Matrix Science Mascot Parser toolkit
 
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Public Types | Public Member Functions | Static Public Attributes | List of all members
ms_log Class Referenceabstract
Error handling and logging

Definitions for logging messages. More...

#include <ms_log.hpp>

Inheritance diagram for ms_log:
Inheritance graph
[legend]

Public Types

typedef int msg_num_t
 Typedef for log and error message numbers.
 
enum  msg_sev {
  sev_fatal = 1 ,
  sev_warn = 2 ,
  sev_info = 3 ,
  sev_debug1 = 4 ,
  sev_debug2 = 5 ,
  sev_debug3 = 6
}
 Message severity levels. More...
 

Public Member Functions

 ms_log ()
 Constructor.
 
virtual ~ms_log ()
 Destructor.
 
void addToCatalog (const msg_catalog_t catalog[], size_t numEntries, ms_loggingmonitor::Source_e src, errorOrLogMessages_e errorOrLogMessages)
 Add messages to the fast lookup map.
 
virtual msg_sev getLoggingLevel () const =0
 Get the logging level.
 
ms_loggingmonitor::Source_e getMessageSource (const ms_log::msg_num_t msgNum) const
 Return the component (library/application) that generated the specified log message.
 
bool willMessageBeLogged (const msg_num_t msgNum) const
 Check to see if the message will be logged to a file or recorded anywhere.
 

Static Public Attributes

static const msg_num_t LOGMSG_AAHELPER_CALC_MASS_MAX_REACHED = 0x0001060F
 [D2] Iteration for seriesID=[num] stops at index=[num] and mass=[mass]: limit is [mass]
 
static const msg_num_t LOGMSG_AAHELPER_CALC_MASS_SKIP_D_PRIME_RES = 0x00010610
 [D2] Skipping d' residue because it doesn't match /[I]/ or /[T]/ (seriesID=[num], pos=[num], residue=[char])
 
static const msg_num_t LOGMSG_AAHELPER_CALC_MASS_SKIP_D_RESIDUE = 0x00010611
 [D2] Skipping d residue because it doesn't match /[ITV]/ or /[CDEKLMNPQRS]/ (seriesID=[num], pos=[num], residue=[char])
 
static const msg_num_t LOGMSG_AAHELPER_CALC_MASS_SKIP_V_RESIDUE = 0x00010612
 [D2] Skipping v residue because it doesn't match /[ARDNCQEHILKMFPSTWYV]/ (seriesID=[num], pos=[num], residue=[char])
 
static const msg_num_t LOGMSG_AAHELPER_CALC_MASS_SKIP_W_PRIME_RES = 0x00010613
 [D2] Skipping w' residue because it doesn't match /[I]/ or /[T]/ (seriesID=[num], pos=[num], residue=[char])
 
static const msg_num_t LOGMSG_AAHELPER_CALC_MASS_SKIP_W_RESIDUE = 0x00010614
 [D2] Skipping w residue because it doesn't match /[ITV]/ or /[RDNCQELKMPS]/ (seriesID=[num], pos=[num], residue=[char])
 
static const msg_num_t LOGMSG_AAHELPER_CFR_INIT_VARMOD_IS_LINKER = 0x0001061D
 [D3] PSM component [num] position i=[num] has intact link, modnum=[num]
 
static const msg_num_t LOGMSG_AAHELPER_CFR_INIT_VARMOD_IS_MONOLINK = 0x0001061E
 [D3] PSM component [num] position i=[num] has monolink modnum=[num] monoLinkNum=[num] title=[name]
 
static const msg_num_t LOGMSG_AAHELPER_CFR_LOOPLINKING_MASK = 0x0001061F
 [D1] PSM component [num] column i=[num] is ignored because there is a looplink at sites [num]-[num], modnum=[num]
 
static const msg_num_t LOGMSG_AAHELPER_CFR_MASSES_VALUE = 0x0001061B
 [D2] Active ms_masses: [name]=[value]
 
static const msg_num_t LOGMSG_AAHELPER_CFR_MOD_DELTA_AT_SITE = 0x0001061C
 [D1] Modification at site i=[num] is [name] with delta=[num]
 
static const msg_num_t LOGMSG_AAHELPER_CFR_NUM_FRAGMENTS = 0x00010600
 [D1] Calculated [num] fragments for psmComponent=[num], seriesID=[num], fragCharge=[num], fragNlType=[num], linkerColumn=[num], linkerMassOffset=[mass]
 
static const msg_num_t LOGMSG_AAHELPER_CFR_SET_QUANT_COMPONENT = 0x0001061A
 [D1] cfr: Initialising isotopes and fixed mods from quant component [name]
 
static const msg_num_t LOGMSG_AAHELPER_CFR_START_FRAGMENTS = 0x00010618
 [D1] cfr(psmComponent=[num], seriesID=[num], fragCharge=[num], minMass=[mass], maxMass=[mass], massType=[num], fragNlType=[num], linkerColumn=[num], linkerMassOffset=[mass])
 
static const msg_num_t LOGMSG_AAHELPER_CROSSLINKED_END = 0x00010619
 [D1] calcCrosslinkedFragments: returning [num] alpha and [num] beta fragments
 
