28 #ifndef _SUBPREP_UTIL_H_
29 #define _SUBPREP_UTIL_H_
58 typedef pair<CSourceRequirements::EWizardType, string>
TWizardName;
125 bool AlreadyHasFeature(objects::CBioseq_Handle bh, objects::CSeqFeatData::ESubtype subtype);
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
User-defined methods of the data storage class.
Include a standard set of the NCBI C++ Toolkit most basic headers.
vector< CRef< CFeatureSeqTableColumnBase > > TFeatureSeqTableColumnList
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n table
const struct ncbi::grid::netcache::search::fields::KEY key
const GenericPointer< typename T::ValueType > T2 value
#define row(bind, expected)
vector< TWizardName > TWizardNameList
int CombineTables(CRef< objects::CSeq_table > dst, const objects::CSeq_table &src)
vector< string > FindNonUniqueStrings(const vector< string > &values)
bool AreAnyColumnValuesMissing(CRef< objects::CSeqTable_column > col)
int CountColumnRowConflicts(CRef< objects::CSeqTable_column > dst_id, CRef< objects::CSeqTable_column > dst_col, CRef< objects::CSeqTable_column > src_id, CRef< objects::CSeqTable_column > src_col)
bool AreAllColumnValuesTheSame(CRef< objects::CSeqTable_column > col, string default_val="")
int AddFeatureToSeqTable(const objects::CSeq_feat &f, CRef< objects::CSeq_table > table)
bool AddSeqEntryToSeqEntry(const objects::CSeq_entry *entry, objects::CSeq_entry_Handle seh, CRef< CCmdComposite > cmd, bool &has_nuc, bool &has_prot, bool create_general_only)
bool SaveTableFile(wxWindow *parent, wxString &save_file_dir, wxString &save_file_name, CRef< objects::CSeq_table > values_table)
CSourceRequirements::EWizardType GetWizardTypeFromName(string wizard_name)
int CountTableColumnConflicts(CRef< objects::CSeq_table > dst, const objects::CSeq_table &src)
CRef< objects::CUser_object > MakeWizardObject()
CRef< objects::CUser_object > MakeBankItSubmissionObject()
bool IsValidEmail(string email)
CRef< objects::CSeq_table > GetIdsFromSeqEntry(const objects::CSeq_entry &entry)
vector< string > SortUniqueStrings(const vector< string > &values)
bool IsWizardObject(const objects::CUser_object &user)
bool IsBankItSubmissionObject(const objects::CUser_object &user)
CRef< CCmdComposite > AddFeatureSeqTableToSeqEntry(CRef< objects::CSeq_table > table, objects::CSeq_entry_Handle entry, objects::CSeqFeatData::ESubtype subtype, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts)
CRef< CCmdComposite > RemoveMatchingFeaturesWithoutLocalIntFeatureIdsFromSeqEntry(objects::CSeq_entry_Handle entry, const objects::CSeq_feat &feat, const TFeatureSeqTableColumnList &reqs)
void AddProblemsColumnToFeatureSeqTable(CRef< objects::CSeq_table > table, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts)
bool IsSynonymForFalse(const string &val)
void SetWizardFieldInSeqEntryNoUndo(objects::CSeq_entry_Handle entry, string field_name, string value)
string GetDescAlternateEmailAddress(const objects::CSeqdesc &desc)
const string kSubmissionPreparationToolVersion
wxString GetAsnSqnExtensions()
void AddIdsFromSeqEntryToTable(const objects::CSeq_entry &entry, CRef< objects::CSeq_table > table)
int FindRowForSeqId(CRef< objects::CSeqTable_column > id_col, CRef< objects::CSeq_id > id)
CRef< CFeatureSeqTableColumnBase > GetColumnRuleForFeatureSeqTable(CRef< objects::CSeqTable_column > col, const TFeatureSeqTableColumnList &reqs, const TFeatureSeqTableColumnList &opts)
CRef< objects::CSeqTable_column > FindSeqIDColumn(const objects::CSeq_table &table)
bool IsSynonymForTrue(const string &val)
string SummarizeIdProblems(CRef< objects::CSeqTable_column > problems)
void DeleteTableRow(CRef< objects::CSeq_table > table, int row)
string GetAlternateEmailAddress(objects::CSeq_entry_Handle entry)
bool AlreadyHasFeature(objects::CBioseq_Handle bh, string key, string comment)
void RemoveProblemsColumn(CRef< objects::CSeq_table > values_table)
void SetAlternateEmailAddress(objects::CSeq_entry_Handle entry, string alt_email)
bool DoesColumnHaveValue(CRef< objects::CSeqTable_column > col, string val)
string GetFieldFromWizardObject(const objects::CUser_object &user, string field_name)
void ApplyReplacementIds(objects::CSeq_entry &entry, CRef< objects::CSeq_table > table)
bool AreAnyColumnValuesPresent(CRef< objects::CSeqTable_column > col, string default_val="")
vector< string > GetTrueFalseList()
pair< CSourceRequirements::EWizardType, string > TWizardName
const string kWizardLabel
string CheckFeatureAnnotation(objects::CSeq_entry_Handle entry, bool &is_ok)
void FixTableAfterImport(CRef< objects::CSeq_table > input_table)
string FindBadRows(CRef< objects::CSeq_table > src, CRef< objects::CSeq_table > dst, objects::CSeq_entry_Handle seh)
CRef< objects::CSeq_table > GetFeaturesFromSeqEntry(objects::CSeq_entry_Handle entry, const objects::CSeq_feat &feat, const TFeatureSeqTableColumnList &reqs)
bool IsTrueFalseList(const vector< string > &choices)
void SetUserAlternateEmailAddress(objects::CUser_object &u, string alt_email)
CRef< objects::CSeqTable_column > GetSeqIdProblems(CRef< objects::CSeq_table > new_ids, CRef< objects::CSeq_table > old_ids, size_t max_len)
bool HasLocalIntFeatureId(const objects::CSeq_feat &feat)
CRef< objects::CSeqTable_column > GetReplacementSeqIds(CRef< objects::CSeq_table > new_ids, CRef< objects::CSeq_table > old_ids, size_t max_len)
void MergeStringVectors(vector< string > &problems, vector< string > add)
TWizardNameList GetWizardNameList()