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NCBI C++ ToolKit: src/gui/packages/pkg_sequence_edit/table_reader.cpp Source File

: m_Table(

), m_Seh(entry), m_id_guesser(id_guesser), m_ColProperties(column_properties),

m_ConstrField(constraint_field), m_StrConstraint(string_constraint),

m_CmdProccessor(cmd_processor)

* kMatchString =

;

adjust_field = field_name;

pos = adjust_field.find(

);

(pos != string::npos) {

adjust_field = adjust_field.substr(pos + 1, string::npos);

(guess_field_type) {

vector<CFieldNamePanel::EFieldType> guess_preference;

(

& it : guess_preference) {

(s_GetFieldType(field_name, it)) {

guess_field_type = it;

field_type = s_GuessFieldType(field_name);

s_GetFieldType(field_name, field_type);

field(field_name);

pos = field_name.find(

);

(pos != string::npos) {

field = field_name.substr(0, pos);

(

(field_name,

) || field_name ==

) {

(field_name.find(

) != string::npos) {

(field_name.find(

) != string::npos) {

(field_name.find(

) != string::npos) {

s_GetPropFromMetaInfo(

& meta_string,

& prop_name)

=

+ prop_name +

;

tag_idx = meta_string.find(

);

(tag_idx != string::npos) {

tag_end_idx = meta_string.find_first_of(

, tag_idx + 1);

start_idx = tag_idx +

(

).length();

(tag_end_idx == string::npos) {

= meta_string.substr(start_idx, meta_string.length() - start_idx);

= meta_string.substr(start_idx, tag_end_idx - start_idx);

s_GetExistingTextInstructionFromText(

& update_rule,

& separator)

(

(update_rule,

)) {

s_IsSequenceIDField(

& field)

(seen_id.

(id_value) != seen_id.

()) {

duplicate_id.

(id_value);

seen_id.

(id_value);

(!duplicate_id.

()) {

report->SetTitle(

(

));

report->Show(

);

(

, eInvalid,

);

(!wxEventLoopBase::GetActive() || !wxEventLoopBase::GetActive()->IsYielding())

modified =

;

desc_present =

;

desc_present =

;

wxGenericProgressDialog progress(

, wxEmptyString);

(

&seh : sehs)

it->SetTopSeqEntry(seh);

it->ResetChangedDescriptors();

it->ResetChangedFeatures();

progress.Update(100*

/

->GetNum_rows());

(!wxEventLoopBase::GetActive() || !wxEventLoopBase::GetActive()->IsYielding())

(

col_num = 0; col_num <

->GetColumns().

(); col_num++) {

(

col_num = 0; col_num <

->GetColumns().

(); col_num++) {

(col_num != id_col_num) {

(

->GetColumns()[col_num]->IsSetHeader()

&&

->GetColumns()[col_num]->GetHeader().IsSetTitle()) {

field_name =

->GetColumns()[col_num]->GetHeader().GetTitle();

(!field_name.empty()) {

field_subtype = s_GetSubtype(field_name, field_type);

field_name = s_AdjustFieldName(field_name, field_type);

(

col_num = 0; col_num <

->GetColumns().

(); col_num++) {

(col_num != id_col_num) {

(col_num < m_ColProperties->GetData().

()) {

col_meta_info = field_meta_info.

().

();

ur = s_GetPropFromMetaInfo(col_meta_info,

);

ts = s_GetPropFromMetaInfo(col_meta_info,

);

.push_back(s_GetExistingTextInstructionFromText(ur, ts));

blanks = s_GetPropFromMetaInfo(col_meta_info,

);

it = value_to_sehs.find(id_value);

(it != value_to_sehs.end())

value_to_sehs.clear();

(s_IsSequenceIDField(id_field_name))

id_field_name =

;

(

&fh : feathdlesmap) {

id_action->SetTopSeqEntry(bseh);

vector<string>& values = id_action->GetChangedValues();

(

v : values)

value_to_sehs[v].insert(bseh);

id_action->ResetChangedValues();

(!descrmap.

