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CycloBranch
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The class representing a theoretical mass spectrum. More...
#include <cTheoreticalSpectrum.h>
Public Member Functions | |
| cTheoreticalSpectrum () | |
| The constructor. | |
| cTheoreticalSpectrum (cParameters *parameters, cCandidate &candidate) | |
| The constructor. More... | |
| void | clear (bool clearpeaklist=true) |
| Clear the spectrum. More... | |
| cCandidate & | getCandidate () |
| Get the peptide spectrum candidate. More... | |
| void | setCandidate (cCandidate &candidate) |
| Set a peptide spectrum candidate. More... | |
| int | getNumberOfPeaks () |
| Get the number of peaks in the spectrum. More... | |
| int | compareBranched (cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) |
| Compare the theoretical spectrum of a branched peptide with an experimental spectrum. More... | |
| int | compareLinear (cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) |
| Compare the theoretical spectrum of a linear peptide with an experimental spectrum. More... | |
| int | compareCyclic (cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) |
| Compare the theoretical spectrum of a cyclic peptide with an experimental spectrum. More... | |
| int | compareBranchCyclic (cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) |
| Compare the theoretical spectrum of a branch-cyclic peptide with an experimental spectrum. More... | |
| int | compareLinearPolyketide (cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) |
| Compare the theoretical spectrum of a linear polyketide with an experimental spectrum. More... | |
| int | compareCyclicPolyketide (cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) |
| Compare the theoretical spectrum of a cyclic polyketide with an experimental spectrum. More... | |
| int | compareOther (cPeaksList &sortedpeaklist, bool writedescription, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) |
| Compare the theoretical spectrum of a metabolite with an experimental spectrum. More... | |
| void | generateMSSpectrum (int sequencestart, int sequencestop, bool &terminatecomputation, bool writedescription) |
| Generate a simple mass spectrum. More... | |
| void | generateFineMSSpectrum (int sequencestart, int sequencestop, bool &terminatecomputation) |
| Generate a simple mass spectrum with fine isotopic patterns. More... | |
| void | getHintsIndex (int id, int peaklistseriesvectorid, cTheoreticalSpectrum &tsfull, cPeaksList &unmatchedpeaksinmatchedpatterns, vector< vector< int > > &hintsindex, bool lcmsrt, bool skipcomparison) |
| Get a map of search hints to identify features in LC-MS data. More... | |
| void | compareMSSpectrum (int id, int peaklistseriesvectorid, cTheoreticalSpectrum &tsfull, cPeaksList &unmatchedpeaksinmatchedpatterns, vector< vector< int > > &hintsindex, bool lcmsrt, bool skipcomparison) |
| Compare theoretical peaks with an experimental spectrum. More... | |
| void | compareAverageMSSpectrum (cPeaksList &averagespectrum, cTheoreticalSpectrum &tsfull, cPeaksList &unmatchedpeaksinmatchedpatterns) |
| Compare theoretical peaks with an average spectrum. More... | |
| void | finalizeMSSpectrum (cPeaksList &unmatchedpeaksinmatchedpatterns, bool writedescription) |
| Finalize MS spectrum after comparison. More... | |
| int | getNumberOfMatchedPeaks () const |
| Get the number of matched peaks between an experimental and a theoretical spectrum. More... | |
| int | getNumberOfScrambledPeaks () |
| Get the number of matched scrambled peaks between an experimental and a theoretical spectrum. More... | |
| int | getNumberOfMatchedPeaks (eFragmentIonType iontype, int neutrallosstype) const |
| Get the number of matched peaks between an experimental and a theoretical spectrum of a specified fragment ion type. More... | |
| int | getNumberOfMatchedPeaksB () const |
| Get the number of matched B ions between an experimental and a theoretical spectrum. More... | |
| int | getNumberOfMatchedPeaksY () const |
| Get the number of matched Y ions between an experimental and a theoretical spectrum. More... | |
| int | getNumberOfMatchedPeaksYB () const |
| Get the number of matched Y and B ions between an experimental and a theoretical spectrum. More... | |
| double | getRatioOfMatchedPeaks () |
| Get a ratio of matched peaks. More... | |
| double | getWeightedRatioOfMatchedPeaks () const |