static const msg_num_t LOGMSG_AAHELPER_CROSSLINKED_START = 0x00010609
 [D1] calcCrosslinkedFragments(seriesID=[num], fragCharge=[num], minMass=[mass], maxMass=[mass], massType=[num], fragNlType=[num]); mass of linker + alpha = [mass]; linker + beta = [mass]
 
static const msg_num_t LOGMSG_AAHELPER_CUMULATIVE_MASS_NL = 0x0001060D
 [D2] Cumulative mass and NL at i=[num] residue=[char]: m[i]=[mass], nl[i]=[mass]
 
static const msg_num_t LOGMSG_AAHELPER_ETMOD_LOOKUP = 0x00010615
 [D1] lookupErrorTolerantModification(q=[num], p=[num], residue=[char]) –> raw name=[string], raw delta=[string], mod name=[name], mod delta=[mass], is mod?=[num], nl=[mass]
 
static const msg_num_t LOGMSG_AAHELPER_IMMONIUM_ION_ADD = 0x00010606
 [D2] Added immonium ion mass=[mass], nl=[mass], psmComponent=[num], seriesID=[num], column=[num], residue=[char], fragCharge=[num]
 
static const msg_num_t LOGMSG_AAHELPER_IMMONIUM_ION_REJECT = 0x00010605
 [D2] Rejected immonium ion mass=[mass], nl=[mass], psmComponent=[num], seriesID=[num], column=[num], residue=[char], fragCharge=[num], because it is outside the range [[mass], [mass]]
 
static const msg_num_t LOGMSG_AAHELPER_INTERNAL_ION_ADD = 0x00010608
 [D2] Added internal ion mass=[mass], nl=[mass], psmComponent=[num], seriesID=[num], start=[num], end=[num], fragCharge=[num]
 
static const msg_num_t LOGMSG_AAHELPER_INTERNAL_ION_REJECT = 0x00010607
 [D2] Rejected internal ion mass=[mass], nl=[mass], psmComponent=[num], seriesID=[num], start=[num], end=[num], fragCharge=[num], because it is outside the range [[mass], [mass]]
 
static const msg_num_t LOGMSG_AAHELPER_MASTER_NL_VALS = 0x0001060B
 [D2] Master neutral loss=[array]
 
static const msg_num_t LOGMSG_AAHELPER_MULTINL_INDICES = 0x0001060A
 [D1] Currently active multi NL indices=[array]
 
static const msg_num_t LOGMSG_AAHELPER_REGULAR_ION_ADD = 0x00010602
 [D2] Added regular ion mass=[mass], nl=[mass], psmComponent=[num], seriesID=[num], column=[num], fragCharge=[num]
 
static const msg_num_t LOGMSG_AAHELPER_REGULAR_ION_REJECT = 0x00010601
 [D2] Rejected regular ion mass=[mass], nl=[mass], psmComponent=[num], seriesID=[num], column=[num], fragCharge=[num], because it is outside the range [[mass], [mass]]
 
static const msg_num_t LOGMSG_AAHELPER_REGULAR_PRIME_ION_ADD = 0x00010604
 [D2] Added regular ion mass=[mass], nl=[mass], psmComponent=[num], seriesID=[num] ([name]), column=[num], fragCharge=[num]
 
static const msg_num_t LOGMSG_AAHELPER_REGULAR_PRIME_ION_REJECT = 0x00010603
 [D2] Rejected regular ion mass=[mass], nl=[mass], psmComponent=[num], seriesID=[num] ([name]), column=[num], fragCharge=[num], because it is outside the range [[mass], [mass]]
 
static const msg_num_t LOGMSG_AAHELPER_SERIES_PARAMS = 0x0001060E
 [D1] Parameters for seriesID=[num]: delta=[mass], start=[num], end=[num], forward=[num]
 
static const msg_num_t LOGMSG_AAHELPER_SETUP_FROM_PRE2_2_ANYCHNG = 0x00010617
 [D1] setupFromPre2_2ResultsFile(peptide=[string], varmods=[string]) –> anyChange=[num], modNum=[num], oldStyleModName=[string], modType=[num]
 
static const msg_num_t LOGMSG_AAHELPER_SETUP_FROM_PRE2_2_INIT = 0x00010616
 [D1] setupFromPre2_2ResultsFile(peptide=[string], varmods=[string]) –> modNum=[num], idx=[num], modType=[num]
 
static const msg_num_t LOGMSG_AAHELPER_TOTAL_NL_VALS = 0x0001060C
 [D2] Currently active multi NL neutral loss=[array]
 
static const msg_num_t LOGMSG_CUSTQUANT_ADD_QUANT_KEY = 0x00010400
 [D2] Adding quantitation key id d to protein s .
 
static const msg_num_t LOGMSG_CUSTQUANT_REMOVE_ALL_KEY = 0x00010401
 [D2] Removing quantitation key d from any proteins.
 
static const msg_num_t LOGMSG_CUSTQUANT_REMOVE_KEY = 0x00010402
 [D2] Removed quantitation key d from protein s.
 