()) {

(descrmap.

(&*desc_iter) != descrmap.

()) {

id_action->SetTopSeqEntry(bseh);

vector<string>& values = id_action->GetChangedValues();

(

v : values)

value_to_sehs[v].insert(bseh);

id_action->ResetChangedValues();

constr_field_subtype = -1;

constr_field_subtype = s_GetSubtype(

, constr_field_type);

TEditingActionVec::iterator iter =

.begin();

(

col_num = 0; col_num <

->GetColumns().

() && rval && iter !=

.end(); col_num++) {

(col_num != id_col_num) {

(

->GetColumns()[col_num]->IsSetHeader()

&&

->GetColumns()[col_num]->GetHeader().IsSetTitle()) {

field_name =

->GetColumns()[col_num]->GetHeader().GetTitle();

(!field_name.empty()) {

field_subtype = s_GetSubtype(field_name, field_type);

field_name = s_AdjustFieldName(field_name, field_type);

(!field_constraint) {

constraint = field_constraint;

(!idfield_constraint) {

*constraint += idfield_constraint;

constraint = idfield_constraint;

(constraint && *iter) {

(*iter)->SetConstraint(constraint);

vector<edit::EExistingText>::iterator existing_text_it =

.begin();

(col_num < id_col_num) {

new_val =

->GetColumns()[col_num]->GetData().GetString()[

];

new_val =

->GetColumns()[col_num + 1]->GetData().GetString()[

];

(new_val.empty()) {

(!new_val.empty()) {

(*action)->SetExistingText(*existing_text_it);

(*action)->Apply(new_val);

User-defined methods of the data storage class.

void AddCommand(IEditCommand &command)

static string AutoMatchRNA(string field_name)

static string AutoMatchFeat(string field_name)

static string AutoMatchSrc(string field_name)

static string AutoMatchMolInfo(string field_name)

static string AutoMatchMisc(string field_name)

static string AutoMatchPub(string field_name)

static string AutoMatchDBLink(string field_name)

static string AutoMatchCGP(string field_name)

@ eFieldType_BankITComment

@ eFieldType_StructuredComment

void SetText(const wxString &text)

implements special composite command, which does not call to its internal commands when run the very ...

CRef< objects::edit::CStringConstraint > m_StrConstraint

TEditingActionVec m_ActionList

void x_GetIdColumnProps(size_t id_col_num)

CRef< objects::CSeq_table > m_Table

bool x_SetConstraints(size_t id_col_num, CRef< edit::CStringConstraint > id_constraint)

objects::CSeq_entry_Handle m_Seh

CFieldNamePanel::EFieldType m_IdFieldType

ICommandProccessor * m_CmdProccessor

vector< bool > m_EraseIfBlank

bool x_ApplyRowToEntry(int row, size_t id_col_num, CRef< CMacroCmdComposite > apply_cmd)

void x_CreateEditingActions(size_t id_col_num)

void x_InterpretColumnProperties(size_t id_col_num)

void x_SetTopSeqEntryForActions(const string &id_value, set< CSeq_entry_Handle > &sehs, const map< string, set< CSeq_entry_Handle > > &value_to_sehs)

static void s_GetValueToSehMap(objects::CSeq_entry_Handle seh, map< string, set< CSeq_entry_Handle > > &value_to_sehs, string id_field_name, CFieldNamePanel::EFieldType id_field_type, int id_subtype)

bool x_ApplyMiscSeqTableToSeqEntry(CRef< CMacroCmdComposite > apply_cmd)

vector< objects::edit::EExistingText > m_ExistingText

CMiscSeqTable(CRef< objects::CSeq_table > table, objects::CSeq_entry_Handle entry, edit::CSeqIdGuesser &id_guesser, CRef< objects::CUser_object > column_properties, const string &constraint_field=kEmptyStr, CRef< objects::edit::CStringConstraint > string_constraint=CRef< edit::CStringConstraint >(NULL), ICommandProccessor *cmd_processor=NULL)

void x_CheckDuplicateIds(CRef< CSeqTable_column > id_col)