| Get weighted ratio of matched peaks. More... | |
| double | getCosineSimilarity () const |
| Get cosine similarity. More... | |
| void | generateNTerminalFragmentIons (int maxcharge, int &peaklistrealsize, vector< int > &intcomposition, eFragmentIonType fragmentiontype, int neutrallosstype, cBricksDatabase &bricksdatabase, bool writedescription, int rotationid, vector< splitSite > &splittingsites, vector< cFragmentIonType > &searchedmodifications, ePeptideType peptidetype, bool regularblocksorder, TRotationInfo *trotation=0, eResidueLossType leftresiduelosstype=h2o_loss, bool hasfirstblockartificial=false) |
| Generate a N-terminal fragment ion series. More... | |
| void | generateCTerminalFragmentIons (int maxcharge, int &peaklistrealsize, vector< int > &intcomposition, eFragmentIonType fragmentiontype, int neutrallosstype, cBricksDatabase &bricksdatabase, bool writedescription, int rotationid, vector< splitSite > &splittingsites, vector< cFragmentIonType > &searchedmodifications, ePeptideType peptidetype, bool regularblocksorder, TRotationInfo *trotation=0, eResidueLossType rightresiduelosstype=h2o_loss, bool haslastblockartificial=false) |
| Generate a C-terminal fragment ion series. More... | |
| void | sortByMass (int limit=-1) |
| Sort peaks by mass. More... | |
| void | resizePeakList (int size) |
| Resize the list of peaks. More... | |
| double | getSumOfRelativeIntensities () const |
| Get the sum of relative intensities of matched peaks. More... | |
| cPeak & | operator[] (int position) |
| Overloaded operator []. More... | |
| cPeaksList & | getExperimentalSpectrum () |
| Get an experimental spectrum which has been compared with the theoretical spectrum. More... | |
| void | setExperimentalSpectrum (cPeaksList &experimentalspectrum) |
| Set the experimental spectrum. More... | |
| set< int > & | getExperimentalMatches (int peakid) |
| Get ids of theoretical peaks which hit an experimental peak. More... | |
| string | getCoverageBySeries () |
| Get coverage of series of fragment ions. More... | |
| int | getUnmatchedExperimentalPeaksCount () |
| Get the number of unmatched experimental peaks. More... | |
| cPeaksList * | getTheoreticalPeaks () |
| Get a list of theoretical peaks. More... | |
| bool | isValid () |
| Check if the candidate sequence corresponds to the searched sequence. More... | |
| int | getValidPosition () |
| Get a position of a rotation of a cyclic peptide sequence corresponding to searched sequence. More... | |
| int | getReverseValidPosition () |
| Get a reverted position of a rotation of a cyclic peptide sequence corresponding to searched sequence. More... | |
| void | setValidSequence (regex &searchedsequence) |
| Set a flag determining if the candidate sequence corresponds to the searched sequence. More... | |
| vector< string > & | getLabelsOfRotations () |
| Get the labels of cyclic rotations. More... | |
| int | getNumberOfCompletedSeries () |
| Get a number of series which identify the peptide. More... | |
| void | setNumberOfCompletedSeries (int numberofcompletedseries) |
| Set a number of series which identify the peptide. More... | |
| void | setPathId (int pathid) |
| Set path id. More... | |
| int | getPathId () const |
| Get path id. More... | |
| void | setParameters (cParameters *parameters) |
| Set a pointer to the parameters of the application. More... | |
| double | getTargetPatternScore (int groupid) |
| Get target pattern score. More... | |
| double | getTargetPatternFDR (int groupid) |
| Get target pattern FDR. More... | |
| map< int, double > & | getTargetScores () |
| Get map of target scores. More... | |
| map< int, double > & | getDecoyScores () |
| Get map of decoy scores. More... | |
| void | setFDRs (vector< double > &targetscoresvector, vector< double > &fdrs, cPeaksList &unmatchedpeaksinmatchedpatterns) |
| Set false discovery rates to peak groups. More... | |
| void | store (ofstream &os) |
| Store the structure into an output stream. More... | |
| void | load (ifstream &is, int fileversionpart1, int fileversionpart2, int fileversionpart3) |
| Load the structure from an input stream. More... | |
| bool | equals (cTheoreticalSpectrum &secondtheoreticalspectrum) |
| Check if the object equals to another object. More... | |
| void | attach (cTheoreticalSpectrum &secondtheoreticalspectrum) |
| Attach another spectrum. More... | |
The class representing a theoretical mass spectrum.
