| 94 | } |
| 95 | |
| 96 | SearchEngineBase::ExitCodes SearchEngineBase::reindex_(std::vector<ProteinIdentification>& protein_identifications, |
| 97 | std::vector<PeptideIdentification>& peptide_identifications) const |
| 98 | { |
| 99 | if (getStringOption_("reindex") == "true") |
| 100 | { |
| 101 | PeptideIndexing indexer; |
| 102 | |
| 103 | // extract parameter subtree |
| 104 | Param param = getParam_().copy("PeptideIndexing:", true); |
| 105 | |
| 106 | Param param_pi = indexer.getParameters(); |
| 107 | // copy search engine specific default parameter for peptide indexing into param_pi |
| 108 | param_pi.update(param, false, false, false, false, OpenMS_Log_debug); // suppress param. update message |
| 109 | indexer.setParameters(param_pi); |
| 110 | indexer.setLogType(this->log_type_); |
| 111 | FASTAContainer<TFI_File> proteins(getDBFilename()); |
| 112 | PeptideIndexing::ExitCodes indexer_exit = indexer.run(proteins, protein_identifications, peptide_identifications); |
| 113 | |
| 114 | if ((indexer_exit != PeptideIndexing::EXECUTION_OK) && |
| 115 | (indexer_exit != PeptideIndexing::PEPTIDE_IDS_EMPTY)) |
| 116 | { |
| 117 | if (indexer_exit == PeptideIndexing::DATABASE_EMPTY) |
| 118 | { |
| 119 | return INPUT_FILE_EMPTY; |
| 120 | } |
| 121 | else if (indexer_exit == PeptideIndexing::UNEXPECTED_RESULT) |
| 122 | { |
| 123 | return UNEXPECTED_RESULT; |
| 124 | } |
| 125 | else |
| 126 | { |
| 127 | return UNKNOWN_ERROR; |
| 128 | } |
| 129 | } |
| 130 | } |
| 131 | return EXECUTION_OK; |
| 132 | } |
| 133 | |
| 134 | void SearchEngineBase::registerPeptideIndexingParameter_(Param peptide_indexing_parameter) |
| 135 | { |
nothing calls this directly
no test coverage detected