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

: m_Name (name), m_Required (required), m_ReportMissing (report_missing), m_Example (

)

vector<string> unwise_names;

unwise_names.push_back(

);

unwise_names.push_back(

);

unwise_names.push_back(

);

unwise_names.push_back(

);

unwise_names.push_back(

);

vector<string>::iterator s = unwise_names.begin();

(s != unwise_names.end()) {

;

;

((*mit)->GetSubtype() ==

&& (*mit)->IsSetSubname()) {

(*mit)->GetSubname();

all_numbers =

;

string::iterator it =

.begin();

(it !=

.end() && all_numbers) {

all_numbers =

;

rval =

;

((*mit)->GetSubtype() ==

&& (*mit)->IsSetName()) {

(*mit)->GetName();

(

.length() < 3) {

rval =

;

rval =

;

rval =

;

(*rit)->SetRequired(

);

(vector<string>, it, list) {

va_start ( arguments, num );

(

x = 0; x < num; x++ ) {

item = va_arg ( arguments,

* );

list.push_back(item );

va_end ( arguments );

(vector<string>, it, list) {

va_start ( arguments, num );

(

x = 0; x < num; x++ ) {

item = va_arg ( arguments,

* );

list.push_back(item );

va_end ( arguments );

this_val =

;

(

= 0;

< cols.size();

++) {

(

< cols[

]->GetData().GetSize()) {

this_val += cols[

]->GetData().GetString()[

] +

;

num_duplicates = 0;

(values_table->

() < 2 || uniqueness_list.size() < 1) {

description = uniqueness_list[0];

(j = 1; j < uniqueness_list.size(); j++) {

description +=

+ uniqueness_list[j];

vector<CRef<CSeqTable_column> > cols;

(j = 0; j < uniqueness_list.size(); j++) {

vector<string> u_list;

(u_list.begin(), u_list.end());

vector<string>::iterator sit = u_list.begin();

vector<string>::iterator sit2 = sit;

is_dup =

;

(sit2 != u_list.end()) {

sit2 = u_list.erase(sit2);

sit = u_list.erase(sit);

(sit2 != u_list.end()) {

(!is_dup && sit != u_list.end()) {

sit = u_list.erase(sit);

sit = u_list.begin();

(sit != u_list.end()) {

is_first =

;

row_problems[

] += description +

;

id_col->

().

()[first_row]->GetLabel(&id_label);

row_problems[

] += description +

+ id_label;

num_duplicates;

(one_of_list.size() < 1) {

description =

+ one_of_list[0];

(j = 1; j < one_of_list.size(); j++) {

description +=

+ one_of_list[j];

vector<CRef<CSeqTable_column> > cols;

(j = 0; j < one_of_list.size(); j++) {

(j = 0; j < cols.size() && !any; j++) {

problems->

().SetString()[

] +=

;

problems->

().SetString()[

] += description;

qual_report =

;

problems->

().SetString().push_back(

);

problems->

().SetString()[

] +=

;

problems->

().SetString()[

] += (*rit)->GetName() +

;

= (*rit)->GetFormatErrors(

);

problems->

().SetString()[

] +=

;

problems->

().SetString()[

] +=

;

problems->

().SetString()[

] += (*rit)->GetName() +

;

found_good_combo =

;

vector<string > uniqueness_problems;

vector<vector<int> > num_problems;

vector<string> this_list;

this_list.push_back(

);

(num_problems > 0) {

(best_num == 0 || best_num > num_problems) {

uniqueness_problems = this_list;

best_num = num_problems;

found_good_combo =

;

(!found_good_combo) {

(

= 0;

< uniqueness_problems.size();

++) {

problems->

().SetString()[

] +=

;

problems->

().SetString()[

] += uniqueness_problems[

];

}

(!

) {

any1 =

, any2 =

;

val_name = (*rit)->GetName();

= (*rit)->GetExample();

val_name +=

+

+

;

new_col->

().SetTitle(val_name);

(new_col->

().SetString().size() < (

) values_table->

()) {

new_col->

().SetString().push_back (

);

values_table->

().push_back(new_col);

{

, -1, -1,

} ,

{

, -1, -1,

} ,

{

, -1, -1,

} ,

{

, -1, -1,

} ,

{

, -1, -1,

} ,

{

, -1, -1,

} ,

{

, -1, -1,

} ,

{

, -1, -1,

} ,

{

, -1, -1,

} ,

{

, -1, -1,

} ,

{

, -1, -1,

} ,

requirements->

(

,

,

);

host =

;

