| OpenMS 2.5.0

Sample.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <list>
38
39 #include <OpenMS/DATASTRUCTURES/String.h>
40 #include <OpenMS/METADATA/MetaInfoInterface.h>
41 #include <OpenMS/CONCEPT/Exception.h>
42
43 namespace OpenMS
44 {
45 class SampleTreatment;
46
59 class OPENMS_DLLAPI Sample :
60 public MetaInfoInterface
61 {
62 public:
64 enum SampleState {SAMPLENULL, SOLID, LIQUID, GAS, SOLUTION, EMULSION, SUSPENSION, SIZE_OF_SAMPLESTATE};
66 static const std::string NamesOfSampleState[SIZE_OF_SAMPLESTATE];
67
69 Sample();
71 Sample(const Sample & source);
73 Sample(Sample&&) = default;
75 ~Sample();
76
78 Sample & operator=(const Sample & source);
80 Sample& operator=(Sample&&) & = default;
81
83 bool operator==(const Sample & rhs) const;
84
86 const String & getName() const;
88 void setName(const String & name);
89
91 const String & getOrganism() const;
93 void setOrganism(const String & organism);
94
96 const String & getNumber() const;
98 void setNumber(const String & number);
99
101 const String & getComment() const;
103 void setComment(const String & comment);
104
106 SampleState getState() const;
108 void setState(SampleState state);
109
111 double getMass() const;
113 void setMass(double mass);
114
116 double getVolume() const;
118 void setVolume(double volume);
119
121 double getConcentration() const;
123 void setConcentration(double concentration);
124
126 std::vector<Sample> & getSubsamples();
128 const std::vector<Sample> & getSubsamples() const;
130 void setSubsamples(const std::vector<Sample> & subsamples);
131
140 void addTreatment(const SampleTreatment & treatment, Int before_position = -1);
141
147 SampleTreatment & getTreatment(UInt position);
148
154 const SampleTreatment & getTreatment(UInt position) const;
155
161 void removeTreatment(UInt position);
162
164 Int countTreatments() const;
165
166 protected:
167 String name_;
168 String number_;
169 String comment_;
170 String organism_;
171 SampleState state_;
172 double mass_;
173 double volume_;
174 double concentration_;
175 std::vector<Sample> subsamples_;
176
177 // note: default move constructor / assignment operator will work on this,
178 // since it will move the whole vector over to the new object who will then
179 // own the memory.
180 std::list<SampleTreatment *> treatments_;
181
182 };
183 } // namespace OpenMS
184
OpenMS::Sample::SampleState
SampleState
state of aggregation of the sample
Definition: Sample.h:64
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Sample::concentration_
double concentration_
Definition: Sample.h:174
OpenMS::Sample::organism_
String organism_
Definition: Sample.h:170
OpenMS::Sample::mass_
double mass_
Definition: Sample.h:172
seqan::position
Size< TNeedle >::Type position(const PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:561
OpenMS::SampleTreatment
Base class for sample treatments (Digestion, Modification, Tagging, ...)
Definition: SampleTreatment.h:51
OpenMS::Sample::number_
String number_
Definition: Sample.h:168
OpenMS::Sample::subsamples_
std::vector< Sample > subsamples_
Definition: Sample.h:175
Exception.h
OpenMS::Sample::comment_
String comment_
Definition: Sample.h:169
OpenMS::Sample::volume_
double volume_
Definition: Sample.h:173
OpenMS::Sample
Meta information about the sample.
Definition: Sample.h:59
OpenMS::Sample::name_
String name_
Definition: Sample.h:167
String.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Sample::SUSPENSION
Definition: Sample.h:64
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::Sample::treatments_
std::list< SampleTreatment * > treatments_
Definition: Sample.h:180
OpenMS::Sample::state_
SampleState state_
Definition: Sample.h:171
int
MetaInfoInterface.h
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806