| OpenMS 2.5.0

RNaseDigestion.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 2002-2020.
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
37 #include <OpenMS/CHEMISTRY/EnzymaticDigestion.h>
38 #include <OpenMS/CHEMISTRY/NASequence.h>
39 #include <OpenMS/METADATA/ID/IdentificationData.h>
40
41 #include <boost/regex.hpp>
42
43 namespace OpenMS
44 {
52 class OPENMS_DLLAPI RNaseDigestion: public EnzymaticDigestion
53 {
54 public:
56 void setEnzyme(const DigestionEnzyme* enzyme) override;
57
59 void setEnzyme(const String& name);
60
66 void digest(const NASequence& rna, std::vector<NASequence>& output,
67 Size min_length = 0, Size max_length = 0) const;
68
75 void digest(IdentificationData& id_data, Size min_length = 0,
76 Size max_length = 0) const;
77
78 protected:
79 const Ribonucleotide* five_prime_gain_;
80 const Ribonucleotide* three_prime_gain_;
81 boost::regex cuts_after_regex_;
82 boost::regex cuts_before_regex_;
83
87 std::vector<std::pair<Size, Size>> getFragmentPositions_(
88 const NASequence& rna, Size min_length, Size max_length)
89 const;
90 };
91
92 } // namespace OpenMS
93
OpenMS::Ribonucleotide
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:51
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::RNaseDigestion::cuts_after_regex_
boost::regex cuts_after_regex_
reg. exp. for enzyme cutting pattern
Definition: RNaseDigestion.h:81
NASequence.h
OpenMS::DigestionEnzyme
Abstract base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
OpenMS::RNaseDigestion::three_prime_gain_
const Ribonucleotide * three_prime_gain_
3&#39; mod added by the enzyme
Definition: RNaseDigestion.h:80
OpenMS::RNaseDigestion::cuts_before_regex_
boost::regex cuts_before_regex_
reg. exp. for enzyme cutting pattern
Definition: RNaseDigestion.h:82
OpenMS::RNaseDigestion::five_prime_gain_
const Ribonucleotide * five_prime_gain_
5&#39; mod added by the enzyme
Definition: RNaseDigestion.h:79
IdentificationData.h
OpenMS::EnzymaticDigestion
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:62
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::RNaseDigestion
Class for the enzymatic digestion of RNAs.
Definition: RNaseDigestion.h:52
OpenMS::NASequence
Representation of a nucleic acid sequence.
Definition: NASequence.h:62
EnzymaticDigestion.h
OpenMS::IdentificationData
Representation of spectrum identification results and associated data.
Definition: IdentificationData.h:89
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127