static const msg_num_t LOGMSG_DBG1_NUM_PROCESSOR_GROUPS = 0x00010160
 [D1] Debug: Number of processor groups : %d.
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_CORE_PER_PHYS = 0x00010178
 [D2] Debug: Number of cores per physical cpu : %d
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_GETAUTODETECT = 0x00010179
 [D2] Debug: getAutoDetectNumThreads(1,4) : %d
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_LOGI_PER_PHYS = 0x00010177
 [D2] Debug: Number of logical cpus / physical cpu: %d
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_MT_NAME = 0x0001017A
 [D2] Debug: Multi-threaded name : %s
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_MT_STATUS = 0x0001017B
 [D2] Debug: Hyper/multi threading status : %d
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_NAME = 0x00010173
 [D2] Debug: Processor name : %s
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_NUM_AVAIL = 0x00010171
 [D2] Debug: Logical number of cpus available : %d
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_NUM_GROUPS = 0x00010172
 [D2] Debug: Number of processor groups : %d
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_NUM_ON_SYS = 0x00010170
 [D2] Debug: Logical number of cpus on the system : %d
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_NUM_PHYSICAL = 0x00010176
 [D2] Debug: Physical number of cpus on the system: %d
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_PROC_AFFINITY = 0x00010174
 [D2] Debug: Process Affinity supported : %s
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_TABLE_LINE = 0x0001017D
 [D2] Debug: %3d : %2d / %5d / %5d / %s / %s
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_TABLE_TITLE = 0x0001017C
 [D2] Debug: logical : physical id / core id / ht id / is primary / is threaded:
 
static const msg_num_t LOGMSG_DBG2_CPU_INF_USE_PROCESSES = 0x00010175
 [D2] Debug: Use processes instead of threads : %s
 
static const msg_num_t LOGMSG_DBG2_NUM_CONFIG_MISMATCH = 0x00010168
 [D2] Debug: Processor configuration detection mismatch: hwloc detects %d and system detects %d configured processors.
 
static const msg_num_t LOGMSG_DBG2_NUM_ONLINE_MISMATCH = 0x00010169
 [D2] Debug: Processor configuration detection mismatch: hwloc detects %d and system detects %d online processors.
 
static const msg_num_t LOGMSG_DBG3_AUTO_DETECT_NUM_THREAD = 0x00010163
 [D3] Debug: getAutoDetectNumThreads. logicalPerPhysical: %d, numCores: %d, numLicensed: %d, numCoresPerCpuLicense: %d, maxLicensable: %d, numAvailableToProcess: %d.
 
static const msg_num_t LOGMSG_DBG3_BINDING_PROCESSORS = 0x00010166
 [D3] Debug: binding processors %s.
 
static const msg_num_t LOGMSG_DBG3_BINDING_THREAD = 0x00010167
 [D3] Debug: binding thread p to logical processor %d.
 
static const msg_num_t LOGMSG_DBG3_CALL_GET_CHIP_MFCTR = 0x00010164
 [D3] Debug: about to call getChipManufacturer()
 
static const msg_num_t LOGMSG_DBG3_HWLOC_GROUPS = 0x00010162
 [D2] Debug: hwloc reports %d processor groups.
 
static const msg_num_t LOGMSG_DBG3_HWLOC_TREE = 0x00010161
 [D3] Debug: iterateHwlocChildren: %%-8s, logical: %d, depth: %d, packageID: %d, coreID: %d.
 
static const msg_num_t LOGMSG_DBG3_PROCESSOR_NAME = 0x00010165
 [D2] Debug: processor name: %s, hyperthreading: %s.
 
static const msg_num_t LOGMSG_GET_THR_LOOP_BODY_MIN_FOUND = 0x00010A05
 [D2] getThresholdForFDR: found a new minimum at i=d, fdr_min=g, target_min=d, decoy_min=d, expect_min=g
 
static const msg_num_t LOGMSG_GET_THR_LOOP_BODY_START = 0x00010A03
 [D2] getThresholdForFDR: i=d, expect=g, target=d, decoy=d, target_count=d, decoy_count=d, fdr=g, too_few=d
 
static const msg_num_t LOGMSG_GET_THR_LOOP_BODY_ZERO_COUNT = 0x00010A04
 [D2] getThresholdForFDR: target or decoy count dropped to zero at i=d, target_count=d, decoy_count=d
 
static const msg_num_t LOGMSG_GET_THR_REACH_COND = 0x00010A06
 [D2] getThresholdForFDR: Result FDR reached; minimum seen at fdr_min=g, expect_min=g, target_min=d, decoy_min=d
 
static const msg_num_t LOGMSG_GET_THRESHOLD_FOR_FDR_FOR_ET = 0x00010A02
 [D1] getThresholdForFDR(g, s, DM_FASTA_SECOND_PASS) returned success = d, closestFDR = g, minProbability = g, numTargetMatches = d, numDecoyMatches = d
 
static const msg_num_t LOGMSG_GET_THRESHOLD_FOR_FIRST_PASS_FDR = 0x00010A01
 [D1] getThresholdForFDR(g, s, DM_FASTA_FIRST_PASS) returned success = d, closestFDR = g, minProbability = g, numTargetMatches = d, numDecoyMatches = d
 
static const msg_num_t LOGMSG_HTTP_GETRETURNSTRING = 0x00010304
 [I] The http GET returned '[text]'.
 
