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OpenMS
2.4.0
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40 #include <OpenMS/OpenMSConfig.h>
41 #include <OpenMS/config.h>
50 #ifndef GLP_PROB_DEFINED
51 #define GLP_PROB_DEFINED
54 #if OPENMS_GLPK_VERSION_MINOR < 48
57 double _opaque_prob[100];
76 message_level(3), branching_tech(4), backtrack_tech(3),
77 preprocessing_tech(2), enable_feas_pump_heuristic(true), enable_gmi_cuts(true),
78 enable_mir_cuts(true), enable_cov_cuts(true), enable_clq_cuts(true), mip_gap(0.0),
79 time_limit((std::numeric_limits<
Int>::max)()), output_freq(5000), output_delay(10000), enable_presolve(true),
80 enable_binarization(true)
133 #if COINOR_SOLVER == 1
151 Int addRow(std::vector<Int> row_indices, std::vector<double> row_values,
const String& name);
155 Int addColumn(std::vector<Int> column_indices, std::vector<double> column_values,
const String& name);
169 Int addRow(std::vector<Int>& row_indices, std::vector<double>& row_values,
const String& name,
double lower_bound,
double upper_bound, Type type);
181 Int addColumn(std::vector<Int>& column_indices, std::vector<double>& column_values,
const String& name,
double lower_bound,
double upper_bound, Type type);
184 void deleteRow(
Int index);
186 void setColumnName(
Int index,
const String& name);
196 double getColumnUpperBound(
Int index);
198 double getColumnLowerBound(
Int index);
200 double getRowUpperBound(
Int index);
202 double getRowLowerBound(
Int index);
204 void setRowName(
Int index,
const String& name);
214 void setColumnBounds(
Int index,
double lower_bound,
double upper_bound, Type type);
224 void setRowBounds(
Int index,
double lower_bound,
double upper_bound, Type type);
232 void setColumnType(
Int index, VariableType type);
240 VariableType getColumnType(
Int index);
243 void setObjective(
Int index,
double obj_value);
245 double getObjective(
Int index);
252 void setObjectiveSense(Sense sense);
253 Sense getObjectiveSense();
256 Int getNumberOfColumns();
258 Int getNumberOfRows();
260 void setElement(
Int row_index,
Int column_index,
double value);
261 double getElement(
Int row_index,
Int column_index);
278 void writeProblem(
const String& filename,
const WriteFormat format)
const;
290 Int solve(SolverParam& solver_param,
const Size verbose_level = 0);
297 SolverStatus getStatus();
300 double getObjectiveValue();
301 double getColumnValue(
Int index);
303 Int getNumberOfNonZeroEntriesInRow(
Int idx);
304 void getMatrixRow(
Int idx, std::vector<Int>& indexes);
308 void setSolver(
const SOLVER s);
311 SOLVER getSolver()
const;
314 #if COINOR_SOLVER == 1
316 std::vector<double> solution_;
Consumer class that writes MS data to disk using the mzML format.
Definition: MSDataWritingConsumer.h:88
Definition: LPWrapper.h:104
Base class for TOPP applications.
Definition: TOPPBase.h:150
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
bool enable_gmi_cuts
Definition: LPWrapper.h:89
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
Type
Definition: LPWrapper.h:101
SolverStatus
Definition: LPWrapper.h:138
Int output_freq
Definition: LPWrapper.h:95
bool enable_clq_cuts
Definition: LPWrapper.h:92
bool enable_feas_pump_heuristic
Definition: LPWrapper.h:88
A class to load an indexedmzML file.
Definition: IndexedMzMLFileLoader.h:53
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
Definition: LPWrapper.h:55
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:57
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
void pickExperiment(const PeakMap &input, PeakMap &output, const bool check_spectrum_type=true) const
Applies the peak-picking algorithm to a map (MSExperiment). This method picks peaks for each scan in ...
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
static bool contains(const std::vector< T > &container, const E &elem)
Checks whether the element elem is contained in the given container.
Definition: ListUtils.h:149
Definition: LPWrapper.h:67
double mip_gap
Definition: LPWrapper.h:93
Int message_level
Definition: LPWrapper.h:84
WriteFormat
Definition: LPWrapper.h:123
SolverParam()
Definition: LPWrapper.h:75
bool enable_cov_cuts
Definition: LPWrapper.h:91
int Int
Signed integer type.
Definition: Types.h:102
UInt getMSLevel() const
Returns the MS level.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
This class implements a fast peak-picking algorithm best suited for high resolution MS data (FT-ICR-M...
Definition: PeakPickerHiRes.h:73
Int time_limit
Definition: LPWrapper.h:94
Definition: LPWrapper.h:106
glp_prob * lp_problem_
Definition: LPWrapper.h:319
Representation of a mass spectrometry experiment on disk.
Definition: OnDiscMSExperiment.h:68
bool load(const String &filename, OnDiscPeakMap &exp)
Load a file.
Definition: IndexedMzMLFileLoader.h:82
Peak picking (conversion from raw to peak data)
Definition: DataProcessing.h:67
Int branching_tech
Definition: LPWrapper.h:85
Int backtrack_tech
Definition: LPWrapper.h:86
Definition: LPWrapper.h:105
Struct that holds the parameters of the LP solver.
Definition: LPWrapper.h:73
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getDefaults() const
Non-mutable access to the default parameters.
bool enable_presolve
Definition: LPWrapper.h:97
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
Sense
Definition: LPWrapper.h:117
void transform(const String &filename_in, Interfaces::IMSDataConsumer *consumer, bool skip_full_count=false, bool skip_first_pass=false)
Transforms a map while loading using the supplied MSDataConsumer.
VariableType
Definition: LPWrapper.h:110
The representation of a chromatogram.
Definition: MSChromatogram.h:54
Definition: LPWrapper.h:113
SOLVER
Definition: LPWrapper.h:130
Management and storage of parameters / INI files.
Definition: Param.h:74
bool enable_mir_cuts
Definition: LPWrapper.h:90
SOLVER solver_
Definition: LPWrapper.h:321
Int preprocessing_tech
Definition: LPWrapper.h:87
Definition: LPWrapper.h:126
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
Int output_delay
Definition: LPWrapper.h:96
bool enable_binarization
Definition: LPWrapper.h:98
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!