OpenMS
ModificationDefinition.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: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 //
35 
36 #pragma once
37 
38 #include <OpenMS/CONCEPT/Types.h>
41 
42 namespace OpenMS
43 {
52  class OPENMS_DLLAPI ModificationDefinition
53  {
54 public:
55 
61 
64 
66  explicit ModificationDefinition(const String& mod, bool fixed = true, UInt max_occur = 0);
67 
69  explicit ModificationDefinition(const ResidueModification& mod, bool fixed = true, UInt max_occur = 0);
70 
74 
79  void setFixedModification(bool fixed);
80 
82  bool isFixedModification() const;
83 
86 
89 
92 
94  void setModification(const String& modification);
95 
103 
110 
115  bool operator==(const ModificationDefinition& rhs) const;
116 
118  bool operator!=(const ModificationDefinition& rhs) const;
119 
123 
124 protected:
125 
128 
131 
134  };
135 
136 } // namespace OpenMS
137 
Representation of modification definition.
Definition: ModificationDefinition.h:53
void setFixedModification(bool fixed)
sets whether this modification definition is fixed or variable (modification must occur vs....
UInt max_occurrences_
maximal number of occurrences per peptide
Definition: ModificationDefinition.h:133
ModificationDefinition(const String &mod, bool fixed=true, UInt max_occur=0)
detailed constructor specifying the modification by name
UInt getMaxOccurrences() const
returns the maximal number of occurrences per peptide
bool operator!=(const ModificationDefinition &rhs) const
inequality operator
ModificationDefinition()
default constructor
bool operator<(const OpenMS::ModificationDefinition &) const
less than operator for e.g. usage in maps; only mod FullIds are compared!
bool isFixedModification() const
returns if the modification if fixed true, else false
void setMaxOccurrences(UInt num)
set the maximal number of occurrences per peptide (unbounded if 0)
const ResidueModification & getModification() const
Returns the modification.
String getModificationName() const
returns the name of the modification
bool operator==(const ModificationDefinition &rhs) const
equality operator
virtual ~ModificationDefinition()
destructor
ModificationDefinition & operator=(const ModificationDefinition &element)
assignment operator
bool fixed_modification_
fixed (true) or variable (false)
Definition: ModificationDefinition.h:130
ModificationDefinition(const ModificationDefinition &rhs)
copy constructor
ModificationDefinition(const ResidueModification &mod, bool fixed=true, UInt max_occur=0)
direct constructor from a residue modification
void setModification(const String &modification)
sets the modification, allowed are unique names provided by ModificationsDB
const ResidueModification * mod_
the modification
Definition: ModificationDefinition.h:127
Representation of a modification on an amino acid residue.
Definition: ResidueModification.h:79
A more convenient string class.
Definition: String.h:60
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48