static const msg_num_t LOGMSG_HTTP_MAXCONECTIONS10FAILED = 0x00010303
 [I] Failed to set maximum connections per 1.0 server
 
static const msg_num_t LOGMSG_HTTP_MAXCONECTIONSFAILED = 0x00010302
 [I] Failed to set maximum connections per server
 
static const msg_num_t LOGMSG_HTTP_QUERYSTATUSRESULT = 0x00010301
 [I] HTTP status is [httpCode] 'httpText'.
 
static const msg_num_t LOGMSG_HTTP_URLSTRING = 0x00010300
 [I] Sending HTTP [httpMethod] to [url] for action [command].
 
static const msg_num_t LOGMSG_INST_ADDINGDATABASE = 0x00010205
 [I] Adding entry for s to mascot.dat.
 
static const msg_num_t LOGMSG_INST_ADDOPTIONSSECTION = 0x00010208
 [I] Added [value] to the options section of mascot.dat.
 
static const msg_num_t LOGMSG_INST_APPENDPARSERULE = 0x00010207
 [I] Added parse rule number [value].
 
static const msg_num_t LOGMSG_INST_APPENDTAXONOMY = 0x00010204
 [I] Appended taxonomy section [value].
 
static const msg_num_t LOGMSG_INST_CHANGEDBTAXONOMY = 0x00010206
 [I] Changed taxonomy entry for [database].
 
static const msg_num_t LOGMSG_INST_CHANGEPARSERULE = 0x0001020C
 [I] Changed [value] parse rule from rule [value] to [value].
 
static const msg_num_t LOGMSG_INST_CHANGEPERCOLATORFEATS = 0x00010210
 [I] Changed PercolatorFeatures section of mascot.dat from [value] to [value].
 
static const msg_num_t LOGMSG_INST_CHANGEPERCOLATORUSERT = 0x00010212
 [I] Changed PercolatorUseRT section of mascot.dat from [value] to [value].
 
static const msg_num_t LOGMSG_INST_CHANGEPROTFAMILYSWITCH = 0x00010211
 [I] Changed ProteinFamilySwitch section of mascot.dat from [value] to [value].
 
static const msg_num_t LOGMSG_INST_CHANGERESULTSCACHE = 0x00010215
 [I] Changed ResultsCache section of mascot.dat from [value] to [value].
 
static const msg_num_t LOGMSG_INST_CHANGESPLITDATAFILESIZE = 0x00010214
 [I] Changed SplitDataFileSize section of mascot.dat from [value] to [value].
 
static const msg_num_t LOGMSG_INST_CHANGESPLITNUMOFQUERIES = 0x00010213
 [I] Changed SplitNumberOfQueries section of mascot.dat from [value] to [value].
 
static const msg_num_t LOGMSG_INST_CLUSTERSECTION = 0x0001020A
 [I] Set the value of [name] to [value] in the cluster section of mascot.dat.
 
static const msg_num_t LOGMSG_INST_FAILSAVEPOSTINSTALLFILE = 0x0001020E
 [I] Failed to save Post Install File [name]. Error [value]
 
static const msg_num_t LOGMSG_INST_LOGICALPERPHYSICALCPU = 0x00010200
 [I] Detected %d logical processors per physical CPU.
 
static const msg_num_t LOGMSG_INST_MASCOTDATOK = 0x00010203
 [I] Successfully loaded existing mascot.dat from [path].
 
static const msg_num_t LOGMSG_INST_NOSUBCLUSTERSET = 0x0001020B
 [I] No SubClusterSet entry in mascot.dat.
 
static const msg_num_t LOGMSG_INST_NOTMASCOTDATOK = 0x00010202
 [I] Successfully loaded not.mascot.dat from [path].
 
static const msg_num_t LOGMSG_INST_NUMTHREADS = 0x00010201
 [I] Setting number of threads to [value].
 
static const msg_num_t LOGMSG_INST_REMOVEOPTIONSSECTION = 0x0001020F
 [I] Removed [value] from the options section of mascot.dat.
 
static const msg_num_t LOGMSG_INST_SAVEDPOSTINSTALLFILE = 0x0001020D
 [I] Saved line ([text]) in Post Install File [name] for Database Manager
 
static const msg_num_t LOGMSG_INST_SETOPTIONSSECTION = 0x00010209
 [I] Set the value of [name] to [value] in the options section of mascot.dat.
 
static const msg_num_t LOGMSG_MATRIX_OUTPUT_VALS = 0x00010500
 [D3] s. d rows and d columns
s
 
static const msg_num_t LOGMSG_MSR2DAT28_SQL_TRACING = 0x00010B00
 [D3] ms_msr2dat28 SQL: [string] –> [string]
 
static const msg_num_t LOGMSG_NON_DEFAULT_HOMOLOGY_THRESHOLD = 0x00010A07
 [D2] getHomologyThreshProtected called with OneInXprobRnd = g, where minProbability_= g, and 1/minProbability_= g, query = d
 
static const msg_num_t LOGMSG_PEPSUM_GETHIT = 0x00010729
 [D3] [function]: [string], [string], [string]
 
static const msg_num_t LOGMSG_PROTINFER_CHOOSE_NEXT_KEEP = 0x00010713
 [D2] choose_next_free_protein(): free count of "[accession]" is [num] => keep
 
static const msg_num_t LOGMSG_PROTINFER_CHOOSE_NEXT_START = 0x00010710
 [D1] choose_next_free_protein(): lead_proteins are [list]
 
static const msg_num_t LOGMSG_PROTINFER_CHOOSE_NEXT_SUPERSET_EMPTY = 0x00010711
 [D2] choose_next_free_protein(): free_count of "[accession]" is [num] but no superset found in lead_proteins; keeping for now
 
static const msg_num_t LOGMSG_PROTINFER_CHOOSE_NEXT_SUPERSET_LIST = 0x00010712
 [D2] choose_next_free_protein(): free count of "[accession]" is [num] => move to subset_list with parents [list]
 
static const msg_num_t LOGMSG_PROTINFER_CLUSTER_FROM_ACC = 0x00010726
 [D1] sortByScore(): Starting point for cluster in hit [num] is [accession]
 
static const msg_num_t LOGMSG_PROTINFER_ELIMINATE_INTERSECTIONS_FREE_COUNT_ZERO = 0x0001070D
 [D2] eliminate_intersections() : ran out of unused_proteins (all free counts are zero)
 
static const msg_num_t LOGMSG_PROTINFER_ELIMINATE_INTERSECTIONS_NEXT = 0x0001070E
 [D2] eliminate_intersections() : next unused protein to try to add is "[accession]"
 
static const msg_num_t LOGMSG_PROTINFER_ELIMINATE_INTERSECTIONS_SUPERSET_LIST = 0x0001070F
 [D2] eliminate_intersections() : fix-up of supersetlist for "[accession]", [changed lists]
 
static const msg_num_t LOGMSG_PROTINFER_FIND_FAMILY_END = 0x00010704
 [D1] findFamily() end for accession "[accession]"
 
static const msg_num_t LOGMSG_PROTINFER_FIND_FAMILY_QUEUE = 0x00010701
 [D1] findFamily(): "[accession]" (node idx = [num]) has [num] PSMs above threshold ([num] PSMs below), [num] homologous proteins, in_queue size=[num], queue size=[num]
 
static const msg_num_t LOGMSG_PROTINFER_FIND_FAMILY_REP_SEQS = 0x00010702
 [D1] findFamily(): "[accession]" has the following [num] representative sequences: [list]
 
static const msg_num_t LOGMSG_PROTINFER_FIND_FAMILY_START = 0x00010700
 [D1] findFamily() start for accession "[accession]"
 
static const msg_num_t LOGMSG_PROTINFER_FIND_MATCHES_PROTEIN_END = 0x00010725
 [D2] findMatchesForThisProteinAndChildren(): Accession: [accession], size of qp = [num]
 
static const msg_num_t LOGMSG_PROTINFER_FIND_MATCHES_PROTEIN_START = 0x00010723
 [D2] findMatchesForThisProteinAndChildren(): Accession: [accession], size of qp = [num]
 
static const msg_num_t LOGMSG_PROTINFER_FIND_MATCHES_SUBSET_START = 0x00010724
 [D2] findMatchesForThisProteinAndChildren(): Subset accession: [accession]
 
static const msg_num_t LOGMSG_PROTINFER_GROUP_FAMILY_DISCARDED_SL_LIST = 0x00010708
 [D2] groupFamily(): discardedSLProteins: [list]
 
static const msg_num_t LOGMSG_PROTINFER_GROUP_FAMILY_ELIMINATION = 0x00010709
 [D1] groupFamily(): eliminate_intersections. lead_proteins size = [num], subset_proteins size = [num]
 
static const msg_num_t LOGMSG_PROTINFER_GROUP_FAMILY_ELIMINATION_LEAD_LIST = 0x0001070B
 [D1] groupFamily(): leadProteins after elimination: [list]
 
static const msg_num_t LOGMSG_PROTINFER_GROUP_FAMILY_ELIMINATION_MEMBER_LIST = 0x0001070A
 [D1] groupFamily(): family members after elimination: [list]
 
static const msg_num_t LOGMSG_PROTINFER_GROUP_FAMILY_ELIMINATION_SUBSET_LIST = 0x0001070C
 [D1] groupFamily(): "[accession]" has parent "[accession]"
 
static const msg_num_t LOGMSG_PROTINFER_GROUP_FAMILY_PULL_IN = 0x0001072B
 [D1] homologous_proteins(): "[accession]" shares q[num]_p[num] with "[accession]" => pull it in to the family
 
static const msg_num_t LOGMSG_PROTINFER_GROUP_FAMILY_SAMESET_LEAD_LIST = 0x00010707
 [D2] groupFamily(): samesetLeadProteins: [list]
 
static const msg_num_t LOGMSG_PROTINFER_GROUP_FAMILY_SAMESET_PARENT_LIST = 0x00010706
 [D2] groupFamily(): samesetParents: [list]
 
