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Public Member Functions | Static Public Member Functions | Static Public Attributes | Protected Member Functions | Static Protected Member Functions | List of all members
CTestAndRepData Class Referenceabstract

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#include <misc/discrepancy_report/hDiscRep_tests.hpp>

+ Inheritance diagram for CTestAndRepData:
+ Collaboration diagram for CTestAndRepData:

Public Member Functions

 CTestAndRepData ()
 
virtual ~CTestAndRepData ()
 
virtual void TestOnObj (const CBioseq_set &bioseq_set)=0
 
virtual void TestOnObj (const CSeq_entry &seq_entry)=0
 
virtual void TestOnObj (const CBioseq &bioseq)=0
 
virtual void TestOnObj (const CSeq_feat &seq_feat)=0
 
virtual void GetReport (CRef< CClickableItem > c_item)=0
 
virtual FAutofix GetAutofixFunc () const
 
virtual string GetName () const =0
 
string GetIsComment (unsigned cnt, const string &str)
 
string GetHasComment (unsigned cnt, const string &str)
 
string GetDoesComment (unsigned cnt, const string &str)
 
string GetOtherComment (unsigned cnt, const string &single_str, const string &plural_str)
 
string GetNoCntComment (unsigned cnt, const string &single_str, const string &plural_str)
 
string GetNoun (unsigned cnt, const string &str)
 
string GetDiscItemText (const CSeq_feat &obj)
 
string GetDiscItemText (const CSeq_submit &seq_submit)
 
string GetDiscItemText (const CBioseq &obj)
 
string GetDiscItemText (const CBioseq_set &objs)
 
string GetDiscItemText (const CSeqdesc &obj, const CSeq_entry &seq_entry)
 
string GetDiscItemText (const CSeqdesc &obj, const CBioseq &bioseq)
 
string GetDiscItemText (const CPerson_id &obj, const CSeq_entry &seq_entry)
 
string GetDiscItemText (const CSeq_entry &seq_entry)
 
string ListAuthNames (const CAuth_list &auths)
 
string ListAllAuths (const CPubdesc &pubdesc)
 
void RmvChar (string &in_out_str, string rm_chars)
 
- Public Member Functions inherited from CObject
 CObject (void)
 Constructor. More...
 
 CObject (const CObject &src)
 Copy constructor. More...
 
virtual ~CObject (void)
 Destructor. More...
 
CObjectoperator= (const CObject &src) THROWS_NONE
 Assignment operator. More...
 
bool CanBeDeleted (void) const THROWS_NONE
 Check if object can be deleted. More...
 
bool IsAllocatedInPool (void) const THROWS_NONE
 Check if object is allocated in memory pool (not system heap) More...
 
bool Referenced (void) const THROWS_NONE
 Check if object is referenced. More...
 
bool ReferencedOnlyOnce (void) const THROWS_NONE
 Check if object is referenced only once. More...
 
void AddReference (void) const
 Add reference to object. More...
 
void RemoveReference (void) const
 Remove reference to object. More...
 
void ReleaseReference (void) const
 Remove reference without deleting object. More...
 
virtual void DoNotDeleteThisObject (void)
 Mark this object as not allocated in heap – do not delete this object. More...
 
virtual void DoDeleteThisObject (void)
 Mark this object as allocated in heap – object can be deleted. More...
 
void * operator new (size_t size)
 Define new operator for memory allocation. More...
 
void * operator new[] (size_t size)
 Define new[] operator for 'array' memory allocation. More...
 
void operator delete (void *ptr)
 Define delete operator for memory deallocation. More...
 
void operator delete[] (void *ptr)
 Define delete[] operator for memory deallocation. More...
 
void * operator new (size_t size, void *place)
 Define new operator. More...
 
void operator delete (void *ptr, void *place)
 Define delete operator. More...
 
void * operator new (size_t size, CObjectMemoryPool *place)
 Define new operator using memory pool. More...
 
void operator delete (void *ptr, CObjectMemoryPool *place)
 Define delete operator. More...
 
virtual void DebugDump (CDebugDumpContext ddc, unsigned int depth) const
 Define method for dumping debug information. More...
 
- Public Member Functions inherited from CDebugDumpable
 CDebugDumpable (void)
 
virtual ~CDebugDumpable (void)
 
void DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const
 
void DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const
 

Static Public Member Functions

static bool AllCapitalLetters (const string &pattern, const string &search)
 
static bool BeginsWithPunct (const string &pattern, const string &search)
 
static bool BeginsOrEndsWithQuotes (const string &pattern, const string &search)
 
static bool ContainsDoubleSpace (const string &pattern, const string &search)
 
static bool ContainsPseudo (const string &pattern, const list< string > &strs)
 
static bool ContainsTwoSetsOfBracketsOrParentheses (const string &pattern, const string &search)
 
static bool ContainsWholeWord (const string &pattern, const string &search)
 
static bool ContainsWholeWord (const string &pattern, const list< string > &strs)
 
static bool ContainsWholeWordCaseSensitive (const string &pattern, const string &search)
 
static bool ContainsUnbalancedParentheses (const string &pattern, const string &search)
 
static bool ContainsUnderscore (const string &pattern, const string &search)
 
static bool ContainsUnknownName (const string &pattern, const string &search)
 
static bool EndsWithFold (const string &pattern, const string &search)
 
static bool EndsWithPattern (const string &pattern, const string &search)
 
static bool EndsWithPunct (const string &pattern, const string &search)
 
static bool IsSingleWord (const string &pattern, const string &search)
 
static bool IsSingleWordOrWeaselPlusSingleWord (const string &pattern, const string &search)
 
static bool IsTooLong (const string &pattern, const string &search)
 
static bool MayContainPlural (const string &pattern, const string &search)
 
static bool NormalSearch (const string &pattern, const string &search)
 
static bool PrefixPlusNumbersOnly (const string &pattern, const string &search)
 
static bool ProductContainsTerm (const string &pattern, const string &search)
 
static bool StartsWithPattern (const string &pattern, const string &search)
 
static bool StartsWithPutativeReplacement (const string &pattern, const string &search)
 
static bool ThreeOrMoreNumbersTogether (const string &pattern, const string &search)
 
static void HaemReplaceFunc (const string &str, const string &str2, const string &str3, const CSeq_feat &feat)
 
static void RemoveBeginningAndEndingQuotes (const string &str, const string &str2, const string &str3, const CSeq_feat &feat)
 
static void ReplaceWholeNameFunc (const string &str, const string &str2, const string &str3, const CSeq_feat &feat)
 
static void ReplaceWholeNameAddNoteFunc (const string &str, const string &str2, const string &str3, const CSeq_feat &feat)
 
static void SimpleReplaceAnywhereFunc (const string &str, const string &str2, const string &str3, const CSeq_feat &feat)
 
static void SimpleReplaceFunc (const string &str, const string &str2, const string &str3, const CSeq_feat &feat)
 
static void UsePutative (const string &str, const string &str2, const string &str3, const CSeq_feat &feat)
 
static string GetContainsComment (unsigned cnt, const string &str)
 
static bool IsmRNASequenceInGenProdSet (const CBioseq &bioseq)
 
static bool IsProdBiomol (const CBioseq &bioseq)
 
static string FindReplaceString (const string &src, const string &search_str, const string &replacement_str, bool case_sensitive=true, bool whole_word=true)
 
static bool DoesStringContainPhrase (const string &str, const string &phrase, bool case_sensitive=true, bool whole_word=true)
 
static string GetSrcQualValue (const CBioSource &biosrc, const string &qual_name, bool is_subsrc=false, const CString_constraint *str_cons=0)
 
static CConstRef< CSeq_featGetGeneForFeature (const CSeq_feat &seq_feat)
 
- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN void ThrowNullPointerException (const type_info &type)
 
static EAllocFillMode GetAllocFillMode (void)
 
static void SetAllocFillMode (EAllocFillMode mode)
 
static void SetAllocFillMode (const string &value)
 Set mode from configuration parameter value. More...
 
- Static Public Member Functions inherited from CDebugDumpable
static void EnableDebugDump (bool on)
 

Static Public Attributes

static vector< const CSeq_feat * > mix_feat
 
static vector< const CSeq_feat * > gene_feat
 
static vector< const CSeq_feat * > cd_feat
 
static vector< const CSeq_feat * > rna_feat
 
static vector< const CSeq_feat * > prot_feat
 
static vector< const CSeq_feat * > intron_feat
 
static vector< const CSeq_feat * > miscfeat_feat
 
static vector< const CSeq_feat * > biosrc_feat
 
static vector< const CSeq_feat * > biosrc_orgmod_feat
 
static vector< const CSeq_feat * > rbs_feat
 
static vector< const CSeq_feat * > biosrc_subsrc_feat
 
static vector< const CSeq_feat * > pub_feat
 
static vector< const CSeq_feat * > D_loop_feat
 
static vector< const CSeq_feat * > rna_not_mrna_feat
 
static vector< const CSeq_feat * > all_feat
 
static vector< const CSeq_feat * > non_prot_feat
 
static vector< const CSeq_feat * > rrna_feat
 
static vector< const CSeq_feat * > otherRna_feat
 
static vector< const CSeq_feat * > org_orgmod_feat
 
static vector< const CSeq_feat * > gap_feat
 
static vector< const CSeq_feat * > utr3_feat
 
static vector< const CSeq_feat * > utr5_feat
 
static vector< const CSeq_feat * > exon_feat
 
static vector< const CSeq_feat * > promoter_feat
 
static vector< const CSeq_feat * > mrna_feat
 
static vector< const CSeq_feat * > trna_feat
 
static vector< const CSeq_feat * > bioseq_biosrc_feat
 
static vector< const CSeqdesc * > bioseq_genbank
 
static vector< const CSeqdesc * > pub_seqdesc
 
static vector< const CSeqdesc * > comm_seqdesc
 
static vector< const CSeqdesc * > biosrc_seqdesc
 
static vector< const CSeqdesc * > title_seqdesc
 
static vector< const CSeqdesc * > biosrc_orgmod_seqdesc
 
static vector< const CSeqdesc * > user_seqdesc
 
static vector< const CSeqdesc * > org_orgmod_seqdesc
 
static vector< const CSeqdesc * > molinfo_seqdesc
 
static vector< const CSeqdesc * > biosrc_subsrc_seqdesc
 
static vector< const CSeqdesc * > bioseq_biosrc_seqdesc
 
static vector< const CSeqdesc * > bioseq_title
 
static vector< const CSeqdesc * > bioseq_user
 
static vector< const CSeq_entry * > pub_seqdesc_seqentry
 
static vector< const CSeq_entry * > comm_seqdesc_seqentry
 
static vector< const CSeq_entry * > biosrc_seqdesc_seqentry
 
static vector< const CSeq_entry * > title_seqdesc_seqentry
 
static vector< const CSeq_entry * > biosrc_orgmod_seqdesc_seqentry
 
static vector< const CSeq_entry * > user_seqdesc_seqentry
 
static vector< const CSeq_entry * > biosrc_subsrc_seqdesc_seqentry
 
static vector< const CSeq_entry * > molinfo_seqdesc_seqentry
 
static vector< const CSeq_entry * > org_orgmod_seqdesc_seqentry
 
- Static Public Attributes inherited from CObject
static const TCount eCounterBitsCanBeDeleted = 1 << 0
 Define possible object states. More...
 
static const TCount eCounterBitsInPlainHeap = 1 << 1
 Heap signature was found. More...
 
static const TCount eCounterBitsPlaceMask
 Mask for 'in heap' state flags. More...
 
static const int eCounterStep = 1 << 2
 Skip over the "in heap" bits. More...
 
static const TCount eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
 Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...
 
static const TCount eCounterStateMask
 Valid object, and object in heap. More...
 