(wizard_type) {

has_gelband_isolate =

;

(

= 0;

< isolate_col->

().GetSize() && !has_gelband_isolate;

++) {

has_gelband_isolate =

;

(has_gelband_isolate) {

(source_type) {

requirements->

(2, host,

);

requirements->

(2, host,

);

requirements->

(2, host,

);

(source_type) {

(source_type) {

requirements->

(5,

,

,

,

,

);

requirements->

(wizard_type, source_type);

vector<string>

;

((*sit)->IsSetName())

new_name = (*sit)->GetName();

(!new_name.empty())

.push_back(new_name);

this_seq =

;

new_seq =

;

((*sit)->IsSetSeq()) {

new_seq = (*sit)->GetSeq();

=

.length();

(

&name,

vector<string>& values)

(name ==

|| name ==

|| name ==

||

name ==

|| name ==

|| name ==

||

name ==

|| name ==

|| name ==

)

(

& name,

& newValue, vector<string> &values)

(name ==

|| name ==

|| name ==

||

name ==

|| name ==

|| name ==

||

name ==

|| name ==

|| name ==

)

values.push_back(newValue);

->SetColumns().push_back(id_col);

expand_col->

().SetTitle(

);

expand_col->

().SetField_name(

);

expand_col->

().SetString();

->SetColumns().push_back(expand_col);

taxname_col->

().SetTitle(

);

taxname_col->

().SetField_name(

);

taxname_col->

().SetString();

->SetColumns().push_back(taxname_col);

( ; b_iter ; ++b_iter ) {

->Assign (*(b_iter->

()));

id_col->

().SetId().push_back(

);

expand_col->

().SetString().push_back(

);

taxname_col->

().SetString().push_back(

);

((*sit)->IsSetName()) {

= (*sit)->GetName();

name_to_values[subtype_name].push_back(

);

(

& name_val : name_to_values)

subtype_name =

;

= (*sit)->GetSubname();

name_to_values[subtype_name].push_back(

);

(

& name_val : name_to_values)

db = (*sit)->GetDb();

((*sit)->GetTag().IsStr())

= (*sit)->GetTag().GetStr();

((*sit)->GetTag().IsId())

fwd_name =

;

rev_name =

;

fwd_seq =

;

rev_seq =

;

this_fwd_name =

;

this_fwd_seq =

;

this_rev_name =

;

this_rev_seq =

;

((*pit)->IsSetForward()) {

((*pit)->IsSetReverse()) {

fwd_name += this_fwd_name +

;

fwd_seq += this_fwd_seq +

;

rev_name += this_rev_name +

;

rev_seq += this_rev_seq +

;

->SetColumns().push_back(id_col);

vector< CRef<CSrcTableColumnBase> > handlers;

(vector<string>, q, qual_names) {

->SetColumns().push_back(col);

( ; b_iter ; ++b_iter ) {

->Assign (*(b_iter->

()));

id_col->

().SetId().push_back(

);

(

= 0;

< handlers.size();

++) {

->SetColumns()[

+ 1]->SetData().SetString().push_back(handlers[

]->GetFromBioSource(it->

()));

->SetColumns()[

+ 1]->SetData().SetString().push_back(

);

vector<CConstRef<CObject> >

;

.

(&(*desc_ci));

vector<CRef<CApplyObject> >

;

vector<string> vals;

vals.insert(vals.begin(), add.begin(), add.end());

vals.insert(vals.begin(), add.begin(), add.end());

vector<string> vals;

vals.push_back(

);

src.

().SetTaxname(orig_val);

in_out_bioSource.

().ResetTaxname();

new_taxname = src.

().substr(0, pos) + orig_val;

src.

().SetTaxname(new_taxname);

taxname = in_out_bioSource.

();

new_taxname = taxname.substr(0, pos);

in_out_bioSource.

().SetTaxname(new_taxname);

vector<string>

;

(

.empty()) {

(

.size() <= pos + 1) {

found_keyword =

;

(pos <

.size() && found_keyword) {

found_keyword =

;

found_keyword =

;

(

= 1;

<

(

)/

(

) && !found_keyword; ++

) {

found_keyword =

;

taxname_after_binomial =

;

(pos <

.size()) {

taxname_after_binomial +=

[pos] +

;

taxname_after_binomial;

(!organelle.empty())

vector<string> problems;

(vector<string>, it, values) {

problems.push_back(

+ *it +

+

);

problems.push_back(

);

vector<string> problems;

(vector<string>, it, values) {

problems.push_back(

+ *it +

+

);

problems.push_back(

);

vector<string> values;

CBioSource::TSubtype::iterator it = src.

