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

showDialog(

);

wxRichMessageDialog dlg(

,

(

), wxEmptyString, wxOK|wxCENTER);

dlg.ShowCheckBox(

);

(dlg.IsCheckBoxChecked()) {

report->SetTitle(

(

));

report->Show(

);

report->SetTitle(

(

));

report->Show(

);

&startingLocusTagNumber,

&startingFeatureId,

&locus_tag,

euk)

startingLocusTagNumber, startingFeatureId, locus_tag, euk);

vector<string> format_ids;

(format_id.empty())

format_ids.push_back(

);

format_ids.push_back(

);

format_ids.push_back(format_id);

fileManager->LoadFormats(format_ids);

fileManager->SetWorkDir(workDir);

vector<CIRef<IOpenObjectsPanelClient> > loadManagers;

dlg.SetSize(710, 480);

(format_id ==

)

dlg.

(

(

));

(format_id ==

)

dlg.

(

(

));

(dlg.ShowModal() != wxID_OK)

(!object_loader) {

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

(!

.empty()) {

(!

.empty()) {

(wxTheClipboard->Open())

wxTextDataObject

;

(wxTheClipboard->IsSupported( wxDF_UNICODETEXT ))

wxTheClipboard->GetData(

);

(

.GetText().length() == 0) {

wxMessageBox(

);

wxTheClipboard->Close();

fname =

.GetFileName();

wxTheClipboard->Close();

vector<wxString> fnames;

wxMessageBox(

(

),

(

), wxOK | wxICON_ERROR);

(!execute_unit->PreExecute())

(!execute_unit->PostExecute())

tmp_file(fname);

(!

.empty()) {

(!

.empty()) {

unordered_set<string> product_ids;

(

& obj_it :

) {

(

& feat_it : ftbl) {

(feat_it->IsSetProduct() &&

feat_it->IsSetData() &&

(

*

= feat_it->GetProduct().GetId()) {

id_string =

->GetSeqIdString(

);

res = product_ids.insert(id_string);

unordered_set<string> product_ids;

(

& obj_it :

) {

(

& feat_it : ftbl) {

(feat_it->IsSetProduct() && feat_it->IsSetData()) {

*

= feat_it->GetProduct().GetId();

(

&& feat_it->GetData().IsCdregion()) {

product_ids.insert(id_string);

vector<string> dupl_product_ids;

(

&& id_it : bseq->GetCompleteBioseq()->GetId()) {

id_string = id_it->GetSeqIdString(

);

(product_ids.find(id_string) != product_ids.end()) {

dupl_product_ids.push_back(id_string);

(

&& it : dupl_product_ids) {

+=

+ it +

;

(

& obj_it :

) {

(ftbl.size() == 1)

feat_it = ftbl.begin();

(feat_it != ftbl.end()) {

feature = *feat_it;

(feature->IsSetData() && feature->GetData().IsCdregion() && !

(*feature)) {

it_cds = feat_it;

(feat_it != ftbl.end() &&

!((*feat_it)->IsSetData() && (*feat_it)->GetData().IsCdregion() && !

(**feat_it))) {

next_cds = feat_it;

(next_cds != ftbl.end()) {

& this_pid = (*it_cds)->GetNamedQual(

);

& next_pid = (*next_cds)->GetNamedQual(

);

has_pid = !this_pid.empty();

next_has_pid = !next_pid.empty();

has_local_pid =

;

next_has_local_pid =

;

(!has_pid != !next_has_pid) {

(!prot_ids.empty() && prot_ids.front()->IsLocal()) {

has_local_pid =

;

(!prot_ids.empty() && prot_ids.front()->IsLocal()) {

next_has_local_pid =

;

(!has_local_pid != !next_has_local_pid) {

=

;

& ptr = obj_it->GetObject();

(!non_matched_ftbl_ids.

()) {

(dlg.ShowModal() == wxID_OK) {

ftbl_seqid_map[it->first] = it->second;

startingLocusTagNumber = 1;

startingFeatureId = 1;

& ptr = obj_it->GetObject();

(!locus_tag.empty())

(!locus_tag.empty())

startingLocusTagNumber = tail;

(

<<

);

(dlg.ShowModal() == wxID_OK)

(locus_tag.empty())

startingLocusTagNumber = 1;

& ptr = obj_it->GetObject();

loc.

(*new_id);

&startingLocusTagNumber,

&startingFeatureId,

&locus_tag,

annot->

(orig_annot);

(*annot, startingLocusTagNumber, startingFeatureId, locus_tag, euk);

vector<CRef<CSeq_feat>> imported_cds;

(!bsh && it == ftbl_seqid_map.

()) {

.assign(

);

(!bsh && it != ftbl_seqid_map.

()) {

bsh =

.GetScope().GetBioseqHandle(it->second.GetSeqId().GetObject());

imported_cds.push_back(new_feat);

(

new_feat : imported_cds) {

->AddCommand(*cds_cmd);

edit::CFeatTableEdit fte(annot, locus_tag, startingLocusTagNumber, startingFeatureId);

fte.GenerateMissingParentFeatures(euk);

fte.GenerateLocusTags();

fte.GenerateProteinAndTranscriptIds();

fte.InstantiateProductsNames();

fte.EliminateBadQualifiers();

fte.SubmitFixProducts();

startingLocusTagNumber = fte.PendingLocusTagNumber();

startingFeatureId = fte.PendingFeatureId();

(prot_str.empty())

prot_str = prot_str.substr(0, prot_str.length() - 1);

protein->

().ResetExt();

protein->

().SetSeq_data().SetIupacaa().Set(prot_str);

protein->

().SetSeq_data().SetNcbieaa().Set(prot_str);

(

& it : prot_ids) {

protein->

().push_back(it);

& prot_id_qual = feat->

(

);

(!prot_id_qual.empty()) {

(

& it : prot_ids) {

protein->

().push_back(it);

feat->

().SetWhole().Assign(*best_id);

feat->

().SetWhole().Assign(*prot_id);

has_protid =

;

(

& it : prot_ids) {

protein->

().push_back(it);

has_protid |= (prot_id->

(*it));

protein->

().push_back(prot_id);

prot_ref->

(*orig_ref);

->SetData().SetProt(*prot_ref);

(!

.IsLocal()) {

(

.GetLocal().IsStr()) {

}

(

.GetLocal().IsId()) {

User-defined methods of the data storage class.

@ eExtreme_Positional

numerical value

@ eExtreme_Biological

5' and 3'

bool GUI_AsyncExecUnit(IExecuteUnit &exec_unit, const wxString &msg)

CRef< objects::CSeq_id > GetNewLocalProtId(const string &id_base, CScope &scope, int &offset)

CRef< CGenetic_code > GetGeneticCodeForBioseq(CBioseq_Handle bh)

GetGeneticCodeForBioseq A function to construct the appropriate CGenetic_code object to use when cons...

static bool ParseCodeBreaks(CSeq_feat &feat, CScope &scope)

Parses all valid transl_except Gb-quals into code-breaks for cdregion, then removes the transl_except...

void AddCommand(IEditCommand &command)

static CIRef< IEditCommand > Create(const objects::CSeq_entry_Handle &seh, const vector< string > &quals)

virtual void SetRegistryPath(const string &path)

void SetText(const wxString &text)

map< string, int > m_OffsetForId

CIRef< IEditCommand > x_CreateCommand(const IObjectLoader::TObjects &objects)

CIRef< IEditCommand > x_DoImportCDS(CRef< objects::CSeq_feat > feat)

objects::CBioseq_Handle x_FindLocalBioseq_Handle(const objects::CSeq_feat &feat, const objects::CTSE_Handle &tseh) const

CIRef< IEditCommand > ImportFeaturesFromClipboard(const wxString &workDir)

string x_CheckCollidingIds(const IObjectLoader::TObjects &objects)

void xPostProcessAnnot(objects::CSeq_annot &annot, unsigned int &startingLocusTagNumber, unsigned int &startingFeatureId, const string &locus_tag, bool euk)

objects::CSeq_id_Handle x_GetFixedId(const objects::CSeq_id &id, const objects::CTSE_Handle &tseh) const

CIRef< IEditCommand > x_DoImportFeaturesFromFile(const wxString &workDir, const string &format_id=kEmptyStr)

CIRef< IEditCommand > x_DoImportFeaturesFromClipboard(const wxString &workDir)

CIRef< IEditCommand > ImportFeaturesFromFile(const wxString &workDir=wxEmptyString, const string &format_id=kEmptyStr)

static void ShowTableInfo()

CIRef< IEditCommand > x_GatherAdditionalChanges(CIRef< IEditCommand > &start_cmd)

CIRef< IEditCommand > AddSeqAnnotToSeqEntry(const objects::CSeq_annot &orig_annot, TFeatSeqIDMap &ftbl_seqid_map, unsigned int &startingLocusTagNumber, unsigned int &startingFeatureId, const string &locus_tag, bool euk)

objects::CSeq_entry_Handle m_Seh

bool x_ContainsDuplicateIds(const IObjectLoader::TObjects &objects)

returns true if the feature table contains at least one pair of duplicate protein/transcript ids

string x_CheckConsistentProteinIds(const IObjectLoader::TObjects &objects)

CIRef< IEditCommand > TestImport(const objects::CSeq_annot &orig_annot, TFeatSeqIDMap &ftbl_seqid_map, unsigned int &startingLocusTagNumber, unsigned int &startingFeatureId, const string &locus_tag, bool euk)

void GetFtableIDToSeqIDMap(TFeatSeqIDMap &ftbl_seqid_map)

IObjectLoader * GetObjectLoader()

void SetManagers(vector< CIRef< IOpenObjectsPanelClient > > &managers)

void SetWorkDir(const wxString &workDir)

ESubtype GetSubtype(void) const

static CTempString SubtypeValueToName(ESubtype eSubtype)

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

SeqVector related exceptions.

bool IsFtable(void) const

namespace ncbi::objects::

const CProt_ref * GetProtXref(void) const

get protein (if present) from Seq-feat.xref list

const string & GetNamedQual(const CTempString &qual_name) const

Return a named qualifier.

void RemoveQualifier(const string &qual_name)

Remove all qualifiers with the given name; do nothing if no such qualifier exists.

const CGene_ref * GetGeneXref(void) const

See related function in util/feature.hpp.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id) const

Get Bioseq handle from this TSE.

Template class for iteration on objects of class C.

void SetHelpUrl(const wxString &url)

virtual bool PreExecute()=0

virtual bool PostExecute()=0

vector< SObject > TObjects

container_type::const_iterator const_iterator

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

void SetMolinfoForProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

CRef< objects::CSeq_feat > AddProteinFeatureToProtein(CRef< objects::CSeq_entry > protein, bool partial5, bool partial3)

static void cleanup(void)

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define LOG_POST(message)

This macro is deprecated and it's strongly recomended to move in all projects (except tests) to macro...

void Error(CExceptionArgs_Base &args)

const string & GetMsg(void) const

Get message string.

void Info(CExceptionArgs_Base &args)

virtual bool Remove(TRemoveFlags flags=eRecursive) const

Remove a directory entry.

@ eIfExists_ReturnCurrent

Return reference to current stream, create new one if it does not exists yet.

@ eNoRemove

Do not remove file.

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

Set object to copy of another one.

virtual bool Equals(const CSerialObject &object, ESerialRecursionMode how=eRecursive) const

Check if both objects contain the same values.

const string AsFastaString(void) const

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

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

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

CConstRef< CSeq_id > GetSeqId(void) const

static SIZE_TYPE ParseFastaIds(CBioseq::TId &ids, const CTempString &s, bool allow_partial_failure=false)

Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

Normal way of getting a handle, works for any seq-id.

static int BestRank(const CRef< CSeq_id > &id)

bool IsBetter(const CSeq_id_Handle &h) const

True if "this" is a better bioseq than "h".