static const msg_num_t LOGMSG_PROTINFER_GROUP_FAMILY_START = 0x00010705
 [D1] groupFamily() for "[accession]": samesetLeadProteins=[num], samesetParents=[num], discardedSLProteins=[num]
 
static const msg_num_t LOGMSG_PROTINFER_GROUP_FROM_ACC = 0x00010727
 [D1] sortByScore(): Starting point for group in hit [num] is [accession]
 
static const msg_num_t LOGMSG_PROTINFER_NUM_PEPTIDES_IN_FAMILY = 0x0001072A
 [D2] findFamily(): Family [num] has [num] peptide matches with keepingThisOne=[boolean]
 
static const msg_num_t LOGMSG_PROTINFER_PEPTIDE_MATRIX = 0x00010703
 [D2] findFamily(): [type] peptide matrix (transposed)
[matrix]
 
static const msg_num_t LOGMSG_PROTINFER_REMOVE_CONFLICTING_DISCARD = 0x00010716
 [D2] remove_conflicting_proteins(): lead protein "[accession]" has free count n < minNumSigUniqueSeqs (n = [num], minNumSiqUniqueSeqs = [num]) => move to subset list with parents [accessions]
 
static const msg_num_t LOGMSG_PROTINFER_REMOVE_CONFLICTING_KEEP = 0x00010715
 [D2] remove_conflicting_proteins(): lead protein "[accession]" does not overlap with any current lead protein => keep
 
static const msg_num_t LOGMSG_PROTINFER_REMOVE_CONFLICTING_START = 0x00010714
 [D2] remove_conflicting_proteins([list])
 
static const msg_num_t LOGMSG_PROTINFER_SINGLETON_FROM_ACC = 0x00010728
 [D1] sortByScore(): No grouping; hit [num] is just "[accession]"
 
static const msg_num_t LOGMSG_PROTINFER_SORT_BY_SCORE_CREATE = 0x00010718
 [D2] sortByScore(): About to create sorted_
 
static const msg_num_t LOGMSG_PROTINFER_SORT_BY_SCORE_CREATED = 0x00010719
 [D2] sortByScore(): Finished creating sorted_
 
static const msg_num_t LOGMSG_PROTINFER_SORT_BY_SCORE_DONE = 0x00010722
 [D1] sortByScore(): reached the end of sorted_, so it's all done
 
static const msg_num_t LOGMSG_PROTINFER_SORT_BY_SCORE_NEXT_PROTEIN = 0x00010721
 [D1] sortByScore(): next accession in sorted_ with significant rank 1 peptide is "[accession]"
 
static const msg_num_t LOGMSG_PROTINFER_SORT_BY_SCORE_NO_PROTEINS = 0x0001071A
 [D1] sortByScore(): proteins_ is empty, so it's all done
 
static const msg_num_t LOGMSG_PROTINFER_SORT_BY_SCORE_REMOVE_CHECKBOLD = 0x00010720
 [D1] sortByScore(): Removing "[accession]" because setBoldAndCheckBoxItems() returned false
 
static const msg_num_t LOGMSG_PROTINFER_SORT_BY_SCORE_REMOVE_LONGESTPEPLEN = 0x0001071D
 [D1] sortByScore(): Removing "[accession]" because longestPeptideLen [num] < minPepLenInPepSummary [num]
 
static const msg_num_t LOGMSG_PROTINFER_SORT_BY_SCORE_REMOVE_LONGESTSIGPEPLEN = 0x0001071E
 [D1] sortByScore(): Removing "[accession]" because longestSigPeptideLen [num] < minPepLenInPepSummary [num]
 
static const msg_num_t LOGMSG_PROTINFER_SORT_BY_SCORE_REMOVE_MAXHITS = 0x0001071C
 [D1] sortByScore(): Removing "[accession]" because numProteins [num] >= maxHitsToReport [num]
 
static const msg_num_t LOGMSG_PROTINFER_SORT_BY_SCORE_REMOVE_MINPROTEINSCORE = 0x0001071B
 [D1] sortByScore(): Removing "[accession]" because its score [num] is less than minProteinScore [num]
 
static const msg_num_t LOGMSG_PROTINFER_SORT_BY_SCORE_START = 0x00010717
 [D1] sortByScore(): Num proteins: [num], num peptides: [num], hitToAdd: [num]
 
static const msg_num_t LOGMSG_PROTINFER_SUBSET_STARTS_NEW_HIT = 0x0001071F
 [D2] sortByScore(): Protein "[accession]" is a subset in hit [num]. Because MSRES_SUBSETS_DIFF_PROT is active, it will now start hit [num]
 
static const msg_num_t LOGMSG_QUANT_ADDED_PROTEIN_HIT = 0x00010417
 [D2] Added quantitation protein hit [accession] to match [value] with sequence [text]
 
static const msg_num_t LOGMSG_QUANT_ADDING_PROTEIN_HIT = 0x00010416
 [D2] Adding quantitation protein hit [accession]
 
static const msg_num_t LOGMSG_QUANT_CALC_COMPLETE_ON_MERGED = 0x0001040F
 [D2] Calling calc_complete() on merged dataset
 
static const msg_num_t LOGMSG_QUANT_CLOSING_CACHE_FILE = 0x00010419
 [D2] Closing quantitation cache file [filename]
 
