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NCBI C++ ToolKit: src/objtools/writers/bed_feature_record.cpp Source File

52 #define BUMP( x, y ) if ( x < (y) ) x = (y) 59

m_strChromStart(

"."

64

m_strThickStart(

"."

67

m_strBlockCount(

"."

68

m_strBlockSizes(

"."

69

m_strBlockStarts(

"."

70

mIdResolve(id_resolve)

91 const auto

& xrefs = mf.

GetXref

();

92 for

(

auto

it = xrefs.begin(); it != xrefs.end(); ++it) {

93 const auto

& xref = **it;

94 if

(xref.CanGetData() && xref.GetData().IsGene()) {

95 return

xref.GetData().GetGene();

119

[](

char

c) ->

char

{ return std::isspace(c) ?

'_'

: c; });

123 if

(geneRef.IsSetLocus()) {

127 if

(geneRef.IsSetLocus_tag()) {

136 if

(geneRef.IsSetDesc()) {

139 if

(geneRef.IsSetSyn()) {

160 const

vector< CRef< CUser_field > >& fields = uo.

GetData

();

161

vector< CRef< CUser_field > >::const_iterator it = fields.begin();

162 for

( ; it != fields.end(); ++it ) {

163 if

( ! (*it)->CanGetLabel() || ! (*it)->GetLabel().IsStr() ) {

166 string

strLabel = (*it)->GetLabel().GetStr();

167 if

( strLabel ==

"name"

) {

169 if

( (*it)->IsSetData() && (*it)->GetData().IsStr() ) {

174 if

( strLabel ==

"score"

&& ! bUseScore ) {

176 if

( (*it)->IsSetData() && (*it)->GetData().IsInt() ) {

181 if

( strLabel ==

"greylevel"

&& bUseScore ) {

183 if

( (*it)->IsSetData() && (*it)->GetData().IsInt() ) {

188 if

( strLabel ==

"thickStart"

) {

190 if

( (*it)->IsSetData() && (*it)->GetData().IsInt() ) {

195 if

( strLabel ==

"thickEnd"

) {

197 if

( (*it)->IsSetData() && (*it)->GetData().IsInt() ) {

202 if

( strLabel ==

"itemRGB"

) {

204 if

( (*it)->IsSetData() && (*it)->GetData().IsInt() ) {

208 if

( (*it)->IsSetData() && (*it)->GetData().IsStr() ) {

214 if

( strLabel ==

"blockCount"

) {

216 if

( (*it)->IsSetData() && (*it)->GetData().IsInt() ) {

221 if

( strLabel ==

"blockSizes"

) {

223 if

( (*it)->IsSetData() && (*it)->GetData().IsStr() ) {

228 if

( strLabel ==

"blockStarts"

) {

230 if

( (*it)->IsSetData() && (*it)->GetData().IsStr() ) {

276 unsigned int

columnCount)

282 if

( columnCount >= 4 ) {

283

ostr <<

"\t"

Name

();

285 if

( columnCount >= 5 ) {

286

ostr <<

"\t"

Score

();

288 if

( columnCount >= 6 ) {

289

ostr <<

"\t"

Strand

();

291 if

( columnCount >= 7 ) {

294 if

( columnCount >= 8 ) {

297 if

( columnCount >= 9 ) {

300 if

( columnCount >= 10 ) {

303 if

( columnCount >= 11 ) {

306 if

( columnCount >= 12 ) {

360 if

(

data

.IsRegion()) {

364 if

(

data

.IsGene()) {

407 if

(

blocks

.IsPacked_int()) {

408 const

list<CRef<CSeq_interval> >& intervals =

blocks

.GetPacked_int().Get();

411

list<string> blockStarts;

412

list<string> blockSizes;

414 for

(

auto

pInterval: intervals) {

456 const string

color

)

459 if

(

color

"0 0 0"

) {

@ eExtreme_Positional

numerical value

const CGene_ref & sGetClosestGeneRef(const CMappedFeat &mf)

void transform(Container &c, UnaryFunction *op)

bool AssignName(const CMappedFeat &)

bool SetThick(const CSeq_loc &)

const string & BlockCount() const

bool SetLocation(const CSeq_loc &)

const string & Chrom() const

bool SetBlocks(const CSeq_loc &, const CSeq_loc &)

const string & ChromEnd() const

bool SetName(const CSeqFeatData &)

const string & ItemRgb() const

const string & ChromStart() const

bool Write(CNcbiOstream &, unsigned int)

CGenbankIdResolve & mIdResolve

const string & Strand() const

bool AssignLocation(CScope &, const CSeq_interval &)

CBedFeatureRecord(CGenbankIdResolve &id_resolve)

bool AssignDisplayData(const CMappedFeat &, bool)

const string & BlockStarts() const

const string & BlockSizes() const

bool SetRgb(const string &)

const string & ThickEnd() const

const string & Name() const

const string & Score() const

const string & ThickStart() const

bool SetNoThick(const CSeq_loc &)

bool GetBestId(CSeq_id_Handle, CScope &, string &) const

TSeqPos GetLength(void) const

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

static CSeq_id_Handle GetHandle(const CSeq_id &id)

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

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

CMappedFeat GetBestGeneForFeat(const CMappedFeat &feat, CFeatTree *feat_tree=0, const SAnnotSelector *base_sel=0, CFeatTree::EBestGeneType lookup_type=CFeatTree::eBestGene_TreeOnly)

const CSeq_feat::TXref & GetXref(void) const

const CSeqFeatData & GetData(void) const

bool IsSetXref(void) const

bool IsSetData(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

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

Convert int to string.

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

Join strings using the specified delimiter.

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

Convert UInt to 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.

bool IsStr(void) const

Check if variant Str is selected.

bool IsSetType(void) const

type of object within class Check if a value has been assigned to Type data member.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TType & GetType(void) const

Get the Type member data.

bool IsUser(void) const

Check if variant User is selected.

const TRegion & GetRegion(void) const

Get the variant data.

bool IsGene(void) const

Check if variant Gene is selected.

const TUser & GetUser(void) const

Get the variant data.

const TGene & GetGene(void) const

Get the variant data.

bool IsRegion(void) const

Check if variant Region is selected.

ENa_strand

strand of nucleic acid

const TId & GetId(void) const

Get the Id member data.

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

TFrom GetFrom(void) const

Get the From member data.

TStrand GetStrand(void) const

Get the Strand member data.

bool IsSetTo(void) const

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

bool CanGetId(void) const

Check if it is safe to call GetId method.

bool IsSetStrand(void) const

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

bool IsSetStrand(void) const

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

TStrand GetStrand(void) const

Get the Strand member data.

TTo GetTo(void) const

Get the To member data.

bool IsSetFrom(void) const

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

bool IsInt(void) const

Check if variant Int is selected.

const TInt & GetInt(void) const

Get the variant data.

bool IsPnt(void) const

Check if variant Pnt is selected.

static DP_BlockInfo * blocks

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NCBI C++ ToolKit: src/objtools/writers/bed_feature_record.cpp Source File

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