OpenMS
2.5.0
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Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but concatenates PSMs. Checks search engine consistency of all inserted runs. It differs from the IDMerger tool, in that it is an algorithm class and it allows inserting multiple peptide hits per peptide sequence (not only the first occurrence). More...
#include <OpenMS/ANALYSIS/ID/IDMergerAlgorithm.h>
Public Member Functions | |
IDMergerAlgorithm (const String &runIdentifier="merged") | |
void | insertRuns (std::vector< ProteinIdentification > &&prots, std::vector< PeptideIdentification > &&peps) |
void | insertRuns (const std::vector< ProteinIdentification > &prots, const std::vector< PeptideIdentification > &peps) |
void | returnResultsAndClear (ProteinIdentification &prots, std::vector< PeptideIdentification > &peps) |
Return the merged results and reset/clear all internal data. More... | |
Public Member Functions inherited from DefaultParamHandler | |
DefaultParamHandler (const String &name) | |
Constructor with name that is displayed in error messages. More... | |
DefaultParamHandler (const DefaultParamHandler &rhs) | |
Copy constructor. More... | |
virtual | ~DefaultParamHandler () |
Destructor. More... | |
virtual DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
Assignment operator. More... | |
virtual bool | operator== (const DefaultParamHandler &rhs) const |
Equality operator. More... | |
void | setParameters (const Param ¶m) |
Sets the parameters. More... | |
const Param & | getParameters () const |
Non-mutable access to the parameters. More... | |
const Param & | getDefaults () const |
Non-mutable access to the default parameters. More... | |
const String & | getName () const |
Non-mutable access to the name. More... | |
void | setName (const String &name) |
Mutable access to the name. More... | |
const std::vector< String > & | getSubsections () const |
Non-mutable access to the registered subsections. More... | |
Public Member Functions inherited from ProgressLogger | |
ProgressLogger () | |
Constructor. More... | |
~ProgressLogger () | |
Destructor. More... | |
ProgressLogger (const ProgressLogger &other) | |
Copy constructor. More... | |
ProgressLogger & | operator= (const ProgressLogger &other) |
Assignment Operator. More... | |
void | setLogType (LogType type) const |
Sets the progress log that should be used. The default type is NONE! More... | |
LogType | getLogType () const |
Returns the type of progress log being used. More... | |
void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
Initializes the progress display. More... | |
void | setProgress (SignedSize value) const |
Sets the current progress. More... | |
void | endProgress () const |
Ends the progress display. More... | |
void | nextProgress () const |
increment progress by 1 (according to range begin-end) More... | |
Private Types | |
using | hash_type = std::size_t(*)(const ProteinHit &) |
using | equal_type = bool(*)(const ProteinHit &, const ProteinHit &) |
Private Member Functions | |
String | getNewIdentifier_ () const |
Returns the new identifier. The initial identifier plus a timestamp. More... | |
bool | checkOldRunConsistency_ (const std::vector< ProteinIdentification > &protRuns, const String &experiment_type) const |
bool | checkOldRunConsistency_ (const std::vector< ProteinIdentification > &protRuns, const ProteinIdentification &ref, const String &experiment_type) const |
void | insertProteinIDs_ (std::vector< ProteinIdentification > &&old_protRuns) |
void | updateAndMovePepIDs_ (std::vector< PeptideIdentification > &&pepIDs, const std::map< String, Size > &runID_to_runIdx, const std::vector< StringList > &originFiles, bool annotate_origin) |
void | movePepIDsAndRefProteinsToResultFaster_ (std::vector< PeptideIdentification > &&pepIDs, std::vector< ProteinIdentification > &&old_protRuns) |
Static Private Member Functions | |
static void | copySearchParams_ (const ProteinIdentification &from, ProteinIdentification &to) |
Copies over search parameters. More... | |
static size_t | accessionHash_ (const ProteinHit &p) |
static bool | accessionEqual_ (const ProteinHit &p1, const ProteinHit &p2) |
Private Attributes | |
ProteinIdentification | prot_result_ |
the resulting new Protein IDs More... | |
std::vector< PeptideIdentification > | pep_result_ |
the resulting new Peptide IDs More... | |
std::unordered_set< ProteinHit, hash_type, equal_type > | collected_protein_hits_ |
bool | filled_ = false |
is the resulting protein ID already filled? More... | |
std::map< String, Size > | file_origin_to_idx_ |
to keep track of the mzML origins of spectra More... | |
String | id_ |
the new identifier string More... | |
Additional Inherited Members | |
Public Types inherited from ProgressLogger | |
enum | LogType { CMD, GUI, NONE } |
Possible log types. More... | |
Protected Member Functions inherited from DefaultParamHandler | |
virtual void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParameters() method. More... | |
void | defaultsToParam_ () |
Updates the parameters after the defaults have been set in the constructor. More... | |
Static Protected Member Functions inherited from ProgressLogger | |
static String | logTypeToFactoryName_ (LogType type) |
Return the name of the factory product used for this log type. More... | |
Protected Attributes inherited from DefaultParamHandler | |
Param | param_ |
Container for current parameters. More... | |
Param | defaults_ |
Container for default parameters. This member should be filled in the constructor of derived classes! More... | |
std::vector< String > | subsections_ |
Container for registered subsections. This member should be filled in the constructor of derived classes! More... | |
String | error_name_ |
Name that is displayed in error messages during the parameter checking. More... | |
bool | check_defaults_ |
If this member is set to false no checking if parameters in done;. More... | |
bool | warn_empty_defaults_ |
If this member is set to false no warning is emitted when defaults are empty;. More... | |
Protected Attributes inherited from ProgressLogger | |
LogType | type_ |
time_t | last_invoke_ |
ProgressLoggerImpl * | current_logger_ |
Static Protected Attributes inherited from ProgressLogger | |
static int | recursion_depth_ |
Creates a new Protein ID run into which other runs can be inserted. Creates union of protein hits but concatenates PSMs. Checks search engine consistency of all inserted runs. It differs from the IDMerger tool, in that it is an algorithm class and it allows inserting multiple peptide hits per peptide sequence (not only the first occurrence).
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inlinestaticprivate |
References ProteinHit::getAccession().
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inlinestaticprivate |
References ProteinHit::getAccession().
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Same as above, if you want to use a specific reference
protRuns | The runs to check (first = reference) |
ref | A possibly external protein run reference |
experiment_type | allow some mismatches in case of other experiment types (e.g. SILAC) |
BaseException | for disagreeing settings |
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Checks consistency of search engines and settings across runs before merging.
protRuns | The runs to check (first = implicit reference) |
experiment_type | allow some mismatches in case of other experiment types (e.g. SILAC) |
BaseException | for disagreeing settings |
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Copies over search parameters.
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Returns the new identifier. The initial identifier plus a timestamp.
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moves and inserts protein IDs if not yet present then clears the input
void insertRuns | ( | const std::vector< ProteinIdentification > & | prots, |
const std::vector< PeptideIdentification > & | peps | ||
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void insertRuns | ( | std::vector< ProteinIdentification > && | prots, |
std::vector< PeptideIdentification > && | peps | ||
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Insert (=move and clear) a run with its peptide IDs into the internal merged data structures, based on the initial mapping from fileorigins to new run
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void returnResultsAndClear | ( | ProteinIdentification & | prots, |
std::vector< PeptideIdentification > & | peps | ||
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Return the merged results and reset/clear all internal data.
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updates the references in pepIDs to the new protein ID run then moves the peptide IDs based on the mapping in
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is the resulting protein ID already filled?
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the new identifier string
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the resulting new Peptide IDs
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the resulting new Protein IDs