().begin();

((*it)->GetSubtype() ==

) {

orig_val =

;

((*it)->IsSetName()) {

orig_val = (*it)->GetName();

(

< values.size())

(*it)->SetName(orig_val);

(;

< values.size();

++)

CBioSource::TSubtype::iterator it = in_out_bioSource.

().begin();

(it != in_out_bioSource.

().end()) {

((*it)->GetSubtype() ==

) {

it = in_out_bioSource.

().erase(it);

(in_out_bioSource.

().empty()) {

CBioSource::TSubtype::const_iterator it = in_out_bioSource.

().begin();

(it != in_out_bioSource.

().end()) {

((*it)->GetSubtype() ==

&& (*it)->IsSetName()) {

= (*it)->GetName();

vector<string> vals;

CBioSource::TSubtype::const_iterator it = biosrc.

().begin();

((*it)->GetSubtype() ==

&& (*it)->IsSetName()) {

= (*it)->GetName();

vals.push_back(

);

vector<string> values;

COrgName::TMod::iterator it = src.

().SetOrgname().SetMod().begin();

(it != src.

().SetOrgname().SetMod().end()) {

((*it)->GetSubtype() ==

) {

orig_val =

;

((*it)->IsSetSubname()) {

orig_val = (*it)->GetSubname();

(

< values.size())

(*it)->SetSubname(orig_val);

(;

< values.size();

++)

src.

().SetOrgname().SetMod().push_back(s);

COrgName::TMod::iterator it = in_out_bioSource.

().SetOrgname().SetMod().begin();

(it != in_out_bioSource.

().SetOrgname().SetMod().end()) {

((*it)->GetSubtype() ==

) {

it = in_out_bioSource.

().SetOrgname().SetMod().erase(it);

in_out_bioSource.

().SetOrgname().ResetMod();

((*it)->GetSubtype() ==

&& (*it)->IsSetSubname()) {

= (*it)->GetSubname();

vector<string> vals;

((*it)->GetSubtype() ==

&& (*it)->IsSetSubname()) {

= (*it)->GetSubname();

vals.push_back(

);

(; iter != sm_VouchMap.end(); ++iter){

(iter->second == stype_part){

(iter != sm_VouchMap.end()){

iter->second;

inst, coll, id;

vector<string> vals;

vals.push_back(

);

COrgName::TMod::iterator it = in_out_bioSource.

().SetOrgname().SetMod().begin();

(it != in_out_bioSource.

().SetOrgname().SetMod().end()) {

((*it)->GetSubtype() ==

&& (*it)->IsSetSubname()) {

inst, coll, id;

it = in_out_bioSource.

().SetOrgname().SetMod().erase(it);

(*it)->SetSubname(new_subname);

in_out_bioSource.

().SetOrgname().ResetMod();

found =

;

COrgName::TMod::iterator it = src.

().SetOrgname().SetMod().begin();

(it != src.

().SetOrgname().SetMod().end()) {

((*it)->GetSubtype() ==

) {

inst, coll, id;

((*it)->IsSetSubname()) {

(*it)->SetSubname(new_subname);

inst, coll, id;

src.

().SetOrgname().SetMod().push_back(s);

(!string_constraint) {

(!

.IsSet() ||

.Get().

() == 0) {

(!

.Get().front()->IsSetSeq()) {

(!

.Get().front()->IsSetName()) {

vector<string> vals;

(add.size() > 0) {

vals.insert(vals.end(), add.begin(), add.end());

vector<string> vals;

(add.size() > 0) {

vals.insert(vals.end(), add.begin(), add.end());

(add.size() > 0) {

vals.insert(vals.end(), add.begin(), add.end());

vector<string> vals;

((*it)->IsSetSeq()) {

vals.push_back((*it)->GetSeq());

((*it)->IsSetName()) {

vals.push_back((*it)->GetName());

try_this =

;

.Set().push_back(primer);

.Set().push_back(primer);

vector<string> values;

= orig_val;

((*it)->IsSetSeq()) {

= (*it)->GetSeq();

= orig_val;

((*it)->IsSetName()) {

= (*it)->GetName();

(*it)->SetName(name);

(;

< values.size();

++)

CPCRReactionSet::Tdata::iterator it = src.

