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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/convert__feat_8hpp_source.html below:

NCBI C++ ToolKit: include/gui/objutils/convert_feat.hpp Source File

1 #ifndef GUI_OBJUTILS___CONVERT_FEAT__HPP 2 #define GUI_OBJUTILS___CONVERT_FEAT__HPP 48

: m_Val(

val

), m_Default (default_val) {};

52 bool GetVal

()

const

{

return

m_Val; };

66

: m_Val (

val

), m_Default(default_val)

67

{ m_Suggested.clear(); m_OnlySuggested =

false

; }

69

: m_Val (

val

), m_Default(default_val), m_Suggested(suggested), m_OnlySuggested(only_suggested)

73 const string

GetVal

()

const

{

return

m_Val; };

96 const string

GetLabel

()

const

{

return

m_Label; };

109 bool IsBool

()

const

{

return

m_Choice == e_Bool; };

110 bool IsString

()

const

{

return

m_Choice == e_String; };

124 CConvertFeatureBase

(objects::CSeqFeatData::ESubtype feat_to = objects::CSeqFeatData::eSubtype_bad,

125

objects::CSeqFeatData::ESubtype feat_from = objects::CSeqFeatData::eSubtype_bad);

128 typedef

vector<CRef<CConversionOption> >

TOptions

;

130 virtual bool

CanConvertFrom(objects::CSeqFeatData::ESubtype subtype);

131 virtual bool

CanConvertTo(objects::CSeqFeatData::ESubtype subtype);

136 string

x_GetCDSProduct(

const

objects::CSeq_feat&

orig

, objects::CScope& scope);

152 bool

x_MoveFeatureToProtein(

const

objects::CSeq_feat&

orig

CRef<objects::CSeq_feat>

new_feat,

bool

keep_orig, objects::CScope& scope);

158

objects::CSeqFeatData::ESubtype

m_To

;

162 void

x_AddCDSSourceConversionOptions();

163 void

x_AddCDSDestinationConversionOptions();

164 void

x_AddRnaDestinationConversionOptions();

165 void

x_AddSiteDestinationConversionOptions();

166 void

x_AddBondDestinationConversionOptions();

167 void

x_AddRegionDestionationConversionOptions();

176 bool

x_IsImportSubtype(objects::CSeqFeatData::ESubtype subtype);

177 bool

x_IsProtSubtype(objects::CSeqFeatData::ESubtype subtype);

178 bool

x_IsRnaSubtype(objects::CSeqFeatData::ESubtype subtype);

179 string

GetSiteName(objects::CSeqFeatData::TSite site_type);

183 bool

m_create_general_only =

false

;

184 int

*m_offset =

nullptr

;

191 static CRef<CConvertFeatureBase>

Create(objects::CSeqFeatData::ESubtype subtype_from, objects::CSeqFeatData::ESubtype subtype_to);

199 virtual string GetDescription

() {

return "Creates gene with locus value from misc_feature comment."

; }

209 virtual bool CanConvertFrom

(objects::CSeqFeatData::ESubtype subtype) {

return

x_IsImportSubtype(subtype); }

210 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype subtype) {

return

x_IsImportSubtype(subtype); }

219 virtual string GetDescription

() {

return "Delete protein product sequence.\nClear product field if transcript ID removal was requested.\nIf converting to tRNA and anticodon value can be parsed from label, set aa value, and add any text that could not be parsed into an anticodon value to the feature note.\nIf converting to other RNA, put label in RNA product."

; }

220 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype subtype) {

return

x_IsRnaSubtype(subtype); }

229 virtual string GetDescription

() {

return "If converting to tRNA and anticodon value can be parsed from label, set aa value, and add any text that could not be parsed into an anticodon value to the feature note. If converting to other RNA, put label in RNA product. Also append gene locus, allele, description, map location, and locus tag to comment (as long as these values are not already in the label and therefore in the RNA product)."

