NCBI C++ ToolKit
Classes | Typedefs | Functions | Variables
sequence_tests.cpp File Reference
#include <ncbi_pch.hpp>
#include <objects/general/User_object.hpp>
#include <objects/seq/MolInfo.hpp>
#include <objects/valid/Comment_rule.hpp>
#include <objmgr/seqdesc_ci.hpp>
#include <objmgr/feat_ci.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/bioseq_ci.hpp>
#include <objmgr/util/create_defline.hpp>
#include <objtools/cleanup/cleanup.hpp>
#include <objtools/edit/loc_edit.hpp>
#include <objects/seq/Seq_ext.hpp>
#include <objects/seq/Delta_ext.hpp>
#include <objects/seq/Delta_seq.hpp>
#include <objects/seq/Seq_literal.hpp>
#include <objects/seq/seqport_util.hpp>
#include <objects/general/Object_id.hpp>
#include <objects/seqfeat/Org_ref.hpp>
#include <objects/seqfeat/OrgMod.hpp>
#include <objects/seqfeat/SubSource.hpp>
#include <objects/seqfeat/Gb_qual.hpp>
#include <objects/pub/Pub.hpp>
#include <objects/pub/Pub_equiv.hpp>
#include <objects/biblio/Auth_list.hpp>
#include <objects/biblio/Author.hpp>
#include <objects/general/Dbtag.hpp>
#include <objects/general/Person_id.hpp>
#include <util/xregexp/regexp.hpp>
#include <util/multipattern_search.hpp>
#include <util/regexp/ctre/ctre.hpp>
#include "discrepancy_core.hpp"
#include "utils.hpp"
#include <util/impl/generated_fsm.hpp>
#include "FLATFILE_FIND.inc"
+ Include dependency graph for sequence_tests.cpp:

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Classes

struct  SpellFixData
 

Typedefs

typedef bool(CBioSource::* FnIsSet) () const
 
typedef const string &(CBioSource::* FnGet) () const
 

Functions

 USING_SCOPE (objects)
 
static bool IsATGC (char ch)
 
static bool EndsWithSequence (const string &title)
 
string GetFieldValueAsString (const CUser_field &field)
 
void AddUserObjectFieldItems (const CSeqdesc *desc, CReportObj &rep_seq, CReportNode &collector, CReportNode &previously_seen, CDiscrepancyContext &context, const string &object_name, const string &field_prefix=kEmptyStr)
 
void AnalyzeField (CReportNode &node, bool &all_present, bool &all_same)
 
void AnalyzeFieldReport (CReportNode &node, bool &all_present, bool &all_same)
 
string GetSummaryLabel (bool all_present, bool all_same)
 
void CopyNode (CReportNode &new_home, CReportNode &original)
 
string AdjustDBLinkFieldName (const string &orig_field_name)
 
static string GetProjectID (const CUser_object &user)
 
static bool IsMolProd (int biomol)
 
static bool CompareOrGetString (const CBioSource &bio_src, FnIsSet is_set_fn, FnGet get_fn, string &val)
 
static bool CompareOrgModValue (const CBioSource &bio_src, COrgMod::TSubtype subtype, string &val)
 
static bool IsSegmentSubtype (const CBioSource &bio_src)
 
static bool IsMicroSatellite (const CSeq_feat &feat)
 
static void FindFlatfileText (const char *str, bool *result)
 
void UnitTest_FLATFILE_FIND ()
 Checking that FLATFILE_FIND.inc is in sync with kSpellFixes If the array is changed, need to regenerate FLATFILE_FIND.inc: multipattern.exe -i FLATFILE_FIND.txt > FLATFILE_FIND.inc. More...
 
static bool FixTextInObject (CSerialObject *obj, size_t misspell_idx)
 
static bool SuspiciousId (const string &s)
 
static bool s_areCompatible (CBioSource::EGenome Location, CSubSource::ESubtype Qualifier)
 

Variables

const string kUniqueDeflines = "[n] definition line[s] [is] unique"
 
const string kIdenticalDeflines = "[n] definition line[s] [is] identical"
 
const string kAllUniqueDeflines = "All deflines are unique"
 
const string kSomeIdenticalDeflines = "Defline Problem Report"
 
static constexpr CDiscrepancyCaseProps s_testcase_props_DUP_DEFLINE = { CDiscrepancyVisitorImpl<eTestNames:: DUP_DEFLINE >::Create, eTestTypes:: SEQUENCE , eTestNames:: DUP_DEFLINE , "DUP_DEFLINE" , "Definition lines should be unique" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_TERMINAL_NS = { CDiscrepancyVisitorImpl<eTestNames:: TERMINAL_NS >::Create, eTestTypes:: SEQUENCE , eTestNames:: TERMINAL_NS , "TERMINAL_NS" , "Ns at end of sequences" , eDisc | eSmart | eBig | eFatal , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_SHORT_PROT_SEQUENCES = { CDiscrepancyVisitorImpl<eTestNames:: SHORT_PROT_SEQUENCES >::Create, eTestTypes:: SEQUENCE , eTestNames:: SHORT_PROT_SEQUENCES , "SHORT_PROT_SEQUENCES" , "Protein sequences should be at least 50 aa, unless they are partial" , eDisc | eOncaller | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_COMMENT_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: COMMENT_PRESENT >::Create, eTestTypes:: DESC , eTestNames:: COMMENT_PRESENT , "COMMENT_PRESENT" , "Comment descriptor present" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MRNA_ON_WRONG_SEQUENCE_TYPE = { CDiscrepancyVisitorImpl<eTestNames:: MRNA_ON_WRONG_SEQUENCE_TYPE >::Create, eTestTypes:: SEQUENCE , eTestNames:: MRNA_ON_WRONG_SEQUENCE_TYPE , "MRNA_ON_WRONG_SEQUENCE_TYPE" , "Eukaryotic sequences that are not genomic or macronuclear should not have mRNA features" , eDisc | eOncaller , nullptr }
 
const string kSequencesWithGaps = "[n] sequence[s] contain[S] gaps"
 
static constexpr CDiscrepancyCaseProps s_testcase_props_GAPS = { CDiscrepancyVisitorImpl<eTestNames:: GAPS >::Create, eTestTypes:: SEQUENCE , eTestNames:: GAPS , "GAPS" , "Sequences with gaps" , eDisc | eSubmitter | eSmart | eBig , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_BIOPROJECT_ID = { CDiscrepancyVisitorImpl<eTestNames:: BIOPROJECT_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: BIOPROJECT_ID , "BIOPROJECT_ID" , "Sequences with BioProject IDs" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_DEFLINES = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_DEFLINES >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_DEFLINES , "MISSING_DEFLINES" , "Missing definition lines" , eAll , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_N_RUNS_14 = { CDiscrepancyVisitorImpl<eTestNames:: N_RUNS_14 >::Create, eTestTypes:: SEQUENCE , eTestNames:: N_RUNS_14 , "N_RUNS_14" , "Runs of more than 14 Ns" , eDisc | eTSA , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_EXTERNAL_REFERENCE = { CDiscrepancyVisitorImpl<eTestNames:: EXTERNAL_REFERENCE >::Create, eTestTypes:: SEQUENCE , eTestNames:: EXTERNAL_REFERENCE , "EXTERNAL_REFERENCE" , "Sequence has external reference" , eDisc | eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_TEN_PERCENTN = { CDiscrepancyVisitorImpl<eTestNames:: TEN_PERCENTN >::Create, eTestTypes:: SEQUENCE , eTestNames:: TEN_PERCENTN , "10_PERCENTN" , "Greater than 10 percent Ns" , eDisc | eSubmitter | eSmart | eTSA , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_FEATURE_COUNT = { CDiscrepancyVisitorImpl<eTestNames:: FEATURE_COUNT >::Create, eTestTypes:: FEAT , eTestNames:: FEATURE_COUNT , "FEATURE_COUNT" , "Count features present or missing from sequences" , eOncaller | eSubmitter | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_EXON_ON_MRNA = { CDiscrepancyVisitorImpl<eTestNames:: EXON_ON_MRNA >::Create, eTestTypes:: SEQUENCE , eTestNames:: EXON_ON_MRNA , "EXON_ON_MRNA" , "mRNA sequences should not have exons" , eOncaller | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_MOLINFO_TECH = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_MOLINFO_TECH >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_MOLINFO_TECH , "INCONSISTENT_MOLINFO_TECH" , "Inconsistent Molinfo Techniques" , eDisc | eSmart , nullptr }
 
static const string kInconsistentMolinfoTechSummary = "Molinfo Technique Report"
 
static const string kInconsistentMolinfoTech = "[n] Molinfo[s] [is] missing field technique"
 
static constexpr CDiscrepancyCaseProps s_testcase_props_TITLE_ENDS_WITH_SEQUENCE = { CDiscrepancyVisitorImpl<eTestNames:: TITLE_ENDS_WITH_SEQUENCE >::Create, eTestTypes:: DESC , eTestNames:: TITLE_ENDS_WITH_SEQUENCE , "TITLE_ENDS_WITH_SEQUENCE" , "Sequence characters at end of defline" , eDisc | eSubmitter | eSmart | eBig , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_FEATURE_MOLTYPE_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: FEATURE_MOLTYPE_MISMATCH >::Create, eTestTypes:: SEQUENCE , eTestNames:: FEATURE_MOLTYPE_MISMATCH , "FEATURE_MOLTYPE_MISMATCH" , "Sequences with rRNA or misc_RNA features should be genomic DNA" , eOncaller , nullptr }
 
const string kMissingDBLink = "[n] Bioseq [is] missing DBLink object"
 
const string kDBLinkObjectList = "DBLink Objects"
 
const string kDBLinkFieldCountTop = "DBLink Fields"
 
const string kDBLinkCollect = "DBLink Collection"
 
const stringkPreviouslySeenFields = "Previously Seen Fields"
 
const stringkPreviouslySeenFieldsThis = "Previously Seen Fields This"
 
const stringkPreviouslySeenObjects = "Previously Seen Objects"
 
static constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_DBLINK = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_DBLINK >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_DBLINK , "INCONSISTENT_DBLINK" , "Inconsistent DBLink fields" , eDisc | eSubmitter | eSmart | eBig , nullptr }
 
const string kStructuredCommentsSeqs = "sequences"
 
const string kStructuredCommentObservedPrefixes = "observed prefixes"
 
const string kStructuredCommentObservedPrefixesThis = "observed prefixes this"
 
const string kStructuredCommentReport = "collection"
 
const string kStructuredCommentPrevious = "previous"
 
const string kStructuredCommentFieldPrefix = "structured comment field "
 
static constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_STRUCTURED_COMMENTS = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_STRUCTURED_COMMENTS >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_STRUCTURED_COMMENTS , "INCONSISTENT_STRUCTURED_COMMENTS" , "Inconsistent structured comments" , eDisc | eSubmitter | eSmart | eBig , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_STRUCTURED_COMMENT = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_STRUCTURED_COMMENT >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_STRUCTURED_COMMENT , "MISSING_STRUCTURED_COMMENT" , "Structured comment not included" , eDisc | eTSA , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_PROJECT = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_PROJECT >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_PROJECT , "MISSING_PROJECT" , "Project not included" , eDisc | eTSA , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_COUNT_UNVERIFIED = { CDiscrepancyVisitorImpl<eTestNames:: COUNT_UNVERIFIED >::Create, eTestTypes:: SEQUENCE , eTestNames:: COUNT_UNVERIFIED , "COUNT_UNVERIFIED" , "Count number of unverified sequences" , eOncaller , nullptr }
 
const string kDeflineExists = "[n] Bioseq[s] [has] definition line"
 
static constexpr CDiscrepancyCaseProps s_testcase_props_DEFLINE_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: DEFLINE_PRESENT >::Create, eTestTypes:: SEQUENCE , eTestNames:: DEFLINE_PRESENT , "DEFLINE_PRESENT" , "Test defline existence" , eDisc , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_UNUSUAL_NT = { CDiscrepancyVisitorImpl<eTestNames:: UNUSUAL_NT >::Create, eTestTypes:: SEQUENCE , eTestNames:: UNUSUAL_NT , "UNUSUAL_NT" , "Sequence contains unusual nucleotides" , eDisc | eSubmitter | eSmart , nullptr }
 
const string kNoTaxnameInDefline = "[n] defline[s] [does] not contain the complete taxname"
 
static constexpr CDiscrepancyCaseProps s_testcase_props_TAXNAME_NOT_IN_DEFLINE = { CDiscrepancyVisitorImpl<eTestNames:: TAXNAME_NOT_IN_DEFLINE >::Create, eTestTypes:: SEQUENCE , eTestNames:: TAXNAME_NOT_IN_DEFLINE , "TAXNAME_NOT_IN_DEFLINE" , "Complete taxname should be present in definition line" , eDisc | eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_HAS_PROJECT_ID = { CDiscrepancyVisitorImpl<eTestNames:: HAS_PROJECT_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: HAS_PROJECT_ID , "HAS_PROJECT_ID" , "Sequences with project IDs (looks for genome project IDs)" , eOncaller | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MULTIPLE_CDS_ON_MRNA = { CDiscrepancyVisitorImpl<eTestNames:: MULTIPLE_CDS_ON_MRNA >::Create, eTestTypes:: SEQUENCE , eTestNames:: MULTIPLE_CDS_ON_MRNA , "MULTIPLE_CDS_ON_MRNA" , "Multiple CDS on mRNA" , eOncaller | eSubmitter | eSmart , nullptr }
 
static const string kMrnaSequenceMinusStrandFeatures = "[n] mRNA sequences have features on the complement strand."
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MRNA_SEQUENCE_MINUS_STRAND_FEATURES = { CDiscrepancyVisitorImpl<eTestNames:: MRNA_SEQUENCE_MINUS_STRAND_FEATURES >::Create, eTestTypes:: SEQUENCE , eTestNames:: MRNA_SEQUENCE_MINUS_STRAND_FEATURES , "MRNA_SEQUENCE_MINUS_STRAND_FEATURES" , "mRNA sequences have CDS/gene on the complement strand" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_LOW_QUALITY_REGION = { CDiscrepancyVisitorImpl<eTestNames:: LOW_QUALITY_REGION >::Create, eTestTypes:: SEQUENCE , eTestNames:: LOW_QUALITY_REGION , "LOW_QUALITY_REGION" , "Sequence contains regions of low quality" , eDisc | eSubmitter | eSmart , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_DEFLINE_ON_SET = { CDiscrepancyVisitorImpl<eTestNames:: DEFLINE_ON_SET >::Create, eTestTypes:: SEQ_SET , eTestNames:: DEFLINE_ON_SET , "DEFLINE_ON_SET" , "Titles on sets" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_MITOCHONDRION_REQUIRED = { CDiscrepancyVisitorImpl<eTestNames:: MITOCHONDRION_REQUIRED >::Create, eTestTypes:: SEQUENCE , eTestNames:: MITOCHONDRION_REQUIRED , "MITOCHONDRION_REQUIRED" , "If D-loop or control region misc_feat is present, source must be mitochondrial" , eDisc | eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_SEQ_SHORTER_THAN_50bp = { CDiscrepancyVisitorImpl<eTestNames:: SEQ_SHORTER_THAN_50bp >::Create, eTestTypes:: SEQUENCE , eTestNames:: SEQ_SHORTER_THAN_50bp , "SEQ_SHORTER_THAN_50bp" , "Find Short Sequences" , eDisc | eSubmitter | eSmart | eBig , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_SEQ_SHORTER_THAN_200bp = { CDiscrepancyVisitorImpl<eTestNames:: SEQ_SHORTER_THAN_200bp >::Create, eTestTypes:: SEQUENCE , eTestNames:: SEQ_SHORTER_THAN_200bp , "SEQ_SHORTER_THAN_200bp" , "Short Contig" , eDisc | eSubmitter | eSmart | eBig | eTSA , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_RNA_PROVIRAL = { CDiscrepancyVisitorImpl<eTestNames:: RNA_PROVIRAL >::Create, eTestTypes:: SEQUENCE , eTestNames:: RNA_PROVIRAL , "RNA_PROVIRAL" , "RNA bioseqs are proviral" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_SMALL_GENOME_SET_PROBLEM = { CDiscrepancyVisitorImpl<eTestNames:: SMALL_GENOME_SET_PROBLEM >::Create, eTestTypes:: SEQ_SET , eTestNames:: SMALL_GENOME_SET_PROBLEM , "SMALL_GENOME_SET_PROBLEM" , "Problems with small genome sets" , eOncaller , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_UNWANTED_SET_WRAPPER = { CDiscrepancyVisitorImpl<eTestNames:: UNWANTED_SET_WRAPPER >::Create, eTestTypes:: FEAT , eTestNames:: UNWANTED_SET_WRAPPER , "UNWANTED_SET_WRAPPER" , "Set wrapper on microsatellites or rearranged genes" , eOncaller , nullptr }
 
static SpellFixData kSpellFixes []
 
static const size_t kSpellFixesSize = ArraySize(kSpellFixes)
 
static const string kFixable = "Fixable"
 
static const string kNonFixable = "Non-fixable"
 
static constexpr std::initializer_list< const char * > g_aliases_FLATFILE_FIND = { "FLATFILE_FIND_ONCALLER", "FLATFILE_FIND_ONCALLER_UNFIXABLE", "FLATFILE_FIND_ONCALLER_FIXABLE" }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_FLATFILE_FIND = { CDiscrepancyVisitorImpl<eTestNames:: FLATFILE_FIND >::Create, eTestTypes:: SEQUENCE , eTestNames:: FLATFILE_FIND , "FLATFILE_FIND" , "Flatfile representation of object contains suspect text" , eOncaller , &g_aliases_FLATFILE_FIND }
 
static const size_t MIN_SEQUENCE_LEN = 20000
 
static constexpr CDiscrepancyCaseProps s_testcase_props_ALL_SEQS_SHORTER_THAN_20kb = { CDiscrepancyVisitorImpl<eTestNames:: ALL_SEQS_SHORTER_THAN_20kb >::Create, eTestTypes:: SEQUENCE , eTestNames:: ALL_SEQS_SHORTER_THAN_20kb , "ALL_SEQS_SHORTER_THAN_20kb" , "Short sequences test" , eDisc | eSubmitter | eSmart | eBig , nullptr }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_ALL_SEQS_CIRCULAR = { CDiscrepancyVisitorImpl<eTestNames:: ALL_SEQS_CIRCULAR >::Create, eTestTypes:: SEQUENCE , eTestNames:: ALL_SEQS_CIRCULAR , "ALL_SEQS_CIRCULAR" , "All sequences circular" , eDisc | eSubmitter | eSmart , nullptr }
 
static constexpr auto suspicious_id_re = ctll::fixed_string{ "chromosome|plasmid|mito|chloroplast|apicoplast|plastid|^chr|^lg|\\bnw_|\\bnz_|\\bnm_|\\bnc_|\\bac_|cp\\d\\d\\d\\d\\d\\d|^x$|^y$|^z$|^w$|^mt$|^pltd$|^chl$" }
 
static constexpr CDiscrepancyCaseProps s_testcase_props_SUSPICIOUS_SEQUENCE_ID = { CDiscrepancyVisitorImpl<eTestNames:: SUSPICIOUS_SEQUENCE_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: SUSPICIOUS_SEQUENCE_ID , "SUSPICIOUS_SEQUENCE_ID" , "Suspicious sequence identifiers" , eOncaller | eSubmitter | eSmart | eBig , nullptr }
 
static const CSubSource::ESubtype eSubtype_unknown = static_cast<CSubSource::ESubtype>(0)
 
static constexpr CDiscrepancyCaseProps s_testcase_props_CHROMOSOME_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: CHROMOSOME_PRESENT >::Create, eTestTypes:: SEQ_SET , eTestNames:: CHROMOSOME_PRESENT , "CHROMOSOME_PRESENT" , "Chromosome present" , eSubmitter | eSmart , nullptr }
 

Typedef Documentation

◆ FnGet

typedef const string&(CBioSource::* FnGet) () const

Definition at line 1447 of file sequence_tests.cpp.

◆ FnIsSet

typedef bool(CBioSource::* FnIsSet) () const

Definition at line 1446 of file sequence_tests.cpp.

Function Documentation

◆ AddUserObjectFieldItems()

void AddUserObjectFieldItems ( const CSeqdesc desc,
CReportObj rep_seq,
CReportNode collector,
CReportNode previously_seen,
CDiscrepancyContext context,
const string object_name,
const string field_prefix = kEmptyStr 
)

◆ AdjustDBLinkFieldName()

string AdjustDBLinkFieldName ( const string orig_field_name)

Definition at line 800 of file sequence_tests.cpp.

References NStr::Equal().

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ AnalyzeField()

void AnalyzeField ( CReportNode node,
bool all_present,
bool all_same 
)

◆ AnalyzeFieldReport()

void AnalyzeFieldReport ( CReportNode node,
bool all_present,
bool all_same 
)

◆ CompareOrGetString()

static bool CompareOrGetString ( const CBioSource bio_src,
FnIsSet  is_set_fn,
FnGet  get_fn,
string val 
)
static

Definition at line 1449 of file sequence_tests.cpp.

References val.

◆ CompareOrgModValue()

static bool CompareOrgModValue ( const CBioSource bio_src,
COrgMod::TSubtype  subtype,
string val 
)
static

◆ CopyNode()

void CopyNode ( CReportNode new_home,
CReportNode original 
)

◆ EndsWithSequence()

static bool EndsWithSequence ( const string title)
static

Definition at line 507 of file sequence_tests.cpp.

References IsATGC().

◆ FindFlatfileText()

static void FindFlatfileText ( const char *  str,
bool result 
)
static

◆ FixTextInObject()

static bool FixTextInObject ( CSerialObject obj,
size_t  misspell_idx 
)
static

◆ GetFieldValueAsString()

string GetFieldValueAsString ( const CUser_field field)

◆ GetProjectID()

static string GetProjectID ( const CUser_object user)
static

◆ GetSummaryLabel()

string GetSummaryLabel ( bool  all_present,
bool  all_same 
)

Definition at line 768 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ IsATGC()

static bool IsATGC ( char  ch)
static

Definition at line 501 of file sequence_tests.cpp.

Referenced by EndsWithSequence().

◆ IsMicroSatellite()

static bool IsMicroSatellite ( const CSeq_feat feat)
static

◆ IsMolProd()

static bool IsMolProd ( int  biomol)
static

◆ IsSegmentSubtype()

static bool IsSegmentSubtype ( const CBioSource bio_src)
static

◆ s_areCompatible()

static bool s_areCompatible ( CBioSource::EGenome  Location,
CSubSource::ESubtype  Qualifier 
)
static

◆ SuspiciousId()

static bool SuspiciousId ( const string s)
static

◆ UnitTest_FLATFILE_FIND()

void UnitTest_FLATFILE_FIND ( )

Checking that FLATFILE_FIND.inc is in sync with kSpellFixes If the array is changed, need to regenerate FLATFILE_FIND.inc: multipattern.exe -i FLATFILE_FIND.txt > FLATFILE_FIND.inc.

Definition at line 1704 of file sequence_tests.cpp.

References eUnknown, FindFlatfileText(), i, kSpellFixes, kSpellFixesSize, SpellFixData::m_misspell, and NCBI_THROW.

Referenced by BOOST_AUTO_TEST_CASE().

◆ USING_SCOPE()

USING_SCOPE ( objects  )

Variable Documentation

◆ eSubtype_unknown

const CSubSource::ESubtype eSubtype_unknown = static_cast<CSubSource::ESubtype>(0)
static

Definition at line 1949 of file sequence_tests.cpp.

Referenced by BEGIN_NAMED_ENUM_IN_INFO().

◆ g_aliases_FLATFILE_FIND

constexpr std::initializer_list<const char*> g_aliases_FLATFILE_FIND = { "FLATFILE_FIND_ONCALLER", "FLATFILE_FIND_ONCALLER_UNFIXABLE", "FLATFILE_FIND_ONCALLER_FIXABLE" }
staticconstexpr

Definition at line 1723 of file sequence_tests.cpp.

◆ kAllUniqueDeflines

const string kAllUniqueDeflines = "All deflines are unique"

Definition at line 75 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kDBLinkCollect

const string kDBLinkCollect = "DBLink Collection"

Definition at line 610 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kDBLinkFieldCountTop

const string kDBLinkFieldCountTop = "DBLink Fields"

Definition at line 609 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kDBLinkObjectList

const string kDBLinkObjectList = "DBLink Objects"

Definition at line 608 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kDeflineExists

const string kDeflineExists = "[n] Bioseq[s] [has] definition line"

Definition at line 1037 of file sequence_tests.cpp.

◆ kFixable

const string kFixable = "Fixable"
static

Definition at line 1688 of file sequence_tests.cpp.

◆ kIdenticalDeflines

const string kIdenticalDeflines = "[n] definition line[s] [is] identical"

Definition at line 74 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kInconsistentMolinfoTech

const string kInconsistentMolinfoTech = "[n] Molinfo[s] [is] missing field technique"
static

Definition at line 449 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kInconsistentMolinfoTechSummary

const string kInconsistentMolinfoTechSummary = "Molinfo Technique Report"
static

Definition at line 448 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kMissingDBLink

const string kMissingDBLink = "[n] Bioseq [is] missing DBLink object"

Definition at line 607 of file sequence_tests.cpp.

◆ kMrnaSequenceMinusStrandFeatures

const string kMrnaSequenceMinusStrandFeatures = "[n] mRNA sequences have features on the complement strand."
static

Definition at line 1206 of file sequence_tests.cpp.

◆ kNonFixable

const string kNonFixable = "Non-fixable"
static

Definition at line 1689 of file sequence_tests.cpp.

◆ kNoTaxnameInDefline

const string kNoTaxnameInDefline = "[n] defline[s] [does] not contain the complete taxname"

Definition at line 1064 of file sequence_tests.cpp.

◆ kPreviouslySeenFields

const string& kPreviouslySeenFields = "Previously Seen Fields"

Definition at line 630 of file sequence_tests.cpp.

Referenced by AddUserObjectFieldItems().

◆ kPreviouslySeenFieldsThis

const string& kPreviouslySeenFieldsThis = "Previously Seen Fields This"

Definition at line 631 of file sequence_tests.cpp.

Referenced by AddUserObjectFieldItems().

◆ kPreviouslySeenObjects

const string& kPreviouslySeenObjects = "Previously Seen Objects"

Definition at line 632 of file sequence_tests.cpp.

Referenced by AddUserObjectFieldItems().

◆ kSequencesWithGaps

const string kSequencesWithGaps = "[n] sequence[s] contain[S] gaps"

Definition at line 212 of file sequence_tests.cpp.

◆ kSomeIdenticalDeflines

const string kSomeIdenticalDeflines = "Defline Problem Report"

Definition at line 76 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kSpellFixes

SpellFixData kSpellFixes[]
static

Definition at line 1602 of file sequence_tests.cpp.

Referenced by FixTextInObject(), and UnitTest_FLATFILE_FIND().

◆ kSpellFixesSize

const size_t kSpellFixesSize = ArraySize(kSpellFixes)
static

◆ kStructuredCommentFieldPrefix

const string kStructuredCommentFieldPrefix = "structured comment field "

Definition at line 870 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kStructuredCommentObservedPrefixes

const string kStructuredCommentObservedPrefixes = "observed prefixes"

Definition at line 866 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kStructuredCommentObservedPrefixesThis

const string kStructuredCommentObservedPrefixesThis = "observed prefixes this"

Definition at line 867 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kStructuredCommentPrevious

const string kStructuredCommentPrevious = "previous"

Definition at line 869 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kStructuredCommentReport

const string kStructuredCommentReport = "collection"

Definition at line 868 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kStructuredCommentsSeqs

const string kStructuredCommentsSeqs = "sequences"

Definition at line 865 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ kUniqueDeflines

const string kUniqueDeflines = "[n] definition line[s] [is] unique"

Definition at line 73 of file sequence_tests.cpp.

Referenced by CDiscrepancyVisitorImpl< _Name >::Summarize().

◆ MIN_SEQUENCE_LEN

const size_t MIN_SEQUENCE_LEN = 20000
static

Definition at line 1815 of file sequence_tests.cpp.

◆ s_testcase_props_ALL_SEQS_CIRCULAR

constexpr CDiscrepancyCaseProps s_testcase_props_ALL_SEQS_CIRCULAR = { CDiscrepancyVisitorImpl<eTestNames:: ALL_SEQS_CIRCULAR >::Create, eTestTypes:: SEQUENCE , eTestNames:: ALL_SEQS_CIRCULAR , "ALL_SEQS_CIRCULAR" , "All sequences circular" , eDisc | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 1840 of file sequence_tests.cpp.

◆ s_testcase_props_ALL_SEQS_SHORTER_THAN_20kb

constexpr CDiscrepancyCaseProps s_testcase_props_ALL_SEQS_SHORTER_THAN_20kb = { CDiscrepancyVisitorImpl<eTestNames:: ALL_SEQS_SHORTER_THAN_20kb >::Create, eTestTypes:: SEQUENCE , eTestNames:: ALL_SEQS_SHORTER_THAN_20kb , "ALL_SEQS_SHORTER_THAN_20kb" , "Short sequences test" , eDisc | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 1818 of file sequence_tests.cpp.

◆ s_testcase_props_BIOPROJECT_ID

constexpr CDiscrepancyCaseProps s_testcase_props_BIOPROJECT_ID = { CDiscrepancyVisitorImpl<eTestNames:: BIOPROJECT_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: BIOPROJECT_ID , "BIOPROJECT_ID" , "Sequences with BioProject IDs" , eOncaller , nullptr }
staticconstexpr

Definition at line 246 of file sequence_tests.cpp.

◆ s_testcase_props_CHROMOSOME_PRESENT

constexpr CDiscrepancyCaseProps s_testcase_props_CHROMOSOME_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: CHROMOSOME_PRESENT >::Create, eTestTypes:: SEQ_SET , eTestNames:: CHROMOSOME_PRESENT , "CHROMOSOME_PRESENT" , "Chromosome present" , eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 1979 of file sequence_tests.cpp.

◆ s_testcase_props_COMMENT_PRESENT

constexpr CDiscrepancyCaseProps s_testcase_props_COMMENT_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: COMMENT_PRESENT >::Create, eTestTypes:: DESC , eTestNames:: COMMENT_PRESENT , "COMMENT_PRESENT" , "Comment descriptor present" , eOncaller , nullptr }
staticconstexpr

Definition at line 160 of file sequence_tests.cpp.

◆ s_testcase_props_COUNT_UNVERIFIED

constexpr CDiscrepancyCaseProps s_testcase_props_COUNT_UNVERIFIED = { CDiscrepancyVisitorImpl<eTestNames:: COUNT_UNVERIFIED >::Create, eTestTypes:: SEQUENCE , eTestNames:: COUNT_UNVERIFIED , "COUNT_UNVERIFIED" , "Count number of unverified sequences" , eOncaller , nullptr }
staticconstexpr

Definition at line 1018 of file sequence_tests.cpp.

◆ s_testcase_props_DEFLINE_ON_SET

constexpr CDiscrepancyCaseProps s_testcase_props_DEFLINE_ON_SET = { CDiscrepancyVisitorImpl<eTestNames:: DEFLINE_ON_SET >::Create, eTestTypes:: SEQ_SET , eTestNames:: DEFLINE_ON_SET , "DEFLINE_ON_SET" , "Titles on sets" , eOncaller , nullptr }
staticconstexpr

Definition at line 1277 of file sequence_tests.cpp.

◆ s_testcase_props_DEFLINE_PRESENT

constexpr CDiscrepancyCaseProps s_testcase_props_DEFLINE_PRESENT = { CDiscrepancyVisitorImpl<eTestNames:: DEFLINE_PRESENT >::Create, eTestTypes:: SEQUENCE , eTestNames:: DEFLINE_PRESENT , "DEFLINE_PRESENT" , "Test defline existence" , eDisc , nullptr }
staticconstexpr

Definition at line 1039 of file sequence_tests.cpp.

◆ s_testcase_props_DUP_DEFLINE

constexpr CDiscrepancyCaseProps s_testcase_props_DUP_DEFLINE = { CDiscrepancyVisitorImpl<eTestNames:: DUP_DEFLINE >::Create, eTestTypes:: SEQUENCE , eTestNames:: DUP_DEFLINE , "DUP_DEFLINE" , "Definition lines should be unique" , eOncaller , nullptr }
staticconstexpr

Definition at line 79 of file sequence_tests.cpp.

◆ s_testcase_props_EXON_ON_MRNA

constexpr CDiscrepancyCaseProps s_testcase_props_EXON_ON_MRNA = { CDiscrepancyVisitorImpl<eTestNames:: EXON_ON_MRNA >::Create, eTestTypes:: SEQUENCE , eTestNames:: EXON_ON_MRNA , "EXON_ON_MRNA" , "mRNA sequences should not have exons" , eOncaller | eSmart , nullptr }
staticconstexpr

Definition at line 395 of file sequence_tests.cpp.

◆ s_testcase_props_EXTERNAL_REFERENCE

constexpr CDiscrepancyCaseProps s_testcase_props_EXTERNAL_REFERENCE = { CDiscrepancyVisitorImpl<eTestNames:: EXTERNAL_REFERENCE >::Create, eTestTypes:: SEQUENCE , eTestNames:: EXTERNAL_REFERENCE , "EXTERNAL_REFERENCE" , "Sequence has external reference" , eDisc | eOncaller , nullptr }
staticconstexpr

Definition at line 298 of file sequence_tests.cpp.

◆ s_testcase_props_FEATURE_COUNT

constexpr CDiscrepancyCaseProps s_testcase_props_FEATURE_COUNT = { CDiscrepancyVisitorImpl<eTestNames:: FEATURE_COUNT >::Create, eTestTypes:: FEAT , eTestNames:: FEATURE_COUNT , "FEATURE_COUNT" , "Count features present or missing from sequences" , eOncaller | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 328 of file sequence_tests.cpp.

◆ s_testcase_props_FEATURE_MOLTYPE_MISMATCH

constexpr CDiscrepancyCaseProps s_testcase_props_FEATURE_MOLTYPE_MISMATCH = { CDiscrepancyVisitorImpl<eTestNames:: FEATURE_MOLTYPE_MISMATCH >::Create, eTestTypes:: SEQUENCE , eTestNames:: FEATURE_MOLTYPE_MISMATCH , "FEATURE_MOLTYPE_MISMATCH" , "Sequences with rRNA or misc_RNA features should be genomic DNA" , eOncaller , nullptr }
staticconstexpr

Definition at line 540 of file sequence_tests.cpp.

◆ s_testcase_props_FLATFILE_FIND

constexpr CDiscrepancyCaseProps s_testcase_props_FLATFILE_FIND = { CDiscrepancyVisitorImpl<eTestNames:: FLATFILE_FIND >::Create, eTestTypes:: SEQUENCE , eTestNames:: FLATFILE_FIND , "FLATFILE_FIND" , "Flatfile representation of object contains suspect text" , eOncaller , &g_aliases_FLATFILE_FIND }
staticconstexpr

Definition at line 1723 of file sequence_tests.cpp.

◆ s_testcase_props_GAPS

constexpr CDiscrepancyCaseProps s_testcase_props_GAPS = { CDiscrepancyVisitorImpl<eTestNames:: GAPS >::Create, eTestTypes:: SEQUENCE , eTestNames:: GAPS , "GAPS" , "Sequences with gaps" , eDisc | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 214 of file sequence_tests.cpp.

◆ s_testcase_props_HAS_PROJECT_ID

constexpr CDiscrepancyCaseProps s_testcase_props_HAS_PROJECT_ID = { CDiscrepancyVisitorImpl<eTestNames:: HAS_PROJECT_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: HAS_PROJECT_ID , "HAS_PROJECT_ID" , "Sequences with project IDs (looks for genome project IDs)" , eOncaller | eSmart , nullptr }
staticconstexpr

Definition at line 1116 of file sequence_tests.cpp.

◆ s_testcase_props_INCONSISTENT_DBLINK

constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_DBLINK = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_DBLINK >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_DBLINK , "INCONSISTENT_DBLINK" , "Inconsistent DBLink fields" , eDisc | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 695 of file sequence_tests.cpp.

◆ s_testcase_props_INCONSISTENT_MOLINFO_TECH

constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_MOLINFO_TECH = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_MOLINFO_TECH >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_MOLINFO_TECH , "INCONSISTENT_MOLINFO_TECH" , "Inconsistent Molinfo Techniques" , eDisc | eSmart , nullptr }
staticconstexpr

Definition at line 430 of file sequence_tests.cpp.

◆ s_testcase_props_INCONSISTENT_STRUCTURED_COMMENTS

constexpr CDiscrepancyCaseProps s_testcase_props_INCONSISTENT_STRUCTURED_COMMENTS = { CDiscrepancyVisitorImpl<eTestNames:: INCONSISTENT_STRUCTURED_COMMENTS >::Create, eTestTypes:: SEQUENCE , eTestNames:: INCONSISTENT_STRUCTURED_COMMENTS , "INCONSISTENT_STRUCTURED_COMMENTS" , "Inconsistent structured comments" , eDisc | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 872 of file sequence_tests.cpp.

◆ s_testcase_props_LOW_QUALITY_REGION

constexpr CDiscrepancyCaseProps s_testcase_props_LOW_QUALITY_REGION = { CDiscrepancyVisitorImpl<eTestNames:: LOW_QUALITY_REGION >::Create, eTestTypes:: SEQUENCE , eTestNames:: LOW_QUALITY_REGION , "LOW_QUALITY_REGION" , "Sequence contains regions of low quality" , eDisc | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 1262 of file sequence_tests.cpp.

◆ s_testcase_props_MISSING_DEFLINES

constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_DEFLINES = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_DEFLINES >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_DEFLINES , "MISSING_DEFLINES" , "Missing definition lines" , eAll , nullptr }
staticconstexpr

Definition at line 272 of file sequence_tests.cpp.

◆ s_testcase_props_MISSING_PROJECT

constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_PROJECT = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_PROJECT >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_PROJECT , "MISSING_PROJECT" , "Project not included" , eDisc | eTSA , nullptr }
staticconstexpr

Definition at line 990 of file sequence_tests.cpp.

◆ s_testcase_props_MISSING_STRUCTURED_COMMENT

constexpr CDiscrepancyCaseProps s_testcase_props_MISSING_STRUCTURED_COMMENT = { CDiscrepancyVisitorImpl<eTestNames:: MISSING_STRUCTURED_COMMENT >::Create, eTestTypes:: SEQUENCE , eTestNames:: MISSING_STRUCTURED_COMMENT , "MISSING_STRUCTURED_COMMENT" , "Structured comment not included" , eDisc | eTSA , nullptr }
staticconstexpr

Definition at line 971 of file sequence_tests.cpp.

◆ s_testcase_props_MITOCHONDRION_REQUIRED

constexpr CDiscrepancyCaseProps s_testcase_props_MITOCHONDRION_REQUIRED = { CDiscrepancyVisitorImpl<eTestNames:: MITOCHONDRION_REQUIRED >::Create, eTestTypes:: SEQUENCE , eTestNames:: MITOCHONDRION_REQUIRED , "MITOCHONDRION_REQUIRED" , "If D-loop or control region misc_feat is present, source must be mitochondrial" , eDisc | eOncaller , nullptr }
staticconstexpr

Definition at line 1298 of file sequence_tests.cpp.

◆ s_testcase_props_MRNA_ON_WRONG_SEQUENCE_TYPE

constexpr CDiscrepancyCaseProps s_testcase_props_MRNA_ON_WRONG_SEQUENCE_TYPE = { CDiscrepancyVisitorImpl<eTestNames:: MRNA_ON_WRONG_SEQUENCE_TYPE >::Create, eTestTypes:: SEQUENCE , eTestNames:: MRNA_ON_WRONG_SEQUENCE_TYPE , "MRNA_ON_WRONG_SEQUENCE_TYPE" , "Eukaryotic sequences that are not genomic or macronuclear should not have mRNA features" , eDisc | eOncaller , nullptr }
staticconstexpr

Definition at line 187 of file sequence_tests.cpp.

◆ s_testcase_props_MRNA_SEQUENCE_MINUS_STRAND_FEATURES

constexpr CDiscrepancyCaseProps s_testcase_props_MRNA_SEQUENCE_MINUS_STRAND_FEATURES = { CDiscrepancyVisitorImpl<eTestNames:: MRNA_SEQUENCE_MINUS_STRAND_FEATURES >::Create, eTestTypes:: SEQUENCE , eTestNames:: MRNA_SEQUENCE_MINUS_STRAND_FEATURES , "MRNA_SEQUENCE_MINUS_STRAND_FEATURES" , "mRNA sequences have CDS/gene on the complement strand" , eOncaller , nullptr }
staticconstexpr

Definition at line 1208 of file sequence_tests.cpp.

◆ s_testcase_props_MULTIPLE_CDS_ON_MRNA

constexpr CDiscrepancyCaseProps s_testcase_props_MULTIPLE_CDS_ON_MRNA = { CDiscrepancyVisitorImpl<eTestNames:: MULTIPLE_CDS_ON_MRNA >::Create, eTestTypes:: SEQUENCE , eTestNames:: MULTIPLE_CDS_ON_MRNA , "MULTIPLE_CDS_ON_MRNA" , "Multiple CDS on mRNA" , eOncaller | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 1179 of file sequence_tests.cpp.

◆ s_testcase_props_N_RUNS_14

constexpr CDiscrepancyCaseProps s_testcase_props_N_RUNS_14 = { CDiscrepancyVisitorImpl<eTestNames:: N_RUNS_14 >::Create, eTestTypes:: SEQUENCE , eTestNames:: N_RUNS_14 , "N_RUNS_14" , "Runs of more than 14 Ns" , eDisc | eTSA , nullptr }
staticconstexpr

Definition at line 284 of file sequence_tests.cpp.

◆ s_testcase_props_RNA_PROVIRAL

constexpr CDiscrepancyCaseProps s_testcase_props_RNA_PROVIRAL = { CDiscrepancyVisitorImpl<eTestNames:: RNA_PROVIRAL >::Create, eTestTypes:: SEQUENCE , eTestNames:: RNA_PROVIRAL , "RNA_PROVIRAL" , "RNA bioseqs are proviral" , eOncaller , nullptr }
staticconstexpr

Definition at line 1426 of file sequence_tests.cpp.

◆ s_testcase_props_SEQ_SHORTER_THAN_200bp

constexpr CDiscrepancyCaseProps s_testcase_props_SEQ_SHORTER_THAN_200bp = { CDiscrepancyVisitorImpl<eTestNames:: SEQ_SHORTER_THAN_200bp >::Create, eTestTypes:: SEQUENCE , eTestNames:: SEQ_SHORTER_THAN_200bp , "SEQ_SHORTER_THAN_200bp" , "Short Contig" , eDisc | eSubmitter | eSmart | eBig | eTSA , nullptr }
staticconstexpr

Definition at line 1385 of file sequence_tests.cpp.

◆ s_testcase_props_SEQ_SHORTER_THAN_50bp

constexpr CDiscrepancyCaseProps s_testcase_props_SEQ_SHORTER_THAN_50bp = { CDiscrepancyVisitorImpl<eTestNames:: SEQ_SHORTER_THAN_50bp >::Create, eTestTypes:: SEQUENCE , eTestNames:: SEQ_SHORTER_THAN_50bp , "SEQ_SHORTER_THAN_50bp" , "Find Short Sequences" , eDisc | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 1368 of file sequence_tests.cpp.

◆ s_testcase_props_SHORT_PROT_SEQUENCES

constexpr CDiscrepancyCaseProps s_testcase_props_SHORT_PROT_SEQUENCES = { CDiscrepancyVisitorImpl<eTestNames:: SHORT_PROT_SEQUENCES >::Create, eTestTypes:: SEQUENCE , eTestNames:: SHORT_PROT_SEQUENCES , "SHORT_PROT_SEQUENCES" , "Protein sequences should be at least 50 aa, unless they are partial" , eDisc | eOncaller | eSmart , nullptr }
staticconstexpr

Definition at line 146 of file sequence_tests.cpp.

◆ s_testcase_props_SMALL_GENOME_SET_PROBLEM

constexpr CDiscrepancyCaseProps s_testcase_props_SMALL_GENOME_SET_PROBLEM = { CDiscrepancyVisitorImpl<eTestNames:: SMALL_GENOME_SET_PROBLEM >::Create, eTestTypes:: SEQ_SET , eTestNames:: SMALL_GENOME_SET_PROBLEM , "SMALL_GENOME_SET_PROBLEM" , "Problems with small genome sets" , eOncaller , nullptr }
staticconstexpr

Definition at line 1501 of file sequence_tests.cpp.

◆ s_testcase_props_SUSPICIOUS_SEQUENCE_ID

constexpr CDiscrepancyCaseProps s_testcase_props_SUSPICIOUS_SEQUENCE_ID = { CDiscrepancyVisitorImpl<eTestNames:: SUSPICIOUS_SEQUENCE_ID >::Create, eTestTypes:: SEQUENCE , eTestNames:: SUSPICIOUS_SEQUENCE_ID , "SUSPICIOUS_SEQUENCE_ID" , "Suspicious sequence identifiers" , eOncaller | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 1911 of file sequence_tests.cpp.

◆ s_testcase_props_TAXNAME_NOT_IN_DEFLINE

constexpr CDiscrepancyCaseProps s_testcase_props_TAXNAME_NOT_IN_DEFLINE = { CDiscrepancyVisitorImpl<eTestNames:: TAXNAME_NOT_IN_DEFLINE >::Create, eTestTypes:: SEQUENCE , eTestNames:: TAXNAME_NOT_IN_DEFLINE , "TAXNAME_NOT_IN_DEFLINE" , "Complete taxname should be present in definition line" , eDisc | eOncaller , nullptr }
staticconstexpr

Definition at line 1066 of file sequence_tests.cpp.

◆ s_testcase_props_TEN_PERCENTN

constexpr CDiscrepancyCaseProps s_testcase_props_TEN_PERCENTN = { CDiscrepancyVisitorImpl<eTestNames:: TEN_PERCENTN >::Create, eTestTypes:: SEQUENCE , eTestNames:: TEN_PERCENTN , "10_PERCENTN" , "Greater than 10 percent Ns" , eDisc | eSubmitter | eSmart | eTSA , nullptr }
staticconstexpr

Definition at line 312 of file sequence_tests.cpp.

◆ s_testcase_props_TERMINAL_NS

constexpr CDiscrepancyCaseProps s_testcase_props_TERMINAL_NS = { CDiscrepancyVisitorImpl<eTestNames:: TERMINAL_NS >::Create, eTestTypes:: SEQUENCE , eTestNames:: TERMINAL_NS , "TERMINAL_NS" , "Ns at end of sequences" , eDisc | eSmart | eBig | eFatal , nullptr }
staticconstexpr

Definition at line 132 of file sequence_tests.cpp.

◆ s_testcase_props_TITLE_ENDS_WITH_SEQUENCE

constexpr CDiscrepancyCaseProps s_testcase_props_TITLE_ENDS_WITH_SEQUENCE = { CDiscrepancyVisitorImpl<eTestNames:: TITLE_ENDS_WITH_SEQUENCE >::Create, eTestTypes:: DESC , eTestNames:: TITLE_ENDS_WITH_SEQUENCE , "TITLE_ENDS_WITH_SEQUENCE" , "Sequence characters at end of defline" , eDisc | eSubmitter | eSmart | eBig , nullptr }
staticconstexpr

Definition at line 528 of file sequence_tests.cpp.

◆ s_testcase_props_UNUSUAL_NT

constexpr CDiscrepancyCaseProps s_testcase_props_UNUSUAL_NT = { CDiscrepancyVisitorImpl<eTestNames:: UNUSUAL_NT >::Create, eTestTypes:: SEQUENCE , eTestNames:: UNUSUAL_NT , "UNUSUAL_NT" , "Sequence contains unusual nucleotides" , eDisc | eSubmitter | eSmart , nullptr }
staticconstexpr

Definition at line 1050 of file sequence_tests.cpp.

◆ s_testcase_props_UNWANTED_SET_WRAPPER

constexpr CDiscrepancyCaseProps s_testcase_props_UNWANTED_SET_WRAPPER = { CDiscrepancyVisitorImpl<eTestNames:: UNWANTED_SET_WRAPPER >::Create, eTestTypes:: FEAT , eTestNames:: UNWANTED_SET_WRAPPER , "UNWANTED_SET_WRAPPER" , "Set wrapper on microsatellites or rearranged genes" , eOncaller , nullptr }
staticconstexpr

Definition at line 1560 of file sequence_tests.cpp.

◆ suspicious_id_re

constexpr auto suspicious_id_re = ctll::fixed_string{ "chromosome|plasmid|mito|chloroplast|apicoplast|plastid|^chr|^lg|\\bnw_|\\bnz_|\\bnm_|\\bnc_|\\bac_|cp\\d\\d\\d\\d\\d\\d|^x$|^y$|^z$|^w$|^mt$|^pltd$|^chl$" }
staticconstexpr

Definition at line 1897 of file sequence_tests.cpp.

Modified on Tue Feb 27 05:56:29 2024 by modify_doxy.py rev. 669887