| cTheoreticalSpectrum::cTheoreticalSpectrum | ( | cParameters * | parameters, |
| cCandidate & | candidate | ||
| ) |
The constructor.
| parameters | a pointer to the parameters of the application |
| candidate | reference to a peptide sequence candidate |
| void cTheoreticalSpectrum::attach | ( | cTheoreticalSpectrum & | secondtheoreticalspectrum | ) |
Attach another spectrum.
| secondtheoreticalspectrum | spectrum to be attached |
| void cTheoreticalSpectrum::clear | ( | bool | clearpeaklist = true | ) |
Clear the spectrum.
| clearpeaklist | if true then all variables including the list of theoretical peaks are cleared else the list of theoretical peaks is not cleared |
| void cTheoreticalSpectrum::compareAverageMSSpectrum | ( | cPeaksList & | averagespectrum, |
| cTheoreticalSpectrum & | tsfull, | ||
| cPeaksList & | unmatchedpeaksinmatchedpatterns | ||
| ) |
Compare theoretical peaks with an average spectrum.
| averagespectrum | average experimental spectrum |
| tsfull | theoretical spectrum with descriptions of peaks |
| unmatchedpeaksinmatchedpatterns | unmatched peaks in matched isotope patterns |
| int cTheoreticalSpectrum::compareBranchCyclic | ( | cPeaksList & | sortedpeaklist, |
| cBricksDatabase & | bricksdatabasewithcombinations, | ||
| bool | writedescription, | ||
| regex & | sequencetag, | ||
| regex & | searchedsequence, | ||
| cPeaksList & | unmatchedpeaksinmatchedpatterns, | ||
| unordered_map< string, int > * | isotopeformuladesctoid | ||
| ) |
Compare the theoretical spectrum of a branch-cyclic peptide with an experimental spectrum.
| sortedpeaklist | reference to an experimental peaklist |
| bricksdatabasewithcombinations | reference to a database of bricks with combinations of bricks |
| writedescription | if true then string descriptions of peaks are filled |
| sequencetag | reference to a regex of a sequence tag |
| searchedsequence | reference to a regex of a searched sequence |
| unmatchedpeaksinmatchedpatterns | unmatched peaks in matched isotope patterns |
| isotopeformuladesctoid | a map of isotope descriptions |
| int | number theoretical peaks generated; -2 when the sequence tag does not match the peptide sequence candidate |
| int cTheoreticalSpectrum::compareBranched | ( | cPeaksList & | sortedpeaklist, |
| cBricksDatabase & | bricksdatabasewithcombinations, | ||
| bool | writedescription, | ||
| regex & | sequencetag, | ||
| regex & | searchedsequence, | ||
| cPeaksList & | unmatchedpeaksinmatchedpatterns, | ||
| unordered_map< string, int > * | isotopeformuladesctoid | ||
| ) |
Compare the theoretical spectrum of a branched peptide with an experimental spectrum.
