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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/biosample__util_8hpp_source.html below:

NCBI C++ ToolKit: include/misc/biosample_util/biosample_util.hpp Source File

33 #ifndef BIOSAMPLE_CHK__UTIL__HPP 34 #define BIOSAMPLE_CHK__UTIL__HPP 69 typedef

pair<string, biosample_util::EStatus>

TStatus

;

83 CBiosampleFieldDiff

(

const string

& sequence_id,

const string

& biosample_id,

const string

& field_name,

const string

& src_val,

const string

& sample_val) :

123 const string

& biosample_accession,

124 size_t

& num_processed,

125

vector<string>& unprocessed_ids,

126 bool

use_dev_server =

false

127 bool

compare_structured_comments =

false

128 const string

& expected_prefix =

""

141 bool

include_comments =

false

const string

& expected_prefix =

""

);

148 const string

& id_prefix,

150 const string

& bioproject_accession,

151 const string

& default_owner,

152 const string

& hup_date,

153 const string

& comment,

155 bool

report_structured_comments,

156 const string

& expected_prefix);

169 const string

& bioSampleAcc,

189 size_t

keyWidth = 20,

190 size_t

valueWidth = 40);

User-defined methods of the data storage class.

string OwnerFromAffil(const CAffil &affil)

vector< CRef< CBiosampleFieldDiff > > TBiosampleFieldDiffList

bool ResolveSuppliedBioSampleAccession(const string &biosample_accession, vector< string > &biosample_ids)

vector< string > GetBioProjectIDs(CBioseq_Handle bh)

map< string, CRef< CSeq_descr > >::iterator TBioSamplesIterator

bool DoDiffsContainConflicts(const TBiosampleFieldDiffList &diffs, CNcbiOstream *log)

string GetBestBioseqLabel(CBioseq_Handle bsh)

EStatus GetBiosampleStatus(const string &accession, bool use_dev_server=false, TStatuses *cache=NULL)

bool UpdateBiosourceFromBiosample(const CBioSource &existingBioSource, CBioSource &newBioource)

map< string, EStatus > TStatuses

void PrintBioseqXML(CBioseq_Handle bh, const string &id_prefix, CNcbiOstream *report_stream, const string &bioproject_accession, const string &default_owner, const string &hup_date, const string &comment, bool first_seq_only, bool report_structured_comments, const string &expected_prefix)

CRef< CSeq_descr > GetBiosampleData(const string &accession, bool use_dev_server=false, TBioSamples *cache=NULL)

string GetBiosampleStatusName(EStatus status)

TBiosampleFieldDiffList GetBioseqDiffs(CBioseq_Handle bh, const string &biosample_accession, size_t &num_processed, vector< string > &unprocessed_ids, bool use_dev_server=false, bool compare_structured_comments=false, const string &expected_prefix="", TBioSamples *cache=NULL)

void GenerateDiffListFromBioSource(const CSeq_descr &bioSample, const CBioSource &bioSource, TBiosampleFieldDiffList &diffs)

bool AttributeNamesAreEquivalent(string name1, string name2)

pair< string, biosample_util::EStatus > TStatus

vector< string > GetBiosampleIDs(CBioseq_Handle bh)

map< string, EStatus >::iterator TStatusesIterator

void AddBioseqToTable(CBioseq_Handle bh, CSeq_table &table, bool with_id, bool include_comments=false, const string &expected_prefix="")

void PrettyPrint(const TBiosampleFieldDiffList &diffList, CNcbiOstream &ostr, size_t keyWidth=20, size_t valueWidth=40)

TBiosampleFieldDiffList GetFieldDiffs(const string &sequence_id, const string &biosample_id, const CBioSource &src, const CBioSource &sample)

@Affil.hpp User-defined methods of the data storage class.

~CBiosampleFieldDiff(void)

string GetSampleVal() const

CBiosampleFieldDiff(const string &sequence_id, const string &biosample_id, const CFieldDiff &diff)

int Compare(const CBiosampleFieldDiff &other)

static void PrintHeader(ncbi::CNcbiOstream &stream, bool show_seq_id=true)

void SetSequenceId(const string &id)

void PrettyPrint(ncbi::CNcbiOstream &stream, size_t keyWidth=20, size_t valueWidth=40) const

void Print(ncbi::CNcbiOstream &stream, bool show_seq_id=true) const

string GetPureSrcVal() const

const string & GetBioSample() const

string GetPureSampleVal() const

const string & GetSequenceId() const

CBiosampleFieldDiff(const string &sequence_id, const string &biosample_id, const string &field_name, const string &src_val, const string &sample_val)

int CompareAllButSequenceID(const CBiosampleFieldDiff &other)

const string & GetFieldName() const

@Seq_descr.hpp User-defined methods of the data storage class.

container_type::iterator iterator

Include a standard set of the NCBI C++ Toolkit most basic headers.

The NCBI C++ standard methods for dealing with std::string.

static DLIST_TYPE *DLIST_NAME() prev(DLIST_LIST_TYPE *list, DLIST_TYPE *item)

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table

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