; }

230 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype subtype) {

return

x_IsRnaSubtype(subtype); }

234 void

x_AddOneGeneField(

string

& product,

string

& comment,

const string

& field);

242 virtual string GetDescription

() {

return "Creates a repeat_region with mobile_element qualifiers for the transposon and/or insertion sequence qualifiers on the BioSource. All other BioSource information is discarded."

; }

252 virtual string GetDescription

() {

return "Copy comment from coding region to new misc_feature and remove product field. If not pseudo coding region, add product name from protein feature to new misc_feature comment and delete product sequence."

; }

257 string

x_GetProteinDesc(

const

objects::CSeq_feat& cds, objects::CScope& scope);

268 virtual string GetDescription

() {

return "Original feature must be on nucleotide sequence and be contained in coding region location. Coding region must have product protein sequence. New feature is created on product protein sequence so that the translated location will be as close as possible to the original nucleotide location (may not be exact because of codon boundaries)."

; }

269 virtual bool CanConvertFrom

(objects::CSeqFeatData::ESubtype feat_from) {

return

x_IsImportSubtype(feat_from); }

270 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype feat_to) {

return

x_IsProtSubtype(feat_to); }

281 "Original feature must be on a protein sequence that is a product of a coding region.\nNew feature will be created on same sequence as coding region.\n" 282 "If protein feature has name, this will be saved as /product qualifier on new feature.\nIf protein feature does not have name but does have description, this will be saved as /product qualifier on new feature.\n" 283 "EC_number values from the protein feature will be saved as /EC_number qualifiers on the new feature.\nActivity values will be saved as /function qualifiers on the new feature.\n" 284 "Db_xref values from the protein feature will be saved as /db_xref qualifers on the new feature."

; }

285 virtual bool CanConvertFrom

(objects::CSeqFeatData::ESubtype feat_from) {

return

x_IsProtSubtype(feat_from); }

286 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype feat_to) {

return

x_IsImportSubtype(feat_to); }

296 virtual string GetDescription

() {

return "Creates an RNA feature of the specified subtype. Import feature key is discarded."

; }

297 virtual bool CanConvertFrom

(objects::CSeqFeatData::ESubtype feat_from) {

return

x_IsImportSubtype(feat_from); }

298 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype feat_to) {

return

x_IsRnaSubtype(feat_to); }

308 virtual string GetDescription

() {

return "Use /product qual or comment for coding region product name."

; }

309 virtual bool CanConvertFrom

(objects::CSeqFeatData::ESubtype feat_from) {

return

x_IsImportSubtype(feat_from); }

318 virtual string GetDescription

() {

return "Use /gene qual or comment for gene locus."

; }

319 virtual bool CanConvertFrom

(objects::CSeqFeatData::ESubtype feat_from) {

return

x_IsImportSubtype(feat_from); }

328 virtual string GetDescription

() {

return "Use region name for new feature comment."

; }

329 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype feat_to) {

return

x_IsImportSubtype(feat_to); }

339 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype feat_to) {

return

x_IsRnaSubtype(feat_to); }

348 virtual string GetDescription

() {

return "Create an import feature with the same note as the comment."

; }

349 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype feat_to) {

return

x_IsImportSubtype(feat_to); }

358 virtual string GetDescription

() {

return "Create an import feature with the gene description and locus prepended to the original comment, separated by semicolons.."

; }

359 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype feat_to) {

return

x_IsImportSubtype(feat_to); }

368 virtual string GetDescription

() {

return "Create an import feature with the RNA product name appended to the original comment, separated by semicolons."

; }

369 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype feat_to) {

return

x_IsImportSubtype(feat_to); }

370 virtual bool CanConvertFrom

(objects::CSeqFeatData::ESubtype feat_from) {

return

x_IsRnaSubtype(feat_from); }

379 virtual string GetDescription

() {

return "Create a coding region feature with the mRNA product name as the protein."

; }

388 virtual string GetDescription

() {

return "Convert tRNA to gene, use tRNA product for gene description."