| sortedpeaklist | reference to an experimental peaklist |
| bricksdatabasewithcombinations | reference to a database of bricks with combinations of bricks |
| writedescription | if true then string descriptions of peaks are filled |
| sequencetag | reference to a regex of a sequence tag |
| searchedsequence | reference to a regex of a searched sequence |
| unmatchedpeaksinmatchedpatterns | unmatched peaks in matched isotope patterns |
| isotopeformuladesctoid | a map of isotope descriptions |
| int | number theoretical peaks generated; -2 when the sequence tag does not match the peptide sequence candidate |
| int cTheoreticalSpectrum::compareCyclic | ( | cPeaksList & | sortedpeaklist, |
| cBricksDatabase & | bricksdatabasewithcombinations, | ||
| bool | writedescription, | ||
| regex & | sequencetag, | ||
| regex & | searchedsequence, | ||
| cPeaksList & | unmatchedpeaksinmatchedpatterns, | ||
| unordered_map< string, int > * | isotopeformuladesctoid | ||
| ) |
Compare the theoretical spectrum of a cyclic peptide with an experimental spectrum.
| sortedpeaklist | reference to an experimental peaklist |
| bricksdatabasewithcombinations | reference to a database of bricks with combinations of bricks |
| writedescription | if true then string descriptions of peaks are filled |
| sequencetag | reference to a regex of a sequence tag |
| searchedsequence | reference to a regex of a searched sequence |
| unmatchedpeaksinmatchedpatterns | unmatched peaks in matched isotope patterns |
| isotopeformuladesctoid | a map of isotope descriptions |
| int | number theoretical peaks generated; -2 when the sequence tag does not match the peptide sequence candidate |
| int cTheoreticalSpectrum::compareCyclicPolyketide | ( | cPeaksList & | sortedpeaklist, |
| cBricksDatabase & | bricksdatabasewithcombinations, | ||
| bool | writedescription, | ||
| regex & | sequencetag, | ||
| regex & | searchedsequence, | ||
| cPeaksList & | unmatchedpeaksinmatchedpatterns, | ||
| unordered_map< string, int > * | isotopeformuladesctoid | ||
| ) |
Compare the theoretical spectrum of a cyclic polyketide with an experimental spectrum.
| sortedpeaklist | reference to an experimental peaklist |
| bricksdatabasewithcombinations | reference to a database of bricks with combinations of bricks |
| writedescription | if true then string descriptions of peaks are filled |
| sequencetag | reference to a regex of a sequence tag |
| searchedsequence | reference to a regex of a searched sequence |
| unmatchedpeaksinmatchedpatterns | unmatched peaks in matched isotope patterns |
| isotopeformuladesctoid | a map of isotope descriptions |
| int | number theoretical peaks generated; -2 when the sequence tag does not match the peptide sequence candidate |
| int cTheoreticalSpectrum::compareLinear | ( | cPeaksList & | sortedpeaklist, |
| cBricksDatabase & | bricksdatabasewithcombinations, | ||
| bool | writedescription, | ||
| regex & | sequencetag, | ||
| regex & | searchedsequence, | ||
| cPeaksList & | unmatchedpeaksinmatchedpatterns, | ||
| unordered_map< string, int > * | isotopeformuladesctoid | ||
| ) |
Compare the theoretical spectrum of a linear peptide with an experimental spectrum.
| sortedpeaklist | reference to an experimental peaklist |
| bricksdatabasewithcombinations | reference to a database of bricks with combinations of bricks |
| writedescription | if true then string descriptions of peaks are filled |
| sequencetag | reference to a regex of a sequence tag |
| searchedsequence | reference to a regex of a searched sequence |
| unmatchedpeaksinmatchedpatterns | unmatched peaks in matched isotope patterns |
| isotopeformuladesctoid | a map of isotope descriptions |
| int | number theoretical peaks generated; -2 when the sequence tag does not match the peptide sequence candidate |
| int cTheoreticalSpectrum::compareLinearPolyketide | ( | cPeaksList & | sortedpeaklist, |
| cBricksDatabase & | bricksdatabasewithcombinations, | ||
| bool | writedescription, | ||
| regex & | sequencetag, | ||
| regex & | searchedsequence, | ||
| cPeaksList & | unmatchedpeaksinmatchedpatterns, | ||
| unordered_map< string, int > * | isotopeformuladesctoid | ||
| ) |
Compare the theoretical spectrum of a linear polyketide with an experimental spectrum.
