Matrix Science Mascot Parser toolkit
 
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ms_mascotresults Member List

This is the complete list of members for ms_mascotresults, including all inherited members.

anyEmPAI() constms_mascotresultsvirtual
anyNumDiscoveredMods() constms_mascotresultsvirtual
cancelCreateSummary(bool newValue=true)ms_mascotresults
createSummary()ms_mascotresultsvirtual
createUnassignedList(sortBy s=QUERY)ms_mascotresults
DB_MATCH_TYPE enum namems_mascotresults
DECOY_STATS_COUNT_TYPE enum namems_mascotresults
DM_BOTH enum valuems_mascotresults
DM_FASTA enum valuems_mascotresults
DM_FASTA_FIRST_PASS enum valuems_mascotresults
DM_FASTA_SECOND_PASS enum valuems_mascotresults
DM_SPECTRAL_LIBRARY enum valuems_mascotresults
DS_COUNT_PSM enum valuems_mascotresults
DS_COUNT_SEQUENCE enum valuems_mascotresults
FC_ALL_PEPTIDES enum valuems_mascotresults
FC_ALL_PEPTITDES enum valuems_mascotresults
FC_CASE_INSENSITIVE enum valuems_mascotresults
FC_CASE_SENSITIVE enum valuems_mascotresults
FC_COMPLETESTR enum valuems_mascotresults
FC_FORWARD enum valuems_mascotresults
FC_LOOP_FROM_UNASSIGNED enum valuems_mascotresults
FC_LOOP_INTO_UNASSIGNED enum valuems_mascotresults
FC_MASK_CASE enum valuems_mascotresults
FC_MASK_DIRECTION enum valuems_mascotresults
FC_MASK_STR_PART enum valuems_mascotresults
FC_PROTEIN_IGN_FAMILY enum valuems_mascotresults
FC_PROTEIN_IGN_MASK enum valuems_mascotresults
FC_PROTEIN_IGN_SAMESETS enum valuems_mascotresults
FC_PROTEIN_IGN_SUBSETS enum valuems_mascotresults
FC_PROTEIN_INC_ALT_ACC enum valuems_mascotresults
FC_RESTRICT_TO_HIT enum valuems_mascotresults
FC_REVERSE enum valuems_mascotresults
FC_SCORING_MASK enum valuems_mascotresults
FC_SEARCH_ALL_RANKS enum valuems_mascotresults
FC_SEARCH_IGNORED_RANKS enum valuems_mascotresults
FC_SIGNIFICANT_PEPTIDES enum valuems_mascotresults
FC_STARTSTR enum valuems_mascotresults
FC_STRTOK enum valuems_mascotresults
FC_SUBSTR enum valuems_mascotresults
FC_UNASSIGNED_MASK enum valuems_mascotresults
FIND_COMPARE_FLAGS enum namems_mascotresults
FIND_FLAGS enum namems_mascotresults
findPeptides(const int startHit, const std::string &str, FIND_FLAGS item, FIND_COMPARE_FLAGS compareFlags, std::vector< int > &q, std::vector< int > &p) const =0ms_mascotresultspure virtual
findProteins(const int startHit, const std::string &str, const int dbIdx, FIND_FLAGS item, FIND_COMPARE_FLAGS compareFlags, std::vector< std::string > &accessions, std::vector< int > &dbIndexes) const =0ms_mascotresultspure virtual
findProteinsByAccession(const int startHit, const std::string &str, const int dbIdx, FIND_COMPARE_FLAGS compareFlags, std::vector< std::string > &accessions, std::vector< int > &dbIndexes) const =0ms_mascotresultspure virtual
findProteinsByDescription(const int startHit, const std::string &str, FIND_COMPARE_FLAGS compareFlags, std::vector< std::string > &accessions, std::vector< int > &dbIndexes) const =0ms_mascotresultspure virtual
FLAGS enum namems_mascotresults
freeHit(const int hit)ms_mascotresultsvirtual
FT_PEPTIDE_CALC_MR enum valuems_mascotresults
FT_PEPTIDE_CALC_MZ enum valuems_mascotresults
FT_PEPTIDE_ETMOD enum valuems_mascotresults
FT_PEPTIDE_EXP_MR enum valuems_mascotresults
FT_PEPTIDE_EXP_MZ enum valuems_mascotresults
FT_PEPTIDE_FIND_MASK enum valuems_mascotresults
FT_PEPTIDE_FIXMOD enum valuems_mascotresults
FT_PEPTIDE_QUERY enum valuems_mascotresults
FT_PEPTIDE_SLMOD enum valuems_mascotresults
FT_PEPTIDE_STRING enum valuems_mascotresults
FT_PEPTIDE_VARMOD enum valuems_mascotresults
FT_PEPTIDE_VARMOD_BYNAME enum valuems_mascotresults
FT_PROTEIN_ACCESSION enum valuems_mascotresults
