OpenMS  2.4.0
RNaseDB.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 2002-2018.
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: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
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 
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:150
OpenMS::DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::getInstance
static RNaseDB * getInstance()
this member function serves as a replacement of the constructor
Definition: DigestionEnzymeDB.h:70
OpenMS::FASTAFile
This class serves for reading in and writing FASTA files.
Definition: FASTAFile.h:64
OpenMS::RNaseDB
Database for enzymes that digest RNA (RNases)
Definition: RNaseDB.h:52
OpenMS::String
A more convenient string class.
Definition: String.h:57
RNaseDigestion.h
OpenMS::DigestionEnzymeDB::getAllNames
void getAllNames(std::vector< String > &all_names) const
returns all the enzyme names (does NOT include synonym names)
Definition: DigestionEnzymeDB.h:122
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
LOG_INFO
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
OpenMS::FASTAFile::FASTAEntry
FASTA entry type (identifier, description and sequence)
Definition: FASTAFile.h:76
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...
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
RNaseDB.h
FASTAFile.h
OpenMS::RNaseDigestion::digest
void digest(const String &rna, std::vector< String > &output, Size min_length, Size max_length) const
Performs the enzymatic digestion of an RNA.
OpenMS::DigestionEnzymeRNA
Representation of a digestion enzyme for RNA (RNase)
Definition: DigestionEnzymeRNA.h:47
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::FASTAFile::load
static void load(const String &filename, std::vector< FASTAEntry > &data)
loads a FASTA file given by 'filename' and stores the information in 'data'
String.h
DigestionEnzymeRNA.h
DigestionEnzymeDB.h
OpenMS::RNaseDigestion::setEnzyme
void setEnzyme(const String &name)
Sets the enzyme for the digestion (by name)
OpenMS::RNaseDigestion
Class for the enzymatic digestion of RNAs.
Definition: RNaseDigestion.h:46
OpenMS::DigestionEnzymeDB
Digestion enzyme database (base class)
Definition: DigestionEnzymeDB.h:58
TOPPBase.h
OpenMS::FASTAFile::store
static void store(const String &filename, const std::vector< FASTAEntry > &data)
stores the data given by 'data' at the file 'filename'