| sortedpeaklist | reference to an experimental peaklist |
| bricksdatabasewithcombinations | reference to a database of bricks with combinations of bricks |
| writedescription | if true then string descriptions of peaks are filled |
| sequencetag | reference to a regex of a sequence tag |
| searchedsequence | reference to a regex of a searched sequence |
| unmatchedpeaksinmatchedpatterns | unmatched peaks in matched isotope patterns |
| isotopeformuladesctoid | a map of isotope descriptions |
| int | number theoretical peaks generated; -2 when the sequence tag does not match the peptide sequence candidate |
| void cTheoreticalSpectrum::compareMSSpectrum | ( | int | id, |
| int | peaklistseriesvectorid, | ||
| cTheoreticalSpectrum & | tsfull, | ||
| cPeaksList & | unmatchedpeaksinmatchedpatterns, | ||
| vector< vector< int > > & | hintsindex, | ||
| bool | lcmsrt, | ||
| bool | skipcomparison | ||
| ) |
Compare theoretical peaks with an experimental spectrum.
| id | identifier of an experimental spectrum |
| peaklistseriesvectorid | id of a peaklistseriesvector |
| tsfull | theoretical spectrum with descriptions of peaks |
| unmatchedpeaksinmatchedpatterns | unmatched peaks in matched isotope patterns |
| hintsindex | index of experimental spectra for every matched theoretical peak |
| lcmsrt | true if LC-MS data are processed and retention time is available |
| skipcomparison | if true, the peak comparison is skipped |
| int cTheoreticalSpectrum::compareOther | ( | cPeaksList & | sortedpeaklist, |
| bool | writedescription, | ||
| cPeaksList & | unmatchedpeaksinmatchedpatterns, | ||
| unordered_map< string, int > * | isotopeformuladesctoid | ||
| ) |
Compare the theoretical spectrum of a metabolite with an experimental spectrum.
| sortedpeaklist | reference to an experimental peaklist |
| writedescription | if true then string descriptions of peaks are filled |
| unmatchedpeaksinmatchedpatterns | unmatched peaks in matched isotope patterns |
| isotopeformuladesctoid | a map of isotope descriptions |
| int | number theoretical peaks generated |
| bool cTheoreticalSpectrum::equals | ( | cTheoreticalSpectrum & | secondtheoreticalspectrum | ) |
Check if the object equals to another object.
| secondtheoreticalspectrum | object for comparison |
| bool | true if the objects are equals |
| void cTheoreticalSpectrum::finalizeMSSpectrum | ( | cPeaksList & | unmatchedpeaksinmatchedpatterns, |
| bool | writedescription | ||
| ) |
Finalize MS spectrum after comparison.
| unmatchedpeaksinmatchedpatterns | unmatched peaks in matched isotope patterns |
| writedescription | if true then string descriptions of fragment ions are generated |
| void cTheoreticalSpectrum::generateCTerminalFragmentIons | ( | int | maxcharge, |
| int & | peaklistrealsize, | ||
| vector< int > & | intcomposition, | ||
| eFragmentIonType | fragmentiontype, | ||
| int | neutrallosstype, | ||
| cBricksDatabase & | bricksdatabase, | ||
| bool | writedescription, | ||
| int | rotationid, | ||
| vector< splitSite > & | splittingsites, | ||
| vector< cFragmentIonType > & | searchedmodifications, | ||
| ePeptideType | peptidetype, | ||
| bool | regularblocksorder, | ||
| TRotationInfo * | trotation = 0, |
||
| eResidueLossType | rightresiduelosstype = h2o_loss, |
||
| bool | haslastblockartificial = false |
||
| ) |
Generate a C-terminal fragment ion series.