FT_PROTEIN_DESCRIPTION enum valuems_mascotresults
getAllFamilyMembersWithThisPepMatch(const int hit, const int q, const int p, std::vector< int > &db, std::vector< std::string > &acc, std::vector< int > &dupe_status) const =0ms_mascotresultspure virtual
getAllProteinsWithThisPepMatch(const int q, const int p, std::vector< int > &start, std::vector< int > &end, std::vector< std::string > &pre, std::vector< std::string > &post, std::vector< int > &frame, std::vector< int > &multiplicity, std::vector< int > &db) const =0ms_mascotresultspure virtual
getAllProteinsWithThisPepMatch(const int q, const int p, std::vector< int > &start, std::vector< int > &end, std::vector< std::string > &pre, std::vector< std::string > &post, std::vector< int > &frame, std::vector< int > &multiplicity, std::vector< int > &db, std::vector< int > &psmComponent) const =0ms_mascotresultspure virtual
getAvePeptideIdentityThreshold(double OneInXprobRnd, DB_MATCH_TYPE dbType=DM_FASTA) constms_mascotresultsvirtual
getComponentIntensity(const int q, const int p, const std::string &componentName, double &value, double &rawValue) const =0ms_mascotresultspure virtual
getComponentProtein(const char *accession, const int dbIdx=1) constms_mascotresultsvirtual
getComponentString(const int q, const int p, const ms_peptide::PSM psmComponent=ms_peptide::PSM_COMPLETE) const =0ms_mascotresultspure virtual
getCreateSummaryProgress(int *cspTotalPercentComplete, unsigned int *cspCurrTask, int *cspCurrTaskPercentageComplete, std::string *cspAccession, int *cspHit, int *cspQuery, std::string *cspKeepAliveText) constms_mascotresults
getDiscoveredErrTolModDeltas(std::vector< std::string > *vecDeltaStrings=NULL) constms_mascotresultsvirtual
getDiscoveredErrTolModNames() constms_mascotresultsvirtual
getDiscoveredLocalModDeltas(std::vector< std::string > *vecDeltaStrings=NULL) constms_mascotresultsvirtual
getDiscoveredLocalModNames() constms_mascotresultsvirtual
getErrTolModDelta(const int q, const int p, std::string *modString=NULL, std::string *deltaAsString=NULL) constms_mascotresultsvirtual
getErrTolModifiedNaSeq(const int q, const int p) constms_mascotresultsvirtual
getErrTolModMasterNeutralLoss(const int q, const int p) constms_mascotresultsvirtual
getErrTolModMasterString(const int q, const int p) const =0ms_mascotresultspure virtual
getErrTolModName(const int q, const int p, std::string *modString=NULL) constms_mascotresultsvirtual
getErrTolModNeutralLoss(const int q, const int p) constms_mascotresultsvirtual
getErrTolModPepNeutralLoss(const int q, const int p) constms_mascotresultsvirtual
getErrTolModPepString(const int q, const int p) const =0ms_mascotresultspure virtual
getErrTolModReqPepNeutralLoss(const int q, const int p) constms_mascotresultsvirtual
getErrTolModReqPepString(const int q, const int p) const =0ms_mascotresultspure virtual
getErrTolModSlaveNeutralLoss(const int q, const int p) constms_mascotresultsvirtual
getErrTolModSlaveString(const int q, const int p) const =0ms_mascotresultspure virtual
getErrTolModString(const int q, const int p) const =0ms_mascotresultspure virtual
getErrTolOriginalNaSeq(const int q, const int p) constms_mascotresultsvirtual
getErrTolProbabilityThreshold() constms_mascotresultsvirtual
getFlags() constms_mascotresults
getFlags2() constms_mascotresults
getHit(const int hit, const int memberNumber=0) constms_mascotresultsvirtual
getHomologyThreshold(const int query, double OneInXprobRnd, const int rank=1) constms_mascotresultsvirtual
getHomologyThresholdForHistogram(double OneInXprobRnd, DB_MATCH_TYPE dbType=DM_FASTA) constms_mascotresultsvirtual
