const String& value);
149 
151  friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzyme& enzyme);
152 
153  protected:
154 
157 
158  // basic
160 
162 
163  std::set<String> synonyms_;
164 
166  };
167 
168  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const DigestionEnzyme& enzyme);
169 }
170 
Base class for digestion enzymes.
Definition: DigestionEnzyme.h:53
bool operator<(const DigestionEnzyme &enzyme) const
order operator
virtual ~DigestionEnzyme()
Destructor.
bool operator==(const String &cleavage_regex) const
equality operator for regex
bool operator!=(const DigestionEnzyme &enzyme) const
inequality operator
DigestionEnzyme & operator=(DigestionEnzyme &&) &=default
Move assignment operator.
bool operator==(const DigestionEnzyme &enzyme) const
equality operator
String regex_description_
Definition: DigestionEnzyme.h:165
String name_
Definition: DigestionEnzyme.h:159
DigestionEnzyme(const DigestionEnzyme &)=default
Copy constructor.
void setSynonyms(const std::set< String > &synonyms)
sets the synonyms
void setRegExDescription(const String &value)
sets the regex description
DigestionEnzyme(const String &name, String cut_before, const String &nocut_after="", String sense="C", const std::set< String > &synonyms=std::set< String >(), String regex_description="")
Detailed constructor 2.
const String & getRegEx() const
returns the cleavage regex
friend std::ostream & operator<<(std::ostream &os, const DigestionEnzyme &enzyme)
ostream iterator to write the enzyme to a stream
void setName(const String &name)
sets the name of the enzyme
const String & getRegExDescription() const
returns the regex description
const std::set< String > & getSynonyms() const
returns the synonyms
DigestionEnzyme(const String &name, const String &cleavage_regex, const std::set< String > &synonyms=std::set< String >(), String regex_description="")
Detailed constructor.
virtual bool setValueFromFile(const String &key, const String &value)
Set the value of a member variable based on an entry from an input file.
const String & getName() const
returns the name of the enzyme
DigestionEnzyme & operator=(const DigestionEnzyme &)=default
Assignment operator.
std::set< String > synonyms_
Definition: DigestionEnzyme.h:163
String cleavage_regex_
Definition: DigestionEnzyme.h:161
DigestionEnzyme()
default constructor
bool operator!=(const String &cleavage_regex) const
equality operator for regex
DigestionEnzyme(DigestionEnzyme &&)=default
Move constructor.
void addSynonym(const String &synonym)
adds a synonym
void setRegEx(const String &cleavage_regex)
sets the cleavage regex
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)