; }

397 virtual string GetDescription

() {

return "Creates an import feature of the specified subtype with the site type name as a /note qualifier."

; }

398 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype feat_to) {

return

x_IsImportSubtype(feat_to); }

408 "If feature is on nucleotide sequence, will create feature on protein product sequence for overlapping coding region. Protein name will be region name."

; }

409 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype feat_to) {

return

x_IsProtSubtype(feat_to); }

419 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype subtype) {

return

x_IsRnaSubtype(subtype); }

420 virtual bool CanConvertFrom

(objects::CSeqFeatData::ESubtype subtype) {

return

x_IsRnaSubtype(subtype); }

429 virtual string GetDescription

() {

return "Create Bond feature with specified site type. Location is a SeqLocBond with a point at the start of the original location and a point at the end of the original location. All feature ID, partialness, except, comment, product, location, genbank qualifiers, title, citation, experimental evidence, gene xrefs, db xrefs, and pseudo-ness information is discarded."

; }

438 virtual string GetDescription

() {

return "Create Site feature with specified site type. All feature ID, partialness, except, product, location, genbank qualifiers, title, citation, experimental evidence, gene xrefs, db xrefs, and pseudo-ness information is discarded."

; }

447 virtual string

GetDescription();

457 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype subtype) {

return

x_IsProtSubtype(subtype); }

458 virtual bool CanConvertFrom

(objects::CSeqFeatData::ESubtype subtype) {

return

x_IsProtSubtype(subtype); }

466 virtual string

GetDescription();

467 virtual bool CanConvertTo

(objects::CSeqFeatData::ESubtype subtype) {

return

x_IsProtSubtype(subtype); }

476 virtual string GetDescription

() {

return "Create gene feature, copy all protein values to gene note."

; }

484 virtual string GetDescription

() {

return "Create pseudo gene feature, copy all protein values to gene note."

; }

void SetDefaultVal(bool val)

CConversionOptionBool(bool val=false, bool default_val=false)

bool GetDefaultVal() const

vector< string > m_Suggested

CConversionOptionString(const string &val, const string &default_val, vector< string > suggested, bool only_suggested)

CConversionOptionString(const string &val, const string &default_val)

const vector< string > & GetSuggestedValues() const

const string & GetDefaultVal() const

const string & GetVal() const

void SetDefaultVal(const string &val)

void SetOnlySuggested(bool val)

bool GetOnlySuggested() const

void ClearSuggestedValues()

void SetVal(const string &val)

void AddSuggestedValue(const string &val)

~CConversionOptionString()

CConversionOption(const string &label)

const string & GetLabel() const

CConvertBioSrcToRptRegion()

virtual string GetDescription()

void SetNonfunctional(bool f)

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype subtype)

CConvertCDSToProt(objects::CSeqFeatData::ESubtype feat_to)

virtual string GetDescription()

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype subtype)

CConvertCDSToRNA(objects::CSeqFeatData::ESubtype feat_to)

virtual string GetDescription()

static const string s_PlaceOnProt

void SetCreateGeneralOnly(bool flag)

static const string s_RemoveTranscriptID

void SetOffset(int *offset)

static const string s_SiteType

const TOptions & GetOptions() const

static const string s_BondType

virtual string GetDescription()

static const string s_NcrnaClass

static const string s_IsPseudo

static const string s_RemovemRNA

objects::CBondList m_BondList

vector< CRef< CConversionOption > > TOptions

objects::CSeqFeatData::ESubtype m_To

objects::CSeqFeatData::ESubtype m_From

static const string s_RemoveGene

objects::CSiteList m_SiteList

virtual string GetDescription()

CConvertGeneToImp(objects::CSeqFeatData::ESubtype feat_to)

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype feat_to)

CConvertGeneToRNA(objects::CSeqFeatData::ESubtype feat_to)

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype subtype)

virtual string GetDescription()

virtual bool CanConvertFrom(objects::CSeqFeatData::ESubtype feat_from)

virtual string GetDescription()

CConvertImpToCDS(objects::CSeqFeatData::ESubtype feat_from)

virtual string GetDescription()

CConvertImpToGene(objects::CSeqFeatData::ESubtype feat_from)

virtual bool CanConvertFrom(objects::CSeqFeatData::ESubtype feat_from)

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype subtype)

virtual bool CanConvertFrom(objects::CSeqFeatData::ESubtype subtype)

virtual string GetDescription()

CConvertImpToImp(objects::CSeqFeatData::ESubtype feat_to, objects::CSeqFeatData::ESubtype feat_from)

CConvertImpToProt(objects::CSeqFeatData::ESubtype feat_to, objects::CSeqFeatData::ESubtype feat_from)

virtual bool CanConvertFrom(objects::CSeqFeatData::ESubtype feat_from)

virtual string GetDescription()

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype feat_to)

virtual string GetDescription()

CConvertImpToRNA(objects::CSeqFeatData::ESubtype feat_to, objects::CSeqFeatData::ESubtype feat_from)

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype feat_to)

virtual bool CanConvertFrom(objects::CSeqFeatData::ESubtype feat_from)

virtual string GetDescription()

virtual bool CanConvertFrom(objects::CSeqFeatData::ESubtype feat_from)

CConvertProtToImp(objects::CSeqFeatData::ESubtype feat_to, objects::CSeqFeatData::ESubtype feat_from)

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype feat_to)

virtual string GetDescription()

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype subtype)

virtual bool CanConvertFrom(objects::CSeqFeatData::ESubtype subtype)

CConvertProtToProt(objects::CSeqFeatData::ESubtype feat_to, objects::CSeqFeatData::ESubtype feat_from)

virtual string GetDescription()

virtual bool CanConvertFrom(objects::CSeqFeatData::ESubtype subtype)

CConvertRNAToRNA(objects::CSeqFeatData::ESubtype feat_to, objects::CSeqFeatData::ESubtype feat_from)

virtual string GetDescription()

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype subtype)

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype feat_to)

virtual string GetDescription()

CConvertRegionToImp(objects::CSeqFeatData::ESubtype feat_to)

virtual string GetDescription()

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype feat_to)

CConvertRegionToProt(objects::CSeqFeatData::ESubtype feat_to)

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype feat_to)

virtual string GetDescription()

CConvertRegionToRna(objects::CSeqFeatData::ESubtype feat_to)

virtual string GetDescription()

virtual bool CanConvertFrom(objects::CSeqFeatData::ESubtype feat_from)

CConvertRnaToImp(objects::CSeqFeatData::ESubtype feat_to, objects::CSeqFeatData::ESubtype feat_from)

virtual bool CanConvertTo(objects::CSeqFeatData::ESubtype feat_to)

CConvertSiteToImp(objects::CSeqFeatData::ESubtype feat_to)

virtual string GetDescription()

CConvertToBond(objects::CSeqFeatData::ESubtype feat_from)

virtual string GetDescription()

CConvertToRegion(objects::CSeqFeatData::ESubtype feat_from)

CConvertToSite(objects::CSeqFeatData::ESubtype feat_from)

virtual string GetDescription()

CConvertmRNAToCDS(objects::CSeqFeatData::ESubtype feat_to, objects::CSeqFeatData::ESubtype feat_from)

virtual string GetDescription()

CConverttRNAToGene(objects::CSeqFeatData::ESubtype feat_to, objects::CSeqFeatData::ESubtype feat_from)

static const string kConversionNotSupported

Include a standard set of the NCBI C++ Toolkit most basic headers.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define NCBI_GUIOBJUTILS_EXPORT

static const char label[]

where boath are integers</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 orig

static void text(MDB_val *v)

@ eExistingText_prefix_semi

const value_slice::CValueConvert< value_slice::SRunTimeCP, FROM > Convert(const FROM &value)

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