| maxcharge | a charge of precursor ion |
| peaklistrealsize | real size of the peak list |
| intcomposition | reference to a vector of ids of bricks as integers |
| fragmentiontype | fragment ion type to be generated |
| neutrallosstype | neutral loss type to be generated |
| bricksdatabase | reference to a database of building blocks |
| writedescription | if true then string descriptions of fragment ions are generated |
| rotationid | id of a cyclic peptide |
| splittingsites | reference to a vector of splitting sites of a cyclic peptide |
| searchedmodifications | reference to a vector of searched modifications |
| peptidetype | the type of searched peptide |
| regularblocksorder | check regular order of ketide blocks |
| trotation | a pointer to a T-permutation of a branched peptide |
| rightresiduelosstype | a residue type of the rightmost building block |
| haslastblockartificial | true when the last block is artificial, false otherwise |
| void cTheoreticalSpectrum::generateFineMSSpectrum | ( | int | sequencestart, |
| int | sequencestop, | ||
| bool & | terminatecomputation | ||
| ) |
Generate a simple mass spectrum with fine isotopic patterns.
| sequencestart | index of the first item to be processed |
| sequencestop | index of the last item to be processed (excluding the last item) |
| terminatecomputation | reference to a variable determining that the computation must be stopped |
| void cTheoreticalSpectrum::generateMSSpectrum | ( | int | sequencestart, |
| int | sequencestop, | ||
| bool & | terminatecomputation, | ||
| bool | writedescription | ||
| ) |
Generate a simple mass spectrum.
| sequencestart | index of the first item to be processed |
| sequencestop | index of the last item to be processed (excluding the last item) |
| terminatecomputation | reference to a variable determining that the computation must be stopped |
| writedescription | if true then string descriptions of peaks are filled |
| void cTheoreticalSpectrum::generateNTerminalFragmentIons | ( | int | maxcharge, |
| int & | peaklistrealsize, | ||
| vector< int > & | intcomposition, | ||
| eFragmentIonType | fragmentiontype, | ||
| int | neutrallosstype, | ||
| cBricksDatabase & | bricksdatabase, | ||
| bool | writedescription, | ||
| int | rotationid, | ||
| vector< splitSite > & | splittingsites, | ||
| vector< cFragmentIonType > & | searchedmodifications, | ||
| ePeptideType | peptidetype, | ||
| bool | regularblocksorder, | ||
| TRotationInfo * | trotation = 0, |
||
| eResidueLossType | leftresiduelosstype = h2o_loss, |
||
| bool | hasfirstblockartificial = false |
||
| ) |
Generate a N-terminal fragment ion series.
| maxcharge | a charge of precursor ion |
| peaklistrealsize | real size of the peak list |
| intcomposition | reference to a vector of ids of bricks as integers |
| fragmentiontype | fragment ion type to be generated |
| neutrallosstype | neutral loss type to be generated |
| bricksdatabase | reference to a database of building blocks |
| writedescription | if true then string descriptions of fragment ions are generated |
| rotationid | id of a cyclic peptide |
| splittingsites | reference to a vector of splitting sites of a cyclic peptide |
| searchedmodifications | reference to a vector of searched modifications |
| peptidetype | the type of searched peptide |
| regularblocksorder | check regular order of ketide blocks |
| trotation | a pointer to a T-permutation of a branched peptide |
| leftresiduelosstype | a residue type of the leftmost building block |
| hasfirstblockartificial | true when the first block is artificial, false otherwise |
| cCandidate & cTheoreticalSpectrum::getCandidate | ( | ) |
Get the peptide spectrum candidate.
| cCandidate | reference to the peptide sequence candidate |
| double cTheoreticalSpectrum::getCosineSimilarity | ( | ) | const |
Get cosine similarity.
| double | cosine similarity |
| string cTheoreticalSpectrum::getCoverageBySeries | ( | ) |
Get coverage of series of fragment ions.
| string | coverage of the series of fragment ions |
| map< int, double > & cTheoreticalSpectrum::getDecoyScores | ( | ) |
Get map of decoy scores.
