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00019 #ifndef MS_INPUTQUERY_HPP
00020 #define MS_INPUTQUERY_HPP
00021
00022
00023 #include <string>
00024
00025 namespace matrix_science {
00026
00032
00033
00038 class MS_MASCOTRESFILE_API ms_inputquery
00039 {
00040 public:
00041
00043 ms_inputquery(const ms_mascotresfile &resfile, const int q);
00044 ~ms_inputquery();
00045
00046 #ifndef SWIGCSHARP
00047
00048 std::string getStringTitle(bool unescaped) const;
00049 #else
00050 std::wstring getStringTitle(bool unescaped) const
00051 {
00052 return getStringTitleWide(unescaped);
00053 };
00054 #endif
00055
00056 std::string getCharge() const;
00057
00059 std::string getSeq(int seq_no) const;
00060
00062 std::string getComp(int comp_no) const;
00063
00065 std::string getTag(int tag_no) const;
00066
00068 double getMassMin() const;
00069
00071 double getMassMax() const;
00072
00074 double getIonMobility() const;
00075
00077 int getNumVals() const;
00078
00080 int getNumUsed() const;
00081
00083 std::string getStringIons1(bool includeCharges = false);
00084
00086 std::string getStringIons2(bool includeCharges = false);
00087
00089 std::string getStringIons3(bool includeCharges = false);
00090
00092 double getIntMax() const;
00093
00095 double getIntMin() const;
00096
00098 std::vector<std::pair<double,double> > getPeakList(const int ions);
00099
00101 double getPeakMass(const int ions, const int peakNo);
00102
00104 double getPeakIntensity(const int ions, const int peakNo);
00105
00107 int getNumberOfPeaks(const int ions);
00108
00110 double getTotalIonsIntensity();
00111
00113 double getPepTol() const;
00114
00116 std::string getPepTolUnits() const;
00117
00119 std::string getPepTolString() const;
00120
00122 std::string getINSTRUMENT(const bool unescaped = true) const;
00123
00125 std::string getRULES() const;
00126
00128 double getMinInternalMass() const;
00129
00131 double getMaxInternalMass() const;
00132
00134 std::string getIT_MODS(const bool unescaped = true) const;
00135
00137 int getNumberOfLocalVarMods() const;
00138
00140 std::string getLocalVarModName(const int num) const;
00141
00143 std::string getScanNumbers(const int rawFileIdx = -1) const;
00144
00146 void getScanNumbers(std::vector<int> &index, std::vector<std::string> &scans) const;
00147
00149 std::string getRawScans(const int rawFileIdx = -1) const;
00150
00152 void getRawScans(std::vector<int> &index, std::vector<std::string> &rawscans) const;
00153
00155 std::string getRetentionTimes(const int rawFileIdx = -1) const;
00156
00158 void getRetentionTimes(std::vector<int> &index, std::vector<std::string> ×) const;
00159
00161 std::string getRawfile() const;
00162
00164 std::string getLocus() const;
00165
00167 int getIndex() const;
00168
00169 #ifndef DOXYGEN_SHOULD_SKIP_THIS
00170 static std::vector<std::string> splitIT_MODS(std::string itmods);
00171 #endif
00172
00173 private:
00174 enum { max_seqs_ = 20, max_comps_ = 20, max_tags_ = 20 };
00175 const ms_mascotresfile &resfile_;
00176 const int q_;
00177
00178 mutable bool has_title_;
00179 mutable std::string title_;
00180 mutable std::string unescapedTitle_;
00181
00182 mutable bool has_charge_;
00183 mutable std::string charge_;
00184
00185 mutable bool has_seq_;
00186 mutable std::string seq_[max_seqs_ +1];
00187
00188 mutable bool has_comp_;
00189 mutable std::string comp_[max_comps_ +1];
00190
00191 mutable bool has_tag_;
00192 mutable std::string tag_[max_tags_ + 1];
00193
00194 mutable bool has_mass_min_;
00195 mutable double mass_min_;
00196
00197 mutable bool has_mass_max_;
00198 mutable double mass_max_;
00199
00200 mutable bool has_ion_mobility_;
00201 mutable double ion_mobility_;
00202
00203 mutable bool has_num_vals_;
00204 mutable int num_vals_;
00205
00206 mutable bool has_num_used_;
00207 mutable int num_used_;
00208
00209 bool has_ions_;
00210 std::string ions_[3], ionsCharges_[3];
00211 std::vector<std::pair<double,double> > peakList_[3];
00212 std::vector<std::string> peakListCharges_[3];
00213
00214 mutable bool has_int_max_;
00215 mutable double int_max_;
00216
00217 mutable bool has_int_min_;
00218 mutable double int_min_;
00219
00220 mutable bool has_tol_;
00221 mutable double tol_;
00222 mutable std::string tol_units_;
00223
00224 mutable bool has_instrument_;
00225 mutable std::string instrument_;
00226 mutable std::string unescaped_instrument_;
00227
00228 mutable bool has_rules_;
00229 mutable std::string rules_;
00230
00231 mutable bool has_internalMasses_;
00232 mutable double minInternalMass_;
00233 mutable double maxInternalMass_;
00234
00235 mutable bool has_it_mods_;
00236 mutable std::string it_mods_;
00237 mutable std::string unescaped_it_mods_;
00238 mutable std::vector<std::string> local_modtitles_;
00239
00240 ms_umod_configfile umodfile_;
00241
00242 mutable bool has_rt_;
00243 mutable std::vector<int> rtIndices_;
00244 mutable std::vector<std::string> rtValues_;
00245
00246 mutable bool has_scans_;
00247 mutable std::vector<int> scansIndices_;
00248 mutable std::vector<std::string> scansValues_;
00249
00250 mutable bool has_rawscans_;
00251 mutable std::vector<int> rawscansIndices_;
00252 mutable std::vector<std::string> rawscansValues_;
00253
00254 mutable bool has_rawfile_;
00255 mutable std::string rawfile_;
00256
00257 mutable bool has_locus_;
00258 mutable std::string locus_;
00259
00260 mutable bool has_index_;
00261 mutable int index_;
00262
00263 void fillPeakList(const int ions);
00264 void loadIons();
00265 void retrieveAllValuesOf(const std::string &prefix, std::vector<int> &index, std::vector<std::string> &values) const;
00266 std::wstring getStringTitleWide(bool unescaped) const;
00267 std::wstring getRawfileWide() const;
00268 std::string getStringIonsWithCharges(const int index);
00269 };
00271 }
00272
00273 #endif // !defined(MS_INPUTQUERY_HPP)
