Matrix Science Mascot Parser toolkit
 
Loading...
Searching...
No Matches
ms_peptidesummary Member List

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

anyEmPAI() constms_peptidesummaryvirtual
anyNumDiscoveredMods() constms_mascotresultsvirtual
BUGFIX_10780 enum valuems_peptidesummary
BUGFIX_10995 enum valuems_peptidesummary
BUGFIX_11002 enum valuems_peptidesummary
BUGFIX_11018 enum valuems_peptidesummary
BUGFIX_11235 enum valuems_peptidesummary
BUGFIX_11254 enum valuems_peptidesummary
BUGFIX_11344 enum valuems_peptidesummary
BUGFIX_11411 enum valuems_peptidesummary
BUGFIX_11425 enum valuems_peptidesummary
BUGFIX_11438 enum valuems_peptidesummary
BUGFIX_11481 enum valuems_peptidesummary
BUGFIX_11483 enum valuems_peptidesummary
BUGFIX_11499 enum valuems_peptidesummary
BUGFIX_11856 enum valuems_peptidesummary
BUGFIX_12123 enum valuems_peptidesummary
BUGFIX_12317 enum valuems_peptidesummary
BUGFIX_12447 enum valuems_peptidesummary
BUGFIX_12538 enum valuems_peptidesummary
BUGFIX_12729 enum valuems_peptidesummary
BUGFIX_12740 enum valuems_peptidesummary
BUGFIX_13324 enum valuems_peptidesummary
BUGFIX_13759 enum valuems_peptidesummary
BUGFIX_NUM enum namems_peptidesummary
CACHE_MISSING_RESFILE enum valuems_peptidesummary
CACHE_STATUS enum namems_peptidesummary
cancelCreateSummary(bool newValue=true)ms_mascotresults
createSummary()ms_peptidesummaryvirtual
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
dumpCDB(const std::string dumpFileName)ms_peptidesummary
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) constms_peptidesummaryvirtual
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) constms_peptidesummaryvirtual
findProteinsByAccession(const int startHit, const std::string &str, const int dbIdx, FIND_COMPARE_FLAGS compareFlags, std::vector< std::string > &accessions, std::vector< int > &dbIndexes) constms_peptidesummaryvirtual
findProteinsByDescription(const int startHit, const std::string &str, FIND_COMPARE_FLAGS compareFlags, std::vector< std::string > &accessions, std::vector< int > &dbIndexes) constms_peptidesummaryvirtual
FLAGS enum namems_mascotresults
freeHit(const int hit)ms_peptidesummaryvirtual
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) constms_peptidesummaryvirtual
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) constms_peptidesummaryvirtual
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) constms_peptidesummaryvirtual
getAvePeptideIdentityThreshold(double OneInXprobRnd, DB_MATCH_TYPE dbType=DM_FASTA) constms_mascotresultsvirtual
getCacheFileName() constms_peptidesummary
getCacheFilename(const ms_mascotresfilebase &resfile, const unsigned int flags, double minProbability=0.0, int maxHitsToReport=50, const char *unigeneIndexFile=0, double ignoreIonsScoreBelow=0.0, int minPepLenInPepSummary=0, const char *singleHit=0, const unsigned int flags2=MSPEPSUM_NONE)ms_peptidesummarystatic
getCacheFilename(const ms_mascotresfilebase &resfile, const ms_mascotresults_params &parameters)ms_peptidesummarystatic
getComponentIntensity(const int q, const int p, const std::string &componentName, double &value, double &rawValue) constms_peptidesummaryvirtual
getComponentProtein(const char *accession, const int dbIdx=1) constms_peptidesummaryvirtual
getComponentString(const int q, const int p, const ms_peptide::PSM psmComponent=ms_peptide::PSM_COMPLETE) constms_peptidesummaryvirtual
getCreateSummaryProgress(int *cspTotalPercentComplete, unsigned int *cspCurrTask, int *cspCurrTaskPercentageComplete, std::string *cspAccession, int *cspHit, int *cspQuery, std::string *cspKeepAliveText) constms_mascotresults
getCrosslinkingMethod() constms_peptidesummary
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) constms_peptidesummaryvirtual
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) constms_peptidesummaryvirtual
getErrTolModReqPepNeutralLoss(const int q, const int p) constms_mascotresultsvirtual