| map<int,double> | map of decoy scores |
| set< int > & cTheoreticalSpectrum::getExperimentalMatches | ( | int | peakid | ) |
Get ids of theoretical peaks which hit an experimental peak.
| set<int> | set of ids of theoretical peaks |
| cPeaksList & cTheoreticalSpectrum::getExperimentalSpectrum | ( | ) |
Get an experimental spectrum which has been compared with the theoretical spectrum.
| cPeaksList | reference to an experimental spectrum |
| void cTheoreticalSpectrum::getHintsIndex | ( | int | id, |
| int | peaklistseriesvectorid, | ||
| cTheoreticalSpectrum & | tsfull, | ||
| cPeaksList & | unmatchedpeaksinmatchedpatterns, | ||
| vector< vector< int > > & | hintsindex, | ||
| bool | lcmsrt, | ||
| bool | skipcomparison | ||
| ) |
Get a map of search hints to identify features in LC-MS data.
| id | identifier of an experimental spectrum |
| peaklistseriesvectorid | id of a peaklistseriesvector |
| tsfull | theoretical spectrum |
| unmatchedpeaksinmatchedpatterns | unmatched peaks in matched isotope patterns |
| hintsindex | index of experimental spectra for every matched theoretical peak |
| lcmsrt | true if LC-MS data are processed and retention time is available |
| skipcomparison | if true, the peak comparison is skipped |
| vector< string > & cTheoreticalSpectrum::getLabelsOfRotations | ( | ) |
Get the labels of cyclic rotations.
| vector<string> | a vector of labels |
| int cTheoreticalSpectrum::getNumberOfCompletedSeries | ( | ) |
Get a number of series which identify the peptide.
| int | number of completed series |
| int cTheoreticalSpectrum::getNumberOfMatchedPeaks | ( | ) | const |
Get the number of matched peaks between an experimental and a theoretical spectrum.
| int | number of matched peaks |
| int cTheoreticalSpectrum::getNumberOfMatchedPeaks | ( | eFragmentIonType | iontype, |
| int | neutrallosstype | ||
| ) | const |
Get the number of matched peaks between an experimental and a theoretical spectrum of a specified fragment ion type.
| iontype | a fragment ion type |
| neutrallosstype | a neutral loss type |
| int | number of matched peaks |
| int cTheoreticalSpectrum::getNumberOfMatchedPeaksB | ( | ) | const |
Get the number of matched B ions between an experimental and a theoretical spectrum.
| int | number of matched peaks |
| int cTheoreticalSpectrum::getNumberOfMatchedPeaksY | ( | ) | const |
Get the number of matched Y ions between an experimental and a theoretical spectrum.
| int | number of matched peaks |
| int cTheoreticalSpectrum::getNumberOfMatchedPeaksYB | ( | ) | const |
Get the number of matched Y and B ions between an experimental and a theoretical spectrum.
| int | number of matched peaks |
| int cTheoreticalSpectrum::getNumberOfPeaks | ( | ) |
Get the number of peaks in the spectrum.
| int | the number of peaks |
| int cTheoreticalSpectrum::getNumberOfScrambledPeaks | ( | ) |
Get the number of matched scrambled peaks between an experimental and a theoretical spectrum.
| int | number of matched scrambled peaks |
| int cTheoreticalSpectrum::getPathId | ( | ) | const |
Get path id.
| int | id of a path |
| double cTheoreticalSpectrum::getRatioOfMatchedPeaks | ( | ) |
Get a ratio of matched peaks.
| double | ratio of matched peaks |
| int cTheoreticalSpectrum::getReverseValidPosition | ( | ) |
Get a reverted position of a rotation of a cyclic peptide sequence corresponding to searched sequence.
| int | reverted position of sequence |
| double cTheoreticalSpectrum::getSumOfRelativeIntensities | ( | ) | const |
Get the sum of relative intensities of matched peaks.
| double | sum of relative intensities of matched peaks |
| double cTheoreticalSpectrum::getTargetPatternFDR | ( | int | groupid | ) |
Get target pattern FDR.