Protected Member Functions

const stringx_GetUserObjType (const CUser_object &user_obj) const
 
bool CommentHasPhrase (string comment, const string &phrase)
 
bool HasLineage (const CBioSource &biosrc, const string &type)
 
bool IsEukaryotic (const CBioseq &bioseq)
 
bool IsBioseqHasLineage (const CBioseq &bioseq, const string &type, bool has_biosrc=true)
 
bool HasTaxonomyID (const CBioSource &biosec)
 
void GetProperCItem (CRef< CClickableItem > c_item, bool *citem1_used)
 
void AddSubcategory (CRef< CClickableItem > c_item, const string &setting_name, const vector< string > *itemlist, const string &desc1, const string &desc2, ECommentTp comm=e_IsComment, bool copy2parent=true, const string &desc3="", bool halfsize=false, unsigned input_cnt=0, bool rm_redundancy=false)
 
void GetTestItemList (const vector< string > &itemlist, Str2Strs &setting2list, const string &delim="$")
 
void GetTestItemList (const set< string > &itemlist, Str2Strs &setting2list, const string &delim="$")
 
void RmvRedundancy (vector< string > &items, vector< CConstRef< CObject > > &objs)
 
bool DoesStringContainPhrase (const string &str, const vector< string > &phrases, bool case_sensitive=true, bool whole_word=true)
 
bool IsOrgModPresent (const CBioSource &biosrc, COrgMod::ESubtype subtype)
 
bool IsSubSrcPresent (const CBioSource &biosrc, CSubSource::ESubtype subtype)
 
bool AllVecElementsSame (const vector< string > arr)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Static Protected Member Functions

static string Get1OrgModValue (const CBioSource &biosrc, const string &type_name)
 
static void GetOrgModValues (const COrg_ref &org, COrgMod::ESubtype subtype, vector< string > &strs)
 
static void GetOrgModValues (const CBioSource &biosrc, const string &type_name, vector< string > &strs)
 
static void GetOrgModValues (const CBioSource &biosrc, COrgMod::ESubtype subtype, vector< string > &strs)
 
static string Get1SubSrcValue (const CBioSource &biosrc, const string &type_name)
 
static void GetSubSrcValues (const CBioSource &biosrc, CSubSource::ESubtype subtype, vector< string > &strs)
 
static void GetSubSrcValues (const CBioSource &biosrc, const string &type_name, vector< string > &strs)
 

Additional Inherited Members

- Public Types inherited from CObject
enum  EAllocFillMode { eAllocFillNone = 1, eAllocFillZero, eAllocFillPattern }
 Control filling of newly allocated memory. More...
 
typedef CObjectCounterLocker TLockerType
 Default locker type for CRef. More...
 
typedef CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 

Detailed Description

Definition at line 611 of file hDiscRep_tests.hpp.

Constructor & Destructor Documentation

CTestAndRepData::CTestAndRepData ( )
inline

Definition at line 615 of file hDiscRep_tests.hpp.

virtual CTestAndRepData::~CTestAndRepData ( )
inlinevirtual

Definition at line 616 of file hDiscRep_tests.hpp.

Member Function Documentation

void CTestAndRepData::AddSubcategory ( CRef< CClickableItem c_item,
const string setting_name,
const vector< string > *  itemlist,
const string desc1,
const string desc2,
ECommentTp  comm = e_IsComment,
bool  copy2parent = true,
const string desc3 = "",
bool  halfsize = false,
unsigned  input_cnt = 0,
bool  rm_redundancy = false 
)
protected

Definition at line 1679 of file cDiscRep_util.cpp.

References cnt, copy(), CClickableItem::description, e_ContainsComment, e_DoesComment, e_HasComment, e_IsComment, e_NoCntComment, e_OtherComment, GetContainsComment(), GetDoesComment(), GetHasComment(), GetIsComment(), GetNoCntComment(), GetOtherComment(), CClickableItem::item_list, NCBI_USER_THROW, CClickableItem::obj_list, RmvRedundancy(), CClickableItem::setting_name, CClickableItem::subcategories, and CDiscRepInfo::test_item_objs.

Referenced by CBioseq_test_on_suspect_phrase::GetRepOfSuspPhrase(), CSeqEntry_DISC_CITSUBAFFIL_CONFLICT::GetReport(), CSeqEntry_DISC_TITLE_AUTHOR_CONFLICT::GetReport(), CSeqEntry_TEST_HAS_PROJECT_ID::GetReport(), CSeqEntry_ONCALLER_MISSING_STRUCTURED_COMMENTS::GetReport(), CSeqEntry_DIVISION_CODE_CONFLICTS::GetReport(), CSeqEntry_DISC_MISSING_VIRAL_QUALS::GetReport(), CSeqEntry_DISC_SUBMITBLOCK_CONFLICT::GetReport(), CSeqEntry_DISC_INCONSISTENT_MOLTYPES::GetReport(), CSeqEntry_DISC_MISMATCHED_COMMENTS::GetReport(), CBioseq_ZERO_BASECOUNT::GetReport(), CBioseq_DISC_DUP_DEFLINE::GetReport(), CBioseq_DISC_EXON_INTRON_CONFLICT::GetReport(), CBioseq_DISC_GENE_PARTIAL_CONFLICT::GetReport(), CBioseq_EXTRA_GENES::GetReport(), CBioseq_DISC_PROTEIN_NAMES::GetReport(), CBioseq_DISC_CDS_PRODUCT_FIND::GetReport(), CBioseq_DISC_FEATURE_LIST::GetReport(), CBioseq_JOINED_FEATURES::GetReport(), CBioseq_SUSPECT_PHRASES::GetReport(), CBioseq_DISC_SUSPECT_RRNA_PRODUCTS::GetReport(), CBioseq_DISC_INCONSISTENT_MOLINFO_TECH::GetReport(), CBioseq_ADJACENT_PSEUDOGENES::GetReport(), CBioseq_CONTAINED_CDS::GetReport(), CBioseq_DISC_SUSPICIOUS_NOTE_TEXT::GetReport(), CBioseq_TEST_BAD_GENE_NAME::GetReport(), CBioseq_DISC_SHORT_INTRON::GetReport(), CBioseq_FEATURE_LOCATION_CONFLICT::GetReport(), CBioseq_DUPLICATE_LOCUS_TAGS_global::GetReport(), CBioseq_DUPLICATE_LOCUS_TAGS::GetReport(), CBioseq_DISC_FEATURE_COUNT_oncaller::GetReport(), CBioseq_RNA_CDS_OVERLAP::GetReport(), CBioseq_DUPLICATE_GENE_LOCUS::GetReport(), CBioseq_OVERLAPPING_CDS::GetReport(), CSeqEntry_test_on_quals::GetReport_quals(), CBioseq_on_SUSPECT_RULE::GetReportForRules(), CBioseq_on_SUSPECT_RULE::GetReportForStaticList(), CSeqEntry_DISC_HAPLOTYPE_MISMATCH::MakeCitem4DiffSeqs(), CSeqEntry_DISC_HAPLOTYPE_MISMATCH::MakeCitem4SameSeqs(), CSeqEntry_test_on_quals::ProcessUniQuals(), CSeqEntry_on_incnst_user::x_GetIncnstTestReport(), and CBioseq_test_on_genprod_set::x_GetReport_dup().

bool CTestAndRepData::AllCapitalLetters ( const string pattern,
const string search 
)
static

Definition at line 256 of file cDiscRep_util.cpp.

References CDiscRepInfo::alpha_str, and IsAllCaps().

bool CTestAndRepData::AllVecElementsSame ( const vector< string arr)
protected

Definition at line 478 of file cDiscRep_util.cpp.

References ITERATE.

bool CTestAndRepData::BeginsOrEndsWithQuotes ( const string pattern,
const string search 
)
static

Definition at line 272 of file cDiscRep_util.cpp.

References len.

bool CTestAndRepData::BeginsWithPunct ( const string pattern,
const string search 
)
static

Definition at line 263 of file cDiscRep_util.cpp.

bool CTestAndRepData::CommentHasPhrase ( string  comment,
const string phrase 
)
protected
bool CTestAndRepData::ContainsDoubleSpace ( const string pattern,
const string search 
)
static

Definition at line 284 of file cDiscRep_util.cpp.

bool CTestAndRepData::ContainsPseudo ( const string pattern,
const list< string > &  strs 
)
static
bool CTestAndRepData::ContainsTwoSetsOfBracketsOrParentheses ( const string pattern,
const string search 
)
static
bool CTestAndRepData::ContainsUnbalancedParentheses ( const string pattern,
const string search 
)
static
bool CTestAndRepData::ContainsUnderscore ( const string pattern,
const string search 
)
static

Definition at line 352 of file cDiscRep_util.cpp.

References CSuspectRuleCheck::StringContainsUnderscore().

bool CTestAndRepData::ContainsUnknownName ( const string pattern,
const string search 
)
static

Definition at line 357 of file cDiscRep_util.cpp.

References NStr::FindNoCase(), and len.

bool CTestAndRepData::ContainsWholeWord ( const string pattern,
const string search 
)
static
bool CTestAndRepData::ContainsWholeWord ( const string pattern,
const list< string > &  strs 
)
static

Definition at line 333 of file cDiscRep_util.cpp.

References ContainsWholeWord(), and ITERATE.

bool CTestAndRepData::ContainsWholeWordCaseSensitive ( const string pattern,
const string search 
)
static

Definition at line 341 of file cDiscRep_util.cpp.

References DoesStringContainPhrase().

bool CTestAndRepData::DoesStringContainPhrase ( const string str,
const string phrase,
bool  case_sensitive = true,
bool  whole_word = true 
)
static
bool CTestAndRepData::DoesStringContainPhrase ( const string str,
const vector< string > &  phrases,
bool  case_sensitive = true,
bool  whole_word = true 
)
protected

Definition at line 644 of file cDiscRep_util.cpp.

References DoesStringContainPhrase(), and ITERATE.

bool CTestAndRepData::EndsWithFold ( const string pattern,
const string search 
)
static

Definition at line 367 of file cDiscRep_util.cpp.

References NStr::EqualNocase(), len, strtmp, and CTempString::substr().

bool CTestAndRepData::EndsWithPattern ( const string pattern,
const string search 
)
static

Definition at line 380 of file cDiscRep_util.cpp.

References NStr::EqualNocase(), and len.

Referenced by CRepConfig::InitParams().

bool CTestAndRepData::EndsWithPunct ( const string pattern,
const string search 
)
static

Definition at line 393 of file cDiscRep_util.cpp.

References len.

string CTestAndRepData::FindReplaceString ( const string src,
const string search_str,
const string replacement_str,
bool  case_sensitive = true,
bool  whole_word = true 
)
static
string CTestAndRepData::Get1OrgModValue ( const CBioSource biosrc,
const string type_name 
)
staticprotected

Definition at line 491 of file cDiscRep_util.cpp.

References GetOrgModValues(), and kEmptyStr.

Referenced by GetSrcQualValue().

string CTestAndRepData::Get1SubSrcValue ( const CBioSource biosrc,
const string type_name 
)
staticprotected

Definition at line 538 of file cDiscRep_util.cpp.

References GetSubSrcValues(), and kEmptyStr.

Referenced by GetSrcQualValue().

virtual FAutofix CTestAndRepData::GetAutofixFunc ( ) const
inlinevirtual

Reimplemented in CBioseq_OVERLAPPING_CDS.

