00001 // -------------------------------------------------------------------------- 00002 // OpenMS -- Open-Source Mass Spectrometry 00003 // -------------------------------------------------------------------------- 00004 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen, 00005 // ETH Zurich, and Freie Universitaet Berlin 2002-2012. 00006 // 00007 // This software is released under a three-clause BSD license: 00008 // * Redistributions of source code must retain the above copyright 00009 // notice, this list of conditions and the following disclaimer. 00010 // * Redistributions in binary form must reproduce the above copyright 00011 // notice, this list of conditions and the following disclaimer in the 00012 // documentation and/or other materials provided with the distribution. 00013 // * Neither the name of any author or any participating institution 00014 // may be used to endorse or promote products derived from this software 00015 // without specific prior written permission. 00016 // For a full list of authors, refer to the file AUTHORS. 00017 // -------------------------------------------------------------------------- 00018 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 00019 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 00020 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 00021 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING 00022 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, 00023 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, 00024 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; 00025 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, 00026 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR 00027 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF 00028 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 00029 // 00030 // -------------------------------------------------------------------------- 00031 // $Maintainer: Witold Wolski, Hannes Roest $ 00032 // $Authors: Witold Wolski, Hannes Roest $ 00033 // -------------------------------------------------------------------------- 00034 00035 #ifndef OPENMS_ANALYSIS_OPENSWATH_DIAHELPER_H 00036 #define OPENMS_ANALYSIS_OPENSWATH_DIAHELPER_H 00037 00038 #include <vector> 00039 #include <OpenMS/CHEMISTRY/AASequence.h> 00040 00041 namespace OpenMS 00042 { 00043 namespace DIAHelpers 00044 { 00048 00049 00050 OPENMS_DLLAPI void getBYSeries(AASequence& a, 00051 std::vector<double>& bseries, std::vector<double>& yseries, UInt charge = 1u); 00052 00054 OPENMS_DLLAPI void getTheorMasses(AASequence& a, std::vector<double>& masses, UInt charge = 1u); 00055 00057 OPENMS_DLLAPI void getAveragineIsotopeDistribution(double product_mz, 00058 std::vector<std::pair<double, double> >& isotopesSpec, 00059 double charge = 1., 00060 int nr_isotopes = 4, 00061 double mannmass = 1.00048); 00062 00064 OPENMS_DLLAPI void simulateSpectrumFromAASequence(AASequence& aa, 00065 std::vector<double>& firstIsotopeMasses, //[out] 00066 std::vector<std::pair<double, double> >& isotopeMasses, //[out] 00067 double charge = 1.); 00068 00070 OPENMS_DLLAPI void modifyMassesByCharge(const std::vector<std::pair<double, double> >& masses, 00071 std::vector<std::pair<double, double> >& modmass, 00072 double charge = 1.); 00073 00075 OPENMS_DLLAPI void addPreisotopeWeights(const std::vector<double>& firstIsotopeMasses, 00076 std::vector<std::pair<double, double> >& isotopeSpec, // output 00077 UInt nrpeaks = 2, //nr of preisotope peaks 00078 double preIsotopePeaksWeight = -0.5, // weight of preisotope peaks 00079 double mannmass = 1.000482, // 00080 double charge = 1.); 00081 00083 OPENMS_DLLAPI void addIsotopes2Spec(const std::vector<std::pair<double, double> >& spec, 00084 std::vector<std::pair<double, double> >& isotopeMasses, //[out] 00085 double charge = 1.); 00086 00088 OPENMS_DLLAPI void sortByFirst(std::vector<std::pair<double, double> >& tmp); 00090 OPENMS_DLLAPI void extractFirst(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass); 00092 OPENMS_DLLAPI void extractSecond(const std::vector<std::pair<double, double> >& peaks, std::vector<double>& mass); 00093 00095 } 00096 } 00097 #endif
| OpenMS / TOPP release 1.10.0 | Documentation generated on Thu Mar 7 2013 09:42:38 using doxygen 1.7.1 |