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Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/showdefline_8cpp_source.html below:

NCBI C++ ToolKit: src/objtools/align_format/showdefline.cpp Source File

123 static const char* kPsiblastNewSeqGif = "

<IMG SRC=\"images/new.gif\" \

124

WIDTH=30 HEIGHT=15 ALT=\"New sequence mark\">";

127 bg.gif\" WIDTH=30 HEIGHT=15 ALT=\" \">"

;

130 /bg.gif\" WIDTH=15 HEIGHT=15 ALT=\" \">"

;

133 if\" WIDTH=15 HEIGHT=15 ALT=\"Checked mark\">"

;

160  bool

found_gi =

false

;

166  if

((*itr)->IsGi()) {

167

id_string += (*itr)->AsFastaString();

181

id_string += id_token;

197

vector< CConstRef<CSeq_id> > original_seqids;

200

original_seqids.push_back(itr->GetSeqId());

222  if

(((*itr)->IsGeneral() &&

223

(*itr)->AsFastaString().find(

"gnl|BL_ORD_ID"

)

225

(*itr)->AsFastaString().find(

"lcl|Subject_"

) != string::npos) {

226

vector<string> title_tokens;

227  string

defline = sequence::CDeflineGenerator().GenerateDefline(bh);

238

obj_id->

SetStr

(id_token);

239

next_seqid->SetLocal(*obj_id);

241

next_seqid->Assign(**itr);

243

ids.push_back(next_seqid);

249

list<TGi>& use_this_gi,

250  string

& seqid,

string

& defline,

256  if

( !handle )

return

;

260  if

(bdlRef.

Empty

()){

261

list<CRef<objects::CSeq_id> > ids;

264

defline = sequence::CDeflineGenerator().GenerateDefline(handle);

267  const

list< CRef< CBlast_def_line > >& bdl = bdlRef->

Get

();

268  bool

is_first =

true

;

273  ITERATE

(list<TGi>, iter_gi, use_this_gi){

274  if

(cur_gi == *iter_gi){

275

gi_in_use_this_gi = *iter_gi;

279  if

(use_this_gi.empty() || gi_in_use_this_gi >

ZERO_GI

) {

283  if

((*iter)->IsSetTitle()){

285

defline = (*iter)->GetTitle();

291  if

( show_gi && cur_gi >

ZERO_GI

){

292

defline = defline +

" >"

+

"gi|"

+

294

concat_acc +

" "

+ (*iter)->GetTitle();

296

defline = defline +

" >"

+ concat_acc +

" "

+

309  if

(descr.length() > maxDescrLength) {

310

descr = descr.substr(0,maxDescrLength);

314

descr = descr.substr(0,end);

324  bool

getIdentProteins)

390

list<string> &use_this_seqid,

394  if

( !handle )

return

;

419

seq_status = itr->second;

438  bool

getIdentProteins = !

m_IsDbNa

&& bdl.size() > 1;

440

iter != bdl.end(); iter++){

444  if

(!use_this_seqid.empty()){

448  if

((use_this_seqid.empty() && sdl->

gi

== cur_gi) ||

match

) {

454  if

(bdl.size() == 0) {

466

sdl->

score_url

= !useTemplates ?

"<a href=#"

:

""

;

472

sdl->

score_url

+= !useTemplates ?

">"

:

""

;

488  if

((*iter_bdl)->IsSetTaxid() && (*iter_bdl)->CanGetTaxid()){

489

seqUrlInfo.

taxid

= (*iter_bdl)->GetTaxid();

500  if

(!(bdl.empty())) {

502

iter != bdl.end(); iter++){

507  if

(use_this_seqid.empty() ||

match

) {

509  if

((*iter)->IsSetTitle()){

510  bool

id_used_already =

false

;

512  if

((*iter_id)->Match(*(sdl->

id

))) {

513

id_used_already =

true

;

517  if

(!id_used_already) {

524

concat_acc +

" "

+ (*iter)->GetTitle();

544  size_t

num_defline_to_show,

545  bool

translated_nuc_alignment,

548

m_AlnSetRef(&seqalign),

550

m_LineLen(line_length),

551

m_NumToShow(num_defline_to_show),

552

m_TranslatedNucAlignment(translated_nuc_alignment),

555

m_MasterRange(master_range),

625  bool

struct_linkout =

false

;

627  const int

k_CountMax = 200;

631  if

( !handle )

continue

;

635

bdl_iter != bdl.end() && struct_linkout ==

false

; bdl_iter++){

636  if

((*bdl_iter)->IsSetLinks())

639

link_iter != (*bdl_iter)->GetLinks().end(); link_iter++)

