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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/editing__actions_8cpp_source.html below:

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

187 if

(cf != created_features.

end

())

212 cmd

->AddCommand(*chgFeat);

214 cmd

->AddCommand(*update_mrna_cmd);

215 if

(retranslate_cds_cmd)

216 cmd

->AddCommand(*retranslate_cds_cmd);

228 if

(cd != created_descriptors.

end

())

238 else if

(dd != deleted_descriptors.

end

())

241 const CSeqdesc

*old_desc = it->first;

246 const CSeqdesc

*old_desc = it->first;

267 auto

ctxt_it = descr_contexts.

find

(old_desc);

268 if

(ctxt_it != descr_contexts.

end

()) {

270 cmd

->AddCommand(*ecmd);

279 const CObject

* actual =

dynamic_cast<const CObject

>

(&submit);

282 cmd

->AddCommand(*chg_submit);

308

prot_product = *name_it;

309 if

(!prot_product.empty())

325

new_mrna->

Assign

(*orig_mrna);

327

new_mrna->

SetData

().SetRna().SetRnaProductName(prot_product, remainder);

337 bool

cds_change(

false

);

432 void IEditingAction::Edit

(

const string

& find,

const string

& replace, macro::CMacroFunction_EditStringQual::ESearchLoc edit_loc,

bool

case_insensitive,

bool

is_regex)

470 source

->SwapContext(

this

);

476 source

->IEditingAction::SwapContext(

this

);

494 source

->SwapContext(

this

);

500 source

->IEditingAction::SwapContext(

this

);

518 source

->SwapContext(

this

);

524 source

->IEditingAction::SwapContext(

this

);

543 source

->SwapContext(

this

);

549 source

->IEditingAction::SwapContext(

this

);

818

parse_options.SetShouldRemove(

false

);

832

action2->ResetChangedFeatures();

833

action2->ResetChangedDescriptors();

834

action2->ResetChangedInstances();

835

action2->ResetChangedIds();

836

action2->ResetChangedValues();

847 const string

& ncRNA_class,

892 if

(!field_name_panel)

899 if

(field_name.empty())

909 if

(field ==

"protein name"

|| field ==

"protein description"

|| field ==

"protein EC number" 910

|| field ==

"protein activity"

|| field ==

"protein comment"

)

914 else if

(field ==

"CDS comment"

|| field ==

"CDS inference"

|| field ==

"codon-start"

)

918 else if

( field ==

"gene description"

|| field ==

"gene comment" 919

|| field ==

"gene inference"

|| field ==

"gene allele"

|| field ==

"gene maploc" 920

|| field ==

"gene locus tag"

|| field ==

"gene synonym"

|| field ==

"gene old_locus_tag" 921

|| field ==

"gene locus"

)

925 else if

(field ==

"mRNA product"

|| field ==

"mRNA comment"

)

929 else if

(field ==

"mat_peptide name"

|| field ==

"mat_peptide description"

|| field ==

"mat_peptide EC number" 930

|| field ==

"mat_peptide activity"

|| field ==

"mat_peptide comment"

)

951 if

(!rna_type.empty())

953 if

(rna_type ==

"preRNA"

)

955 else if

(rna_type ==

"mRNA"

)

957 else if

(rna_type ==

"tRNA"

)

959 else if

(rna_type ==

"rRNA"

)

961 else if

(rna_type ==

"ncRNA"

) {

962

ncRNA_class = ncrna_class;

965 else if

(rna_type ==

"tmRNA"

)

967 else if

(rna_type ==

"miscRNA"

)

978

ncRNA_class =

"any"

;

982

ncRNA_class =

"snRNA"

;

986

ncRNA_class =

"scRNA"

;

990

ncRNA_class =

"snoRNA"

;

997 const CSeqdesc

* old_desc =

dynamic_cast<const CSeqdesc

>

(

object

.GetPointer());