Definition at line 624 of file hDiscRep_tests.hpp.

string CTestAndRepData::GetContainsComment ( unsigned  cnt,
const string str 
)
static
string CTestAndRepData::GetDiscItemText ( const CSeq_feat obj)

Definition at line 1539 of file cDiscRep_util.cpp.

References GetDiscrepancyItemText(), CRef< C, Locker >::GetPointer(), and CDiscRepInfo::scope.

Referenced by CSeqEntryTestAndRepData::AddBioseqsInSeqentryToReport(), CSeqEntryTestAndRepData::AddBioseqsOfSetToReport(), CSeqEntry_test_on_biosrc::AddEukaryoticBioseqsToReport(), CSeqEntry_INCONSISTENT_BIOSOURCE::AddSeqEntry(), CBioseq_OVERLAPPING_CDS::AddToDiscRep(), CSeqEntry_test_on_user::CheckCommentCountForSet(), CBioseq_test_on_suspect_phrase::CheckForProdAndComment(), CBioseq_test_on_missing_genes::CheckGenesForFeatureType(), CBioseq_on_Aa::CompareIntronExonList(), CBioseq_test_on_suspect_phrase::FindBadMiscFeatures(), CBioseq_test_on_rna::FindDupRNAsInList(), CBioseq_test_on_rna::FindMissingRNAsInList(), CBioseq_PSEUDO_MISMATCH::FindPseudoDiscrepancies(), CBioseq_SUSPECT_PHRASES::FindSuspectPhrases(), CBioseq_on_SUSPECT_RULE::FindSuspectProductNamesWithRules(), CBioseq_on_SUSPECT_RULE::FindSuspectProductNamesWithStaticList(), CBioseq_test_on_rna::FindtRNAsOnSameStrand(), CFlatfileTextFind::notify_bioseq(), CSeqEntry_DISC_HAPLOTYPE_MISMATCH::ReportHaplotypeSequenceMismatchForList(), CBioseq_on_Aa::ReportPartialConflictsForFeatureType(), CSeqEntry_DISC_HAPLOTYPE_MISMATCH::ReportSameTaxHaplotypeDiffSequenceMismatch(), CSeqEntry_test_on_biosrc::RunTests(), CBioseqSet_TEST_SMALL_GENOME_SET_PROBLEM::TestOnObj(), CBioseqSet_on_class::TestOnObj(), CSeqEntry_on_incnst_user::TestOnObj(), CSeqEntry_on_biosrc_subsrc::TestOnObj(), CSeqEntry_test_on_pub::TestOnObj(), CSeqEntry_test_on_defline::TestOnObj(), CSeqEntry_test_on_tax_cflts::TestOnObj(), CSeqEntry_test_on_quals::TestOnObj(), CSeqEntry_test_on_biosrc_orgmod::TestOnObj(), CSeqEntry_test_on_user::TestOnObj(), CSeqEntry_test_on_biosrc::TestOnObj(), CSeqEntry_ONCALLER_STRAIN_TAXNAME_CONFLICT::TestOnObj(), CSeqEntry_DISC_SUBMITBLOCK_CONFLICT::TestOnObj(), CSeqEntry_DISC_INCONSISTENT_MOLTYPES::TestOnObj(), CSeqEntry_INCONSISTENT_BIOSOURCE::TestOnObj(), CSeqEntry_on_comment::TestOnObj(), CBioseq_on_base::TestOnObj(), CBioseq_on_tax_def::TestOnObj(), CBioseq_on_Aa::TestOnObj(), CBioseq_on_mRNA::TestOnObj(), CBioseq_on_cd_feat::TestOnObj(), CBioseq_missing_genes_regular::TestOnObj(), CBioseq_missing_genes_oncaller::TestOnObj(), CBioseq_test_on_bac_partial::TestOnObj(), CBioseq_test_on_rrna::TestOnObj(), CBioseq_test_on_protfeat::TestOnObj(), CBioseq_test_on_genprod_set::TestOnObj(), CBioseq_test_on_prot::TestOnObj(), CBioseq_test_on_cd_4_transl::TestOnObj(), CBioseq_test_on_rna::TestOnObj(), CBioseq_test_on_molinfo::TestOnObj(), CBioseq_test_on_all_annot::TestOnObj(), CBioseq_TEST_TERMINAL_NS::TestOnObj(), CBioseq_DISC_MISSING_DEFLINES::TestOnObj(), CBioseq_DISC_BAD_BGPIPE_QUALS::TestOnObj(), CBioseq_NO_PRODUCT_STRING::TestOnObj(), CBioseq_DISC_SUSPECT_RRNA_PRODUCTS::TestOnObj(), CBioseq_TEST_ORGANELLE_PRODUCTS::TestOnObj(), CBioseq_DISC_GAPS::TestOnObj(), CBioseq_DISC_INCONSISTENT_MOLINFO_TECH::TestOnObj(), CBioseq_TEST_MRNA_OVERLAPPING_PSEUDO_GENE::TestOnObj(), CBioseq_TEST_UNWANTED_SPACER::TestOnObj(), CBioseq_ONCALLER_HIV_RNA_INCONSISTENT::TestOnObj(), CBioseq_DISC_MITOCHONDRION_REQUIRED::TestOnObj(), CBioseq_DISC_MICROSATELLITE_REPEAT_TYPE::TestOnObj(), CBioseq_DISC_mRNA_ON_WRONG_SEQUENCE_TYPE::TestOnObj(), CBioseq_DISC_FEATURE_MOLTYPE_MISMATCH::TestOnObj(), CBioseq_ADJACENT_PSEUDOGENES::TestOnObj(), CBioseq_DISC_FEAT_OVERLAP_SRCFEAT::TestOnObj(), CBioseq_CDS_TRNA_OVERLAP::TestOnObj(), CBioseq_CONTAINED_CDS::TestOnObj(), CBioseq_EC_NUMBER_NOTE::TestOnObj(), CBioseq_NON_GENE_LOCUS_TAG::TestOnObj(), CBioseq_SHOW_TRANSL_EXCEPT::TestOnObj(), CBioseq_DISC_BACTERIA_SHOULD_NOT_HAVE_MRNA::TestOnObj(), CBioseq_on_mrna::TestOnObj(), CBioseq_GENE_PRODUCT_CONFLICT::TestOnObj(), CBioseq_TEST_UNUSUAL_MISC_RNA::TestOnObj(), CBioseq_DISC_PARTIAL_PROBLEMS::TestOnObj(), CBioseq_DISC_SUSPICIOUS_NOTE_TEXT::TestOnObj(), CBioseq_SHOW_HYPOTHETICAL_CDS_HAVING_GENE_NAME::TestOnObj(), CBioseq_TEST_LOW_QUALITY_REGION::TestOnObj(), CBioseq_on_bad_gene_name::TestOnObj(), CBioseq_DISC_BAD_GENE_STRAND::TestOnObj(), CBioseq_DISC_SHORT_INTRON::TestOnObj(), CBioseq_RNA_NO_PRODUCT::TestOnObj(), CBioseq_on_locus_tags::TestOnObj(), CBioseq_on_feat_cnt::TestOnObj(), CBioseq_RNA_CDS_OVERLAP::TestOnObj(), CBioseq_DISC_COUNT_NUCLEOTIDES::TestOnObj(), CBioseq_DUPLICATE_GENE_LOCUS::TestOnObj(), CBioseqTestAndRepData::TestOverlapping_ed_Feats(), CFlatfileTextFind::unified_notify(), CBioseq_FEATURE_LOCATION_CONFLICT::x_CheckFeatureTypeForLocationDiscrepancies(), CSeqEntry_TEST_ALIGNMENT_HAS_SCORE::x_CheckSeqEntryAlign(), CSeqEntry_on_incnst_user::x_ClassifyFlds(), CBioseq_on_locus_tags::x_CollectDupLocusTagGenes(), CFlatfileTextFind::x_GetDescAndObjRef4Seqdesc(), CSeqEntry_test_on_defline::x_HasDefline(), and CBioseq_FEATURE_LOCATION_CONFLICT::x_ReportFeat().

string CTestAndRepData::GetDiscItemText ( const CSeq_submit seq_submit)

Definition at line 958 of file cDiscRep_util.cpp.

References GetDiscrepancyItemText().

string CTestAndRepData::GetDiscItemText ( const CBioseq obj)
string CTestAndRepData::GetDiscItemText ( const CBioseq_set objs)

Definition at line 1025 of file cDiscRep_util.cpp.

References GetDiscrepancyItemText().

string CTestAndRepData::GetDiscItemText ( const CSeqdesc obj,
const CSeq_entry seq_entry 
)

Definition at line 1193 of file cDiscRep_util.cpp.

References GetDiscrepancyItemText().

string CTestAndRepData::GetDiscItemText ( const CSeqdesc obj,
const CBioseq bioseq 
)

Definition at line 1174 of file cDiscRep_util.cpp.

References GetDiscrepancyItemText().

string CTestAndRepData::GetDiscItemText ( const CPerson_id obj,
const CSeq_entry seq_entry 
)
string CTestAndRepData::GetDiscItemText ( const CSeq_entry seq_entry)

Definition at line 930 of file cDiscRep_util.cpp.

References GetDiscrepancyItemText().

string CTestAndRepData::GetDoesComment ( unsigned  cnt,
const string str 
)
CConstRef< CSeq_feat > CTestAndRepData::GetGeneForFeature ( const CSeq_feat seq_feat)
static
string CTestAndRepData::GetHasComment ( unsigned  cnt,
const string str 
)

Definition at line 1622 of file cDiscRep_util.cpp.

References NStr::UIntToString().

Referenced by AddSubcategory(), CSeqEntry_UNCULTURED_NOTES_ONCALLER::GetReport(), CSeqEntry_ONCALLER_SUSPECTED_ORG_COLLECTED::GetReport(), CSeqEntry_ONCALLER_SUSPECTED_ORG_IDENTIFIED::GetReport(), CSeqEntry_ONCALLER_MORE_NAMES_COLLECTED_BY::GetReport(), CSeqEntry_ONCALLER_MORE_OR_SPEC_NAMES_IDENTIFIED_BY::GetReport(), CSeqEntry_DISC_UNPUB_PUB_WITHOUT_TITLE::GetReport(), CSeqEntry_DISC_CITSUBAFFIL_CONFLICT::GetReport(), CSeqEntry_DISC_CITSUB_AFFIL_DUP_TEXT::GetReport(), CSeqEntry_DISC_CHECK_AUTH_CAPS::GetReport(), CSeqEntry_TEST_DEFLINE_PRESENT::GetReport(), CSeqEntry_TEST_AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE::GetReport(), CSeqEntry_DISC_HUMAN_HOST::GetReport(), CSeqEntry_ONCALLER_MULTIPLE_CULTURE_COLLECTION::GetReport(), CSeqEntry_ONCALLER_CHECK_AUTHORITY::GetReport(), CSeqEntry_DISC_METAGENOME_SOURCE::GetReport(), CSeqEntry_DISC_BACTERIA_MISSING_STRAIN::GetReport(), CSeqEntry_DUP_DISC_ATCC_CULTURE_CONFLICT::GetReport(), CSeqEntry_DUP_DISC_CBS_CULTURE_CONFLICT::GetReport(), CSeqEntry_DISC_BACTERIAL_TAX_STRAIN_MISMATCH::GetReport(), CSeqEntry_ONCALLER_STRAIN_CULTURE_COLLECTION_MISMATCH::GetReport(), CSeqEntry_TEST_UNNECESSARY_ENVIRONMENTAL::GetReport(), CSeqEntry_ONCALLER_DUPLICATE_PRIMER_SET::GetReport(), CSeqEntry_ONCALLER_COUNTRY_COLON::GetReport(), CSeqEntry_TEST_MISSING_PRIMER::GetReport(), CSeqEntry_TEST_SP_NOT_UNCULTURED::GetReport(), CSeqEntry_DISC_METAGENOMIC::GetReport(), CSeqEntry_DISC_BACTERIA_SHOULD_NOT_HAVE_ISOLATE::GetReport(), CSeqEntry_ONCALLER_MULTISRC::GetReport(), CSeqEntry_TEST_ALIGNMENT_HAS_SCORE::GetReport(), CSeqEntry_ONCALLER_STRAIN_TAXNAME_CONFLICT::GetReport(), CSeqEntry_DISC_INCONSISTENT_MOLTYPES::GetReport(), CSeqEntry_INCONSISTENT_BIOSOURCE::GetReport(), CBioseq_ZERO_BASECOUNT::GetReport(), CBioseq_DISC_PERCENT_N::GetReport(), CBioseq_DISC_10_PERCENTN::GetReport(), CBioseq_MULTIPLE_CDS_ON_MRNA::GetReport(), CBioseq_TEST_MRNA_SEQUENCE_MINUS_STRAND_FEATURES::GetReport(), CBioseq_TEST_EXON_ON_MRNA::GetReport(), CBioseq_TEST_BAD_MRNA_QUAL::GetReport(), CBioseq_TEST_CDS_HAS_CDD_XREF::GetReport(), CBioseq_DISC_CDS_HAS_NEW_EXCEPTION::GetReport(), CBioseq_MISSING_GENES::GetReport(), CBioseq_ONCALLER_GENE_MISSING::GetReport(), CBioseq_DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_EXCEPTION::GetReport(), CBioseq_DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS::GetReport(), CBioseq_DISC_PROTEIN_NAMES::GetReport(), CBioseq_EC_NUMBER_ON_UNKNOWN_PROTEIN::GetReport(), CBioseq_MISSING_GENPRODSET_PROTEIN::GetReport(), CBioseq_MISSING_GENPRODSET_TRANSCRIPT_ID::GetReport(), CBioseq_MISSING_PROTEIN_ID::GetReport(), CBioseq_INCONSISTENT_PROTEIN_ID::GetReport(), CBioseq_TRANSL_NO_NOTE::GetReport(), CBioseq_NOTE_NO_TRANSL::GetReport(), CBioseq_TRANSL_TOO_LONG::GetReport(), CBioseq_COUNT_RRNAS::GetReport(), CBioseq_ONCALLER_HAS_STANDARD_NAME::GetReport(), CBioseq_ONCALLER_ORDERED_LOCATION::GetReport(), CBioseq_JOINED_FEATURES::GetReport(), CBioseq_NO_ANNOTATION::GetReport(), CBioseq_TEST_TERMINAL_NS::GetReport(), CBioseq_DISC_MISSING_DEFLINES::GetReport(), CBioseq_NO_PRODUCT_STRING::GetReport(), CBioseq_TEST_MRNA_OVERLAPPING_PSEUDO_GENE::GetReport(), CBioseq_ONCALLER_HIV_RNA_INCONSISTENT::GetReport(), CBioseq_DISC_MITOCHONDRION_REQUIRED::GetReport(), CBioseq_DISC_FEATURE_MOLTYPE_MISMATCH::GetReport(), CBioseq_CDS_TRNA_OVERLAP::GetReport(), CBioseq_EC_NUMBER_NOTE::GetReport(), CBioseq_NON_GENE_LOCUS_TAG::GetReport(), CBioseq_SHOW_TRANSL_EXCEPT::GetReport(), CBioseq_DISC_BACTERIA_SHOULD_NOT_HAVE_MRNA::GetReport(), CBioseq_GENE_PRODUCT_CONFLICT::GetReport(), CBioseq_DISC_PARTIAL_PROBLEMS::GetReport(), CBioseq_SHOW_HYPOTHETICAL_CDS_HAVING_GENE_NAME::GetReport(), CBioseq_RNA_NO_PRODUCT::GetReport(), CBioseq_FEATURE_LOCATION_CONFLICT::GetReport(), CBioseq_MISSING_LOCUS_TAGS::GetReport(), CBioseq_DUPLICATE_LOCUS_TAGS_global::GetReport(), CBioseq_DUPLICATE_LOCUS_TAGS::GetReport(), CBioseq_INCONSISTENT_LOCUS_TAG_PREFIX::GetReport(), CBioseq_DISC_FEATURE_COUNT_oncaller::GetReport(), CBioseq_DUPLICATE_GENE_LOCUS::GetReport(), CSeqEntry_test_on_tax_cflts::GetReport_cflts(), CSeqEntry_test_on_quals::GetReport_quals(), CBioseq_test_on_rna::GetReport_trna(), CSeqEntry_test_on_quals::MultiItem(), CSeqEntry_test_on_quals::ProcessUniQuals(), CBioseq_on_base::x_AddNsReport(), and CBioseq_test_on_genprod_set::x_GetReport_dup().

string CTestAndRepData::GetIsComment ( unsigned  cnt,
const string str 
)

Definition at line 1616 of file cDiscRep_util.cpp.

References NStr::UIntToString().

Referenced by AddSubcategory(), CBioseqSet_DISC_NONWGS_SETS_PRESENT::GetReport(), CBioseqSet_DISC_SEGSETS_PRESENT::GetReport(), CSeqEntry_DISC_MISSING_AFFIL::GetReport(), CSeqEntry_DISC_USA_STATE::GetReport(), CSeqEntry_ONCALLER_SWITCH_STRUCTURED_COMMENT_PREFIX::GetReport(), CSeqEntry_MISSING_GENOMEASSEMBLY_COMMENTS::GetReport(), CSeqEntry_DISC_REQUIRED_STRAIN::GetReport(), CSeqEntry_DISC_REQUIRED_CLONE::GetReport(), CSeqEntry_DISC_MISSING_VIRAL_QUALS::GetReport(), CSeqEntry_TAX_LOOKUP_MISSING::GetReport(), CBioseq_DISC_DUP_DEFLINE::GetReport(), CBioseq_RNA_PROVIRAL::GetReport(), CBioseq_NON_RETROVIRIDAE_PROVIRAL::GetReport(), CBioseq_TEST_COUNT_UNVERIFIED::GetReport(), CBioseq_SHORT_PROT_SEQUENCES::GetReport(), CBioseq_TEST_ORGANELLE_NOT_GENOMIC::GetReport(), CBioseq_DISC_EXON_INTRON_CONFLICT::GetReport(), CBioseq_SHORT_CONTIG::GetReport(), CBioseq_SHORT_SEQUENCES_200::GetReport(), CBioseq_SHORT_SEQUENCES::GetReport(), CBioseq_EXTRA_GENES::GetReport(), CBioseq_ONCALLER_SUPERFLUOUS_GENE::GetReport(), CBioseq_DISC_SHORT_RRNA::GetReport(), CBioseq_RRNA_NAME_CONFLICTS::GetReport(), CBioseq_TEST_SHORT_LNCRNA::GetReport(), CBioseq_FIND_BADLEN_TRNAS::GetReport(), CBioseq_MOLTYPE_NOT_MRNA::GetReport(), CBioseq_TECHNIQUE_NOT_TSA::GetReport(), CBioseq_DISC_LONG_NO_ANNOTATION::GetReport(), CBioseq_TEST_ORGANELLE_PRODUCTS::GetReport(), CBioseq_TEST_UNWANTED_SPACER::GetReport(), CBioseq_DISC_mRNA_ON_WRONG_SEQUENCE_TYPE::GetReport(), CBioseq_CONTAINED_CDS::GetReport(), CBioseq_DISC_SHORT_INTRON::GetReport(), CBioseq_DUPLICATE_LOCUS_TAGS_global::GetReport(), CBioseq_DUPLICATE_LOCUS_TAGS::GetReport(), CBioseq_BAD_LOCUS_TAG_FORMAT::GetReport(), CBioseq_DISC_COUNT_NUCLEOTIDES::GetReport(), CBioseq_DISC_DUP_DEFLINE::x_AddUniDef(), and CSeqEntry_on_incnst_user::x_GetIncnstTestReport().

virtual string CTestAndRepData::GetName ( ) const
pure virtual

Implemented in CSeqFeatTestAndRepData, CBioseq_OVERLAPPING_CDS, CBioseq_DUPLICATE_GENE_LOCUS, CBioseq_DISC_COUNT_NUCLEOTIDES, CBioseq_RNA_CDS_OVERLAP, CBioseq_DISC_QUALITY_SCORES, CBioseq_FIND_OVERLAPPED_GENES, CBioseq_OVERLAPPING_GENES, CBioseq_DISC_FEATURE_COUNT, CBioseq_DISC_FEATURE_COUNT_oncaller, CBioseq_on_feat_cnt, CBioseq_BAD_LOCUS_TAG_FORMAT, CBioseq_INCONSISTENT_LOCUS_TAG_PREFIX, CBioseq_DUPLICATE_LOCUS_TAGS, CBioseq_DUPLICATE_LOCUS_TAGS_global, CBioseq_MISSING_LOCUS_TAGS, CBioseq_on_locus_tags, CBioseq_FEATURE_LOCATION_CONFLICT, CBioseq_RNA_NO_PRODUCT, CBioseq_DISC_SHORT_INTRON, CBioseq_DISC_BAD_GENE_STRAND, CBioseq_DISC_BAD_BACTERIAL_GENE_NAME, CBioseq_TEST_BAD_GENE_NAME, CBioseq_on_bad_gene_name, CBioseq_TEST_LOW_QUALITY_REGION, CBioseq_TEST_OVERLAPPING_RRNAS, CBioseq_SHOW_HYPOTHETICAL_CDS_HAVING_GENE_NAME, CBioseq_DISC_SUSPICIOUS_NOTE_TEXT, CBioseq_DISC_PARTIAL_PROBLEMS, CBioseq_TEST_UNUSUAL_MISC_RNA, CBioseq_GENE_PRODUCT_CONFLICT, CBioseq_DISC_CDS_WITHOUT_MRNA, CBioseq_MRNA_SHOULD_HAVE_PROTEIN_TRANSCRIPT_IDS, CBioseq_on_mrna, CBioseq_DISC_BACTERIA_SHOULD_NOT_HAVE_MRNA, CBioseq_SHOW_TRANSL_EXCEPT, CBioseq_NON_GENE_LOCUS_TAG, CBioseq_EC_NUMBER_NOTE, CBioseq_PSEUDO_MISMATCH, CBioseq_CONTAINED_CDS, CBioseq_CDS_TRNA_OVERLAP, CBioseq_DISC_FEAT_OVERLAP_SRCFEAT, CBioseq_ADJACENT_PSEUDOGENES, CBioseq_DISC_FEATURE_MOLTYPE_MISMATCH, CBioseq_DISC_mRNA_ON_WRONG_SEQUENCE_TYPE, CBioseq_DISC_MICROSATELLITE_REPEAT_TYPE, CBioseq_DISC_MITOCHONDRION_REQUIRED, CBioseq_ONCALLER_HIV_RNA_INCONSISTENT, CBioseq_TEST_UNWANTED_SPACER, CBioseq_TEST_MRNA_OVERLAPPING_PSEUDO_GENE, CBioseq_DISC_INCONSISTENT_MOLINFO_TECH, CBioseq_DISC_GAPS, CBioseq_TEST_ORGANELLE_PRODUCTS, CBioseq_DISC_SUSPECT_RRNA_PRODUCTS, CBioseq_SUSPECT_PHRASES, CBioseq_NO_PRODUCT_STRING, CBioseq_DISC_BAD_BGPIPE_QUALS, CBioseq_DISC_MISSING_DEFLINES, CBioseq_SEQ_ID_PHRASES, CBioseq_TEST_TERMINAL_NS, CBioseq_DISC_LONG_NO_ANNOTATION, CBioseq_NO_ANNOTATION, CBioseq_JOINED_FEATURES, CBioseq_ONCALLER_ORDERED_LOCATION, CBioseq_DISC_FEATURE_LIST, CBioseq_ONCALLER_HAS_STANDARD_NAME, CBioseq_test_on_all_annot, CBioseq_TECHNIQUE_NOT_TSA, CBioseq_MOLTYPE_NOT_MRNA, CBioseq_PARTIAL_CDS_COMPLETE_SEQUENCE, CBioseq_DISC_POSSIBLE_LINKER, CBioseq_test_on_molinfo, CBioseq_FIND_DUP_RRNAS, CBioseq_COUNT_RRNAS, CBioseq_COUNT_TRNAS, CBioseq_FIND_DUP_TRNAS, CBioseq_FIND_BADLEN_TRNAS, CBioseq_FIND_STRAND_TRNAS, CBioseq_TEST_SHORT_LNCRNA, CBioseq_test_on_rna, CBioseq_TRANSL_TOO_LONG, CBioseq_NOTE_NO_TRANSL, CBioseq_TRANSL_NO_NOTE, CBioseq_test_on_cd_4_transl, CBioseq_INCONSISTENT_PROTEIN_ID, CBioseq_MISSING_PROTEIN_ID, CBioseq_COUNT_PROTEINS, CBioseq_test_on_prot, CBioseq_DISC_DUP_GENPRODSET_TRANSCRIPT_ID, CBioseq_MISSING_GENPRODSET_TRANSCRIPT_ID, CBioseq_DUP_GENPRODSET_PROTEIN, CBioseq_MISSING_GENPRODSET_PROTEIN, CBioseq_test_on_genprod_set, CBioseq_EC_NUMBER_ON_UNKNOWN_PROTEIN, CBioseq_DISC_CDS_PRODUCT_FIND, CBioseq_DISC_PROTEIN_NAMES, CBioseq_DISC_PROTEIN_NAMES_global, CBioseq_test_on_protfeat, CBioseq_DISC_CHECK_RNA_PRODUCTS_AND_COMMENTS, CBioseq_DISC_SUSPECT_MISC_FEATURES, CBioseq_test_on_suspect_phrase, CBioseq_RRNA_NAME_CONFLICTS, CBioseq_DISC_INTERNAL_TRANSCRIBED_SPACER_RRNA, CBioseq_DISC_SHORT_RRNA, CBioseq_test_on_rrna, CBioseq_DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS, CBioseq_DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_EXCEPTION, CBioseq_test_on_bac_partial, CBioseq_ONCALLER_SUPERFLUOUS_GENE, CBioseq_ONCALLER_GENE_MISSING, CBioseq_missing_genes_oncaller, CBioseq_EXTRA_GENES, CBioseq_MISSING_GENES, CBioseq_missing_genes_regular, CBioseq_test_on_missing_genes, CBioseq_DISC_CDS_HAS_NEW_EXCEPTION, CBioseq_TEST_CDS_HAS_CDD_XREF, CBioseq_on_cd_feat, CBioseq_TEST_BAD_MRNA_QUAL, CBioseq_TEST_EXON_ON_MRNA, CBioseq_TEST_MRNA_SEQUENCE_MINUS_STRAND_FEATURES, CBioseq_MULTIPLE_CDS_ON_MRNA, CBioseq_on_mRNA, CBioseq_SHORT_SEQUENCES, CBioseq_SHORT_SEQUENCES_200, CBioseq_SHORT_CONTIG, CBioseq_DISC_GENE_PARTIAL_CONFLICT, CBioseq_DISC_EXON_INTRON_CONFLICT, CBioseq_DISC_RBS_WITHOUT_GENE, CBioseq_TEST_UNNECESSARY_VIRUS_GENE, CBioseq_TEST_ORGANELLE_NOT_GENOMIC, CBioseq_SHORT_PROT_SEQUENCES, CBioseq_TEST_DUP_GENES_OPPOSITE_STRANDS, CBioseq_TEST_COUNT_UNVERIFIED, CBioseq_NON_RETROVIRIDAE_PROVIRAL, CBioseq_DISC_RETROVIRIDAE_DNA, CBioseq_RNA_PROVIRAL, CBioseq_EUKARYOTE_SHOULD_HAVE_MRNA, CBioseq_on_Aa, CBioseq_TEST_TAXNAME_NOT_IN_DEFLINE, CBioseq_INCONSISTENT_SOURCE_DEFLINE, CBioseq_DISC_DUP_DEFLINE, CBioseq_on_tax_def, CBioseq_on_SUSPECT_RULE, CBioseq_TEST_UNUSUAL_NT, CBioseq_DISC_10_PERCENTN, CBioseq_DISC_PERCENT_N, CBioseq_ZERO_BASECOUNT, CBioseq_N_RUNS_14, CBioseq_N_RUNS, CBioseq_on_base, CBioseqTestAndRepData, CSeqEntry_DISC_MISMATCHED_COMMENTS, CSeqEntry_ONCALLER_COMMENT_PRESENT, CSeqEntry_on_comment, CSeqEntry_INCONSISTENT_BIOSOURCE, CSeqEntry_DISC_HAPLOTYPE_MISMATCH, CSeqEntry_DISC_INCONSISTENT_MOLTYPES, CSeqEntry_DISC_SUBMITBLOCK_CONFLICT, CSeqEntry_ONCALLER_STRAIN_TAXNAME_CONFLICT, CSeqEntry_DISC_FLATFILE_FIND_ONCALLER, CSeqEntry_TEST_ALIGNMENT_HAS_SCORE, CFlatfileTextFind, CSeqEntry_ONCALLER_MULTISRC, CSeqEntry_DISC_BACTERIA_SHOULD_NOT_HAVE_ISOLATE, CSeqEntry_TAX_LOOKUP_MISMATCH, CSeqEntry_TAX_LOOKUP_MISSING, CSeqEntry_DISC_INFLUENZA_DATE_MISMATCH, CSeqEntry_DISC_MISSING_VIRAL_QUALS, CSeqEntry_DIVISION_CODE_CONFLICTS, CSeqEntry_DISC_MAP_CHROMOSOME_CONFLICT, CSeqEntry_DISC_REQUIRED_CLONE, CSeqEntry_DISC_TRINOMIAL_SHOULD_HAVE_QUALIFIER, CSeqEntry_DISC_METAGENOMIC, CSeqEntry_TEST_SP_NOT_UNCULTURED, CSeqEntry_TEST_MISSING_PRIMER, CSeqEntry_ONCALLER_COUNTRY_COLON, CSeqEntry_ONCALLER_DUPLICATE_PRIMER_SET, CSeqEntry_DISC_REQUIRED_STRAIN, CSeqEntry_TEST_UNNECESSARY_ENVIRONMENTAL, CSeqEntry_test_on_biosrc, CSeqEntry_MISSING_PROJECT, CSeqEntry_ONCALLER_MISSING_STRUCTURED_COMMENTS, CSeqEntry_TEST_HAS_PROJECT_ID, CSeqEntry_MISSING_GENOMEASSEMBLY_COMMENTS, CSeqEntry_ONCALLER_BIOPROJECT_ID, CSeqEntry_MISSING_STRUCTURED_COMMENT, CSeqEntry_ONCALLER_SWITCH_STRUCTURED_COMMENT_PREFIX, CSeqEntry_test_on_user, CSeqEntry_ONCALLER_STRAIN_CULTURE_COLLECTION_MISMATCH, CSeqEntry_DISC_BACTERIAL_TAX_STRAIN_MISMATCH, CSeqEntry_DUP_DISC_CBS_CULTURE_CONFLICT, CSeqEntry_DUP_DISC_ATCC_CULTURE_CONFLICT, CSeqEntry_DISC_BACTERIA_MISSING_STRAIN, CSeqEntry_DISC_METAGENOME_SOURCE, CSeqEntry_ONCALLER_CHECK_AUTHORITY, CSeqEntry_ONCALLER_MULTIPLE_CULTURE_COLLECTION, CSeqEntry_DISC_HUMAN_HOST, CSeqEntry_TEST_AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE, CSeqEntry_test_on_biosrc_orgmod, CSeqEntry_DISC_SOURCE_QUALS_ASNDISC_oncaller, CSeqEntry_DISC_SOURCE_QUALS_ASNDISC, CSeqEntry_DISC_SRC_QUAL_PROBLEM, CSeqEntry_DISC_DUP_SRC_QUAL, CSeqEntry_DISC_DUP_SRC_QUAL_DATA, CSeqEntry_DISC_MISSING_SRC_QUAL, CSeqEntry_test_on_quals, CSeqEntry_DISC_SPECVOUCHER_TAXNAME_MISMATCH, CSeqEntry_DISC_STRAIN_TAXNAME_MISMATCH, CSeqEntry_DISC_CULTURE_TAXNAME_MISMATCH, CSeqEntry_DISC_BIOMATERIAL_TAXNAME_MISMATCH, CSeqEntry_test_on_tax_cflts, CSeqEntry_ONCALLER_DEFLINE_ON_SET, CSeqEntry_DISC_TITLE_ENDS_WITH_SEQUENCE, CSeqEntry_TEST_DEFLINE_PRESENT, CSeqEntry_test_on_defline, CSeqEntry_DISC_CHECK_AUTH_CAPS, CSeqEntry_DISC_CITSUB_AFFIL_DUP_TEXT, CSeqEntry_DISC_USA_STATE, CSeqEntry_DISC_TITLE_AUTHOR_CONFLICT, CSeqEntry_DISC_CITSUBAFFIL_CONFLICT, CSeqEntry_DISC_UNPUB_PUB_WITHOUT_TITLE, CSeqEntry_DISC_MISSING_AFFIL, CSeqEntry_ONCALLER_CONSORTIUM, CSeqEntry_DISC_CHECK_AUTH_NAME, CSeqEntry_test_on_pub, CSeqEntry_ONCALLER_MORE_OR_SPEC_NAMES_IDENTIFIED_BY, CSeqEntry_ONCALLER_MORE_NAMES_COLLECTED_BY, CSeqEntry_ONCALLER_SUSPECTED_ORG_IDENTIFIED, CSeqEntry_ONCALLER_SUSPECTED_ORG_COLLECTED, CSeqEntry_END_COLON_IN_COUNTRY, CSeqEntry_UNCULTURED_NOTES_ONCALLER, CSeqEntry_on_biosrc_subsrc, CSeqEntry_DISC_INCONSISTENT_DBLINK, CSeqEntry_DISC_INCONSISTENT_STRUCTURED_COMMENTS, CSeqEntry_on_incnst_user, CSeqEntryTestAndRepData, CBioseqSet_DISC_SEGSETS_PRESENT, CBioseqSet_DISC_NONWGS_SETS_PRESENT, CBioseqSet_TEST_UNWANTED_SET_WRAPPER, CBioseqSet_on_class, CBioseqSet_TEST_SMALL_GENOME_SET_PROBLEM, and CBioseqSetTestAndRepData.

string CTestAndRepData::GetNoCntComment ( unsigned  cnt,
const string single_str,
const string plural_str 
)

Definition at line 1639 of file cDiscRep_util.cpp.

Referenced by AddSubcategory().

string CTestAndRepData::GetNoun ( unsigned  cnt,
const string str 
)
void CTestAndRepData::GetOrgModValues ( const COrg_ref org,
COrgMod::ESubtype  subtype,
vector< string > &  strs 
)
staticprotected
void CTestAndRepData::GetOrgModValues ( const CBioSource biosrc,
const string type_name,
vector< string > &  strs 
)
staticprotected
void CTestAndRepData::GetOrgModValues ( const CBioSource biosrc,
COrgMod::ESubtype  subtype,
vector< string > &  strs 
)
staticprotected

Definition at line 524 of file cDiscRep_util.cpp.

References CBioSource_Base::GetOrg(), and GetOrgModValues().

string CTestAndRepData::GetOtherComment ( unsigned  cnt,
const string single_str,
const string plural_str 
)
void CTestAndRepData::GetProperCItem ( CRef< CClickableItem c_item,
bool citem1_used 
)
protected

Definition at line 722 of file cDiscRep_util.cpp.

References CDiscRepInfo::disc_report_data, and CClickableItem::item_list.

virtual void CTestAndRepData::GetReport ( CRef< CClickableItem c_item)
pure virtual

Implemented in CSeqFeatTestAndRepData, CBioseq_OVERLAPPING_CDS, CBioseq_DUPLICATE_GENE_LOCUS, CBioseq_DISC_COUNT_NUCLEOTIDES, CBioseq_RNA_CDS_OVERLAP, CBioseq_DISC_QUALITY_SCORES, CBioseq_FIND_OVERLAPPED_GENES, CBioseq_OVERLAPPING_GENES, CBioseq_DISC_FEATURE_COUNT, CBioseq_DISC_FEATURE_COUNT_oncaller, CBioseq_on_feat_cnt, CBioseq_BAD_LOCUS_TAG_FORMAT, CBioseq_INCONSISTENT_LOCUS_TAG_PREFIX, CBioseq_DUPLICATE_LOCUS_TAGS, CBioseq_DUPLICATE_LOCUS_TAGS_global, CBioseq_MISSING_LOCUS_TAGS, CBioseq_on_locus_tags, CBioseq_FEATURE_LOCATION_CONFLICT, CBioseq_RNA_NO_PRODUCT, CBioseq_DISC_SHORT_INTRON, CBioseq_DISC_BAD_GENE_STRAND, CBioseq_DISC_BAD_BACTERIAL_GENE_NAME, CBioseq_TEST_BAD_GENE_NAME, CBioseq_on_bad_gene_name, CBioseq_TEST_LOW_QUALITY_REGION, CBioseq_TEST_OVERLAPPING_RRNAS, CBioseq_SHOW_HYPOTHETICAL_CDS_HAVING_GENE_NAME, CBioseq_DISC_SUSPICIOUS_NOTE_TEXT, CBioseq_DISC_PARTIAL_PROBLEMS, CBioseq_TEST_UNUSUAL_MISC_RNA, CBioseq_GENE_PRODUCT_CONFLICT, CBioseq_DISC_CDS_WITHOUT_MRNA, CBioseq_MRNA_SHOULD_HAVE_PROTEIN_TRANSCRIPT_IDS, CBioseq_on_mrna, CBioseq_DISC_BACTERIA_SHOULD_NOT_HAVE_MRNA, CBioseq_SHOW_TRANSL_EXCEPT, CBioseq_NON_GENE_LOCUS_TAG, CBioseq_EC_NUMBER_NOTE, CBioseq_PSEUDO_MISMATCH, CBioseq_CONTAINED_CDS, CBioseq_CDS_TRNA_OVERLAP, CBioseq_DISC_FEAT_OVERLAP_SRCFEAT, CBioseq_ADJACENT_PSEUDOGENES, CBioseq_DISC_FEATURE_MOLTYPE_MISMATCH, CBioseq_DISC_mRNA_ON_WRONG_SEQUENCE_TYPE, CBioseq_DISC_MICROSATELLITE_REPEAT_TYPE, CBioseq_DISC_MITOCHONDRION_REQUIRED, CBioseq_ONCALLER_HIV_RNA_INCONSISTENT, CBioseq_TEST_UNWANTED_SPACER, CBioseq_TEST_MRNA_OVERLAPPING_PSEUDO_GENE, CBioseq_DISC_INCONSISTENT_MOLINFO_TECH, CBioseq_DISC_GAPS, CBioseq_TEST_ORGANELLE_PRODUCTS, CBioseq_DISC_SUSPECT_RRNA_PRODUCTS, CBioseq_SUSPECT_PHRASES, CBioseq_NO_PRODUCT_STRING, CBioseq_DISC_BAD_BGPIPE_QUALS, CBioseq_DISC_MISSING_DEFLINES, CBioseq_SEQ_ID_PHRASES, CBioseq_TEST_TERMINAL_NS, CBioseq_DISC_LONG_NO_ANNOTATION, CBioseq_NO_ANNOTATION, CBioseq_JOINED_FEATURES, CBioseq_ONCALLER_ORDERED_LOCATION, CBioseq_DISC_FEATURE_LIST, CBioseq_ONCALLER_HAS_STANDARD_NAME, CBioseq_test_on_all_annot, CBioseq_TECHNIQUE_NOT_TSA, CBioseq_MOLTYPE_NOT_MRNA, CBioseq_PARTIAL_CDS_COMPLETE_SEQUENCE, CBioseq_DISC_POSSIBLE_LINKER, CBioseq_test_on_molinfo, CBioseq_FIND_DUP_RRNAS, CBioseq_COUNT_RRNAS, CBioseq_COUNT_TRNAS, CBioseq_FIND_DUP_TRNAS, CBioseq_FIND_BADLEN_TRNAS, CBioseq_FIND_STRAND_TRNAS, CBioseq_TEST_SHORT_LNCRNA, CBioseq_test_on_rna, CBioseq_TRANSL_TOO_LONG, CBioseq_NOTE_NO_TRANSL, CBioseq_TRANSL_NO_NOTE, CBioseq_test_on_cd_4_transl, CBioseq_INCONSISTENT_PROTEIN_ID, CBioseq_MISSING_PROTEIN_ID, CBioseq_COUNT_PROTEINS, CBioseq_test_on_prot, CBioseq_DISC_DUP_GENPRODSET_TRANSCRIPT_ID, CBioseq_MISSING_GENPRODSET_TRANSCRIPT_ID, CBioseq_DUP_GENPRODSET_PROTEIN, CBioseq_MISSING_GENPRODSET_PROTEIN, CBioseq_test_on_genprod_set, CBioseq_EC_NUMBER_ON_UNKNOWN_PROTEIN, CBioseq_DISC_CDS_PRODUCT_FIND, CBioseq_DISC_PROTEIN_NAMES, CBioseq_DISC_PROTEIN_NAMES_global, CBioseq_test_on_protfeat, CBioseq_DISC_CHECK_RNA_PRODUCTS_AND_COMMENTS, CBioseq_DISC_SUSPECT_MISC_FEATURES, CBioseq_test_on_suspect_phrase, CBioseq_RRNA_NAME_CONFLICTS, CBioseq_DISC_INTERNAL_TRANSCRIBED_SPACER_RRNA, CBioseq_DISC_SHORT_RRNA, CBioseq_test_on_rrna, CBioseq_DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_PROBLEMS, CBioseq_DISC_BACTERIAL_PARTIAL_NONEXTENDABLE_EXCEPTION, CBioseq_test_on_bac_partial, CBioseq_ONCALLER_SUPERFLUOUS_GENE, CBioseq_ONCALLER_GENE_MISSING, CBioseq_missing_genes_oncaller, CBioseq_EXTRA_GENES, CBioseq_MISSING_GENES, CBioseq_missing_genes_regular, CBioseq_test_on_missing_genes, CBioseq_DISC_CDS_HAS_NEW_EXCEPTION, CBioseq_TEST_CDS_HAS_CDD_XREF, CBioseq_on_cd_feat, CBioseq_TEST_BAD_MRNA_QUAL, CBioseq_TEST_EXON_ON_MRNA, CBioseq_TEST_MRNA_SEQUENCE_MINUS_STRAND_FEATURES, CBioseq_MULTIPLE_CDS_ON_MRNA, CBioseq_on_mRNA, CBioseq_SHORT_SEQUENCES, CBioseq_SHORT_SEQUENCES_200, CBioseq_SHORT_CONTIG, CBioseq_DISC_GENE_PARTIAL_CONFLICT, CBioseq_DISC_EXON_INTRON_CONFLICT, CBioseq_DISC_RBS_WITHOUT_GENE, CBioseq_TEST_UNNECESSARY_VIRUS_GENE, CBioseq_TEST_ORGANELLE_NOT_GENOMIC, CBioseq_SHORT_PROT_SEQUENCES, CBioseq_TEST_DUP_GENES_OPPOSITE_STRANDS, CBioseq_TEST_COUNT_UNVERIFIED, CBioseq_NON_RETROVIRIDAE_PROVIRAL, CBioseq_DISC_RETROVIRIDAE_DNA, CBioseq_RNA_PROVIRAL, CBioseq_EUKARYOTE_SHOULD_HAVE_MRNA, CBioseq_on_Aa, CBioseq_TEST_TAXNAME_NOT_IN_DEFLINE, CBioseq_INCONSISTENT_SOURCE_DEFLINE, CBioseq_DISC_DUP_DEFLINE, CBioseq_on_tax_def, CBioseq_on_SUSPECT_RULE, CBioseq_TEST_UNUSUAL_NT, CBioseq_DISC_10_PERCENTN, CBioseq_DISC_PERCENT_N, CBioseq_ZERO_BASECOUNT, CBioseq_N_RUNS_14, CBioseq_N_RUNS, CBioseq_on_base, CBioseqTestAndRepData, CSeqEntry_DISC_MISMATCHED_COMMENTS, CSeqEntry_ONCALLER_COMMENT_PRESENT, CSeqEntry_on_comment, CSeqEntry_INCONSISTENT_BIOSOURCE, CSeqEntry_DISC_HAPLOTYPE_MISMATCH, CSeqEntry_DISC_INCONSISTENT_MOLTYPES, CSeqEntry_DISC_SUBMITBLOCK_CONFLICT, CSeqEntry_ONCALLER_STRAIN_TAXNAME_CONFLICT, CSeqEntry_DISC_FLATFILE_FIND_ONCALLER, CSeqEntry_TEST_ALIGNMENT_HAS_SCORE, CFlatfileTextFind, CSeqEntry_ONCALLER_MULTISRC, CSeqEntry_DISC_BACTERIA_SHOULD_NOT_HAVE_ISOLATE, CSeqEntry_TAX_LOOKUP_MISMATCH, CSeqEntry_TAX_LOOKUP_MISSING, CSeqEntry_DISC_INFLUENZA_DATE_MISMATCH, CSeqEntry_DISC_MISSING_VIRAL_QUALS, CSeqEntry_DIVISION_CODE_CONFLICTS, CSeqEntry_DISC_MAP_CHROMOSOME_CONFLICT, CSeqEntry_DISC_REQUIRED_CLONE, CSeqEntry_DISC_TRINOMIAL_SHOULD_HAVE_QUALIFIER, CSeqEntry_DISC_METAGENOMIC, CSeqEntry_TEST_SP_NOT_UNCULTURED, CSeqEntry_TEST_MISSING_PRIMER, CSeqEntry_ONCALLER_COUNTRY_COLON, CSeqEntry_ONCALLER_DUPLICATE_PRIMER_SET, CSeqEntry_DISC_REQUIRED_STRAIN, CSeqEntry_TEST_UNNECESSARY_ENVIRONMENTAL, CSeqEntry_test_on_biosrc, CSeqEntry_MISSING_PROJECT, CSeqEntry_ONCALLER_MISSING_STRUCTURED_COMMENTS, CSeqEntry_TEST_HAS_PROJECT_ID, CSeqEntry_MISSING_GENOMEASSEMBLY_COMMENTS, CSeqEntry_ONCALLER_BIOPROJECT_ID, CSeqEntry_MISSING_STRUCTURED_COMMENT, CSeqEntry_ONCALLER_SWITCH_STRUCTURED_COMMENT_PREFIX, CSeqEntry_test_on_user, CSeqEntry_ONCALLER_STRAIN_CULTURE_COLLECTION_MISMATCH, CSeqEntry_DISC_BACTERIAL_TAX_STRAIN_MISMATCH, CSeqEntry_DUP_DISC_CBS_CULTURE_CONFLICT, CSeqEntry_DUP_DISC_ATCC_CULTURE_CONFLICT, CSeqEntry_DISC_BACTERIA_MISSING_STRAIN, CSeqEntry_DISC_METAGENOME_SOURCE, CSeqEntry_ONCALLER_CHECK_AUTHORITY, CSeqEntry_ONCALLER_MULTIPLE_CULTURE_COLLECTION, CSeqEntry_DISC_HUMAN_HOST, CSeqEntry_TEST_AMPLIFIED_PRIMERS_NO_ENVIRONMENTAL_SAMPLE, CSeqEntry_test_on_biosrc_orgmod, CSeqEntry_DISC_SOURCE_QUALS_ASNDISC_oncaller, CSeqEntry_DISC_SOURCE_QUALS_ASNDISC, CSeqEntry_DISC_SRC_QUAL_PROBLEM, CSeqEntry_DISC_DUP_SRC_QUAL, CSeqEntry_DISC_DUP_SRC_QUAL_DATA, CSeqEntry_DISC_MISSING_SRC_QUAL, CSeqEntry_test_on_quals, CSeqEntry_DISC_SPECVOUCHER_TAXNAME_MISMATCH, CSeqEntry_DISC_STRAIN_TAXNAME_MISMATCH, CSeqEntry_DISC_CULTURE_TAXNAME_MISMATCH, CSeqEntry_DISC_BIOMATERIAL_TAXNAME_MISMATCH, CSeqEntry_test_on_tax_cflts, CSeqEntry_ONCALLER_DEFLINE_ON_SET, CSeqEntry_DISC_TITLE_ENDS_WITH_SEQUENCE, CSeqEntry_TEST_DEFLINE_PRESENT, CSeqEntry_test_on_defline, CSeqEntry_DISC_CHECK_AUTH_CAPS, CSeqEntry_DISC_CITSUB_AFFIL_DUP_TEXT, CSeqEntry_DISC_USA_STATE, CSeqEntry_DISC_TITLE_AUTHOR_CONFLICT, CSeqEntry_DISC_CITSUBAFFIL_CONFLICT, CSeqEntry_DISC_UNPUB_PUB_WITHOUT_TITLE, CSeqEntry_DISC_MISSING_AFFIL, CSeqEntry_ONCALLER_CONSORTIUM, CSeqEntry_DISC_CHECK_AUTH_NAME, CSeqEntry_test_on_pub, CSeqEntry_ONCALLER_MORE_OR_SPEC_NAMES_IDENTIFIED_BY, CSeqEntry_ONCALLER_MORE_NAMES_COLLECTED_BY, CSeqEntry_ONCALLER_SUSPECTED_ORG_IDENTIFIED, CSeqEntry_ONCALLER_SUSPECTED_ORG_COLLECTED, CSeqEntry_END_COLON_IN_COUNTRY, CSeqEntry_UNCULTURED_NOTES_ONCALLER, CSeqEntry_on_biosrc_subsrc, CSeqEntry_DISC_INCONSISTENT_DBLINK, CSeqEntry_DISC_INCONSISTENT_STRUCTURED_COMMENTS, CSeqEntry_on_incnst_user, CSeqEntryTestAndRepData, CBioseqSet_DISC_SEGSETS_PRESENT, CBioseqSet_DISC_NONWGS_SETS_PRESENT, CBioseqSet_TEST_UNWANTED_SET_WRAPPER, CBioseqSet_on_class, CBioseqSet_TEST_SMALL_GENOME_SET_PROBLEM, and CBioseqSetTestAndRepData.

string CTestAndRepData::GetSrcQualValue ( const CBioSource biosrc,
const string qual_name,
bool  is_subsrc = false,
const CString_constraint str_cons = 0 
)
static
void CTestAndRepData::GetSubSrcValues ( const CBioSource biosrc,
CSubSource::ESubtype  subtype,
vector< string > &  strs 
)
staticprotected
void CTestAndRepData::GetSubSrcValues ( const CBioSource biosrc,
const string type_name,
vector< string > &  strs 
)
staticprotected
void CTestAndRepData::GetTestItemList ( const vector< string > &  itemlist,
Str2Strs setting2list,
const string delim = "$" 
)
protected

Definition at line 1655 of file cDiscRep_util.cpp.

References map_checker< Container >::clear(), NStr::eMergeDelims, ITERATE, and NStr::Tokenize().

Referenced by CSeqEntry_DISC_FLATFILE_FIND_ONCALLER::AddCItemToReport(), CBioseq_test_on_suspect_phrase::GetRepOfSuspPhrase(), CBioseqSet_TEST_SMALL_GENOME_SET_PROBLEM::GetReport(), CSeqEntry_DISC_CITSUBAFFIL_CONFLICT::GetReport(), CSeqEntry_DISC_TITLE_AUTHOR_CONFLICT::GetReport(), CSeqEntry_TEST_HAS_PROJECT_ID::GetReport(), CSeqEntry_ONCALLER_MISSING_STRUCTURED_COMMENTS::GetReport(), CSeqEntry_DIVISION_CODE_CONFLICTS::GetReport(), CSeqEntry_DISC_MISSING_VIRAL_QUALS::GetReport(), CSeqEntry_DISC_FLATFILE_FIND_ONCALLER::GetReport(), CSeqEntry_DISC_SUBMITBLOCK_CONFLICT::GetReport(), CSeqEntry_DISC_INCONSISTENT_MOLTYPES::GetReport(), CSeqEntry_DISC_HAPLOTYPE_MISMATCH::GetReport(), CSeqEntry_DISC_MISMATCHED_COMMENTS::GetReport(), CBioseq_ZERO_BASECOUNT::GetReport(), CBioseq_DISC_DUP_DEFLINE::GetReport(), CBioseq_INCONSISTENT_SOURCE_DEFLINE::GetReport(), CBioseq_DISC_EXON_INTRON_CONFLICT::GetReport(), CBioseq_DISC_GENE_PARTIAL_CONFLICT::GetReport(), CBioseq_EXTRA_GENES::GetReport(), CBioseq_DISC_PROTEIN_NAMES::GetReport(), CBioseq_DISC_CDS_PRODUCT_FIND::GetReport(), CBioseq_COUNT_PROTEINS::GetReport(), CBioseq_INCONSISTENT_PROTEIN_ID::GetReport(), CBioseq_FIND_BADLEN_TRNAS::GetReport(), CBioseq_COUNT_RRNAS::GetReport(), CBioseq_DISC_FEATURE_LIST::GetReport(), CBioseq_JOINED_FEATURES::GetReport(), CBioseq_SUSPECT_PHRASES::GetReport(), CBioseq_DISC_SUSPECT_RRNA_PRODUCTS::GetReport(), CBioseq_DISC_INCONSISTENT_MOLINFO_TECH::GetReport(), CBioseq_ADJACENT_PSEUDOGENES::GetReport(), CBioseq_DISC_FEAT_OVERLAP_SRCFEAT::GetReport(), CBioseq_CDS_TRNA_OVERLAP::GetReport(), CBioseq_CONTAINED_CDS::GetReport(), CBioseq_MRNA_SHOULD_HAVE_PROTEIN_TRANSCRIPT_IDS::GetReport(), CBioseq_GENE_PRODUCT_CONFLICT::GetReport(), CBioseq_DISC_SUSPICIOUS_NOTE_TEXT::GetReport(), CBioseq_TEST_BAD_GENE_NAME::GetReport(), CBioseq_DISC_BAD_GENE_STRAND::GetReport(), CBioseq_DISC_SHORT_INTRON::GetReport(), CBioseq_FEATURE_LOCATION_CONFLICT::GetReport(), CBioseq_DUPLICATE_LOCUS_TAGS_global::GetReport(), CBioseq_DUPLICATE_LOCUS_TAGS::GetReport(), CBioseq_INCONSISTENT_LOCUS_TAG_PREFIX::GetReport(), CBioseq_DISC_FEATURE_COUNT_oncaller::GetReport(), CBioseq_DISC_FEATURE_COUNT::GetReport(), CBioseq_RNA_CDS_OVERLAP::GetReport(), CBioseq_DUPLICATE_GENE_LOCUS::GetReport(), CBioseq_OVERLAPPING_CDS::GetReport(), CSeqEntry_test_on_tax_cflts::GetReport_cflts(), CSeqEntry_test_on_quals::GetReport_quals(), CBioseq_test_on_rna::GetReport_trna(), CBioseq_on_SUSPECT_RULE::GetReportForRules(), CBioseq_on_SUSPECT_RULE::GetReportForStaticList(), CSeqEntry_DISC_HAPLOTYPE_MISMATCH::MakeCitem4DiffSeqs(), CSeqEntry_DISC_HAPLOTYPE_MISMATCH::MakeCitem4SameSeqs(), CBioseq_on_base::x_AddNsReport(), CBioseq_DISC_FEATURE_COUNT_oncaller::x_AddSeqToAllSeqList(), CSeqEntry_on_incnst_user::x_GetIncnstTestReport(), CBioseq_test_on_genprod_set::x_GetReport_dup(), and CBioseq_test_on_rna::x_GetReport_dup().

void CTestAndRepData::GetTestItemList ( const set< string > &  itemlist,
Str2Strs setting2list,
const string delim = "$" 
)
protected
static void CTestAndRepData::HaemReplaceFunc ( const string str,
const string str2,
const string str3,
const CSeq_feat feat 
)
inlinestatic

Definition at line 656 of file hDiscRep_tests.hpp.

bool CTestAndRepData::HasLineage ( const CBioSource biosrc,
const string type 
)
protected
bool CTestAndRepData::HasTaxonomyID ( const CBioSource biosec)
protected
bool CTestAndRepData::IsBioseqHasLineage ( const CBioseq bioseq,
const string type,
bool  has_biosrc = true 
)
protected
bool CTestAndRepData::IsEukaryotic ( const CBioseq bioseq)
protected
bool CTestAndRepData::IsmRNASequenceInGenProdSet ( const CBioseq bioseq)
static
bool CTestAndRepData::IsOrgModPresent ( const CBioSource biosrc,
COrgMod::ESubtype  subtype 
)
protected
bool CTestAndRepData::IsProdBiomol ( const CBioseq bioseq)
static
bool CTestAndRepData::IsSingleWord ( const string pattern,
const string search 
)
static

Definition at line 403 of file cDiscRep_util.cpp.

References NStr::EqualNocase().

bool CTestAndRepData::IsSingleWordOrWeaselPlusSingleWord ( const string pattern,
const string search 
)
static
bool CTestAndRepData::IsSubSrcPresent ( const CBioSource biosrc,
CSubSource::ESubtype  subtype 
)
protected
bool CTestAndRepData::IsTooLong ( const string pattern,
const string search 
)
static

Definition at line 424 of file cDiscRep_util.cpp.