CRef< objects::CUser_object > m_ColProperties

edit::CSeqIdGuesser & m_id_guesser

static CRef< CCmdComposite > GetPropagateUpCommand(objects::CSeq_entry_Handle seh)

static CRef< CCmdComposite > GetPropagateDownCommand(objects::CSeq_entry_Handle seh)

@ eSubtype_mat_peptide_aa

static ESubtype SubtypeNameToValue(CTempString sName)

Turn a string into its ESubtype which is NOT necessarily related to the identifier of the enum.

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

Undo/Redo interface for editing operations.

virtual void Execute(IEditCommand *command, wxWindow *window=0)=0

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

CRef< CEditingActionConstraint > CreateEditingActionConstraint(const string &field, CFieldNamePanel::EFieldType field_type, int subtype, const string &ncRNA_class, const string &const_field, CFieldNamePanel::EFieldType const_field_type, int const_subtype, string &const_ncRNA_class, CRef< CConstraintMatcher >constraint)

CIRef< IEditingAction > CreateAction(CSeq_entry_Handle seh, const string &field, CFieldNamePanel::EFieldType field_type, int subtype, const string &ncRNA_class=kEmptyStr, CConstRef< objects::CSeq_submit > submit=CConstRef< objects::CSeq_submit >(NULL))

const char * kDefinitionLineLabel

const char * kFieldTypeSeqId

const char * kBankITComment

const char * kSequenceIdColLabel

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

const string & GetMsg(void) const

Get message string.

#define NCBI_RETHROW_SAME(prev_exception, message)

Generic macro to re-throw the same exception.

virtual void Execute()

Do the editing action.

virtual void Unexecute()

Undo (opposite to Execute())

EDialogReturnValue NcbiMessageBox(const string &message, TDialogType type=eDialog_Ok, EDialogIcon icon=eIcon_Exclamation, const string &title="Error", EDialogTextMode text_mode=eRaw)

@ eContent

Untagged human-readable accession or the like.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

@ fIncludeGivenEntry

Include the top (given) entry.

@ fRecursive

Iterate recursively.

TObjectType & GetObject(void)

Get object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

static string Join(const TContainer &arr, const CTempString &delim)

Join strings using the specified delimiter.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static bool EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static enable_if< is_arithmetic< TNumeric >::value||is_convertible< TNumeric, Int8 >::value, string >::type NumericToString(TNumeric value, TNumToStringFlags flags=0, int base=10)

Convert numeric value to string.

static bool Equal(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2, ECase use_case=eCase)

Test for equality of a substring with another string.

@ eNocase

Case insensitive compare.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool IsId(void) const

Check if variant Id is selected.

const TTitle & GetTitle(void) const

Get the Title member data.

bool IsString(void) const

Check if variant String is selected.

const THeader & GetHeader(void) const

Get the Header member data.

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

const TString & GetString(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TId & GetId(void) const

Get the variant data.

@ e_not_set

No variant selected.

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

constexpr bool empty(list< Ts... >) noexcept

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

Defines NCBI C++ exception handling.

bool QualifierNamesAreEquivalent(string name1, string name2)

#define row(bind, expected)

@ eExistingText_append_semi

@ eExistingText_append_space

@ eExistingText_prefix_colon

@ eExistingText_append_none

@ eExistingText_leave_old

@ eExistingText_prefix_none

@ eExistingText_prefix_space

@ eExistingText_append_colon

@ eExistingText_prefix_comma

@ eExistingText_append_comma

@ eExistingText_prefix_semi

@ eExistingText_replace_old

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