998 const CSeq_feat

* old_feat =

dynamic_cast<const CSeq_feat

>

(

object

.GetPointer());

1004

new_desc->

Assign

(*old_desc);

1005

new_obj = (

CObject

*)new_desc;

1006

}

else if

(old_feat) {

1009

new_feat->

Assign

(*old_feat);

1010

new_obj = (

CObject

*)new_feat;

1019 bool

success =

false

;

1027 if

(seh && new_desc) {

1029 cmd

->AddCommand(*ecmd);

1032

}

else if

(old_feat) {

1046 const string

&field,

1049 const string

& ncRNA_class,

1054

action->SetConstraint(constraint);

1061

vector<CConstRef<CObject> > objs;

1062 for

(

auto

&fh : feathdlesmap)

1064

objs.emplace_back(fh.first.GetSeq_feat());

1066 for

(

auto

&dh : descrmap)

1070 for

(

auto

&bh : instmap)

1079 if

(!descrmap.

empty

() && descr_context) {

1081

descr_context->clear();

1082 for

(

auto

& it : contextmap) {

1083

descr_context->emplace_back(it.second);

CSeq_entry_Handle GetSeqEntryForSeqdesc(CRef< CScope > scope, const CSeqdesc &seq_desc)

bool IsGeneralIdProtPresent(objects::CSeq_entry_Handle tse)

virtual string GetFieldName(const bool subfield=false)

Returns the name of the field as selected in the panel.

void Add(CObject *obj, const CObject *new_obj)

string GetRnaTypeOnly(void)

string GetNcrnaType(void)

virtual bool Match(const string &value)

@ eFieldType_BankITComment

@ eFieldType_TaxnameAfterBinomial

@ eFieldType_StructuredComment

string GetRnaTypeOnly(void)

string GetNcrnaType(void)

static CRef< CCmdComposite > RetranslateCDSCommand(CScope &scope, const CSeq_feat &old_cds, CSeq_feat &cds, bool &cds_change, int &offset, bool create_general_only)

ESubtype GetSubtype(void) const

static E_Choice GetTypeFromSubtype(ESubtype subtype)

@ 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.

namespace ncbi::objects::

void SetExistingText(edit::EExistingText existing_text)

const string GetName(void) const

void SetTopSeqEntry(CSeq_entry_Handle seh)

virtual void FindRelated(EActionType action)=0

virtual void SetValue(const string &value)=0

edit::EExistingText m_existing_text

map< const CSeqdesc *, CSeq_entry_Handle > m_ContextForDescriptors

CRef< CSubmit_block > GetChangedSubmitBlock(void)

void ResetChangedFeatures(void)

virtual void Find(EActionType action)=0

void ConvertFrom(ECapChange cap_change, bool leave_on_original, const string &strip_name, IEditingAction *destination)

void Apply(const string &value)

virtual void Modify(EActionType action)=0

map< const CSeqdesc *, CSeq_entry_Handle > m_CreatedDescriptors

void SetConstraint(CRef< CEditingActionConstraint > constraint)

const vector< string > & GetChangedValues(void)

const map< const CSeqdesc *, CSeq_entry_Handle > & GetDeletedDescriptors(void)

CSeq_entry_Handle m_TopSeqEntry

void ResetChangedDescriptors(void)

CConstRef< objects::CSeq_submit > m_SeqSubmit

const map< CSeq_feat_Handle, CRef< CSeq_feat > > & GetChangedFeatures(void)

const map< CBioseq_Handle, CRef< CSeq_inst > > & GetChangedInstances(void)

void ConvertTo(const string &value, IEditingAction *source)

void ResetChangedIds(void)

map< const CSeqdesc *, CRef< CSeqdesc > > m_ChangedDescriptors

IEditingAction(CSeq_entry_Handle seh, const string &name, CConstRef< objects::CSeq_submit > submit=CConstRef< objects::CSeq_submit >(NULL))

macro::CMacroFunction_EditStringQual::ESearchLoc m_edit_loc

map< CSeq_feat_Handle, CRef< CSeq_feat > > m_ChangedFeatures

CRef< CCmdComposite > GetActionCommand(void)