().Set().begin();

(!(*it)->IsSetForward() && !(*it)->IsSetReverse()) {

(

.IsSet()) {

CPCRPrimerSet::Tdata::iterator it =

.Set().

();

(it !=

.Set().

()) {

is_empty =

;

((*it)->IsSetName()) {

= (*it)->GetName();

((*it)->IsSetSeq()) {

= (*it)->GetSeq();

vector<string> values;

= newValue;

(;

< values.size();

++)

(vals.size() > 0) {

vector<string> vals;

(add.size() > 0) {

vals.insert(vals.end(), add.begin(), add.end());

primer_value = fwdseq->GetFromBioSource(src);

primer_value = revseq->GetFromBioSource(src);

primer_value = fwdname->GetFromBioSource(src);

primer_value = revname->GetFromBioSource(src);

primer_value;

vector <string> vals;

note = fwdseq->GetFromBioSource(src);

(!note.empty()) {

vals.push_back(note);

note = revseq->GetFromBioSource(src);

(!note.empty()) {

vals.push_back(note);

note = fwdname->GetFromBioSource(src);

(!note.empty()) {

vals.push_back(note);

note = revname->GetFromBioSource(src);

(!note.empty()) {

vals.push_back(note);

(*db)->GetTag().AsString(oss);

vector<string> vals;

(*db)->GetLabel(&

);

vals.push_back(

);

vector<string> values;

(

: values)

(!db.empty() && !

.empty())

(*db)->GetTag().AsString(oss);

.SetStr(orig_val);

(exception &) {

in_out_bioSource.

().SetDb().push_back(db_tag);

(in_out_bioSource.IsSetOrg() && in_out_bioSource.GetOrg().IsSetDb()) {

in_out_bioSource.SetOrg().ResetDb();

vector <string> vals;

(!note.empty()) {

vals.push_back(note);

(!note.empty()) {

vals.push_back(note);

( !note_values.empty() ){

note_values.front();

in_out_bioSource.

().SetTaxId(

);

}

(exception &) {

COrg_ref::TDb::iterator it = in_out_bioSource.

().SetDb().begin();

(it != in_out_bioSource.

().SetDb().end()) {

it = in_out_bioSource.

().SetDb().erase(it);

(in_out_bioSource.

()) {

}

(exception &) {

sTitle = column_name;

( nl_pos !=

) {

sTitle = sTitle.substr(0, nl_pos);

(desc_pos !=

) {

sTitle = sTitle.substr(0, desc_pos);

}

(feat_pos !=

) {

sTitle = sTitle.substr(0, feat_pos);

(sTitle.empty()) {

organelle = sTitle.substr(6,

);

( pos !=

) {

subtype = sTitle.substr(0, pos);

( !

.IsSetHeader() || !

.GetHeader().IsSetTitle() ) {

sTitle =

.GetHeader().GetTitle();

num_cols =

.size();

vector< CRef<CSrcTableColumnBase> > vecColEditFactories;

vecColEditFactories.push_back(bogus);

(

= 0;

< values_table->

() && (

) row < id_col->GetData().GetSize();

++) {

new_source_desc->

(*desc_ci);

(

col = 1; col < num_cols; ++col ) {

(vecColEditFactories[col])

vecColEditFactories[col]->ClearInBioSource(bioSource);

(

col = 1; col < num_cols; ++col ) {

(vecColEditFactories[col] &&

[col]->GetData().GetSize() > (

)

) {

vecColEditFactories[col]->AddToBioSource(

->AddCommand (*ecmd);

found =

;

id1_label =

;

id2_label =

;

pos =

(id2_label, id1_label);

(

(id2_label.substr(id1_label.length(), 1),

)) {

}

(pos != string::npos &&

(id2_label, id1_label)) {

delim = id2_label.substr(pos - 1, 1);

(!

|| !id_col) {

found =

;

(row < id_col->GetData().GetSize() && !found) {

->Assign(*row_id);

(row < id_col->GetData().GetSize() && !found) {

->Assign(*row_id);

->Assign(*row_id);

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.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

static bool AutoFill(objects::COrg_ref &org)

const string & GetLineage(void) const

bool IsSetCommon(void) const

const string & GetTaxname(void) const

bool IsSetOrgMod(void) const

static string GetOrganelleByGenome(unsigned int genome)

const string & GetCommon(void) const

const COrgName & GetOrgname(void) const

const string & GetDivision(void) const

static CBioSource::EOrigin GetOriginByString(const string &origin, NStr::ECase use_case=NStr::eCase, bool starts_with=false)

bool IsSetLineage(void) const

bool IsSetDivision(void) const

static CBioSource::EGenome GetGenomeByOrganelle(const string &organelle, NStr::ECase use_case=NStr::eCase, bool starts_with=false)

static string GetStringFromOrigin(unsigned int origin)

bool IsSetTaxname(void) const

virtual string GetValue(const objects::CBioSource &src)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

objects::COrgMod::TSubtype m_Subtype

COrgModQual()