static const msg_num_t LOGMSG_QUANT_EXCLUDING_PEPTIDE = 0x00010411
 [D2] Excluding peptide for query: [value], rank: [value] because [string]
 
static const msg_num_t LOGMSG_QUANT_EXCLUDING_PEPTIDE_GREATHAN = 0x00010413
 [D2] Excluding peptide for query: [value], rank: [value] because [string]. [value] > [value]
 
static const msg_num_t LOGMSG_QUANT_EXCLUDING_PEPTIDE_LESSTHAN = 0x00010412
 [D2] Excluding peptide for query: [value], rank: [value] because [string]. [value] < [value]
 
static const msg_num_t LOGMSG_QUANT_FINISH_CALC_COMPLETE = 0x00010406
 [D2] Finished calc_complete() call
 
static const msg_num_t LOGMSG_QUANT_FINISH_LOAD_CDB = 0x00010409
 [D2] Finished loadCdbFile() call
 
static const msg_num_t LOGMSG_QUANT_FINISH_REORDER_AFTER_MERGE = 0x0001041B
 [D1] Finished reordering of peptide matches after merge
 
static const msg_num_t LOGMSG_QUANT_FINISH_UPDATE_PROT_MATCHES = 0x00010404
 [D2] Finished updating protein matches
 
static const msg_num_t LOGMSG_QUANT_HELPER_TEST_REQUIRED = 0x00010800
 [D3] testRequiredMods(): sorted required mods="[string]", sequence="[string]", mods="[string]", iter=[char]
 
static const msg_num_t LOGMSG_QUANT_LOAD_PEP_STATUS_MATCHES = 0x0001040A
 [D2] Loading all peptide status values
 
static const msg_num_t LOGMSG_QUANT_LOADING_MATCHES = 0x0001040B
 [D2] Loading quantitation matches
 
static const msg_num_t LOGMSG_QUANT_MERGE_COMPONENT_DUPE_FI = 0x0001041D
 [D1] Duplicate file_index: d when trying to merge file_index for same component. Name: s, Mods: s, m/z: f
 
static const msg_num_t LOGMSG_QUANT_MERGE_COMPONENT_INCONSIST = 0x0001041C
 [D1] Incompatibility trying to merge file_index for same component. Name: s (s), Mods: s (s), m/z: f (f)
 
static const msg_num_t LOGMSG_QUANT_MERGE_COMPONENT_SUCCESS = 0x0001041E
 [D2] Successfully merging file_index: d into existing component. Name: s, Mods: s, m/z: f
 
static const msg_num_t LOGMSG_QUANT_OPENING_CACHE_FILE = 0x00010418
 [D2] Opening quantitation cache file [filename]
 
static const msg_num_t LOGMSG_QUANT_REAPPLY_THRESHOLDS = 0x0001040D
 [D2] Reapplying quantitation quality thresholds
 
static const msg_num_t LOGMSG_QUANT_REMATCHING_INFERRED = 0x00010410
 [D2] Rematching [value] inferred matches
 
static const msg_num_t LOGMSG_QUANT_REMOVE_INFERRED_MATCH = 0x00010415
 [D1] Removing inferred quantitation match [value] - [value] < [value]
 
static const msg_num_t LOGMSG_QUANT_REMOVE_MATCH_NO_EVIDENCE = 0x00010414
 [D1] Removing quantitation match [value] - no remaining evidence
 
static const msg_num_t LOGMSG_QUANT_RT_OFFSET_LOOKUP = 0x00010420
 [D2] Retention time: f, from project: d, gives an offset of: f for project: d. (m/z: f)
 
static const msg_num_t LOGMSG_QUANT_START_CALC_COMPLETE = 0x00010405
 [D2] Calling calc_complete()
 
static const msg_num_t LOGMSG_QUANT_START_LOAD_CDB = 0x00010408
 [D2] Start of loadCdbFile() call. Cdb file: [filename], cache file: [filename]
 
static const msg_num_t LOGMSG_QUANT_START_REORDER_AFTER_MERGE = 0x0001041A
 [D1] Starting reordering of peptide matches after merge
 
static const msg_num_t LOGMSG_QUANT_START_UPDATE_PROT_MATCHES = 0x00010403
 [D2] Starting to update protein matches
 
static const msg_num_t LOGMSG_QUANT_TIME_ALIGN_INDEX_MZ_RANGE = 0x0001041F
 [D1] Invalid index when getting RT offset - expected for some Waters MS^E peptides. This project id: d, other project id: d. Rt in other project: f, m/z: f. Combined min bin number: d. bin number: d, Array size: d
 
static const msg_num_t LOGMSG_QUANT_TIME_ALIGN_INDEX_MZ_RANGE1 = 0x00010421
 [D1] In getEstimatedFeatureWidth(), for subProject: [num], m/z: [value], rt: [value], binIndex: [num], but max bin for this sub project: [num], min bin: 0
 
static const msg_num_t LOGMSG_QUANT_UPDATE_EXCLUDED_MATCHES = 0x0001040E
 [D2] Updating excluded matches
 