References NStr::FindNoCase().

string CTestAndRepData::ListAllAuths ( const CPubdesc pubdesc)
string CTestAndRepData::ListAuthNames ( const CAuth_list auths)
bool CTestAndRepData::MayContainPlural ( const string pattern,
const string search 
)
static

Definition at line 433 of file cDiscRep_util.cpp.

References CSuspectRuleCheck::StringMayContainPlural().

bool CTestAndRepData::NormalSearch ( const string pattern,
const string search 
)
static

Definition at line 438 of file cDiscRep_util.cpp.

References NStr::FindNoCase().

bool CTestAndRepData::PrefixPlusNumbersOnly ( const string pattern,
const string search 
)
static

Definition at line 444 of file cDiscRep_util.cpp.

References CSuspectRuleCheck::IsPrefixPlusNumbers().

bool CTestAndRepData::ProductContainsTerm ( const string pattern,
const string search 
)
static

Definition at line 449 of file cDiscRep_util.cpp.

References CSuspectRuleCheck::ProductContainsTerm().

static void CTestAndRepData::RemoveBeginningAndEndingQuotes ( const string str,
const string str2,
const string str3,
const CSeq_feat feat 
)
inlinestatic

Definition at line 660 of file hDiscRep_tests.hpp.

static void CTestAndRepData::ReplaceWholeNameAddNoteFunc ( const string str,
const string str2,
const string str3,
const CSeq_feat feat 
)
inlinestatic

Definition at line 668 of file hDiscRep_tests.hpp.

static void CTestAndRepData::ReplaceWholeNameFunc ( const string str,
const string str2,
const string str3,
const CSeq_feat feat 
)
inlinestatic

Definition at line 664 of file hDiscRep_tests.hpp.

void CTestAndRepData::RmvChar ( string in_out_str,
string  rm_chars 
)
void CTestAndRepData::RmvRedundancy ( vector< string > &  items,
vector< CConstRef< CObject > > &  objs 
)
protected
static void CTestAndRepData::SimpleReplaceAnywhereFunc ( const string str,
const string str2,
const string str3,
const CSeq_feat feat 
)
inlinestatic

Definition at line 672 of file hDiscRep_tests.hpp.

static void CTestAndRepData::SimpleReplaceFunc ( const string str,
const string str2,
const string str3,
const CSeq_feat feat 
)
inlinestatic

Definition at line 676 of file hDiscRep_tests.hpp.

bool CTestAndRepData::StartsWithPattern ( const string pattern,
const string search 
)
static

Definition at line 454 of file cDiscRep_util.cpp.

References NStr::EqualNocase(), and len.

Referenced by CRepConfig::InitParams(), and StartsWithPutativeReplacement().

bool CTestAndRepData::StartsWithPutativeReplacement ( const string pattern,
const string search 
)
static
virtual void CTestAndRepData::TestOnObj ( const CBioseq_set bioseq_set)
pure virtual
virtual void CTestAndRepData::TestOnObj ( const CSeq_entry seq_entry)
pure virtual
virtual void CTestAndRepData::TestOnObj ( const CBioseq bioseq)
pure virtual

Implemented in CSeqFeatTestAndRepData, CBioseq_OVERLAPPING_CDS, CBioseq_DUPLICATE_GENE_LOCUS, CBioseq_DISC_COUNT_NUCLEOTIDES, CBioseq_RNA_CDS_OVERLAP, CBioseq_DISC_QUALITY_SCORES, CBioseq_FIND_OVERLAPPED_GENES, CBioseq_OVERLAPPING_GENES, CBioseq_on_feat_cnt, CBioseq_on_locus_tags, CBioseq_FEATURE_LOCATION_CONFLICT, CBioseq_RNA_NO_PRODUCT, CBioseq_DISC_SHORT_INTRON, CBioseq_DISC_BAD_GENE_STRAND, CBioseq_on_bad_gene_name, CBioseq_TEST_LOW_QUALITY_REGION, CBioseq_TEST_OVERLAPPING_RRNAS, CBioseq_SHOW_HYPOTHETICAL_CDS_HAVING_GENE_NAME, CBioseq_DISC_SUSPICIOUS_NOTE_TEXT, CBioseq_DISC_PARTIAL_PROBLEMS, CBioseq_TEST_UNUSUAL_MISC_RNA, CBioseq_GENE_PRODUCT_CONFLICT, CBioseq_on_mrna, CBioseq_DISC_BACTERIA_SHOULD_NOT_HAVE_MRNA, CBioseq_SHOW_TRANSL_EXCEPT, CBioseq_NON_GENE_LOCUS_TAG, CBioseq_EC_NUMBER_NOTE, CBioseq_PSEUDO_MISMATCH, CBioseq_CONTAINED_CDS, CBioseq_CDS_TRNA_OVERLAP, CBioseq_DISC_FEAT_OVERLAP_SRCFEAT, CBioseq_ADJACENT_PSEUDOGENES, CBioseq_DISC_FEATURE_MOLTYPE_MISMATCH, CBioseq_DISC_mRNA_ON_WRONG_SEQUENCE_TYPE, CBioseq_DISC_MICROSATELLITE_REPEAT_TYPE, CBioseq_DISC_MITOCHONDRION_REQUIRED, CBioseq_ONCALLER_HIV_RNA_INCONSISTENT, CBioseq_TEST_UNWANTED_SPACER, CBioseq_TEST_MRNA_OVERLAPPING_PSEUDO_GENE, CBioseq_DISC_INCONSISTENT_MOLINFO_TECH, CBioseq_DISC_GAPS, CBioseq_TEST_ORGANELLE_PRODUCTS, CBioseq_DISC_SUSPECT_RRNA_PRODUCTS, CBioseq_SUSPECT_PHRASES, CBioseq_NO_PRODUCT_STRING, CBioseq_DISC_BAD_BGPIPE_QUALS, CBioseq_DISC_MISSING_DEFLINES, CBioseq_SEQ_ID_PHRASES, CBioseq_TEST_TERMINAL_NS, CBioseq_test_on_all_annot, CBioseq_test_on_molinfo, CBioseq_test_on_rna, CBioseq_test_on_cd_4_transl, CBioseq_test_on_prot, CBioseq_test_on_genprod_set, CBioseq_test_on_protfeat, CBioseq_test_on_suspect_phrase, CBioseq_test_on_rrna, CBioseq_test_on_bac_partial, CBioseq_missing_genes_oncaller, CBioseq_missing_genes_regular, CBioseq_test_on_missing_genes, CBioseq_on_cd_feat, CBioseq_on_mRNA, CBioseq_on_Aa, CBioseq_on_tax_def, CBioseq_on_SUSPECT_RULE, CBioseq_on_base, CBioseqTestAndRepData, CFlatfileTextFind, CSeqEntryTestAndRepData, and CBioseqSetTestAndRepData.

virtual void CTestAndRepData::TestOnObj ( const CSeq_feat seq_feat)
pure virtual
bool CTestAndRepData::ThreeOrMoreNumbersTogether ( const string pattern,
const string search 
)
static
static void CTestAndRepData::UsePutative ( const string str,
const string str2,
const string str3,
const CSeq_feat feat 
)
inlinestatic

Definition at line 680 of file hDiscRep_tests.hpp.

const string & CTestAndRepData::x_GetUserObjType ( const CUser_object user_obj) const
protected

Member Data Documentation

vector< const CSeq_feat * > CTestAndRepData::all_feat
static
vector< const CSeq_feat * > CTestAndRepData::bioseq_biosrc_feat
static
vector< const CSeqdesc * > CTestAndRepData::bioseq_biosrc_seqdesc
static
vector< const CSeqdesc * > CTestAndRepData::bioseq_genbank
static
vector< const CSeqdesc * > CTestAndRepData::bioseq_title
static
vector< const CSeqdesc * > CTestAndRepData::bioseq_user
static
vector< const CSeq_feat * > CTestAndRepData::biosrc_feat
static
vector< const CSeq_feat * > CTestAndRepData::biosrc_orgmod_feat
static
vector< const CSeqdesc * > CTestAndRepData::biosrc_orgmod_seqdesc
static
vector< const CSeq_entry * > CTestAndRepData::biosrc_orgmod_seqdesc_seqentry
static
vector< const CSeqdesc * > CTestAndRepData::biosrc_seqdesc
static
vector< const CSeq_entry * > CTestAndRepData::biosrc_seqdesc_seqentry
static
vector< const CSeq_feat * > CTestAndRepData::biosrc_subsrc_feat
static
vector< const CSeqdesc * > CTestAndRepData::biosrc_subsrc_seqdesc
static
vector< const CSeq_entry * > CTestAndRepData::biosrc_subsrc_seqdesc_seqentry
static
vector< const CSeq_feat * > CTestAndRepData::cd_feat
static
vector< const CSeqdesc * > CTestAndRepData::comm_seqdesc
static
vector< const CSeq_entry * > CTestAndRepData::comm_seqdesc_seqentry
static
vector< const CSeq_feat * > CTestAndRepData::D_loop_feat
static
vector< const CSeq_feat * > CTestAndRepData::exon_feat
static
vector< const CSeq_feat * > CTestAndRepData::gap_feat
static
vector< const CSeq_feat * > CTestAndRepData::gene_feat
static
vector< const CSeq_feat * > CTestAndRepData::intron_feat
static
vector< const CSeq_feat * > CTestAndRepData::miscfeat_feat
static
vector< const CSeq_feat * > CTestAndRepData::mix_feat
static
vector< const CSeqdesc * > CTestAndRepData::molinfo_seqdesc
static
vector< const CSeq_entry * > CTestAndRepData::molinfo_seqdesc_seqentry
static
vector< const CSeq_feat * > CTestAndRepData::mrna_feat
static
vector< const CSeq_feat * > CTestAndRepData::non_prot_feat
static
vector< const CSeq_feat * > CTestAndRepData::org_orgmod_feat
static
vector< const CSeqdesc * > CTestAndRepData::org_orgmod_seqdesc
static
vector< const CSeq_entry * > CTestAndRepData::org_orgmod_seqdesc_seqentry
static
vector< const CSeq_feat * > CTestAndRepData::otherRna_feat
static
vector< const CSeq_feat * > CTestAndRepData::promoter_feat
static
vector< const CSeq_feat * > CTestAndRepData::prot_feat
static
vector< const CSeq_feat * > CTestAndRepData::pub_feat
static
vector< const CSeqdesc * > CTestAndRepData::pub_seqdesc
static
vector< const CSeq_entry * > CTestAndRepData::pub_seqdesc_seqentry
static
vector< const CSeq_feat * > CTestAndRepData::rbs_feat
static
vector< const CSeq_feat * > CTestAndRepData::rna_feat
static
vector< const CSeq_feat * > CTestAndRepData::rna_not_mrna_feat
static
vector< const CSeq_feat * > CTestAndRepData::rrna_feat
static
vector< const CSeqdesc * > CTestAndRepData::title_seqdesc
static
vector< const CSeq_entry * > CTestAndRepData::title_seqdesc_seqentry
static
vector< const CSeq_feat * > CTestAndRepData::trna_feat
static
vector< const CSeqdesc * > CTestAndRepData::user_seqdesc
static
vector< const CSeq_entry * > CTestAndRepData::user_seqdesc_seqentry
static
vector< const CSeq_feat * > CTestAndRepData::utr3_feat
static
vector< const CSeq_feat * > CTestAndRepData::utr5_feat
static

The documentation for this class was generated from the following files:
Modified on Thu Sep 03 14:33:09 2015 by modify_doxy.py rev. 426318