Constructors.

virtual string GetValue(const objects::CBioSource &src)

virtual string GetFormatErrors(string value)

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

static bool IsValidSubtypeName(const string &str, EVocabulary vocabulary=eVocabulary_raw)

static string GetSubtypeName(TSubtype stype, EVocabulary vocabulary=eVocabulary_raw)

static TSubtype GetSubtypeValue(const string &str, EVocabulary vocabulary=eVocabulary_raw)

static string MakeStructuredVoucher(const string &inst, const string &coll, const string &id)

static bool ParseStructuredVoucher(const string &str, string &inst, string &coll, string &id)

size_t GetSize(void) const

namespace ncbi::objects::

void AddColumnsToSeqTable(CRef< objects::CSeq_table > values_table)

void x_AddOneOfProblems(CRef< objects::CSeq_table >, vector< string > one_of_list, CRef< objects::CSeqTable_column > problems)

int x_AddUniquenessProblems(CRef< objects::CSeq_table > values_table, vector< string > uniqueness_list, vector< string > &row_problems)

void SetExamples(EWizardType wizard_type, EWizardSrcType src_type)

@ eWizardSrcType_cultured_fungus

@ eWizardSrcType_virus_norovirus

@ eWizardSrcType_virus_foot_and_mouth

@ eWizardSrcType_bacteria_or_archaea

@ eWizardSrcType_virus_influenza

@ eWizardSrcType_vouchered_fungus

@ eWizardSrcType_virus_rotavirus

CSourceRequirements()

Constructors.

virtual ~CSourceRequirements()

Destructor.

void AddUniquenessList(vector< string > list)

void AddOneOfList(vector< string > list)

TSrcQualList m_Requirements

vector< vector< string > > m_UniquenessLists

void AddRequirement(string name, bool required, string example="")

vector< vector< string > > m_OneOfLists

@ eWizardType_uncultured_samples

@ eWizardType_microsatellite

@ eWizardType_rrna_its_igs

void PreferentiallyAddRequirement(CRef< objects::CSeq_table > values_table, string choice1, string choice2, bool required)

CRef< objects::CSeqTable_column > CheckSourceQuals(CRef< objects::CSeq_table > values_table)

virtual ~CSrcQual()

Destructor.

virtual string GetValue(const objects::CBioSource &src)

void x_ParsePartsFromStructuredVoucher(const string &qualifier, string &inst, string &coll, string &id) const

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &src) const

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

static const string & GetName_StrVoucherPart(EStructVouchPart stype_part)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

EStructVouchPart m_SubtypePart

static EStructVouchPart GetStrVoucherPart_FromName(const string &name)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &biosrc) const

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual string GetFromBioSource(const objects::CBioSource &src) const

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &src) const

static CRef< CSrcTableColumnBase > Create(const objects::CSeqTable_column &column)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &src) const

vector< CRef< objects::edit::CApplyObject > > GetApplyObjects(CBioseq_Handle bsh)

string GetVal(const CObject &object)

vector< string > GetVals(const CObject &object)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const =0

vector< CConstRef< CObject > > GetObjects(CBioseq_Handle bsh)

void SetSourceType(ESourceType type)

void ClearVal(CObject &object)

virtual string GetFromBioSource(const objects::CBioSource &biosrc) const

virtual bool AllowMultipleValues()

virtual bool AddToBioSource(objects::CBioSource &in_out_bioSource, const string &newValue, objects::edit::EExistingText existing_text)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &biosrc) const

virtual string GetFromBioSource(const objects::CBioSource &biosrc) const

virtual string GetFromBioSource(const objects::CBioSource &biosrc) const

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual vector< string > IsValid(const vector< string > &values)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

CSrcTableGenomeColumn(const string &organelle=kEmptyStr)

virtual string GetFromBioSource(const objects::CBioSource &biosrc) const

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &biosrc) const

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

objects::COrgMod::TSubtype m_Subtype

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual vector< string > IsValid(const vector< string > &values)

