37 #ifndef OBJECTS_SEQFEAT_BIOSOURCE_HPP
38 #define OBJECTS_SEQFEAT_BIOSOURCE_HPP
68 int GetGenCode(
int def = 1)
const;
74 static string GetOrganelleByGenome (
unsigned int genome);
80 static string GetStringFromOrigin (
unsigned int origin);
84 bool IsSetTaxname(
void)
const;
85 const string& GetTaxname(
void)
const;
87 bool IsSetCommon(
void)
const;
88 const string& GetCommon(
void)
const;
90 bool IsSetLineage(
void)
const;
91 const string& GetLineage(
void)
const;
93 bool IsSetGcode(
void)
const;
96 bool IsSetMgcode(
void)
const;
97 int GetMgcode(
void)
const;
99 bool IsSetPgcode(
void)
const;
100 int GetPgcode(
void)
const;
102 bool IsSetDivision(
void)
const;
103 const string& GetDivision(
void)
const;
105 bool IsSetOrgname(
void)
const;
106 const COrgName& GetOrgname(
void)
const;
108 bool IsSetOrgMod(
void)
const;
111 string GetRepliconName (
void)
const;
112 string GetBioprojectType (
void)
const;
113 string GetBioprojectLocation (
void)
const;
116 void SetDisableStrainForwarding(
bool val);
117 bool GetDisableStrainForwarding()
const;
120 void UpdateWithBioSample(
const CBioSource& biosample,
bool force,
bool is_local_copy =
false);
121 static bool ShouldIgnoreConflict(
const string&
label,
string src_val,
string sample_val,
bool is_local_copy =
false);
124 bool BiosampleDiffsOkForUpdate(
const TFieldDiffList& diffs)
const;
131 static bool IsStopWord(
const string&
value);
134 void RemoveCultureNotes(
bool is_species_level =
true);
135 bool RemoveLineageSourceNotes();
137 bool RemoveSubSource(
int subtype);
138 bool RemoveSubSource(
int subtype,
const string&
val);
139 bool RemoveOrgMod(
int subtype);
140 bool RemoveOrgMod(
int subtype,
const string&
val);
148 bool FixEnvironmentalSample();
151 bool RemoveNullTerms();
154 static bool AllowSexQualifier(
const string& lineage);
155 bool AllowSexQualifier()
const;
158 static bool AllowMatingTypeQualifier(
const string& lineage);
159 bool AllowMatingTypeQualifier()
const;
164 bool FixSexMatingTypeInconsistencies();
167 bool RemoveUnexpectedViralQualifiers();
169 bool FixGenomeForQualifiers();
171 static bool IsViral(
const string& lineage);
172 bool IsViral()
const;
184 void x_ClearCoordinatedBioSampleSubSources();
189 bool x_ShouldIgnoreNoteForBiosample()
const;
194 static void x_RemoveStopWords(
COrg_ref& org_ref);
219 CFieldDiff(
string field_name,
string src_val,
string sample_val) :
220 m_FieldName(field_name), m_SrcVal(src_val), m_SampleVal(sample_val)
vector< CRef< CFieldDiff > > TFieldDiffList
********************************************************************
void x_ClearCoordinatedBioSampleOrgMods()
CBioSource(const CBioSource &value)
pair< string, string > TNameVal
vector< TNameVal > TNameValList
CBioSource & operator=(const CBioSource &value)
static void x_InitStopWords(void)
CFieldDiff(string field_name, string src_val, string sample_val)
const string & GetSampleVal() const
const string & GetFieldName() const
const string & GetSrcVal() const
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
ECase
Which type of string comparison.
@ eCase
Case sensitive compare.
#define NCBI_SEQFEAT_EXPORT
static const char label[]
EGenome
biological context
static const GLdouble origin[]