OpenMS  3.0.0
RNaseDB.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
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34 
35 #pragma once
36 
40 
41 #include <vector>
42 
43 namespace OpenMS
44 {
52  class OPENMS_DLLAPI RNaseDB: public DigestionEnzymeDB<DigestionEnzymeRNA, RNaseDB>
53  {
54  // allow access to constructor in DigestionEnzymeDB::getInstance():
56 
57  protected:
59  RNaseDB();
60  };
61 }
62 
LogStream.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
Size
OpenMS::NASequence
Representation of a nucleic acid sequence.
Definition: NASequence.h:61
OpenMS::DigestionEnzymeDB::getInstance
static InstanceType * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:69
OpenMS::FASTAFile
This class serves for reading in and writing FASTA files If the protein/gene sequence contains unusua...
Definition: FASTAFile.h:60
OpenMS::RNaseDB
Database for enzymes that digest RNA (RNases)
Definition: RNaseDB.h:52
OpenMS::NASequence::NASFragmentType
NASFragmentType
an enum of all possible fragment ion types
Definition: NASequence.h:69
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::RNaseDigestion::digest
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.
RNaseDigestion.h
OpenMS::String::trim
String & trim()
removes whitespaces (space, tab, line feed, carriage return) at the beginning and the end of the stri...
Int
OpenMS::Exception::ConversionError
Invalid conversion exception.
Definition: Exception.h:354
OpenMS::RNaseDigestion::setEnzyme
void setEnzyme(const DigestionEnzyme *enzyme) override
Sets the enzyme for the digestion.
NASequence.h
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:55
OpenMS::NASequence::getFormula
EmpiricalFormula getFormula(NASFragmentType type=Full, Int charge=0) const
OPENMS_LOG_WARN
#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
OpenMS::FASTAFile::FASTAEntry
FASTA entry type (identifier, description and sequence) The first String corresponds to the identifie...
Definition: FASTAFile.h:71
OpenMS::EnzymaticDigestion::setMissedCleavages
void setMissedCleavages(Size missed_cleavages)
Sets the number of missed cleavages for the digestion (default is 0). This setting is ignored when lo...
ListUtils.h
OpenMS::EmpiricalFormula::toString
String toString() const
returns the formula as a string (charges are not included)
OpenMS::FASTAFile::store
void store(const String &filename, const std::vector< FASTAEntry > &data) const
stores the data given by 'data' at the file 'filename'
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
RNaseDB.h
FASTAFile.h
OpenMS::SVOutStream
Stream class for writing to comma/tab/...-separated values files.
Definition: SVOutStream.h:56
OpenMS::DigestionEnzymeRNA
Representation of a digestion enzyme for RNA (RNase)
Definition: DigestionEnzymeRNA.h:57
OpenMS::String::unquote
String & unquote(char q='"', QuotingMethod method = ESCAPE)
Reverses changes made by the quote method.
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
SVOutStream.h
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
OPENMS_LOG_ERROR
#define OPENMS_LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:455
OpenMS::Exception::ParseError
Parse Error exception.
Definition: Exception.h:622
OpenMS::String::substr
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...
OpenMS::NASequence::getAverageWeight
double getAverageWeight(NASFragmentType type=Full, Int charge=0) const
OpenMS::FASTAFile::load
void load(const String &filename, std::vector< FASTAEntry > &data) const
loads a FASTA file given by 'filename' and stores the information in 'data' This uses more RAM than r...
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:84
OpenMS::NASequence::fromString
static NASequence fromString(const String &s)
create NASequence object by parsing an OpenMS string
String.h
OpenMS::NASequence::toString
std::string toString() const
DigestionEnzymeRNA.h
OpenMS::StringUtils::prefix
static String prefix(const String &this_s, size_t length)
Definition: StringUtilsSimple.h:147
DigestionEnzymeDB.h
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
OpenMS::RNaseDigestion
Class for the enzymatic digestion of RNAs.
Definition: RNaseDigestion.h:52
OpenMS::DigestionEnzymeDB
Digestion enzyme database (base class)
Definition: DigestionEnzymeDB.h:57
OpenMS::NASequence::getMonoWeight
double getMonoWeight(NASFragmentType type=Full, Int charge=0) const
utility functions
OpenMS::String::toInt
Int toInt() const
Conversion to int.
File.h
TOPPBase.h