CRef< CCmdComposite > GetRetranslateCdsCmd(const CSeq_feat_Handle fh, const CRef< CSeq_feat > feat, int &offset, bool create_general_only)

void DoRemoveOutside(void)

void RemoveOutside(CRef< macro::CRemoveTextOptions > options)

CRef< CSubmit_block > m_ChangedSubmitBlock

virtual bool SameObject()=0

const map< const CSeqdesc *, CSeq_entry_Handle > & GetContextForDescriptors(void)

bool IsTo(EActionType action)

int CheckForExistingText(CIRef< IEditingAction > action2, EActionType action_type, edit::CParseTextOptions parse_options=edit::CParseTextOptions())

void CopyTo(const string &value, IEditingAction *source)

CIRef< IEditCommand > GetUpdateMRNAProductNameCmd(const CSeq_feat_Handle fh, const CRef< CSeq_feat > feat)

CSeq_entry_Handle m_CurrentSeqEntry

void SwapFrom(IEditingAction *destination)

CConstRef< objects::CSeq_submit > GetSeqSubmit(void)

void CopyFrom(IEditingAction *destination)

void Action(EActionType action)

vector< string > m_ChangedValues

const map< const CSeqdesc *, CRef< CSeqdesc > > & GetChangedDescriptors(void)

void SwapTo(const string &value, IEditingAction *source)

void ParseFrom(edit::CParseTextOptions parse_options, IEditingAction *destination)

CRef< macro::CRemoveTextOptions > m_remove_options

map< CSeq_feat_Handle, CSeq_entry_Handle > m_CreatedFeatures

void ResetChangedInstances(void)

const vector< string > & GetValues(void)

@ eActionType_RemoveOutside

@ eActionType_ConvertFrom

edit::CParseTextOptions m_parse_options

virtual void SwapContext(IEditingAction *source)

bool IsFrom(EActionType action)

virtual bool IsSetValue(void)=0

const map< CSeq_feat_Handle, CSeq_entry_Handle > & GetCreatedFeatures(void)

virtual void ResetValue(void)=0

CRef< CEditingActionConstraint > m_constraint

void ResetChangedValues(void)

bool IsCreateNew(EActionType action)

const map< const CSeqdesc *, CSeq_entry_Handle > & GetCreatedDescriptors(void)

virtual void ResetScope()

map< const CSeqdesc *, CSeq_entry_Handle > m_DeletedDescriptors

void Edit(const string &find, const string &replace, macro::CMacroFunction_EditStringQual::ESearchLoc edit_loc, bool case_insensitive, bool is_regex)

void ParseTo(const string &value, IEditingAction *source)

virtual string GetValue(void)=0

bool IsNOOP(EActionType action)

void HandleValue(const string &value)

map< CBioseq_Handle, CRef< CSeq_inst > > m_ChangedInstances

const_iterator begin() const

const_iterator end() const

const_iterator find(const key_type &key) const

CChangeUnindexedObjectCommand< objects::CSubmit_block > CChangeSubmitBlockCommand

static auto & RemoveFieldNameFromString

static auto & FixCapitalizationInString

IEditingActionBiosource * CreateActionBiosource(CSeq_entry_Handle seh, string field)

IEditingActionDesc * CreateActionDesc(CSeq_entry_Handle seh, const string &field, CConstRef< objects::CSeq_submit > submit=CConstRef< objects::CSeq_submit >(NULL))

IEditingActionFeat * CreateActionCdsGeneProt(CSeq_entry_Handle seh, string field, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class=kEmptyStr)

IEditingActionFeat * CreateActionFeat(CSeq_entry_Handle seh, string field, const CSeqFeatData::ESubtype subtype, const CSeqFeatData::E_Choice feat_type, const string &ncRNA_class)

IEditingActionFeat * CreateActionRna(CSeq_entry_Handle seh, string field, const CSeqFeatData::ESubtype subtype, const string &ncRNA_class)

IEditingAction * CreateActionMisc(CSeq_entry_Handle seh, const string &field)

CEditingActionSeqid * CreateActionSeqid(CSeq_entry_Handle seh, const string &field)

int CorrectForncRNASubtypes(CSeqFeatData::ESubtype subtype, string &ncRNA_class)

int GetSubtype(CFieldNamePanel *field_name_panel, string &ncRNA_class)

CRef< CCmdComposite > GetReplacementCommand(CConstRef< CObject > oldobj, CRef< CObject > newobj, CScope &scope, const string &cmd_name)

vector< CConstRef< CObject > > GetObjects(CSeq_entry_Handle seh, const string &field, CFieldNamePanel::EFieldType field_type, int subtype, const string &ncRNA_class, CConstRef< CSeq_submit > submit, CRef< CEditingActionConstraint > constraint, vector< CSeq_entry_Handle > *descr_context)

CRef< CObject > GetNewObject(CConstRef< CObject > object)

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

static void cleanup(void)

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

void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)

void CleanupForTaxnameChange(CObjectInfo oi)

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

Set object to copy of another one.

const CSeq_feat * GetCDSForProduct(const CBioseq &product, CScope *scope)

Get the encoding CDS feature of a given protein sequence.

CConstRef< CSeq_feat > GetmRNAforCDS(const CSeq_feat &cds, CScope &scope)

GetmRNAforCDS A function to find a CSeq_feat representing the appropriate mRNA for a given CDS.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_feat_Handle GetSeq_featHandle(const CSeq_feat &feat, EMissing action=eMissing_Default)

TClass GetClass(void) const

virtual const CSeq_loc & GetLocation(void) const

CSeq_entry_Handle GetTopLevelEntry(void) const

Get top level Seq-entry handle.

bool IsSetClass(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CConstRef< CSeq_feat > GetOriginalSeq_feat(void) const

bool HasParentEntry(void) const

Check if current seq-entry has a parent.

CSeq_entry_Handle GetParentEntry(void) const

Get parent Seq-entry handle.

TObjectType * GetPointer(void) const THROWS_NONE

Get pointer,.

CRef< C > Ref(C *object)

Helper functions to get CRef<> and CConstRef<> objects.

TObjectType * GetPointer(void) THROWS_NONE

Get pointer,.

void Reset(void)

Reset reference object.

void Reset(void)

Reset reference object.

#define numeric_limits

Pre-declaration of the "numeric_limits<>" template Forcibly overrides (using preprocessor) the origin...

#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 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 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.

bool IsSetOrg(void) const

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

const TOrg & GetOrg(void) const

Get the Org member data.

const TTaxname & GetTaxname(void) const

Get the Taxname member data.

bool IsSetTaxname(void) const

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

bool IsSetData(void) const

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

bool IsCdregion(void) const

Check if variant Cdregion is selected.

const TData & GetData(void) const

Get the Data member data.

const TExcept_text & GetExcept_text(void) const

Get the Except_text member data.

bool IsSetExcept_text(void) const

explain if except=TRUE Check if a value has been assigned to Except_text data member.

void SetData(TData &value)

Assign a value to Data data member.

const TProt & GetProt(void) const

Get the variant data.

@ 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.

TSource & SetSource(void)

Select the variant.

const TSub & GetSub(void) const

Get the Sub member data.

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

Utility macros and typedefs for exploring NCBI objects from seqfeat.asn.

#define FOR_EACH_NAME_ON_PROTREF(Itr, Var)

FOR_EACH_NAME_ON_PROTREF EDIT_EACH_NAME_ON_PROTREF.

@ 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...

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