| 159 | } |
| 160 | |
| 161 | void OMSSAXMLFile::characters(const XMLCh* const chars, const XMLSize_t /*length*/) |
| 162 | { |
| 163 | if (tag_.empty()) return; |
| 164 | |
| 165 | String value = ((String)sm_.convert(chars)).trim(); |
| 166 | // MSPepHit section |
| 167 | // <MSPepHit_start>0</MSPepHit_start> |
| 168 | // <MSPepHit_stop>8</MSPepHit_stop> |
| 169 | // <MSPepHit_accession>6599</MSPepHit_accession> |
| 170 | // <MSPepHit_defline>CRHU2 carbonate dehydratase (EC 4.2.1.1) II [validated] - human</MSPepHit_defline> |
| 171 | // <MSPepHit_protlength>260</MSPepHit_protlength> |
| 172 | // <MSPepHit_oid>6599</MSPepHit_oid> |
| 173 | |
| 174 | if (tag_ == "MSPepHit_start") |
| 175 | { |
| 176 | tag_ = ""; |
| 177 | return; |
| 178 | } |
| 179 | else if (tag_ == "MSPepHit_stop") |
| 180 | { |
| 181 | tag_ = ""; |
| 182 | return; |
| 183 | } |
| 184 | else if (tag_ == "MSPepHit_accession") |
| 185 | { |
| 186 | if (load_proteins_) |
| 187 | { |
| 188 | actual_peptide_evidence_.setProteinAccession(value); |
| 189 | } |
| 190 | tag_ = ""; |
| 191 | return; |
| 192 | } |
| 193 | else if (tag_ == "MSPepHit_defline") |
| 194 | { |
| 195 | // TODO add defline to ProteinHit? |
| 196 | tag_ = ""; |
| 197 | return; |
| 198 | } |
| 199 | else if (tag_ == "MSPepHit_protlength") |
| 200 | { |
| 201 | tag_ = ""; |
| 202 | return; |
| 203 | } |
| 204 | else if (tag_ == "MSPepHit_oid") |
| 205 | { |
| 206 | tag_ = ""; |
| 207 | // end of MSPepHit so we add the evidence |
| 208 | actual_peptide_evidences_.push_back(actual_peptide_evidence_); |
| 209 | return; |
| 210 | } |
| 211 | // MSHits section |
| 212 | // <MSHits_evalue>0.00336753988893542</MSHits_evalue> |
| 213 | // <MSHits_pvalue>1.30819399070598e-08</MSHits_pvalue> |
| 214 | // <MSHits_charge>1</MSHits_charge> |
| 215 | // <MSHits_pepstring>MSHHWGYGK</MSHits_pepstring> |
| 216 | // <MSHits_mass>1101492</MSHits_mass> |
| 217 | // <MSHits_pepstart></MSHits_pepstart> |
| 218 | // <MSHits_pepstop>H</MSHits_pepstop> |
nothing calls this directly
no test coverage detected