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OpenMS
2.6.0
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Base class for TOPP applications.
Definition: TOPPBase.h:144
Representation of a nucleic acid sequence.
Definition: NASequence.h:62
static RNaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
Database for enzymes that digest RNA (RNases)
Definition: RNaseDB.h:52
NASFragmentType
an enum of all possible fragment ion types
Definition: NASequence.h:70
A more convenient string class.
Definition: String.h:59
void digest(const NASequence &rna, std::vector< NASequence > &output, Size min_length=0, Size max_length=0) const
Performs the enzymatic digestion of a (potentially modified) RNA.
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
Invalid conversion exception.
Definition: Exception.h:362
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
void setEnzyme(const DigestionEnzyme *enzyme) override
Sets the enzyme for the digestion.
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
EmpiricalFormula getFormula(NASFragmentType type=Full, Int charge=0) const
#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
void setMissedCleavages(Size missed_cleavages)
Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when lo...
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Stream class for writing to comma/tab/...-separated values files.
Definition: SVOutStream.h:54
Representation of a digestion enzyme for RNA (RNase)
Definition: DigestionEnzymeRNA.h:57
String & unquote(char q='"', QuotingMethod method = ESCAPE)
Reverses changes made by the quote method.
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
Parse Error exception.
Definition: Exception.h:622
String substr(size_t pos=0, size_t n=npos) const
Wrapper for the STL substr() method. Returns a String object with its contents initialized to a subst...
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
double getAverageWeight(NASFragmentType type=Full, Int charge=0) const
static NASequence fromString(const String &s)
create NASequence object by parsing an OpenMS string
std::string toString() const
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
Class for the enzymatic digestion of RNAs.
Definition: RNaseDigestion.h:52
Digestion enzyme database (base class)
Definition: DigestionEnzymeDB.h:57
double getMonoWeight(NASFragmentType type=Full, Int charge=0) const
utility functions
Int toInt() const
Conversion to int.
static void store(const String &filename, const std::vector< FASTAEntry > &data)
stores the data given by 'data' at the file 'filename'