getIonsScore(const int q, const int p, const bool decoy) const =0ms_mascotresultspure virtual
getIonsScoreCorrected(const double ionsScore, const long multiplicity) constms_mascotresultsprotected
getIonsScoreHistogram(IONS_HISTOGRAM flags=IH_INCLUDE_TOP_MATCHES, DB_MATCH_TYPE dbType=DM_FASTA) constms_mascotresultsvirtual
getLibraryModString(const int q, const int p) const =0ms_mascotresultspure virtual
getMaxPeptideIdentityThreshold(double OneInXprobRnd, DB_MATCH_TYPE dbType=DM_FASTA) constms_mascotresultsvirtual
getMaxRankValue() constms_mascotresultsvirtual
getMinPepLenInPepSummary() constms_mascotresults
getNextFamilyProtein(const int masterHit, const int id) constms_mascotresultsvirtual
getNextSimilarProtein(const int masterHit, const int id) constms_mascotresultsvirtual
getNextSimilarProteinOf(const char *masterAccession, const int masterDB, const int id) constms_mascotresultsvirtual
getNextSubsetProtein(const int masterHit, const int id, const bool searchWholeFamily=true) constms_mascotresultsvirtual
getNextSubsetProteinOf(const char *masterAccession, const int masterDB, const int id) constms_mascotresultsvirtual
getNumberOfFamilyMembers() constms_mascotresultsvirtual
getNumberOfHits() constms_mascotresultsvirtual
getNumberOfUnassigned() constms_mascotresults
getNumDecoyHitsAboveHomology(double OneInXprobRnd, DECOY_STATS_COUNT_TYPE countType=DS_COUNT_PSM, DB_MATCH_TYPE dbType=DM_FASTA)ms_mascotresultsvirtual
getNumDecoyHitsAboveIdentity(double OneInXprobRnd, DECOY_STATS_COUNT_TYPE countType=DS_COUNT_PSM, DB_MATCH_TYPE dbType=DM_FASTA)ms_mascotresultsvirtual
getNumDiscoveredErrTolMods(const std::string modName, std::vector< std::string > &positions, std::vector< std::string > &sites) constms_mascotresultsvirtual
getNumDiscoveredFixedMods(const int num, std::vector< std::string > &positions, std::vector< std::string > &sites) constms_mascotresultsvirtual
getNumDiscoveredIntactLinks(std::vector< int > &varModNum1, std::vector< std::string > &position1, std::vector< std::string > &site1, std::vector< int > &varModNum2, std::vector< std::string > &position2, std::vector< std::string > &site2, std::vector< int > &numLinkedPeptides) constms_mascotresults
getNumDiscoveredLibraryMods(const int modId, std::vector< std::string > &positions, std::vector< std::string > &sites) constms_mascotresults
getNumDiscoveredLocalMods(const std::string modName, std::vector< std::string > &positions, std::vector< std::string > &sites) constms_mascotresultsvirtual
getNumDiscoveredNonSpecCleavage() constms_mascotresultsvirtual
getNumDiscoveredVariableMods(const int num, std::vector< std::string > &positions, std::vector< std::string > &sites, std::vector< double > &deltas, std::vector< std::string > &names) constms_mascotresultsvirtual
getNumDiscoveredVariableMods(const int num, std::vector< std::string > &positions, std::vector< std::string > &sites) constms_mascotresultsvirtual
getNumHitsAboveHomology(double OneInXprobRnd, DECOY_STATS_COUNT_TYPE countType=DS_COUNT_PSM, DB_MATCH_TYPE dbType=DM_FASTA)ms_mascotresultsvirtual
getNumHitsAboveIdentity(double OneInXprobRnd, DECOY_STATS_COUNT_TYPE countType=DS_COUNT_PSM, DB_MATCH_TYPE dbType=DM_FASTA)ms_mascotresultsvirtual
getPepsWithSameScore(const int q, const int p) const =0ms_mascotresultspure virtual
getPeptide(const int q, const int p) const =0ms_mascotresultspure virtual
getPeptide(const int q, const int p, ms_peptide *&pep) const =0ms_mascotresultspure virtual
getPeptideExpectationValue(const double score, const int query, const int rank=0) constms_mascotresultsvirtual
getPeptideIdentityThreshold(const int query, double OneInXprobRnd, DB_MATCH_TYPE dbType=DM_FASTA) constms_mascotresultsvirtual
