00001 // -*- Mode: C++; tab-width: 2; -*- 00002 // vi: set ts=2: 00003 // 00004 // -------------------------------------------------------------------------- 00005 // OpenMS Mass Spectrometry Framework 00006 // -------------------------------------------------------------------------- 00007 // Copyright (C) 2003-2008 -- Oliver Kohlbacher, Knut Reinert 00008 // 00009 // This library is free software; you can redistribute it and/or 00010 // modify it under the terms of the GNU Lesser General Public 00011 // License as published by the Free Software Foundation; either 00012 // version 2.1 of the License, or (at your option) any later version. 00013 // 00014 // This library is distributed in the hope that it will be useful, 00015 // but WITHOUT ANY WARRANTY; without even the implied warranty of 00016 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 00017 // Lesser General Public License for more details. 00018 // 00019 // You should have received a copy of the GNU Lesser General Public 00020 // License along with this library; if not, write to the Free Software 00021 // Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA 00022 // 00023 // -------------------------------------------------------------------------- 00024 // $Maintainer: Andreas Bertsch $ 00025 // -------------------------------------------------------------------------- 00026 // 00027 00028 #ifndef OPENMS_CHEMISTRY_RESIDUEMODIFICATION_H 00029 #define OPENMS_CHEMISTRY_RESIDUEMODIFICATION_H 00030 00031 #include <OpenMS/CHEMISTRY/EmpiricalFormula.h> 00032 #include <OpenMS/CONCEPT/Types.h> 00033 #include <OpenMS/DATASTRUCTURES/String.h> 00034 00035 #include <set> 00036 00037 namespace OpenMS 00038 { 00039 // forward declaration 00040 class Residue; 00041 00045 class ResidueModification 00046 { 00047 public: 00048 00052 00053 ResidueModification(); 00054 00056 ResidueModification(const ResidueModification& modification); 00057 00059 virtual ~ResidueModification(); 00061 00064 00065 ResidueModification& operator = (const ResidueModification& modification); 00067 00071 00072 void setName(const String& name); 00073 00075 const String& getName() const; 00076 00078 void setShortName(const String& name); 00079 00081 const String& getShortName() const; 00082 00084 void setNamePrefix(const String& name_prefix); 00085 00087 const String& getNamePrefix() const; 00088 00090 void setSynonyms(const std::set<String>& synonyms); 00091 00093 void addSynonym(const String& synonym); 00094 00096 const std::set<String>& getSynonyms() const; 00097 00099 void setAddFormula(const EmpiricalFormula& formula); 00100 00102 const EmpiricalFormula& getAddFormula() const; 00103 00105 void setAddAverageWeight(DoubleReal weight); 00106 00108 DoubleReal getAddAverageWeight() const; 00109 00111 void setAddMonoWeight(DoubleReal weight); 00112 00114 DoubleReal getAddMonoWeight() const; 00115 00117 void setDelFormula(const EmpiricalFormula& formula); 00118 00120 const EmpiricalFormula& getDelFormula() const; 00121 00123 void setDelAverageWeight(DoubleReal weight); 00124 00126 DoubleReal getDelAverageWeight() const; 00127 00129 void setDelMonoWeight(DoubleReal weight); 00130 00132 DoubleReal getDelMonoWeight() const; 00133 00135 void setValidResidues(const std::set<Residue*>& valid_residues); 00136 00138 void addValidResidue(Residue* valid_residue); 00139 00141 const std::set<Residue*>& getValidResidues() const; 00143 00147 00148 bool operator == (const ResidueModification& modification) const; 00149 00151 bool operator != (const ResidueModification& modification) const; 00153 00154 protected: 00155 00156 // basic 00157 String name_; 00158 00159 String short_name_; 00160 00161 String name_prefix_; 00162 00163 std::set<String> synonyms_; 00164 00165 // additions 00166 EmpiricalFormula add_formula_; 00167 00168 DoubleReal add_average_weight_; 00169 00170 DoubleReal add_mono_weight_; 00171 00172 // deletions 00173 EmpiricalFormula del_formula_; 00174 00175 DoubleReal del_average_weight_; 00176 00177 DoubleReal del_mono_weight_; 00178 00179 // residues 00180 std::set<Residue*> valid_residues_; 00181 }; 00182 } 00183 00184 #endif
Generated Tue Apr 1 15:36:37 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |