|
CycloBranch
|
|
CycloBranch
|
This is the complete list of members for cTheoreticalSpectrum, including all inherited members.
| attach(cTheoreticalSpectrum &secondtheoreticalspectrum) | cTheoreticalSpectrum | |
| clear(bool clearpeaklist=true) | cTheoreticalSpectrum | |
| compareAverageMSSpectrum(cPeaksList &averagespectrum, cTheoreticalSpectrum &tsfull, cPeaksList &unmatchedpeaksinmatchedpatterns) | cTheoreticalSpectrum | |
| compareBranchCyclic(cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) | cTheoreticalSpectrum | |
| compareBranched(cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) | cTheoreticalSpectrum | |
| compareCyclic(cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) | cTheoreticalSpectrum | |
| compareCyclicPolyketide(cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) | cTheoreticalSpectrum | |
| compareLinear(cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) | cTheoreticalSpectrum | |
| compareLinearPolyketide(cPeaksList &sortedpeaklist, cBricksDatabase &bricksdatabasewithcombinations, bool writedescription, regex &sequencetag, regex &searchedsequence, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) | cTheoreticalSpectrum | |
| compareMSSpectrum(int id, int peaklistseriesvectorid, cTheoreticalSpectrum &tsfull, cPeaksList &unmatchedpeaksinmatchedpatterns, vector< vector< int > > &hintsindex, bool lcmsrt, bool skipcomparison) | cTheoreticalSpectrum | |
| compareOther(cPeaksList &sortedpeaklist, bool writedescription, cPeaksList &unmatchedpeaksinmatchedpatterns, unordered_map< string, int > *isotopeformuladesctoid) | cTheoreticalSpectrum | |
| cTheoreticalSpectrum() | cTheoreticalSpectrum | |
| cTheoreticalSpectrum(cParameters *parameters, cCandidate &candidate) | cTheoreticalSpectrum | |
| equals(cTheoreticalSpectrum &secondtheoreticalspectrum) | cTheoreticalSpectrum | |
| finalizeMSSpectrum(cPeaksList &unmatchedpeaksinmatchedpatterns, bool writedescription) | 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) | cTheoreticalSpectrum | |
| generateFineMSSpectrum(int sequencestart, int sequencestop, bool &terminatecomputation) | cTheoreticalSpectrum | |
| generateMSSpectrum(int sequencestart, int sequencestop, bool &terminatecomputation, bool writedescription) | 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) | cTheoreticalSpectrum | |
| getCandidate() | cTheoreticalSpectrum | |
| getCosineSimilarity() const | cTheoreticalSpectrum | |
| getCoverageBySeries() | cTheoreticalSpectrum | |
| getDecoyScores() | cTheoreticalSpectrum | |
| getExperimentalMatches(int peakid) | cTheoreticalSpectrum | |
| getExperimentalSpectrum() | cTheoreticalSpectrum | |
| getHintsIndex(int id, int peaklistseriesvectorid, cTheoreticalSpectrum &tsfull, cPeaksList &unmatchedpeaksinmatchedpatterns, vector< vector< int > > &hintsindex, bool lcmsrt, bool skipcomparison) | cTheoreticalSpectrum | |
| getLabelsOfRotations() | cTheoreticalSpectrum | |
| getNumberOfCompletedSeries() | cTheoreticalSpectrum | |
| getNumberOfMatchedPeaks() const | cTheoreticalSpectrum | |
| getNumberOfMatchedPeaks(eFragmentIonType iontype, int neutrallosstype) const | cTheoreticalSpectrum | |
| getNumberOfMatchedPeaksB() const | cTheoreticalSpectrum | |
| getNumberOfMatchedPeaksY() const | cTheoreticalSpectrum | |
| getNumberOfMatchedPeaksYB() const | cTheoreticalSpectrum | |
| getNumberOfPeaks() | cTheoreticalSpectrum | |
| getNumberOfScrambledPeaks() | cTheoreticalSpectrum | |
| getPathId() const | cTheoreticalSpectrum | |
| getRatioOfMatchedPeaks() | cTheoreticalSpectrum | |
| getReverseValidPosition() | cTheoreticalSpectrum | |
| getSumOfRelativeIntensities() const | cTheoreticalSpectrum | |
| getTargetPatternFDR(int groupid) | cTheoreticalSpectrum | |
| getTargetPatternScore(int groupid) | cTheoreticalSpectrum | |
| getTargetScores() | cTheoreticalSpectrum | |
| getTheoreticalPeaks() | cTheoreticalSpectrum | |
| getUnmatchedExperimentalPeaksCount() | cTheoreticalSpectrum | |
| getValidPosition() | cTheoreticalSpectrum | |
| getWeightedRatioOfMatchedPeaks() const | cTheoreticalSpectrum | |
| isValid() | cTheoreticalSpectrum | |
| load(ifstream &is, int fileversionpart1, int fileversionpart2, int fileversionpart3) | cTheoreticalSpectrum | |
| operator[](int position) | cTheoreticalSpectrum | |
| resizePeakList(int size) | cTheoreticalSpectrum | |
| setCandidate(cCandidate &candidate) | cTheoreticalSpectrum | |
| setExperimentalSpectrum(cPeaksList &experimentalspectrum) | cTheoreticalSpectrum | |
| setFDRs(vector< double > &targetscoresvector, vector< double > &fdrs, cPeaksList &unmatchedpeaksinmatchedpatterns) | cTheoreticalSpectrum | |
| setNumberOfCompletedSeries(int numberofcompletedseries) | cTheoreticalSpectrum | |
| setParameters(cParameters *parameters) | cTheoreticalSpectrum | |
| setPathId(int pathid) | cTheoreticalSpectrum | |
| setValidSequence(regex &searchedsequence) | cTheoreticalSpectrum | |
| sortByMass(int limit=-1) | cTheoreticalSpectrum | |
| store(ofstream &os) | cTheoreticalSpectrum |
1.9.4 
