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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/genbank__formatter_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/format/genbank_formatter.cpp Source File

m_uFeatureCount( 0 ), m_bHavePrintedSourceFeatureJavascript(

),

m_bSourceDescriptorDone(

)

SetIndent(

(12,

));

SetFeatIndent(

(21,

));

SetBarcodeIndent(

(35,

));

<

TFlatItemClass>

CWrapperForFlatTextOStream(

TFlatItemClass& item ) :

m_block_callback(block_callback),

m_orig_text_os(orig_text_os),

~CWrapperForFlatTextOStream()

(2,

m_block_callback->notify(m_block_text_str, *m_ctx, m_item);

);

m_orig_text_os.AddLine(m_block_text_str,

, eAddNewline_No);

add_size = m_block_text_str.size();

add_size += (line->

() + 1);

m_block_text_str.reserve(

(m_block_text_str.capacity(), add_size));

(*line, obj, eAddNewline_Yes);

EAddNewline add_newline )

m_block_text_str.reserve(

(m_block_text_str.capacity(),

m_block_text_str.length() +

(add_newline == eAddNewline_Yes?1:0) ) );

m_block_text_str.append(line.

(), line.

());

( add_newline == eAddNewline_Yes ) {

m_block_text_str +=

;

TFlatItemClass& m_item;

m_block_text_str;

<

TFlatItemClass>

TFlatItemClass& item,

item.GetContext()->Config().GetGenbankBlockCallback();

( block_callback ) {

p_text_os.

(

CWrapperForFlatTextOStream<TFlatItemClass>(

block_callback, orig_text_os,

, item) );

( loc.

() &&

<<

<< (point+1) <<

<< (point+2) <<

;

is_first =

;

( ; loc_piece_iter ; ++loc_piece_iter ) {

( seq_id_handle && bioseq_handle && ! bioseq_handle.

(seq_id_handle) ) {

<<

<< (from + 1) <<

<< (to + 1) <<

;

accn =

.GetAccession();

period_pos = accn.find_first_of(

);

( period_pos !=

) {

accn.resize(period_pos);

<<

<< sAnchorName <<

<<

->GetAccession() <<

;

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, end_item, orig_text_os);

bHtml = cfg.

();

.push_back(

);

.push_back(

);

* strands[] = {

,

,

,

};

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, locus, orig_text_os);

ostringstream locus_line;

* units =

;

( !

.IsProt() ) {

( (

.IsWGSMaster() && !

.IsRSWGSNuc() ) ||

.IsTSAMaster() ||

.IsTLSMaster() )

locus_line.setf(IOS_BASE::left, IOS_BASE::adjustfield);

locuslength = locusname.length();

locus_line << setw(16) << locusname;

spaceForLength =

( 12, (

)(12 - (locuslength - 16)) );

locus_line.setf(IOS_BASE::right, IOS_BASE::adjustfield);

<< setw(spaceForLength-1) << locus.

()

locus_line.setf(IOS_BASE::left, IOS_BASE::adjustfield);

locus_line_str = locus_line.str();

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, defline, orig_text_os);

(

,

, defline_text);

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, acc, orig_text_os);

acc_line =

;

acc_line += link_base + acc_str +

+ acc_str +

;

acc_line +=

;

.push_back(

);

(

,

, acc_line);

ostringstream version_line;

(

.GetAccession().empty() ) {

.push_back(

);

version_line <<

.GetAccession();

version_line <<

<<

.GetGi();

version_line_str = version_line.str();

(

.GetContext()->Config().DoHTML() ) {

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, gp, orig_text_os);

*prefix =

;

ostringstream project_line;

project_line <<

;

project_line <<

;

proj_num = *proj_num_iter;

project_line << proj_num;

project_line_str = project_line.str();

( !

.empty() ) {

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, html_anchor, orig_text_os);

( csh.

() ) {

vector<string>* rcx = csh.

();

prefix = (csh.

() ?

:

);

(

&

: *rcx) {

text_os.

(

.substr(0, pos + 2) + prefix +

+ suffix);

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, keys, orig_text_os);

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, seg, orig_text_os);

ostringstream segment_line;

(

,

, segment_line.str());

ostringstream source_line;

prefix =

.IsUsingAnamorph() ?

:

;

source_line <<

.GetOrganelle() <<

.GetTaxname();

( !

.GetCommon().empty() ) {

source_line << prefix <<

.GetCommon() <<

;

line = source_line.str();

(

.GetContext()->Config().DoHTML() ) {

(

.GetContext()->Config().DoHTML()) {

lineage =

.GetLineage();

strBaseUrlCambiaPatentLensHead(

);

strPatString =

;

strPatString +=

;

strPatString += strBaseUrlCambiaPatentLensHead;

strPatString +=

;

strPatString +=

;

strPatString +=

;

strPatString =

(

);

strFeatureLink;

strFeatureLink;

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, ref, orig_text_os);

(

.Config().DoHTML() ) {

vector<string>* rc =

.GetRefCache();

(

:

) {

rc->push_back(

);

strDummyProt(

);

( uLinkStart !=

) {

uLinkStop = strText.find_first_of(

, uLinkStart );

( uLinkStop ==

) {

uLinkStop = strText.length();

( uLinkStart > 0 && ( strText[uLinkStart-1] ==

|| strText[uLinkStart-1] ==

) ) {

strLink = strText.substr( uLinkStart, uLinkStop - uLinkStart );

string::size_type last_good_char = strLink.find_last_not_of(

);

( last_good_char !=

) {

strLink.resize( last_good_char + 1 );

strDummyLink =

( strLink, strProtocol, strDummyProt );

strReplace(

);

strReplace += strDummyLink;

strReplace +=

;

strReplace += strDummyLink;

strReplace +=

;

uLinkStart =

( strText, strProtocol +

, uLinkStart + strReplace.length() );

ostringstream ref_line;

ref_line << serial <<

;

ref_line.setf(IOS_BASE::left, IOS_BASE::adjustfield);

ref_line << setw(3) << serial;

ref_line <<

;

ref_line_str = ref_line.str();

( authors.empty() ) {

(

.Config().IsFormatGenbank() ) {

}

(

.Config().IsFormatEMBL() ) {

string::size_type last_periods = authors.find_last_not_of(

);

( last_periods != string::npos ) {

( last_periods < authors.length() ) {

authors.resize( last_periods );

bHtml =

.Config().DoHTML();

strDummy(

);

strLink =

;

strLink += strPubmed;

strLink += strPubmed;

strPubmed = strLink;

(

.Config().DoHTML() ) {

strRaw = strPubmed;

strPubmed =

;

strPubmed += strRaw;

strPubmed +=

;

strPubmed += strRaw;

strPubmed +=

;

is_html =

.Config().DoHTML();

.Config().DoHTML() );

( ! strCambiaPatentLens.empty() ) {

(

,

, strCambiaPatentLens,

);

( !

.Config().IsModeEntrez() ) {

first_line =

+ first_line;

has_comment =

;

( desc_ci1 || desc_ci2 || desc_ci3 ) {

has_comment =

;

( ; user_iter; ++user_iter ) {

& desc = *user_iter;

( type_str ==

||

type_str ==

||

type_str ==

)

has_comment =

;

( ! has_comment ) {

(

.CanGetDate() && !

.GetIds().empty() )

has_comment =

;

(

.CanGetDate() && !

.GetIds().empty() )

has_comment =

;

has_contig =

;

do_contig_style =

.DoContigStyle();

show_contig = ( (

.IsSegmented() &&

.HasParts()) ||

(

.IsDelta() && !

.IsDeltaLitOnly()) );

has_sequence =

;

has_sequence =

;

& accn =

.GetAccession();

<<

;

( has_comment ) {

<<

<< accn <<

;

<<

<< accn <<

;

<<

<< accn <<

;

( has_sequence ) {

<<

<< accn <<

;

(

.GetPrevHandle() ||

.GetNextHandle() ) {

<<

;

(

.GetNextHandle() ) {

gi =

.GetNextHandle().GetAccessSeq_id_Handle().GetGi();

<<

<< gi <<

<< accn <<

;

(

.GetPrevHandle() ) {

gi =

.GetPrevHandle().GetAccessSeq_id_Handle().GetGi();

<<

<< gi <<

<< accn <<

;

<<

<<

;

<<

;

first_line =

.str();

ostringstream pre_feature_html;

pre_feature_html <<

<<

.GetAccession()

<<

<< strKey <<

<< feat_type_count <<

;

pre_feature_html <<

;

pre_feature_html <<

<<

.GetGI() <<

<<

;

<<

<< strKey

<<

<< strKey

<<

<< strKey <<

;

pre_feature_html <<

;

temp = pre_feature_html.str();

( it != wrapped.end() ) {

( strContent.size() && strContent.size() <= uMaxSize ) {

wrapped.erase( delete_me );

list<string>::iterator l_first_new_line;

( l_old_last !=

.end() ) {

l_first_new_line = l_old_last;

l_first_new_line =

.begin();

( l_first_new_line ==

.end() ) {

list<string>::iterator l_second_new_line = l_first_new_line;

++l_second_new_line;

( l_second_new_line ==

.end() ) {

( (

)l_first_new_line->length() <=

) {

.erase( l_second_new_line );

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, comment, orig_text_os);

is_first = comment.

();

list<string>::iterator l_old_last =

.end();

( !

.empty() ) {

& comm = *comment_it;

(

,

, comm,

, bHtml, internalIndent);

( internalIndent > 0 ) {

& txt = *line;

x.push_back(

+ txt);

}

(

(txt,

) !=

||

x.push_back(

+ txt);

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, fh, orig_text_os);

& iFrom,

& iTo )

( idh && idh.

() ) {

iGi = idh.

();

& strRawKey,

uItemNumber = 0 )

( strRawKey ==

|| strRawKey ==

)

( strRawKey ==

&& uItemNumber == 0) {

iFrom = 0, iTo = 0;

( iFrom == 0 && iFrom == iTo ) {

strLink.reserve(100);

(

.find_first_not_of(

) ==

&& s.

() == 22) {

vector<CRef<CFormatQual> > & quals = ff.

();

& qual = (*it)->GetName();

((*it)->GetTrim()) {

= (*it)->GetValue();

((*it)->GetStyle()) {

(bHtml) sanitized +=

;

+=

;

(l_new.size() > 1) {

&last_line = l_new.back();

list<string>::const_iterator end_iter = l_new.end();

&second_to_last_line = *end_iter;

l_new.back() +=

;

(p_source_feature_item) {

text_os = &s_WrapOstreamIfCallbackExists(p_text_os, *p_source_feature_item, orig_text_os);

(! text_os && p_feature_item) {

text_os = &s_WrapOstreamIfCallbackExists(p_text_os, *p_feature_item, orig_text_os);

bHtml =

.GetContext()->Config().DoHTML();

& strKey = feat->GetKey();

fkey = strKey;

(

.GetContext()->IsProt()) {

(

.GetContext()->IsRefSeq()) {

(

.GetContext()->Config().IsModeEntrez() ||

.GetContext()->Config().IsModeRelease()) {

(bHtml &&

.GetContext()->Config().IsModeEntrez() &&

.GetContext()->Config().ShowSeqSpans()) {

(

, fkey, feat->GetLoc().GetString(),

);

(bHtml &&

.GetContext()->Config().IsModeEntrez() &&

.GetContext()->Config().ShowSeqSpans()) {

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, bc, orig_text_os);

ostringstream bc_line;

bc_line.setf(IOS_BASE::right, IOS_BASE::adjustfield);

<< setw(7) << bc.

() <<

<< setw(7) << bc.

() <<

<< setw(7) << bc.

() <<

<< setw(7) << bc.

() <<

;

bc_line << setw(7) << bc.

() <<

;

(

,

, bc_line.str());

}

( (v /= 10) && --

);

*

initial_p = p;

*p =

+base_count%10;

}

( (base_count /= 10) > 0 );

reverse( initial_p, p );

dist_to_gap_or_end = 0;

dist_to_gap_or_end += seg_len;

( 0 == space_left_on_line ) {

( iter && iter.

() && gap_size < space_left_on_line ) {

( gap_size >= space_left_on_line ) {

dist_to_gap_or_end += gap_size;

dist_to_gap_or_end;

kSeqPosWidth = 9;

kLineBufferSize = 170;

line[kLineBufferSize];

fill(line, line+kLineBufferSize,

);

kCloseSpan =

;

length_of_span_before_base_count = 0;

kSpan =

;

( kSpan.begin(), kSpan.end(), line + kSeqPosWidth );

length_of_span_before_base_count = kSpan.length();

( 0 == initial_indent ) {

( total > 0 ) {

(base_count >= 1000000000) {

(kSeqPosWidth == 9) {

fill(line, line+kLineBufferSize,

);

length_of_span_before_base_count = 0;

kSpan =

;

( kSpan.begin(), kSpan.end(), line + kSeqPosWidth );

length_of_span_before_base_count = (

) kSpan.length();

( 0 == initial_indent ) {

* linep = line + kSeqPosWidth;

linep += length_of_span_before_base_count;

*

linep_right_after_span_tag = (linep + 1);

bases_to_skip = 0;

( initial_indent != 0 ) {

bases_to_skip = initial_indent;

linep += (bases_to_skip + chunks_to_skip);

ch = *iter;

base_count += total;

( ; total > 0 && j <

; ++j, ++iter, --total, ++linep) {

ch = *iter;

doneWithEntireSequence = ( ! iter );

( ! doneWithEntireSequence ) {

*

linep_at_close_span =

fill( linep, linep_at_close_span,

);

linep = linep_at_close_span;

( kCloseSpan.begin(), kCloseSpan.end(), linep );

linep += kCloseSpan.length();

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, seq, orig_text_os);

bGapsHiddenUntilClicked = (

total = from <= to? to - from + 1 : 0;

( ! bGapsHiddenUntilClicked ) {

( iter && total > 0 ) {

distance_until_next_significant_gap =

( 0 == distance_until_next_significant_gap ) {

( iter && iter.

() ) {

( total >= gap_size ) {

base_count += gap_size;

( gap_started_before_this_point && ! seq.

() ) {

ostringstream gap_link;

text_os.

(gap_link.str());

fake_total = distance_until_next_significant_gap;

amount_to_subtract_from_total =

( distance_until_next_significant_gap - fake_total );

( total >= amount_to_subtract_from_total ) {

total -= amount_to_subtract_from_total;

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, dbs, orig_text_os);

=

;

db_src = *it;

( !

.empty() ) {

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, wgs, orig_text_os);

=

;

=

;

first_id_equals_second_id =

;

first_id_equals_second_id =

;

wgs_line = ( first_id_equals_second_id ? first_id : first_id +

+ last_id );

( first_id_equals_second_id ) {

link =

+ first_id;

prefix_len = first_id.find_first_of(

);

bIsWGSScafldWithS =

first_id.length() > 7 && first_id[prefix_len+2] ==

);

(bIsWGSProject || bIsWGSScafldWithS) {

url_arg = first_id.substr(0,prefix_len+2);

link =

+

url_arg +

+ ( bIsWGSScafldWithS ?

:

);

link =

+ first_id +

+ last_id +

;

wgs_line =

+ link +

+ wgs_line +

;

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, tsa, orig_text_os);

id_range = first_id;

id_range = first_id +

+ last_id;

prefix_len = tls_master.find_first_of(

);

tls_master = tls_master.substr(0, prefix_len+2);

( ! tls_master.empty() ) {

id_range =

+ tls_master +

+ id_range +

;

id_range = first_id;

id_range = first_id +

+ last_id;

prefix_len = tsa_master.find_first_of(

);

tsa_master = tsa_master.substr(0, prefix_len+2);

( ! tsa_master.empty() ) {

id_range =

+ tsa_master +

+ id_range +

;

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, primary, orig_text_os);

primary_str = primary.

();

(

,

, primary_str);

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, contig, orig_text_os);

(assembly.empty()) {

assembly =

;

assembly =

+ assembly +

;

(

,

, assembly);

strOrigin =

.GetOrigin();

( strOrigin ==

) {

( strOrigin.empty() ) {

.push_back(

);

(

,

, strOrigin );

& text_os = s_WrapOstreamIfCallbackExists(p_text_os, gap, orig_text_os);

isGapOfLengthZero = ( gapStart > gapEnd );

( isGapOfLengthZero ) {

( isGapOfLengthZero ) {

estimated_length;

estimated_length =

;

@ eExtreme_Positional

numerical value

User-defined methods of the data storage class.

const CSeq_loc & GetRegion(void) const

bool IsSetRegion(void) const

SIZE_TYPE GetOther(void) const

SIZE_TYPE GetT(void) const

SIZE_TYPE GetA(void) const

SIZE_TYPE GetG(void) const

SIZE_TYPE GetC(void) const

const string & GetTSAMasterName(void) const

const CFlatFileConfig & Config(void) const

const CSeq_loc & GetLocation(void) const

const string & GetTLSMasterName(void) const

const string & GetAccession(void) const

const TCache & GetCache(void) const

int GetLength(void) const

const CSeq_loc & GetLoc(void) const

const TDBSource & GetDBSource(void) const

const string & GetDefline(void) const

const CMappedFeat & GetFeat(void) const

const TQuals & GetQuals(void) const

@ eAction_Skip

skip this block (i.e. don't print it)

@ eAction_HaltFlatfileGeneration

If for some reason you don't want the rest of the flatfile generated, this will trigger a CFlatExcept...

const IHTMLFormatter & GetHTMLFormatter() const

bool IsPolicyFtp(void) const

bool ShowSeqSpans(void) const

bool IsPolicyGenomes(void) const

bool LongLocusNames(void) const

bool ExpandGaps(void) const

bool ShowContigAndSeq(void) const

bool IsModeEntrez(void) const

const CFlatFileConfig & GetConfig(void) const

static const string s_GenbankMol[]

const CFlatFileContext & GetContext(void) const

string x_FormatAccession(const CAccessionItem &acc, char separator) const

const string & GetIndent(void) const

void x_FormatRefJournal(const CReferenceItem &ref, string &journal, CBioseqContext &ctx) const

void x_GetKeywords(const CKeywordsItem &kws, const string &prefix, list< string > &l) const

const string & GetFeatIndent(void) const

void x_FormatRefLocation(ostream &os, const CSeq_loc &loc, const string &to, const string &delim, CBioseqContext &ctx) const

virtual list< string > & Wrap(list< string > &l, SIZE_TYPE width, const string &tag, const string &body, EPadContext where=ePara, bool htmlaware=false) const

TWrapFlags & SetWrapFlags(void)

CBioseqContext * GetContext(void)

const CSerialObject * GetObject(void) const

const string & GetString(void) const

TSeqPos GetTo(void) const

TSeqPos GetEstimatedLength(void) const

TSeqPos GetFrom(void) const

std::vector< std::string > TEvidence

const std::string & GetType(void) const

bool HasEstimatedLength(void) const

const TEvidence & GetEvidence(void) const

const std::string & GetFeatureName(void) const

CGenbankFormatterWrapDest(IFlatTextOStream &s)

virtual void Append(const string &s)

virtual void Append(const CTempString &s)

IFlatTextOStream & m_text_os

void FormatBasecount(const CBaseCountItem &bc, IFlatTextOStream &text_os) override

void x_SmartWrapQuals(const class CFeatureItemBase &f, const class CFlatFeature &feat, IFlatTextOStream &text_os)

void FormatWGS(const CWGSItem &wgs, IFlatTextOStream &text_os) override

void FormatSource(const CSourceItem &source, IFlatTextOStream &text_os) override

void FormatTSA(const CTSAItem &tsa, IFlatTextOStream &text_os) override

void FormatContig(const CContigItem &contig, IFlatTextOStream &text_os) override

void EndSection(const CEndSectionItem &, IFlatTextOStream &text_os) override

void x_LocusHtmlPrefix(std::string &first_line, CBioseqContext &ctx)

bool m_bSourceDescriptorDone

bool m_bHavePrintedSourceFeatureJavascript

void x_Title(list< string > &l, const CReferenceItem &ref, CBioseqContext &ctx) const

void FormatGap(const CGapItem &gap, IFlatTextOStream &text_os) override

void FormatOrigin(const COriginItem &origin, IFlatTextOStream &text_os) override

void x_FormatSourceLine(list< string > &l, const CSourceItem &source) const

void x_Pubmed(list< string > &l, const CReferenceItem &ref, CBioseqContext &ctx) const

void x_GetFeatureSpanAndScriptStart(IFlatTextOStream &os, const CTempString &strKey, const CSeq_loc &feat_loc, CBioseqContext &ctx)

void FormatCache(const CCacheItem &csh, IFlatTextOStream &text_os) override

void x_Journal(list< string > &l, const CReferenceItem &ref, CBioseqContext &ctx) const

void x_Remark(list< string > &l, const CReferenceItem &ref, CBioseqContext &ctx) const

void x_Reference(list< string > &l, const CReferenceItem &ref, CBioseqContext &ctx) const

SIZE_TYPE GetWidth() const override

void FormatVersion(const CVersionItem &version, IFlatTextOStream &text_os) override

void FormatReference(const CReferenceItem &keys, IFlatTextOStream &text_os) override

void FormatPrimary(const CPrimaryItem &prim, IFlatTextOStream &text_os) override

void x_FormatOrganismLine(list< string > &l, const CSourceItem &source) const

unsigned int m_uFeatureCount

void x_Medline(list< string > &l, const CReferenceItem &ref, CBioseqContext &ctx) const

void FormatDefline(const CDeflineItem &defline, IFlatTextOStream &text_os) override

void FormatGenomeProject(const CGenomeProjectItem &, IFlatTextOStream &) override

void FormatHtmlAnchor(const CHtmlAnchorItem &, IFlatTextOStream &) override

void FormatFeatHeader(const CFeatHeaderItem &fh, IFlatTextOStream &text_os) override

void FormatSequence(const CSequenceItem &seq, IFlatTextOStream &text_os) override

void FormatLocus(const CLocusItem &locus, IFlatTextOStream &text_os) override

void x_Authors(list< string > &l, const CReferenceItem &ref, CBioseqContext &ctx) const

void FormatFeature(const CFeatureItemBase &feat, IFlatTextOStream &text_os) override

TFeatureKeyCountMap m_FeatureKeyToLocMap

void FormatSegment(const CSegmentItem &seg, IFlatTextOStream &text_os) override

void x_Consortium(list< string > &l, const CReferenceItem &ref, CBioseqContext &ctx) const

void FormatGenome(const CGenomeItem &genome, IFlatTextOStream &text_os) override

void FormatKeywords(const CKeywordsItem &keys, IFlatTextOStream &text_os) override

void FormatComment(const CCommentItem &keys, IFlatTextOStream &text_os) override

void FormatAccession(const CAccessionItem &acc, IFlatTextOStream &text_os) override

void FormatDBSource(const CDBSourceItem &dbs, IFlatTextOStream &text_os) override

const TDBLinkLineVec & GetDBLinkLines(void) const

vector< TDBLinkLine > TDBLinkLineVec

const vector< int > & GetProjectNumbers(void) const

const string & GetLabelCore(void) const

const string & GetName(void) const

size_t GetLength(void) const

TBiomol GetBiomol(void) const

const string & GetDate(void) const

TTopology GetTopology(void) const

const string & GetDivision(void) const

TStrand GetStrand(void) const

const string & GetFullName(void) const

const string & GetString(void) const

TEntrezId GetMUID(void) const

const string & GetTitle(void) const

const CCit_pat & GetPatent(void) const

const string & GetRemark(void) const

int GetSerial(void) const

TEntrezId GetPMID(void) const

TReftype GetReftype(void) const

const CAuth_list & GetAuthors(void) const

static void FormatAuthors(const CAuth_list &alp, string &auth)

bool IsSetPatent(void) const

const CSeq_loc & GetLoc(void) const

const string & GetConsortium(void) const

bool IsSetAuthors(void) const

size_t GetNum(void) const

size_t GetCount(void) const

SeqVector related exceptions.

Seq-loc iterator class – iterates all intervals from a seq-loc in the correct order.

const CSeqVector & GetSequence(void) const

TSeqPos GetTo(void) const

TSeqPos GetFrom(void) const

Base class for all serializable objects.

const string & GetLastID(void) const

const string & GetFirstID(void) const

TTSAType GetType(void) const

CTempString implements a light-weight string on top of a storage buffer whose lifetime management is ...

const string & GetLastID(void) const

TWGSType GetType(void) const

const string & GetFirstID(void) const

virtual void AddLine(const CTempString &, const CSerialObject *=nullptr, EAddNewline=eAddNewline_Yes)

This adds its given argument, appending a newline only if the add_newline argument is eAddNewline_Yes...

virtual void AddParagraph(const list< string > &, const CSerialObject *=nullptr)

This adds a list of strings to the stream one at a time, unconditionally adding a newline to each one...

virtual void FormatLocation(string &str, const CSeq_loc &loc, TIntId gi, const string &visible_text) const =0

virtual void FormatGapLink(ostream &os, TSeqPos gap_size, const string &id, bool is_prot) const =0

virtual void FormatTaxid(string &str, const TTaxId taxid, const string &taxname) const =0

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

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

static void s_FixListIfBadWrap(list< string > &l, list< string >::iterator l_old_last, int indent)

static const TSeqPos s_kFullLineSize

bool s_GetFeatureKeyLinkLocation(const CMappedFeat &feat, TGi &iGi, unsigned int &iFrom, unsigned int &iTo)

static string s_get_anchor_html(const string &sAnchorName, CBioseqContext *ctx)

static char * s_FormatSeqSpanTag(char *p, int base_count)

static const TSeqPos s_kChunkCount

static TSeqPos s_CalcDistanceUntilNextSignificantGapOrEnd(const CSequenceItem &seq, CSeqVector_CI iter)

static const TSeqPos s_kChunkSize

string s_GetLinkCambiaPatentLens(const CReferenceItem &ref, bool bHtml)

bool s_GetLinkFeatureKey(const CFeatureItemBase &item, const CFlatFeature &feat, const string &strRawKey, string &strLink, unsigned int uItemNumber=0)

static string s_GetAccessionWithoutPeriod(const CBioseqContext &ctx)

static char * s_FormatSeqPosBack(char *p, TSeqPos v, size_t l)

static void s_FormatRegularSequencePiece(const CSequenceItem &seq, IFlatTextOStream &text_os, CSeqVector_CI &iter, TSeqPos &total, TSeqPos &base_count)

void s_OrphanFixup(list< string > &wrapped, size_t uMaxSize=0)

static void s_PrintLocAsJavascriptArray(CBioseqContext &ctx, CNcbiOstream &text_os, const CSeq_loc &loc)

string s_GetLinkFeature(const CReferenceItem &ref, bool bHtml)

void s_GenerateWeblinks(const string &strProtocol, string &strText)

unsigned int TSeqPos

Type for sequence locations and lengths.

#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.

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

#define ERR_POST_X(err_subcode, message)

Error posting with default error code and given error subcode.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

void Warning(CExceptionArgs_Base &args)

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

TSeqPos GetStart(ESeqLocExtremes ext) const

Return start and stop positions of the seq-loc.

bool IsSetStrand(void) const

Get strand.

CSeq_id_Handle GetSeq_id_Handle(void) const

TRange GetRange(void) const

Get the range.

ENa_strand GetStrand(void) const

TSeqPos GetStop(ESeqLocExtremes ext) const

@ eOrder_Biological

Iterate sub-locations in positional order.

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,...

@ eGetId_Best

return the "best" gi (uses FindBestScore(), with CSeq_id::CalculateScore() as the score function

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

const TInst_Hist & GetInst_Hist(void) const

bool IsSetInst_Hist(void) const

bool CanGetInst_Length(void) const

TInst_Length GetInst_Length(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

bool IsSynonym(const CSeq_id &id) const

Check if this id can be used to obtain this bioseq handle.

TSeqPos SkipGap(void)

skip current gap forward returns number of skipped gap symbols does nothing and returns 0 if current ...

TSeqPos GetPos(void) const

const CSeq_loc & GetLocation(void) const

TSeqPos GetBufferSize(void) const

Get number of chars from current position to the current buffer end.

TSeqPos GetGapSizeBackward(void) const

returns number of gap symbols before current symbol returns 0 if current position is not in gap

bool IsInGap(void) const

true if current position of CSeqVector_CI is inside of sequence gap

void Reset(void)

Reset reference object.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

NCBI_NS_STD::string::size_type SIZE_TYPE

static CTempString TruncateSpaces_Unsafe(const CTempString str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

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 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.

const char * data(void) const

Return a pointer to the array represented.

static string & Replace(const string &src, const string &search, const string &replace, string &dst, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

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

Convert UInt to 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 EqualNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive equality of a substring with another string.

static void Wrap(const string &str, SIZE_TYPE width, IWrapDest &dest, TWrapFlags flags, const string *prefix, const string *prefix1)

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 & ReplaceInPlace(string &src, const string &search, const string &replace, SIZE_TYPE start_pos=0, SIZE_TYPE max_replace=0, SIZE_TYPE *num_replace=0)

Replace occurrences of a substring within a string.

static string TruncateSpaces(const string &str, ETrunc where=eTrunc_Both)

Truncate whitespace in a string.

const char *const kEmptyCStr

Empty "C" string (points to a '\0').

size_type size(void) const

Return the length of the represented array.

@ eTrunc_End

Truncate trailing whitespace only.

bool CanGetCountry(void) const

Check if it is safe to call GetCountry method.

bool CanGetNumber(void) const

Check if it is safe to call GetNumber method.

const TNumber & GetNumber(void) const

Get the Number member data.

const TCountry & GetCountry(void) const

Get the Country member data.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

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.

bool IsLim(void) const

Check if variant Lim is selected.

TLim GetLim(void) const

Get the variant data.

const TStr & GetStr(void) const

Get the variant data.

const TType & GetType(void) const

Get the Type member data.

@ eLim_tr

space to right of position

const TPnt & GetPnt(void) const

Get the variant data.

TPoint GetPoint(void) const

Get the Point member data.

bool IsSetFuzz(void) const

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

const TFuzz & GetFuzz(void) const

Get the Fuzz member data.

bool IsWhole(void) const

Check if variant Whole is selected.

bool IsPnt(void) const

Check if variant Pnt is selected.

const TUser & GetUser(void) const

Get the variant data.

bool CanGetReplaced_by(void) const

Check if it is safe to call GetReplaced_by method.

bool IsSetReplaces(void) const

seq makes these seqs obsolete Check if a value has been assigned to Replaces data member.

const TReplaces & GetReplaces(void) const

Get the Replaces member data.

const TReplaced_by & GetReplaced_by(void) const

Get the Replaced_by member data.

@ eReftype_sites

refers to unspecified features

@ eReftype_no_target

nothing specified (EMBL)

@ eReftype_feats

refers to specified features

@ eTech_tsa

transcriptome shotgun assembly

@ eTech_wgs

whole genome shotgun sequencing

@ eBiomol_transcribed_RNA

transcribed RNA other than existing classes

@ e_User

user defined object

@ e_Comment

a more extensive comment

@ e_Region

overall region (globin locus)

@ e_Maploc

map location of this sequence

unsigned int

A callback function used to compare two keys in a database.

static void text(MDB_val *v)

const string version

version string

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

void copy(Njn::Matrix< S > *matrix_, const Njn::Matrix< T > &matrix0_)

bool TrimSpacesAndJunkFromEnds(string &str, bool allow_ellipsis=false)

const char * strLinkBaseGenomePrj

const char * strLinkBaseProt

const char * strLinkBaseNuc

void TryToSanitizeHtmlList(std::list< std::string > &strs)

const char * strLinkBasePubmed

void CleanAndCompress(string &dest, const CTempString &instr)

void TryToSanitizeHtml(std::string &str)

static const GLdouble origin[]

CRef< CPub > journal(ParserPtr pp, char *bptr, char *eptr, CRef< CAuth_list > &auth_list, CRef< CTitle::C_E > &title, bool has_muid, CRef< CCit_art > &cit_art, Int4 er)

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

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