@ eContent

Untagged human-readable accession or the like.

bool IsPartialStart(ESeqLocExtremes ext) const

check start or stop of location for e_Lim fuzz

void SetId(CSeq_id &id)

set the 'id' field in all parts of this location

const CSeq_id * GetId(void) const

Get the id of the location return NULL if has multiple ids or no id at all.

bool IsPartialStop(ESeqLocExtremes ext) const

TSeqPos GetStop(ESeqLocExtremes ext) const

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

bool IsPseudo(const CSeq_feat &feat, CScope &scope)

Determines whether given feature is pseudo, using gene associated with feature if necessary Checks to...

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

vector< CSeq_id_Handle > TId

TSeqPos GetBioseqLength(void) const

CSeq_entry_Handle GetSeq_entry_Handle(void) const

Get parent Seq-entry handle.

CScope & GetScope(void) const

Get scope this handle belongs to.

const TId & GetId(void) const

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

static int StringToNonNegativeInt(const CTempString str, TStringToNumFlags flags=0)

Convert string to non-negative integer value.

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 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 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 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.

@ eCase

Case sensitive compare.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

C::value_type FindBestChoice(const C &container, F score_func)

Find the best choice (lowest score) for values in a container.

bool IsSetLocus_tag(void) const

systematic gene name (e.g., MI0001, ORF0069) Check if a value has been assigned to Locus_tag data mem...

const TLocus_tag & GetLocus_tag(void) const

Get the Locus_tag member data.

TStr & SetStr(void)

Select the variant.

TId & SetId(void)

Select the variant.

bool IsSetData(void) const

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

bool IsSetCode(void) const

genetic code used Check if a value has been assigned to Code data member.

bool IsCdregion(void) const

Check if variant Cdregion is selected.

void SetProduct(TProduct &value)

Assign a value to Product data member.

void SetCode(TCode &value)

Assign a value to Code data member.

const TLocation & GetLocation(void) const

Get the Location member data.

bool IsGene(void) const

Check if variant Gene is selected.

const TData & GetData(void) const

Get the Data member data.

void SetData(TData &value)

Assign a value to Data data member.

TPseudo GetPseudo(void) const

Get the Pseudo member data.

const TProduct & GetProduct(void) const

Get the Product member data.

bool IsSetPseudo(void) const

annotated on pseudogene? Check if a value has been assigned to Pseudo data member.

const TGene & GetGene(void) const

Get the variant data.

bool IsSetProduct(void) const

product of process Check if a value has been assigned to Product data member.

void SetFrame(TFrame value)

Assign a value to Frame data member.

bool IsSetFrame(void) const

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

bool IsGenbank(void) const

Check if variant Genbank is selected.

const TWhole & GetWhole(void) const

Get the variant data.

bool IsGeneral(void) const

Check if variant General is selected.

TLocal & SetLocal(void)

Select the variant.

bool IsLocal(void) const

Check if variant Local is selected.

bool IsWhole(void) const

Check if variant Whole is selected.

TSeq & SetSeq(void)

Select the variant.

TId & SetId(void)

Assign a value to Id data member.

list< CRef< CSeq_id > > TId

void SetInst(TInst &value)

Assign a value to Inst data member.

const TFtable & GetFtable(void) const

Get the variant data.

list< CRef< CSeq_feat > > TFtable

const TData & GetData(void) const

Get the Data member data.

@ eRepr_raw

continuous sequence

static string s_GetIdBase(const CSeq_id &id)

static void s_RemapFeatureSeqIds(CSeq_feat &feat, const CSeq_id &set_id)

const wxString kfeaturetableinstructions

static bool s_IsPseudo(const CSeq_feat &feat)

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

wxString ToWxString(const string &s)

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