getPeptideThreshold(const int query, double OneInXprobRnd, const int rank=1, const THRESHOLD_TYPE thresholdType=TT_PEPSUM_DEFAULT) constms_mascotresults
getProbabilityThreshold() constms_mascotresultsvirtual
getProbFromScore(const double score) constms_mascotresultsvirtual
getProbOfPepBeingRandomMatch(const double score, const int query) constms_mascotresultsvirtual
getProbOfProteinBeingRandomMatch(const double score) constms_mascotresultsvirtual
getProtein(const char *accession, const int dbIdx=1) constms_mascotresultsvirtual
getProteinDescription(const char *accession, const int dbIdx=1) constms_mascotresults
getProteinEmPAI(const char *accession, const int dbIdx=1, const int length=-1) constms_mascotresultsvirtual
getProteinExpectationValue(const double score) constms_mascotresultsvirtual
getProteinMass(const char *accession, const int dbIdx=1) constms_mascotresults
getProteinScoreCutoff(double OneInXprobRnd) const =0ms_mascotresultspure virtual
getProteinScoreForHistogram(const int num) constms_mascotresultsvirtual
getProteinsWithThisPepMatch(const int q, const int p, const bool quotes=false)=0ms_mascotresultspure virtual
getProteinTaxonomyIDs(const char *accession, const int dbIdx, std::vector< int > &gpt_ids, std::vector< std::string > &gpt_accessions) constms_mascotresults
getProteinThreshold(double OneInXprobRnd) constms_mascotresultsvirtual
getQmatch(const int query) constms_mascotresultsvirtual
getQmatch(const int query, const ms_mascotresfile_dat::section sec) constms_mascotresultsvirtual
getQuantitationComponentForPeptide(const matrix_science::ms_peptide &peptide, matrix_science::ms_quant_component &component, const matrix_science::ms_quant_method *method=NULL) const =0ms_mascotresultspure virtual
getReadableVarMods(const int q, const int p, const int numDecimalPlaces=2, const ms_peptide::PSM psmComponent=ms_peptide::PSM_COMPLETE) constms_mascotresultsvirtual
getResfile() constms_mascotresults
getResultsParameters() constms_mascotresults
getSequenceMass(const char *seq) constms_mascotresults
getTagDeltaRangeEnd(const int q, const int p) const =0ms_mascotresultspure virtual
getTagDeltaRangeStart(const int q, const int p) const =0ms_mascotresultspure virtual
getTagEnd(const int q, const int p, const int tagNumber) constms_mascotresultsvirtual
getTagSeries(const int q, const int p, const int tagNumber) constms_mascotresultsvirtual
getTagStart(const int q, const int p, const int tagNumber) constms_mascotresultsvirtual
getTagString(const int q, const int p) const =0ms_mascotresultspure virtual
getTerminalResiduesString(const int q, const int p, const ms_peptide::PSM psmComponent=ms_peptide::PSM_COMPLETE) const =0ms_mascotresultspure virtual
getThresholdForFDRAboveHomology(double targetFDR, double *closestFDR, double *minProbability, int *numTargetMatches=0, int *numDecoyMatches=0)ms_mascotresults
getThresholdForFDRAboveHomology(double targetFDR, DECOY_STATS_COUNT_TYPE countType, DB_MATCH_TYPE dbType, double *closestFDR, double *minProbability, int *numTargetMatches=0, int *numDecoyMatches=0)ms_mascotresults
getThresholdForFDRAboveIdentity(double targetFDR, double *closestFDR, double *minProbability, int *numTargetMatches=0, int *numDecoyMatches=0)ms_mascotresults
getThresholdForFDRAboveIdentity(double targetFDR, DECOY_STATS_COUNT_TYPE countType, DB_MATCH_TYPE dbType, double *closestFDR, double *minProbability, int *numTargetMatches=0, int *numDecoyMatches=0)ms_mascotresults
getToleranceInDalton(bool &needMass, const double *const pMass=NULL) constms_mascotresults