static const msg_num_t LOGMSG_QUANT_UPDATING_PEP_EVIDENCE = 0x0001040C
 [D2] Updating Peptide Evidence
 
static const msg_num_t LOGMSG_REPORT_FUNCTION_CALLED_BY = 0x00010900
 [D3] [function], called by [string]
 
static const msg_num_t LOGMSG_REPORT_FUNCTION_ENTRY = 0x00010901
 [D3] [function] entered
 
static const msg_num_t LOGMSG_REPORT_FUNCTION_ENTRY_WITH_ARGS1 = 0x00010902
 [D3] [function]([args]) entered
 
static const msg_num_t LOGMSG_REPORT_FUNCTION_ENTRY_WITH_ARGS2 = 0x00010903
 [D3] [function]([args]) entered
 
static const msg_num_t LOGMSG_REPORT_FUNCTION_ENTRY_WITH_ARGS3 = 0x00010904
 [D3] [function]([args]) entered
 
static const msg_num_t LOGMSG_REPORT_FUNCTION_ENTRY_WITH_ARGS4 = 0x00010905
 [D3] [function]([args]) entered
 
static const msg_num_t LOGMSG_REPORT_FUNCTION_EXIT = 0x00010910
 [D3] [function] exited
 
static const msg_num_t LOGMSG_REPORT_FUNCTION_EXIT_WITH = 0x00010911
 [D3] [function] exited with [string]
 
static const msg_num_t LOGMSG_RESFILE_APPEND = 0x00010A00
 [D2] [string] numQueries=[num] cachedExpValues=[num]
 

Detailed Description

Definitions for logging messages.

Member Typedef Documentation

◆ msg_num_t

typedef int msg_num_t

Typedef for log and error message numbers.

See Using enumerated values and static const ints in Perl, Java, Python and C#.

Logging messages are classified as:

  • [I] information
  • [D1] Debug level 1 message
  • [D2] Debug level 2 message
  • [D3] Debug level 3 message

Ranges:

ProductClassificationFirstLast
Parser sev_fatal, sev_warn 0x00000000 0x0000FFFF
sev_info, sev_debug1, sev_debug2, sev_debug3 0x00010000 0x0001FFFF
MSQuantlib sev_fatal, sev_warn 0x00020000 0x0002FFFF
sev_info, sev_debug1, sev_debug2, sev_debug3 0x00030000 0x0003FFFF
Purifier API sev_fatal, sev_warn, sev_info, sev_debug1, sev_debug2, sev_debug3 0x00040000 0x0004FFFF
Purifier sev_fatal, sev_warn, sev_info, sev_debug1, sev_debug2, sev_debug3 0x00050000 0x0005FFFF
Mascot Server sev_fatal, sev_warn 0x00000000 0x0000FFFF
sev_info, sev_debug1, sev_debug2, sev_debug3 0x00060000 0x0006FFFF
MDRO sev_fatal, sev_warn, sev_info, sev_debug1, sev_debug2, sev_debug3 0x4C020000 0x4C03FFFF

Member Enumeration Documentation

◆ msg_sev

enum msg_sev

Message severity levels.

See Using enumerated values and static const ints in Perl, Java, Python and C#.

See also: ms_loggingmonitor::Level_e

Enumerator
sev_fatal 

A fatal error that results in the object being 'invalid'.

sev_warn 

A warning message.

sev_info 

Information message.

sev_debug1 

Debug level 1 message.

sev_debug2 

Debug level 2 message.

sev_debug3 

Debug level 3 message.

Constructor & Destructor Documentation

◆ ms_log()

ms_log ( )

Constructor.

Initialisation by adding the message text and severity to a lookup

◆ ~ms_log()

~ms_log ( )
virtual

Destructor.

Nothing to delete, but a virtual destructor needs to be defined as we have virtual methods

Member Function Documentation

◆ addToCatalog()

void addToCatalog ( const msg_catalog_t  catalog[],
size_t  numEntries,
ms_loggingmonitor::Source_e  src,
errorOrLogMessages_e  errorOrLogMessages 
)

Add messages to the fast lookup map.

Parameters
catalogis a pointer to an array of messages and severities
numEntriesis the number of entries in catalog
srcis used to check if the messages have already been added to the static catalog_ map.
errorOrLogMessagesis used, with src to check if the messages have already been added to the static catalog_ map.

◆ getMessageSource()

ms_loggingmonitor::Source_e getMessageSource ( const ms_log::msg_num_t  msgNum) const

Return the component (library/application) that generated the specified log message.

The return value is based on the message number and determined from the table shown for msg_num_t above. If the value isn't in one of the above ranges, then ms_loggingmonitor::SRC_ALL will be returned.

Parameters
msgNumNumeric code of the messaged to be logged
Returns
the ms_loggingmonitor::Source_e value.

◆ willMessageBeLogged()

bool willMessageBeLogged ( const msg_num_t  msgNum) const

Check to see if the message will be logged to a file or recorded anywhere.

If the code to format a log message might take some time to run, it is worth calling this function first to see if the message will be logged or used anywhere.

Parameters
msgNummust be a valid error number
Returns
true if the message will be logged, or returned by getErrorString()
The documentation for this class was generated from the following files: