35 #ifndef OPENMS_ANALYSIS_QUANTITATION_PROTEINRESOLVER_H 36 #define OPENMS_ANALYSIS_QUANTITATION_PROTEINRESOLVER_H 90 enum type {primary, secondary, primary_indistinguishable, secondary_indistinguishable} protein_type;
94 std::list<ProteinEntry *>
indis;
147 enum type {PeptideIdent, Consensus} input_type;
168 void resolveID(std::vector<PeptideIdentification> & peptide_identifications);
222 void countTargetDecoy(std::vector<MSDGroup> & msd_groups,
ConsensusMap & consensus);
230 void countTargetDecoy(std::vector<MSDGroup> & msd_groups, std::vector<PeptideIdentification> & peptide_nodes);
234 void setProteinData(std::vector<FASTAFile::FASTAEntry> & protein_data);
236 const std::vector<ResolverResult> & getResults();
242 static const PeptideHit & getPeptideHit(
const std::vector<PeptideIdentification> & peptide_nodes,
const PeptideEntry * peptide);
249 void computeIntensityOfMSD_(std::vector<MSDGroup> & msd_groups);
255 Size findPeptideEntry_(
String seq, std::vector<PeptideEntry> & nodes);
257 Size binarySearchNodes_(
String & seq, std::vector<PeptideEntry> & nodes,
Size start,
Size end);
259 Size includeMSMSPeptides_(std::vector<PeptideIdentification> & peptide_identifications, std::vector<PeptideEntry> & peptide_nodes);
262 Size includeMSMSPeptides_(
ConsensusMap & consensus, std::vector<PeptideEntry> & peptide_nodes);
264 void reindexingNodes_(std::vector<MSDGroup> & msd_groups, std::vector<Size> & reindexed_proteins, std::vector<Size> & reindexed_peptides);
266 void primaryProteins_(std::vector<PeptideEntry> & peptide_nodes, std::vector<Size> & reindexed_peptides);
267 void buildingMSDGroups_(std::vector<MSDGroup> & msd_groups, std::vector<ISDGroup> & isd_groups);
268 void buildingISDGroups_(std::vector<ProteinEntry> & protein_nodes, std::vector<PeptideEntry> & peptide_nodes,
269 std::vector<ISDGroup> & isd_groups);
277 #endif // OPENMS_ANALYSIS_QUANTITATION_PROTEINRESOLVER_H std::list< ProteinEntry * > proteins
Definition: ProteinResolver.h:132
Definition: ProteinResolver.h:130
std::list< ProteinEntry * > proteins
Definition: ProteinResolver.h:120
Size index
Definition: ProteinResolver.h:109
std::vector< Size > * reindexed_proteins
Definition: ProteinResolver.h:146
Size msd_group
Definition: ProteinResolver.h:110
A more convenient string class.
Definition: String.h:57
ISDGroup * isd_group
Definition: ProteinResolver.h:123
Size index
Definition: ProteinResolver.h:134
std::vector< PeptideIdentification > * peptide_identification
Definition: ProteinResolver.h:148
Size peptide_hit
Definition: ProteinResolver.h:108
std::vector< PeptideEntry > * peptide_entries
Definition: ProteinResolver.h:144
std::list< PeptideEntry * > peptides
Definition: ProteinResolver.h:87
Size isd_group
Definition: ProteinResolver.h:97
String identifier
Definition: ProteinResolver.h:140
representation of an msd group. Contains peptides, proteins and a pointer to its ISD group ...
Definition: ProteinResolver.h:118
std::vector< FASTAFile::FASTAEntry > protein_data_
Definition: ProteinResolver.h:247
Size number_of_decoy
Definition: ProteinResolver.h:124
Size index
Definition: ProteinResolver.h:95
A container for consensus elements.
Definition: ConsensusMap.h:72
Size peptide_identification
Definition: ProteinResolver.h:107
float coverage
Definition: ProteinResolver.h:92
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::vector< Size > * reindexed_peptides
Definition: ProteinResolver.h:145
std::list< PeptideEntry * > peptides
Definition: ProteinResolver.h:121
std::list< ProteinEntry * > indis
Definition: ProteinResolver.h:94
float intensity
Definition: ProteinResolver.h:113
Size index
Definition: ProteinResolver.h:122
Size number_of_target_plus_decoy
Definition: ProteinResolver.h:126
bool traversed
Definition: ProteinResolver.h:105
Helper class for peptide and protein quantification based on feature data annotated with IDs...
Definition: ProteinResolver.h:59
Size isd_group
Definition: ProteinResolver.h:111
Size number_of_experimental_peptides
Definition: ProteinResolver.h:98
std::vector< ProteinEntry > * protein_entries
Definition: ProteinResolver.h:143
type
Definition: ProteinResolver.h:147
String origin
Definition: ProteinResolver.h:114
Size msd_group
Definition: ProteinResolver.h:96
std::list< PeptideEntry * > peptides
Definition: ProteinResolver.h:133
std::list< Size > msd_groups
Definition: ProteinResolver.h:135
Representation of a peptide hit.
Definition: PeptideHit.h:55
represents a protein from FASTA file
Definition: ProteinResolver.h:85
bool experimental
Definition: ProteinResolver.h:112
FASTAFile::FASTAEntry * fasta_entry
Definition: ProteinResolver.h:89
Definition: ProteinResolver.h:138
ConsensusMap * consensus_map
Definition: ProteinResolver.h:149
String sequence
Definition: ProteinResolver.h:106
Size number_of_target
Definition: ProteinResolver.h:125
std::vector< ResolverResult > resolver_result_
Definition: ProteinResolver.h:246
std::vector< MSDGroup > * msds
Definition: ProteinResolver.h:142
bool traversed
Definition: ProteinResolver.h:88
std::vector< ISDGroup > * isds
Definition: ProteinResolver.h:141
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
represents a peptide. First in silico. If experimental is set to true it is MS/MS derived...
Definition: ProteinResolver.h:102
FASTA entry type (identifier, description and sequence)
Definition: FASTAFile.h:74
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
std::list< ProteinEntry * > proteins
Definition: ProteinResolver.h:104
type
Definition: ProteinResolver.h:90
float intensity
Definition: ProteinResolver.h:127
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
double weight
Definition: ProteinResolver.h:91