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OpenMS
2.5.0
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39 #include <OpenMS/OpenMSConfig.h>
118 void setParameters(
const Param& param);
121 const Param& getParameters()
const;
124 const Param& getDefaults()
const;
127 const String& getName()
const;
130 void setName(
const String& name);
133 const std::vector<String>& getSubsections()
const;
143 virtual void updateMembers_();
146 void defaultsToParam_();
Base class for TOPP applications.
Definition: TOPPBase.h:144
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
An algorithm to decharge features (i.e. as found by FeatureFinder).
Definition: FeatureDeconvolution.h:59
void store(const String &filename, const ConsensusMap &consensus_map)
Stores a consensus map to file.
void setEnzyme(const String &name)
Sets the enzyme for the digestion (by name)
String error_name_
Name that is displayed in error messages during the parameter checking.
Definition: DefaultParamHandler.h:166
String identifier
Definition: FASTAFile.h:78
static ProteaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
String sequence
Definition: FASTAFile.h:80
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
void compute(const FeatureMapType &fm_in, FeatureMapType &fm_out, ConsensusMap &cons_map, ConsensusMap &cons_map_p)
Compute a zero-charge feature map from a set of charged features.
A more convenient string class.
Definition: String.h:58
This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object.
Definition: MRMDecoy.h:88
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
void getAllNames(std::vector< String > &all_names) const
returns all the enzyme names (does NOT include synonym names)
Definition: DigestionEnzymeDB.h:122
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
const DataValue & getValue(const String &key) const
Returns a value of a parameter.
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
FASTA entry type (identifier, description and sequence)
Definition: FASTAFile.h:76
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
static String concatenate(const std::vector< T > &container, const String &glue="")
Concatenates all elements of the container and puts the glue string between elements.
Definition: ListUtils.h:193
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool toBool() const
Conversion to bool.
String sequence
Definition: TargetedExperimentHelper.h:437
static OpenMS::TargetedExperiment::Peptide reversePeptide(const OpenMS::TargetedExperiment::Peptide &peptide, const bool keepN, const bool keepC, const String &const_pattern=String())
Reverse a peptide sequence (with its modifications)
bool warn_empty_defaults_
If this member is set to false no warning is emitted when defaults are empty;.
Definition: DefaultParamHandler.h:183
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
Size digest(const AASequence &protein, std::vector< AASequence > &output, Size min_length=1, Size max_length=0) const
: Performs the enzymatic digestion of a protein.
void setParameters(const Param ¶m)
Sets the parameters.
void writeNext(const FASTAEntry &protein)
Stores the data given by protein. Call writeStart() once before calling writeNext().
const Param & getDefaults() const
Non-mutable access to the default parameters.
const Param & getParameters() const
Non-mutable access to the parameters.
A container for consensus elements.
Definition: ConsensusMap.h:79
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
void append(const T &i, String &target)
Definition: StringUtils.h:77
Charge deconvolution.
Definition: DataProcessing.h:61
void writeStart(const String &filename)
Prepares a FASTA file given by 'filename' for streamed writing using writeNext().
StopWatch Class.
Definition: StopWatch.h:59
Definition: MetaData.h:67
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
A container for features.
Definition: FeatureMap.h:95
Class for the enzymatic digestion of proteins.
Definition: ProteaseDigestion.h:60
bool readNext(FASTAEntry &protein)
Reads the next FASTA entry from file.
void readStart(const String &filename)
Prepares a FASTA file given by 'filename' for streamed reading using readNext().
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
String & reverse()
inverts the direction of the string
Param defaults_
Container for default parameters. This member should be filled in the constructor of derived classes!
Definition: DefaultParamHandler.h:156
Management and storage of parameters / INI files.
Definition: Param.h:73
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
std::vector< String > subsections_
Container for registered subsections. This member should be filled in the constructor of derived clas...
Definition: DefaultParamHandler.h:163
void insert(const String &prefix, const Param ¶m)
bool check_defaults_
If this member is set to false no checking if parameters in done;.
Definition: DefaultParamHandler.h:175
std::ifstream infile
Questionable file tested by TEST_FILE_EQUAL.
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:61
Param param_
Container for current parameters.
Definition: DefaultParamHandler.h:149