getErrTolModReqPepString(const int q, const int p) constms_peptidesummaryvirtual
getErrTolModSlaveNeutralLoss(const int q, const int p) constms_mascotresultsvirtual
getErrTolModSlaveString(const int q, const int p) constms_peptidesummaryvirtual
getErrTolModString(const int q, const int p) constms_peptidesummaryvirtual
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_peptidesummaryvirtual
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) constms_peptidesummaryvirtual
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
getLibraryEntryId(const int q, const int p, std::vector< int > &dbIdx, std::vector< int > &offset, std::vector< std::string > &checksum, std::vector< std::string > &mods) constms_peptidesummary
getLibraryModString(const int q, const int p) constms_peptidesummaryvirtual
getMaxPeptideIdentityThreshold(double OneInXprobRnd, DB_MATCH_TYPE dbType=DM_FASTA) constms_mascotresultsvirtual
getMaxRankValue() constms_mascotresultsvirtual
getMinPepLenInPepSummary() constms_mascotresults
getMinProbabilityForSLScore(double score)ms_peptidesummarystatic
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
getNumberOfAccessionDBTypes(int q, int p) constms_peptidesummary
getNumberOfFamilyAccessionDBTypes(int hit, int q, int p, bool includeSamesets=true) constms_peptidesummary
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) constms_peptidesummaryvirtual
getPeptide(const int q, const int p) constms_peptidesummaryvirtual
getPeptide(const int q, const int p, ms_peptide *&pep) constms_peptidesummaryvirtual
getPeptideAmbiguityRanks(const int q, const int p)ms_peptidesummary
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_peptidesummaryvirtual
getProteinDescription(const char *accession, const int dbIdx=1) constms_mascotresults
getProteinEmPAI(const char *accession, const int dbIdx=1, const int length=-1) constms_peptidesummaryvirtual
getProteinExpectationValue(const double score) constms_mascotresultsvirtual
getProteinMass(const char *accession, const int dbIdx=1) constms_mascotresults
getProteinScoreCutoff(double OneInXprobRnd) constms_peptidesummaryvirtual
getProteinScoreForHistogram(const int num) constms_mascotresultsvirtual
getProteinsWithThisPepMatch(const int q, const int p, const bool quotes=false)ms_peptidesummaryvirtual
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 ms_peptide &peptide, ms_quant_component &component, const ms_quant_method *method=NULL) constms_peptidesummaryvirtual
getQuantMethod() constms_peptidesummary
getQueryList(QL_FLAG flag, bool outputListOfQueries=true)ms_peptidesummary
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
getSLThresholdFromMinProbability(double minProbability)ms_peptidesummarystatic
getSrcRank(int q, int p) constms_peptidesummary
getSrcSection(int q, int p) constms_peptidesummary
getTagDeltaRangeEnd(const int q, const int p) constms_peptidesummaryvirtual
getTagDeltaRangeStart(const int q, const int p) constms_peptidesummaryvirtual
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) constms_peptidesummaryvirtual
getTerminalResiduesString(const int q, const int p, const ms_peptide::PSM psmComponent=ms_peptide::PSM_COMPLETE) constms_peptidesummaryvirtual
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, ms_mascotresults::TREE_CLUSTER_METHOD tcm=ms_mascotresults::TCM_PAIRWISE_MAXIMUM, double ***reserved1=0, unsigned int *reserved2=0) constms_peptidesummaryvirtual
getUnassigned(const int num) constms_mascotresults
getUnassignedIsBold(const int num) constms_mascotresults
getUnassignedShowCheckbox(const int num) constms_mascotresults
hasCrosslinkingMethod() constms_peptidesummary
hasQuantMethod() constms_peptidesummary
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
isDataCached(ms_peptidesummary::BUGFIX_NUM bugNum) constms_peptidesummary
isEmPAIallowed() constms_mascotresults