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

virtual vector< string > GetValsFromBioSource(const CBioSource &src) const

bool x_ApplyStringToReaction(const string &val, CPCRReaction &reaction, objects::edit::EExistingText existing_text)

bool x_DoesPrimerSetHaveSpace(const CPCRPrimerSet &set)

bool x_DoesReactionMatchConstraint(const CPCRReaction &reaction) const

virtual void SetConstraint(const string &field_name, CConstRef< edit::CStringConstraint > string_constraint)

bool x_AddFieldToPrimerSet(const string &val, CPCRPrimerSet &set)

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

bool x_ApplyStringToPrimerSet(const string &val, CPCRPrimerSet &set, objects::edit::EExistingText existing_text)

bool x_DoesReactionHaveSpace(const CPCRReaction &reaction)

void x_RemoveEmptyValues(CBioSource &src)

static EPrimerColType GetPrimerColumnType(const string &field_name)

virtual void ClearInBioSource(objects::CBioSource &src)

virtual string GetFromBioSource(const objects::CBioSource &src) const

CRef< edit::CStringConstraint > m_StringConstraint

EPrimerColType m_ConstraintCol

vector< string > x_GetValues(EPrimerColType col, const CBioSource &src) const

objects::CSubSource::TSubtype m_Subtype

virtual vector< string > GetValsFromBioSource(const objects::CBioSource &biosrc) const

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual bool AddToBioSource(objects::CBioSource &in_out_bioSource, const string &newValue, objects::edit::EExistingText existing_text)

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

string x_GetTextAfterNomial(const string &taxname) const

virtual void ClearInBioSource(objects::CBioSource &in_out_bioSource)

virtual string GetFromBioSource(const objects::CBioSource &in_out_bioSource) const

virtual bool AddToBioSource(objects::CBioSource &src, const string &newValue, objects::edit::EExistingText existing_text)

class CStaticArrayMap<> provides access to a static array in much the same way as CStaticArraySet<>,...

TBase::const_iterator const_iterator

static TSubtype GetSubtypeValue(const string &str, EVocabulary vocabulary=eVocabulary_raw)

static bool IsValidSubtypeName(const string &str, EVocabulary vocabulary=eVocabulary_raw)

static string GetSubtypeName(CSubSource::TSubtype stype, EVocabulary vocabulary=eVocabulary_raw)

static bool NeedsNoText(const TSubtype &subtype)

vector< string > m_BadIsolationSourceValues

objects::CSubSource::TSubtype m_Subtype

virtual string GetFormatErrors(string value)

CSubSrcQual()

Constructors.

virtual string GetValue(const objects::CBioSource &src)

virtual string GetValue(const objects::CBioSource &src)

virtual string GetFormatErrors(string value)

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

const char * kGenomeProjectID

const char * kSubSourceNote

const char * kSequenceIdColLabel

static const struct name_t names[]

static const char * str(char *buf, int n)

static const char * column

static const column_t columns[]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

#define ENUM_METHOD_NAME(EnumName)

void GetLabel(string *label, ELabelType type=eDefault, TLabelFlags flags=fLabel_Default) const

Append a label for this Seq-id to the supplied string.

E_SIC

Compare return values.

@ e_YES

SeqIds compared, but are different.

@ eContent

Untagged human-readable accession or the like.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TClass GetClass(void) const

CBioseq_set_Handle GetParentBioseq_set(void) const

Return a handle for the parent Bioseq-set, or null handle.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id) const

Get Bioseq handle from the TSE of this Seq-entry.

CSeq_entry_Handle GetParentEntry(void) const

Return a handle for the parent seq-entry of the bioseq.

bool IsSetClass(void) const

const CSeq_feat & GetOriginalFeature(void) const

Get original feature with unmapped location/product.

CSeq_entry_Handle GetSeq_entry_Handle(void) const

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

NCBI_NS_STD::string::size_type SIZE_TYPE

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

static SIZE_TYPE FindNoCase(const CTempString str, const CTempString pattern, SIZE_TYPE start, SIZE_TYPE end, EOccurrence which=eFirst)

Find the pattern in the specified range of a string using a case insensitive search.

static bool EndsWith(const CTempString str, const CTempString end, ECase use_case=eCase)

Check if a string ends with a specified suffix value.

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

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

static void TruncateSpacesInPlace(string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string (in-place)

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

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

Join strings using the specified delimiter.

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

Case-sensitive equality of a substring with another string.

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 SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

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.

static string & ToUpper(string &str)

Convert string to upper case – string& version.

@ fSplit_Tokenize

All delimiters are merged and trimmed, to get non-empty tokens only.

