Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
BaseFeature.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 2002-2013.
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: Hendrik Weisser $
32 // $Authors: Hendrik Weisser, Chris Bielow $
33 // --------------------------------------------------------------------------
34 
35 #ifndef OPENMS_KERNEL_BASEFEATURE_H
36 #define OPENMS_KERNEL_BASEFEATURE_H
37 
40 
41 namespace OpenMS
42 {
43 
55  class OPENMS_DLLAPI BaseFeature :
56  public RichPeak2D
57  {
58 public:
60 
61  typedef Real QualityType;
64  typedef Int ChargeType;
66  typedef Real WidthType;
67 
70  {
75  SIZE_OF_ANNOTATIONSTATE
76  };
77 
78  static const std::string NamesOfAnnotationState[SIZE_OF_ANNOTATIONSTATE];
79 
81 
85  BaseFeature();
87 
89  BaseFeature(const BaseFeature & feature);
90 
92  explicit BaseFeature(const Peak2D & point);
93 
95  explicit BaseFeature(const RichPeak2D & point);
96 
98  ~BaseFeature();
100 
102 
103  QualityType getQuality() const;
106  void setQuality(QualityType q);
108  struct QualityLess :
109  std::binary_function<BaseFeature, BaseFeature, bool>
110  {
111  bool operator()(const BaseFeature & left, const BaseFeature & right) const
112  {
113  return left.getQuality() < right.getQuality();
114  }
115 
116  bool operator()(const BaseFeature & left, const QualityType & right) const
117  {
118  return left.getQuality() < right;
119  }
120 
121  bool operator()(const QualityType & left, const BaseFeature & right) const
122  {
123  return left < right.getQuality();
124  }
125 
126  bool operator()(const QualityType & left, const QualityType & right) const
127  {
128  return left < right;
129  }
130 
131  };
133 
135  WidthType getWidth() const;
137  void setWidth(WidthType fwhm);
138 
140  const ChargeType & getCharge() const;
141 
143  void setCharge(const ChargeType & ch);
144 
146  BaseFeature & operator=(const BaseFeature & rhs);
147 
149  bool operator==(const BaseFeature & rhs) const;
150 
152  bool operator!=(const BaseFeature & rhs) const;
153 
155  const std::vector<PeptideIdentification> & getPeptideIdentifications() const;
156 
158  std::vector<PeptideIdentification> & getPeptideIdentifications();
159 
161  void setPeptideIdentifications(const std::vector<PeptideIdentification> & peptides);
162 
164  AnnotationState getAnnotationState() const;
165 
166 protected:
167 
170 
173 
176 
178  std::vector<PeptideIdentification> peptides_;
179  };
180 
181 } // namespace OpenMS
182 
183 #endif // OPENMS_KERNEL_BASEFEATURE_H
bool operator()(const BaseFeature &left, const QualityType &right) const
Definition: BaseFeature.h:116
float Real
Real type.
Definition: Types.h:109
Definition: BaseFeature.h:71
A 2-dimensional raw data point or peak.
Definition: Peak2D.h:55
Int ChargeType
Type of charge values.
Definition: BaseFeature.h:64
Compare by quality.
Definition: BaseFeature.h:108
A basic LC-MS feature.
Definition: BaseFeature.h:55
bool operator()(const QualityType &left, const BaseFeature &right) const
Definition: BaseFeature.h:121
QualityType quality_
Overall quality measure of the feature.
Definition: BaseFeature.h:169
bool operator()(const QualityType &left, const QualityType &right) const
Definition: BaseFeature.h:126
QualityType getQuality() const
Non-mutable access to the overall quality.
Real WidthType
Type of feature width/FWHM (RT)
Definition: BaseFeature.h:66
bool operator()(const BaseFeature &left, const BaseFeature &right) const
Definition: BaseFeature.h:111
Real QualityType
Type of quality values.
Definition: BaseFeature.h:62
Definition: BaseFeature.h:72
WidthType width_
Width (FWHM) for the feature. The default value is 0.0, a feature finding algorithm can compute this ...
Definition: BaseFeature.h:175
A 2-dimensional raw data point or peak with meta information.
Definition: RichPeak2D.h:53
AnnotationState
state of identification, use getIDState() to query it
Definition: BaseFeature.h:69
std::vector< PeptideIdentification > peptides_
Peptide PeptideIdentifications belonging to the feature.
Definition: BaseFeature.h:178
int Int
Signed integer type.
Definition: Types.h:100
ChargeType charge_
Charge of the peptide represented by this feature. The default value is 0, which represents an unknow...
Definition: BaseFeature.h:172

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:11 using doxygen 1.8.5