isNA() constms_mascotresults
isPeptideComponentMatch(const ms_quant_component &component, const ms_peptide &peptide) constms_peptidesummary
isPeptideModificationMatch(const ms_quant_modgroup &group, const ms_peptide &peptide) constms_peptidesummary
isPeptideUnique(const int q, const int p, const UNIQUE_PEP_RULES rules=UPR_DEFAULT) constms_peptidesummaryvirtual
mascotresfile() constms_peptidesummary
ms_mascotresults()ms_mascotresults
ms_peptidesummary(const ms_mascotresfilebase &resfile, const unsigned int flags=ms_mascotresults::MSRES_GROUP_PROTEINS, double minProbability=0.0, int maxHits=50, const char *unigeneIndexFile=0, double ignoreIonsScoreBelow=0.0, int minPepLenInPepSummary=0, const char *singleHit=0, const unsigned int flags2=MSPEPSUM_NONE)ms_peptidesummary
ms_peptidesummary(const ms_mascotresfilebase &resfile, const ms_mascotresults_params &parameters)ms_peptidesummary
MSPEPSUM enum namems_peptidesummary
MSPEPSUM_CACHE_IGNORE_DATE_CHANGE enum valuems_peptidesummary
MSPEPSUM_CROSSLINK_INTEGRATED enum valuems_peptidesummary
MSPEPSUM_CROSSLINK_ONLY enum valuems_peptidesummary
MSPEPSUM_DEFERRED_CREATE enum valuems_peptidesummary
MSPEPSUM_DISCARD_RELOADABLE enum valuems_peptidesummary
MSPEPSUM_NO_PROTEIN_GROUPING enum valuems_peptidesummary
MSPEPSUM_NONE enum valuems_peptidesummary
MSPEPSUM_PERCOLATOR enum valuems_peptidesummary
MSPEPSUM_REMOVE_CHIMERIC_DUPES enum valuems_peptidesummary
MSPEPSUM_SINGLE_HIT_DBIDX enum valuems_peptidesummary
MSPEPSUM_SL_INTEGRATED enum valuems_peptidesummary
MSPEPSUM_SL_ONLY enum valuems_peptidesummary
MSPEPSUM_USE_CACHE enum valuems_peptidesummary
MSPEPSUM_USE_HOMOLOGY_THRESH enum valuems_peptidesummary
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
PEPSUMMARY_CACHE_BEING_CREATED enum valuems_peptidesummary
PEPSUMMARY_CACHE_CAN_CREATE enum valuems_peptidesummary
PEPSUMMARY_CACHE_DISABLED_IN_OPTIONS enum valuems_peptidesummary
PEPSUMMARY_CACHE_FILE_NOT_PRESENT enum valuems_peptidesummary
PEPSUMMARY_CACHE_NOT_FOR_PMF enum valuems_peptidesummary
PEPSUMMARY_CACHE_STATUS_NOT_AVAILABLE enum valuems_peptidesummary
PEPSUMMARY_CACHE_VALID enum valuems_peptidesummary
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
QL_ALL enum valuems_peptidesummary
QL_BELOW_HOMOLOGY enum valuems_peptidesummary
QL_BELOW_IDENTITY enum valuems_peptidesummary
QL_FLAG enum namems_peptidesummary
QL_IGNORE_IONS_SCORE_BELOW enum valuems_peptidesummary
QL_LAST enum valuems_peptidesummary
QL_UNASSIGNED enum valuems_peptidesummary
QUANT_COMPONENT_STATUS enum namems_mascotresults
QUERY enum valuems_mascotresults
RESFILE_CACHE_BEING_CREATED enum valuems_peptidesummary
RESFILE_CACHE_CAN_CREATE enum valuems_peptidesummary
RESFILE_CACHE_DISABLED_IN_OPTIONS enum valuems_peptidesummary
RESFILE_CACHE_FILE_NOT_PRESENT enum valuems_peptidesummary
RESFILE_CACHE_VALID enum valuems_peptidesummary
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
willCreateCache(const ms_mascotresfilebase &resfile, const unsigned int flags=ms_mascotresults::MSRES_GROUP_PROTEINS, double minProbability=0.0, int maxHits=50, const char *unigeneIndexFile=0, double ignoreIonsScoreBelow=0.0, int minPepLenInPepSummary=0, const char *singleHit=0, const unsigned int flags2=MSPEPSUM_NONE)ms_peptidesummarystatic
willCreateCache(const ms_mascotresfilebase &resfile, const ms_mascotresults_params &parameters)ms_peptidesummarystatic
willCreateCache(const char *resultsFileName, const ms_mascotoptions &opts, const char *unigeneIndexFile, const char *singleHit, const char *applicationName, std::string &resfileCacheFileName, std::string &peptideSummaryCacheFileName, unsigned int &cacheStatus)ms_peptidesummarystatic
willCreateCache(const ms_mascotresfilebase &resfile, const ms_mascotresults_params &parameters, const ms_mascotoptions &opts, std::string &peptideSummaryCacheFileName, unsigned int &cacheStatus)ms_peptidesummarystatic