@ eReverseSearch

Search in a backward direction.

@ eTrunc_End

Truncate trailing whitespace only.

@ eNocase

Case insensitive compare.

@ eCase

Case sensitive compare.

static const char label[]

const Tdata & Get(void) const

Get the member data.

const TSubtype & GetSubtype(void) const

Get the Subtype member data.

const TPcr_primers & GetPcr_primers(void) const

Get the Pcr_primers member data.

TGenome GetGenome(void) const

Get the Genome member data.

TOrigin GetOrigin(void) const

Get the Origin member data.

void ResetGenome(void)

Reset Genome data member.

void ResetOrigin(void)

Reset Origin data member.

const Tdata & Get(void) const

Get the member data.

bool IsSetOrg(void) const

Check if a value has been assigned to Org data member.

list< CRef< CSubSource > > TSubtype

bool IsSetSubtype(void) const

Check if a value has been assigned to Subtype data member.

bool IsSetPcr_primers(void) const

Check if a value has been assigned to Pcr_primers data member.

void SetOrigin(TOrigin value)

Assign a value to Origin data member.

const TForward & GetForward(void) const

Get the Forward member data.

void SetSeq(const TSeq &value)

Assign a value to Seq data member.

const TOrg & GetOrg(void) const

Get the Org member data.

bool IsSetOrigin(void) const

Check if a value has been assigned to Origin data member.

void SetGenome(TGenome value)

Assign a value to Genome data member.

void SetForward(TForward &value)

Assign a value to Forward data member.

bool IsSetGenome(void) const

Check if a value has been assigned to Genome data member.

void ResetReverse(void)

Reset Reverse data member.

void SetPcr_primers(TPcr_primers &value)

Assign a value to Pcr_primers data member.

void SetReverse(TReverse &value)

Assign a value to Reverse data member.

void SetName(const TName &value)

Assign a value to Name data member.

void SetOrg(TOrg &value)

Assign a value to Org data member.

bool IsSetReverse(void) const

Check if a value has been assigned to Reverse data member.

void ResetForward(void)

Reset Forward data member.

const TReverse & GetReverse(void) const

Get the Reverse member data.

list< CRef< CPCRReaction > > Tdata

bool IsSetForward(void) const

Check if a value has been assigned to Forward data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

bool IsSet(void) const

Check if a value has been assigned to data member.

TSubtype & SetSubtype(void)

Assign a value to Subtype data member.

void ResetPcr_primers(void)

Reset Pcr_primers data member.

void ResetSubtype(void)

Reset Subtype data member.

list< CRef< CPCRPrimer > > Tdata

@ eSubtype_isolation_source

void SetTag(TTag &value)

Assign a value to Tag data member.

void SetDb(const TDb &value)

Assign a value to Db data member.

const TMod & GetMod(void) const

Get the Mod member data.

bool IsSetDb(void) const

ids in taxonomic or culture dbases Check if a value has been assigned to Db data member.

void SetSubtype(TSubtype value)

Assign a value to Subtype data member.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

const TDb & GetDb(void) const

Get the Db member data.

bool IsSetMod(void) const

Check if a value has been assigned to Mod data member.

list< CRef< COrgMod > > TMod

bool IsSetOrgname(void) const

Check if a value has been assigned to Orgname data member.

bool IsSetTaxname(void) const

preferred formal name Check if a value has been assigned to Taxname data member.

void SetSubname(const TSubname &value)

Assign a value to Subname data member.

const TOrgname & GetOrgname(void) const

Get the Orgname member data.

@ eSubtype_other

ASN5: old-name (254) will be added to next spec.

@ eSubtype_nat_host

natural host of this specimen

const TColumns & GetColumns(void) const

Get the Columns member data.

void SetHeader(THeader &value)

Assign a value to Header data member.

vector< CRef< CSeqTable_column > > TColumns

void SetData(TData &value)

Assign a value to Data data member.

TNum_rows GetNum_rows(void) const

Get the Num_rows member data.

const TString & GetString(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

bool IsSetColumns(void) const

data in columns Check if a value has been assigned to Columns data member.

TColumns & SetColumns(void)

Assign a value to Columns data member.

const TId & GetId(void) const

Get the variant data.

@ eField_id_location_id

location Seq-id

bool IsSetData(void) const

the specific data Check if a value has been assigned to Data data member.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

const TBiosrc & GetBiosrc(void) const

Get the variant data.

bool IsBiosrc(void) const

Check if variant Biosrc is selected.

bool IsLocal(void) const

Check if variant Local is selected.