| groupid | id of a group of peaks forming a target pattern |
| double | target pattern FDR |
| double cTheoreticalSpectrum::getTargetPatternScore | ( | int | groupid | ) |
Get target pattern score.
| groupid | id of a group of peaks forming a target pattern |
| double | target pattern score |
| map< int, double > & cTheoreticalSpectrum::getTargetScores | ( | ) |
Get map of target scores.
| map<int,double> | map of target scores |
| cPeaksList * cTheoreticalSpectrum::getTheoreticalPeaks | ( | ) |
Get a list of theoretical peaks.
| cPeaksList | a pointer to a list of theoretical peaks |
| int cTheoreticalSpectrum::getUnmatchedExperimentalPeaksCount | ( | ) |
Get the number of unmatched experimental peaks.
| number | of unmatched experimental peaks |
| int cTheoreticalSpectrum::getValidPosition | ( | ) |
Get a position of a rotation of a cyclic peptide sequence corresponding to searched sequence.
| int | position of sequence |
| double cTheoreticalSpectrum::getWeightedRatioOfMatchedPeaks | ( | ) | const |
Get weighted ratio of matched peaks.
| double | weighted ratio of matched peaks |
| bool cTheoreticalSpectrum::isValid | ( | ) |
Check if the candidate sequence corresponds to the searched sequence.
| bool | if true then the theoretical spectrum corresponds to a searched sequence |
| void cTheoreticalSpectrum::load | ( | ifstream & | is, |
| int | fileversionpart1, | ||
| int | fileversionpart2, | ||
| int | fileversionpart3 | ||
| ) |
Load the structure from an input stream.
| is | an input stream |
| fileversionpart1 | first number of .res the file version |
| fileversionpart2 | second number of .res the file version |
| fileversionpart3 | third number of .res the file version |
| cPeak & cTheoreticalSpectrum::operator[] | ( | int | position | ) |
Overloaded operator [].
| position | position of a peak in the peak list |
| cPeak | reference to the peak |
| void cTheoreticalSpectrum::resizePeakList | ( | int | size | ) |
Resize the list of peaks.
| size | the number of peaks |
| void cTheoreticalSpectrum::setCandidate | ( | cCandidate & | candidate | ) |
Set a peptide spectrum candidate.
| candidate | reference to the peptide sequence candidate |
| void cTheoreticalSpectrum::setExperimentalSpectrum | ( | cPeaksList & | experimentalspectrum | ) |
Set the experimental spectrum.
| experimentalspectrum | an experimental spectrum |
| void cTheoreticalSpectrum::setFDRs | ( | vector< double > & | targetscoresvector, |
| vector< double > & | fdrs, | ||
| cPeaksList & | unmatchedpeaksinmatchedpatterns | ||
| ) |
Set false discovery rates to peak groups.
| targetscoresvector | vector of target scores |
| fdrs | vector of FDRs |
| unmatchedpeaksinmatchedpatterns | unmatched peaks in matched isotope patterns |
| void cTheoreticalSpectrum::setNumberOfCompletedSeries | ( | int | numberofcompletedseries | ) |
Set a number of series which identify the peptide.
| numberofcompletedseries | number of completed series |
| void cTheoreticalSpectrum::setParameters | ( | cParameters * | parameters | ) |
Set a pointer to the parameters of the application.
| parameters | the pointer to the parameters of the application |
| void cTheoreticalSpectrum::setPathId | ( | int | pathid | ) |
Set path id.
| pathid | id of a path |
| void cTheoreticalSpectrum::setValidSequence | ( | regex & | searchedsequence | ) |
Set a flag determining if the candidate sequence corresponds to the searched sequence.
| searchedsequence | searched sequence |
| void cTheoreticalSpectrum::sortByMass | ( | int | limit = -1 | ) |
Sort peaks by mass.
| limit | sort first limit peaks only; if limit == -1 then all peaks are sorted |
| void cTheoreticalSpectrum::store | ( | ofstream & | os | ) |
Store the structure into an output stream.
| os | an output stream |