OpenMS  2.5.0
MultiplexSatelliteCentroided.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 2002-2020.
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: Lars Nilse $
32 // $Authors: Lars Nilse $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
38 
39 #include <map>
40 #include <vector>
41 #include <algorithm>
42 #include <iostream>
43 
44 namespace OpenMS
45 {
54  class OPENMS_DLLAPI MultiplexSatelliteCentroided
55  {
56  public:
57 
61  MultiplexSatelliteCentroided(size_t rt_idx, size_t mz_idx);
62 
66  size_t getMZidx() const;
67 
71  size_t getRTidx() const;
72 
73  private:
74 
80  size_t rt_idx_;
81  size_t mz_idx_;
82 
83  };
84 
85 }
86 
ConsensusXMLFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:144
OpenMS::ConsensusMap::applyMemberFunction
Size applyMemberFunction(Size(Type::*member_function)())
Applies a member function of Type to the container itself and all consensus features....
Definition: ConsensusMap.h:337
OpenMS::Param::setMinFloat
void setMinFloat(const String &key, double min)
Sets the minimum value for the floating point or floating point list parameter key.
OpenMS::ConsensusXMLFile::store
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
OpenMS::MultiplexSatelliteCentroided::rt_idx_
size_t rt_idx_
indices of the satellite peak position in the centroided experiment
Definition: MultiplexSatelliteCentroided.h:80
OpenMS::Exception::InvalidSize
Invalid UInt exception.
Definition: Exception.h:303
OpenMS::Exception::InvalidValue
Invalid value exception.
Definition: Exception.h:335
OpenMS::MultiplexDeltaMasses::LabelSet
std::multiset< String > LabelSet
set of labels associated with a mass shift
Definition: MultiplexDeltaMasses.h:73
OpenMS::Param::setValue
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:58
MzMLFile.h
ConsensusMap.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::ConsensusFeature::HandleSetType
std::set< FeatureHandle, FeatureHandle::IndexLess > HandleSetType
Type definitions.
Definition: ConsensusFeature.h:75
OpenMS::Peak2D::getIntensity
IntensityType getIntensity() const
Definition: Peak2D.h:166
Constants.h
OpenMS::BaseFeature::getPeptideIdentifications
const std::vector< PeptideIdentification > & getPeptideIdentifications() const
returns a const reference to the PeptideIdentification vector
OpenMS::Peak2D::setIntensity
void setIntensity(IntensityType intensity)
Non-mutable access to the data point intensity (height)
Definition: Peak2D.h:172
MultiplexDeltaMassesGenerator.h
OpenMS::BaseFeature::setPeptideIdentifications
void setPeptideIdentifications(const std::vector< PeptideIdentification > &peptides)
sets the PeptideIdentification vector
OpenMS::FeatureHandle::setMapIndex
void setMapIndex(UInt64 i)
Set the map index.
OpenMS::MultiplexSatelliteCentroided
data structure storing a single satellite peak
Definition: MultiplexSatelliteCentroided.h:54
OpenMS::FeatureHandle::setCharge
void setCharge(ChargeType charge)
Sets the charge.
OpenMS::MultiplexDeltaMassesGenerator::printDeltaMassesList
void printDeltaMassesList(std::ostream &stream) const
write the list of all mass patterns
OpenMS::Param::ParamIterator
Forward const iterator for the Param class.
Definition: Param.h:197
OpenMS::BaseFeature::setQuality
void setQuality(QualityType q)
Set the overall quality.
OpenMS::Peak2D::setRT
void setRT(CoordinateType coordinate)
Mutable access to the RT coordinate (index 0)
Definition: Peak2D.h:214
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
PeptideHit.h
OpenMS::MultiplexSatelliteCentroided::mz_idx_
size_t mz_idx_
Definition: MultiplexSatelliteCentroided.h:81
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
OpenMS::Param::setMinInt
void setMinInt(const String &key, Int min)
Sets the minimum value for the integer or integer list parameter key.
MultiplexIsotopicPeakPattern.h
OpenMS::BaseFeature::getCharge
const ChargeType & getCharge() const
Non-mutable access to charge state.
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::ConsensusMap::ConstIterator
std::vector< ConsensusFeature >::const_iterator ConstIterator
Non-mutable iterator.
Definition: ConsensusMap.h:162
OpenMS::Peak2D::setMZ
void setMZ(CoordinateType coordinate)
Mutable access to the m/z coordinate (index 1)
Definition: Peak2D.h:202
OpenMS::DefaultParamHandler::getParameters
const Param & getParameters() const
Non-mutable access to the parameters.
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
OpenMS::Peak2D::getRT
CoordinateType getRT() const
Returns the RT coordinate (index 0)
Definition: Peak2D.h:208
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
OpenMS::MultiplexDeltaMassesGenerator::printSamplesLabelsList
void printSamplesLabelsList(std::ostream &stream) const
write the list of labels for each of the sample
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
MultiplexDeltaMasses.h
MSExperiment.h
OpenMS::ConsensusMap::getColumnHeaders
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
OpenMS::Param::end
ParamIterator end() const
End iterator for the internal tree.
OpenMS::Param::begin
ParamIterator begin() const
Begin iterator for the internal tree.
OpenMS::FeatureHandle
Representation of a Peak2D, RichPeak2D or Feature .
Definition: FeatureHandle.h:57
OpenMS::ConsensusFeature::size
Size size() const
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::MultiplexDeltaMassesGenerator::extractLabelSet
MultiplexDeltaMasses::LabelSet extractLabelSet(AASequence sequence)
extract the label set from the sequence
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::MSExperiment::ConstIterator
std::vector< SpectrumType >::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSExperiment.h:113
OpenMS::MultiplexDeltaMassesGenerator::getDeltaMassesList
std::vector< MultiplexDeltaMasses > getDeltaMassesList()
returns the list of mass shift patterns
OpenMS::Exception::MissingInformation
Not all required information provided.
Definition: Exception.h:195
OpenMS::Peak2D::getMZ
CoordinateType getMZ() const
Returns the m/z coordinate (index 1)
Definition: Peak2D.h:196
OpenMS::ConsensusFeature::getFeatures
const HandleSetType & getFeatures() const
Non-mutable access to the contained feature handles.
OpenMS::Constants::C13C12_MASSDIFF_U
const double C13C12_MASSDIFF_U
OpenMS::MSSpectrum::ConstIterator
ContainerType::const_iterator ConstIterator
Non-mutable iterator.
Definition: MSSpectrum.h:104
OpenMS::MultiplexDeltaMassesGenerator
generates complete list of all possible mass shifts due to isotopic labelling
Definition: MultiplexDeltaMassesGenerator.h:61
PeptideIdentification.h
StandardTypes.h
OpenMS::BaseFeature::setCharge
void setCharge(const ChargeType &ch)
Set charge state.
OpenMS::BaseFeature::getQuality
QualityType getQuality() const
Non-mutable access to the overall quality.
TOPPBase.h
OpenMS::ConsensusFeature::insert
void insert(const ConsensusFeature &cf)
Adds all feature handles (of the CF) into the consensus feature.
OpenMS::MSExperiment::RTEnd
ConstIterator RTEnd(CoordinateType rt) const
Fast search for spectrum range end (returns the past-the-end iterator)
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
OpenMS::MSExperiment::RTBegin
ConstIterator RTBegin(CoordinateType rt) const
Fast search for spectrum range begin.