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);
 
  231     void countTargetDecoy(std::vector<MSDGroup> & msd_groups, std::vector<PeptideIdentification> & peptide_nodes);
 
  235     void setProteinData(std::vector<FASTAFile::FASTAEntry> & protein_data);
 
  237     const  std::vector<ResolverResult> & getResults();
 
  243     static const PeptideHit & getPeptideHit(
const std::vector<PeptideIdentification> & peptide_nodes, 
const PeptideEntry * peptide);
 
  250     void computeIntensityOfMSD_(std::vector<MSDGroup> & msd_groups);
 
  258     Size findPeptideEntry_(
String seq, std::vector<PeptideEntry> & nodes);
 
  260     Size binarySearchNodes_(
String & seq, std::vector<PeptideEntry> & nodes, 
Size start, 
Size end);
 
  262     Size includeMSMSPeptides_(std::vector<PeptideIdentification> & peptide_identifications, std::vector<PeptideEntry> & peptide_nodes);
 
  265     Size includeMSMSPeptides_(
ConsensusMap & consensus, std::vector<PeptideEntry> & peptide_nodes);
 
  267     void reindexingNodes_(std::vector<MSDGroup> & msd_groups, std::vector<Size> & reindexed_proteins, std::vector<Size> & reindexed_peptides);
 
  269     void primaryProteins_(std::vector<PeptideEntry> & peptide_nodes, std::vector<Size> & reindexed_peptides);
 
  270     void buildingMSDGroups_(std::vector<MSDGroup> & msd_groups, std::vector<ISDGroup> & isd_groups);
 
  271     void buildingISDGroups_(std::vector<ProteinEntry> & protein_nodes, std::vector<PeptideEntry> & peptide_nodes,
 
  272                             std::vector<ISDGroup> & isd_groups);
 
  280 #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
float Real
Real type. 
Definition: Types.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:56
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
Real intensity
Definition: ProteinResolver.h:127
String identifier
Definition: ProteinResolver.h:140
Definition: ProteinResolver.h:118
std::vector< FASTAFile::FASTAEntry > protein_data_
Definition: ProteinResolver.h:248
Size number_of_decoy
Definition: ProteinResolver.h:124
Size index
Definition: ProteinResolver.h:95
A container for consensus elements. 
Definition: ConsensusMap.h:60
Size peptide_identification
Definition: ProteinResolver.h:107
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
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
Real coverage
Definition: ProteinResolver.h:92
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:54
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
DoubleReal weight
Definition: ProteinResolver.h:91
Size number_of_target
Definition: ProteinResolver.h:125
std::vector< ResolverResult > resolver_result_
Definition: ProteinResolver.h:247
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:144
Definition: ProteinResolver.h:102
FASTA entry type (identifier, description and sequence) 
Definition: FASTAFile.h:61
Real intensity
Definition: ProteinResolver.h:113
A base class for all classes handling default parameters. 
Definition: DefaultParamHandler.h:90
std::list< ProteinEntry * > proteins
Definition: ProteinResolver.h:104
type
Definition: ProteinResolver.h:90
Represents the peptide hits for a spectrum. 
Definition: PeptideIdentification.h:63