getTreeClusterNodes(const int hit, std::vector< int > &left, std::vector< int > &right, std::vector< double > &distance, TREE_CLUSTER_METHOD tcm=TCM_PAIRWISE_MAXIMUM, double ***reserved1=0, unsigned int *reserved2=0) constms_mascotresultsvirtual
getUnassigned(const int num) constms_mascotresults
getUnassignedIsBold(const int num) constms_mascotresults
getUnassignedShowCheckbox(const int num) constms_mascotresults
HOMOLOGY_THRESHOLD_SOURCE enum namems_mascotresults
HOMTHR_FASTA enum valuems_mascotresults
HOMTHR_SL enum valuems_mascotresults
IH_INCLUDE_TOP_10_MATCHES enum valuems_mascotresults
IH_INCLUDE_TOP_MATCHES enum valuems_mascotresults
INTENSITY enum valuems_mascotresults
IONS_HISTOGRAM enum namems_mascotresults
isEmPAIallowed() constms_mascotresults
isNA() constms_mascotresults
isPeptideUnique(const int q, const int p, const UNIQUE_PEP_RULES rules=UPR_DEFAULT) const =0ms_mascotresultspure virtual
ms_mascotresults()ms_mascotresults
MSRES_CLUSTER_PROTEINS enum valuems_mascotresults
MSRES_DECOY enum valuems_mascotresults
MSRES_DUPE_DEFAULT enum valuems_mascotresults
MSRES_DUPE_INCL_IN_SCORE_A enum valuems_mascotresults
MSRES_DUPE_INCL_IN_SCORE_B enum valuems_mascotresults
MSRES_DUPE_INCL_IN_SCORE_C enum valuems_mascotresults
MSRES_DUPE_INCL_IN_SCORE_D enum valuems_mascotresults
MSRES_DUPE_INCL_IN_SCORE_E enum valuems_mascotresults
MSRES_DUPE_INCL_IN_SCORE_F enum valuems_mascotresults
MSRES_DUPE_INCL_IN_SCORE_G enum valuems_mascotresults
MSRES_DUPE_INCL_IN_SCORE_H enum valuems_mascotresults
MSRES_DUPE_INCL_IN_SCORE_I enum valuems_mascotresults
MSRES_DUPE_INCL_IN_SCORE_NONE enum valuems_mascotresults
MSRES_DUPE_REMOVE_A enum valuems_mascotresults
MSRES_DUPE_REMOVE_B enum valuems_mascotresults
MSRES_DUPE_REMOVE_C enum valuems_mascotresults
MSRES_DUPE_REMOVE_D enum valuems_mascotresults
MSRES_DUPE_REMOVE_E enum valuems_mascotresults
MSRES_DUPE_REMOVE_F enum valuems_mascotresults
MSRES_DUPE_REMOVE_G enum valuems_mascotresults
MSRES_DUPE_REMOVE_H enum valuems_mascotresults
MSRES_DUPE_REMOVE_I enum valuems_mascotresults
MSRES_DUPE_REMOVE_NONE enum valuems_mascotresults
MSRES_ERR_TOL enum valuems_mascotresults
MSRES_GROUP_PROTEINS enum valuems_mascotresults
MSRES_IGNORE_PMF_MIXTURE enum valuems_mascotresults
MSRES_INTEGRATED_ERR_TOL enum valuems_mascotresults
MSRES_MAXHITS_OVERRIDES_MINPROB enum valuems_mascotresults
MSRES_MUDPIT_PROTEIN_SCORE enum valuems_mascotresults
MSRES_NOFLAG enum valuems_mascotresults
MSRES_REQUIRE_BOLD_RED enum valuems_mascotresults
MSRES_SHOW_ALL_FROM_ERR_TOL enum valuems_mascotresults
MSRES_SHOW_SUBSETS enum valuems_mascotresults
MSRES_SUBSETS_DIFF_PROT enum valuems_mascotresults
QCS_ERROR_BAD_COMPONENT_NAME enum valuems_mascotresults
QCS_ERROR_NO_COMPONENTS enum valuems_mascotresults
QCS_ERROR_NO_METHOD enum valuems_mascotresults
QCS_OK enum valuems_mascotresults
QCS_OK_MULTIPLE_MATCHES enum valuems_mascotresults
QCS_OK_NO_MATCH enum valuems_mascotresults
QUANT_COMPONENT_STATUS enum namems_mascotresults
QUERY enum valuems_mascotresults
SCORE enum valuems_mascotresults
setSubsetsThreshold(const double scoreFraction)ms_mascotresultsvirtual
sortBy enum namems_mascotresults
TCM_PAIRWISE_AVERAGE enum valuems_mascotresults
TCM_PAIRWISE_MAXIMUM enum valuems_mascotresults
TCM_PAIRWISE_SINGLE enum valuems_mascotresults
THRESHOLD_TYPE enum namems_mascotresults
TREE_CLUSTER_METHOD enum namems_mascotresults
TT_HOMOLOGY enum valuems_mascotresults
TT_IDENTITY enum valuems_mascotresults
TT_PEPSUM_DEFAULT enum valuems_mascotresults
UNIQUE_PEP_RULES enum namems_mascotresults
UPR_DEFAULT enum valuems_mascotresults
UPR_IGNORE_SUBSET_PROTEINS enum valuems_mascotresults
UPR_WITHIN_FAMILY enum valuems_mascotresults
UPR_WITHIN_FAMILY_MEMBER enum valuems_mascotresults