@ eClass_nuc_prot

nuc acid and coded proteins

const TSource & GetSource(void) const

Get the variant data.

bool IsSource(void) const

Check if variant Source is selected.

list< CRef< CSeq_id > > TId

TSource & SetSource(void)

Select the variant.

@ e_Source

source of materials, includes Org-ref

@ eMol_na

just a nucleic acid

char * dbname(DBPROCESS *dbproc)

Get name of current database.

fallback to Cassandra storage</td > n</tr > n</table > n</td > n< td > no and not provided</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is smart and slim</td> n<td> orig</td> n</tr> n<tr> n<td> exclude_blobs</td> n<td> optional</td> n<td> String</td> n<td class=\"description\"> A comma separated list of blob identifiers which client already has If provided then n if the resolution of sequence identifier sequence identifier type matches one of the n blob identifiers in the list then the blob will not be sent The format of the blob n identifier depends on a processor For example

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

constexpr auto sort(_Init &&init)

const GenericPointer< typename T::ValueType > T2 value

static const GLdouble origin[]

#define FOR_EACH_DBXREF_ON_ORGREF(Itr, Var)

FOR_EACH_DBXREF_ON_ORGREF EDIT_EACH_DBXREF_ON_ORGREF.

#define EDIT_EACH_DBXREF_ON_ORGREF(Itr, Var)

bool MatchColumnName(string name1, string name2)

bool IsOrgColumnName(string name)

CRef< CSeqTable_column > FindSeqTableColumnByName(CRef< objects::CSeq_table > values_table, string column_name)

void AddValueToTable(CRef< CSeq_table > table, string subtype_name, string value, size_t row, edit::EExistingText existing_text=edit::eExistingText_replace_old)

static SLJIT_INLINE sljit_ins st(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

CRef< CCmdComposite > ApplySrcTableToSeqEntry(CRef< CSeq_table >values_table, CSeq_entry_Handle seh)

static bool IsExampleTableRowAcceptable(const ExampleTableData *e1, string field_name, CSourceRequirements::EWizardType wizard_type, CSourceRequirements::EWizardSrcType src_type)

CRef< CSeq_table > GetSeqTableForSrcQualFromSeqEntry(CSeq_entry_Handle seh, vector< string > qual_names)

static bool s_IsAllNumbers(string val)

void SplitValues(const string &name, const string &newValue, vector< string > &values)

static const TStructVoucherPart s_StrVouchPartName[]

bool IsFwdPrimerSeq(string name)

static string s_MakeUniquenessVal(vector< CRef< CSeqTable_column > > cols, size_t row)

bool RelaxedMatch(CRef< CSeq_id > id1, CRef< CSeq_id > id2)

string GetPrimerSetNameValues(const CPCRPrimerSet &primer_set)

static int CompareExampleTableRows(const ExampleTableData *e1, const ExampleTableData *e2)

CRef< CSeq_table > GetSeqTableFromSeqEntry(CSeq_entry_Handle seh)

string JoinValues(const string &name, const vector< string > &values)

string GetPrimerSetSeqValues(const CPCRPrimerSet &primer_set)

static bool OneRowOk(CRef< CSeq_id > id, CRef< CSeqTable_column > id_col, CSeq_entry_Handle seh)

SStaticPair< const char *, CSrcStructuredVoucherPartColumn::EStructVouchPart > TStructVoucherPart

DEFINE_STATIC_ARRAY_MAP(TStrcVouchMap, sm_VouchMap, s_StrVouchPartName)

bool IsRevPrimerSeq(string name)

static const int k_NumExampleTableRows

struct exampletable ExampleTableData

static const string nomial_keywords[]

bool IsFwdPrimerName(string name)

CStaticArrayMap< string, CSrcStructuredVoucherPartColumn::EStructVouchPart > TStrcVouchMap

bool IsRevPrimerName(string name)

CSourceRequirements * GetSrcRequirements(CSourceRequirements::EWizardType wizard_type, CSourceRequirements::EWizardSrcType source_type, CRef< CSeq_table > values_table)

static const ExampleTableData s_ExampleTable[]

void RemoveLastCharacter(string &str)

vector< CSrcQual * > TSrcQualList

#define row(bind, expected)

@ eExistingText_leave_old

@ eExistingText_replace_old

bool AddValueToString(string &str, const string &value, EExistingText existing_text)

Add text to an existing string, using the "existing_text" directive to combine new text with existing...

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

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