, including all inherited members.
| binarySearchNodes_(String &seq, std::vector< PeptideEntry > &nodes, Size start, Size end) | ProteinResolver | [private] |
| buildingISDGroups_(std::vector< ProteinEntry > &protein_nodes, std::vector< PeptideEntry > &peptide_nodes, std::vector< ISDGroup > &isd_groups) | ProteinResolver | [private] |
| buildingMSDGroups_(std::vector< MSDGroup > &msd_groups, std::vector< ISDGroup > &isd_groups) | ProteinResolver | [private] |
| check_defaults_ | DefaultParamHandler | [protected] |
| clearResult() | ProteinResolver | |
| computeIntensityOfMSD_(std::vector< MSDGroup > &msd_groups) | ProteinResolver | [private] |
| countTargetDecoy(std::vector< MSDGroup > &msd_groups, ConsensusMap &consensus) | ProteinResolver | |
| countTargetDecoy(std::vector< MSDGroup > &msd_groups, std::vector< PeptideIdentification > &peptide_nodes) | ProteinResolver | |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| defaults_ | DefaultParamHandler | [protected] |
| defaultsToParam_() | DefaultParamHandler | [protected] |
| error_name_ | DefaultParamHandler | [protected] |
| findPeptideEntry_(String seq, std::vector< PeptideEntry > &nodes) | ProteinResolver | [private] |
| getDefaults() const | DefaultParamHandler | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getPeptideHit(const ConsensusMap &consensus, const PeptideEntry *peptide) | ProteinResolver | |
| getPeptideHit(const std::vector< PeptideIdentification > &peptide_nodes, const PeptideEntry *peptide) | ProteinResolver | |
| getPeptideIdentification(const ConsensusMap &consensus, const PeptideEntry *peptide) | ProteinResolver | |
| getPeptideIdentification(const std::vector< PeptideIdentification > &peptide_nodes, const PeptideEntry *peptide) | ProteinResolver | |
| getResults() | ProteinResolver | |
| getSubsections() const | DefaultParamHandler | |
| includeMSMSPeptides_(std::vector< PeptideIdentification > &peptide_identifications, std::vector< PeptideEntry > &peptide_nodes) | ProteinResolver | [private] |
| includeMSMSPeptides_(ConsensusMap &consensus, std::vector< PeptideEntry > &peptide_nodes) | ProteinResolver | [private] |
| operator=(const ProteinResolver &rhs) | ProteinResolver | |
| OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | [virtual] |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | [virtual] |
| param_ | DefaultParamHandler | [protected] |
| primaryProteins_(std::vector< PeptideEntry > &peptide_nodes, std::vector< Size > &reindexed_peptides) | ProteinResolver | [private] |
| protein_data_ | ProteinResolver | [private] |
| ProteinResolver() | ProteinResolver | |
| ProteinResolver(const ProteinResolver &rhs) | ProteinResolver | |
| reindexingNodes_(std::vector< MSDGroup > &msd_groups, std::vector< Size > &reindexed_proteins, std::vector< Size > &reindexed_peptides) | ProteinResolver | [private] |
| resolveConsensus(ConsensusMap &consensus) | ProteinResolver | |
| resolveID(std::vector< PeptideIdentification > &peptide_identifications) | ProteinResolver | |
| resolver_result_ | ProteinResolver | [private] |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setProteinData(std::vector< FASTAFile::FASTAEntry > &protein_data) | ProteinResolver | |
| subsections_ | DefaultParamHandler | [protected] |
| traversPeptide_(PeptideEntry *pep_node, ISDGroup &group) | ProteinResolver | [private] |
| traversPeptide_(PeptideEntry *pep_node, MSDGroup &group) | ProteinResolver | [private] |
| traversProtein_(ProteinEntry *prot_node, ISDGroup &group) | ProteinResolver | [private] |
| traversProtein_(ProteinEntry *prot_node, MSDGroup &group) | ProteinResolver | [private] |
| updateMembers_() | DefaultParamHandler | [protected, virtual] |
| warn_empty_defaults_ | DefaultParamHandler | [protected] |
| writePeptideTable(std::vector< PeptideEntry > &peptides, std::vector< Size > &reindexed_peptides, std::vector< PeptideIdentification > &identifications, String &output_file) | ProteinResolver | |
| writePeptideTable(std::vector< PeptideEntry > &peptides, std::vector< Size > &reindexed_peptides, ConsensusMap &consensus, String &output_file) | ProteinResolver | |
| writeProteinGroups(std::vector< ISDGroup > &isd_groups, std::vector< MSDGroup > &msd_groups, String &output_file) | ProteinResolver | |
| writeProteinTable(std::vector< ProteinEntry > &proteins, std::vector< Size > &reindexed_proteins, String &output_file) | ProteinResolver | |
| ~DefaultParamHandler() | DefaultParamHandler | [virtual] |
| ~ProteinResolver() | ProteinResolver | [virtual] |