642

struct_linkout =

true

;

648  if

(struct_linkout ==

true

||

count

> k_CountMax)

652  return

struct_linkout;

664  bool

is_first_aln =

true

;

665  size_t

num_align = 0;

682  bool

master_is_na =

false

;

686  for

(CSeq_align_set::Tdata::const_iterator

690  if

(ialn < m_SkipTo && ialn >=

m_SkipFrom

)

continue

;

698

subid = &((*iter)->GetSeq_id(1));

699  if

(is_first_aln || (!is_first_aln && !subid->

Match

(*previous_id))) {

703  if

(m_MaxScoreLen < sci->bit_string.size()){

706  if

(m_MaxEvalueLen < sci->evalue_string.size()){

710  if

(m_MaxTotalScoreLen < sci->total_bit_string.size()){

724

is_first_aln =

false

;

739  buf

[

sizeof

(

buf

)-1] =

'\0'

;

748  buf

[

sizeof

(

buf

)-1] =

'\0'

;

851  bool

first_new =

true

;

854  size_t

line_length = 0;

855  string

line_component;

889  out

<< line_component;

890

line_length += line_component.size();

894  if

(!(sdl->

id

->AsFastaString().find(

"gnl|BL_ORD_ID"

) != string::npos ||

895

sdl->

id

->AsFastaString().find(

"lcl|Subject_"

) != string::npos)){

898

idStr = sdl->

id

->AsFastaString();

903  if

(

strncmp

(idStr.c_str(),

"lcl|"

, 4) == 0) {

904

idStr = sdl->

id

->AsFastaString().substr(4);

907

line_length += idStr.size();

913

line_component = (line_component.empty() ?

""

:

" "

) + sdl->

defline

;

914  string

actual_line_component;

915  if

(line_component.size()+line_length >

m_LineLen

){

916

actual_line_component = line_component.substr(0,

m_LineLen

-

920

actual_line_component = line_component.substr(0,

m_LineLen

-

926  out

<< actual_line_component;

928

line_length += actual_line_component.size();

936  out

<< (*iter)->bit_string;

944

(*iter)->total_bit_string.size());

949  int

percent_coverage = (*iter)->percent_coverage;

967  int

percent_identity =(

int

) (0.5 + (*iter)->percent_identity);

968  if

(percent_identity > 100) {

969

percent_identity =

min

(99, percent_identity);

976  bool

is_first =

true

;

982  out

<< *iter_linkout;

992  const string

& param,

993  const string

& entrez_term)

997

snprintf(

buf

,

sizeof

(

buf

), structure_Overview.c_str(), rid.c_str(),

998

0, 0, param.c_str(),

"overview"

,

999

(entrez_term.empty()?

"none"

: entrez_term.c_str()));

1000  buf

[

sizeof

(

buf

)-1] =

'\0'

;

1001  out

<<

' '

<<

buf

<<

"\n\n"

;

1015  int

currDisplaySort,

1017  int

columnDisplSort,

1026  if

(currDisplaySort == columnDisplSort) {

1027  out

<<

"<th class=\"sel\">"

;

1033  out

<<

"<a href=\"Blast.cgi?" 1034

<<

"CMD=Get&"

<< query_buf

1035

<<

"&DISPLAY_SORT="

<< columnDisplSort

1036

<<

"&HSP_SORT="

<< columnHspSort

1037

<<

"#sort_mark\">"

;

1042  out

<<

"</a></th>\n"

;

1056  bool

is_first_aln =

true

;

1057  size_t

num_align = 0;

1064  int

percent_identity = 0;

1078  bool

master_is_na =

false

;

1082  for

(CSeq_align_set::Tdata::const_iterator

1087  if

(ialn < m_SkipTo && ialn >=

m_SkipFrom

)

continue

;

1091  m_ScopeRef

->GetBioseqHandle((*iter)->GetSeq_id(0)).GetBioseqLength();

1092

master_is_na =

m_ScopeRef

->GetBioseqHandle((*iter)->GetSeq_id(0)).

1093

GetBioseqCore()->IsNa();

1096

subid = &((*iter)->GetSeq_id(1));

1100  if

(!is_first_aln && !(subid->

Match

(*previous_id))) {

1104  if

(m_MaxScoreLen < sci->bit_string.size()){

1107  if

(m_MaxTotalScoreLen < sci->total_bit_string.size()){

1114  if

(m_MaxEvalueLen < sci->evalue_string.size()){

1121

hit.

Set

().clear();

1127

hit.

Set

().push_back(*iter);

1129

is_first_aln =

false

;

1130

previous_id = subid;

1137  if

(m_MaxScoreLen < sci->bit_string.size()){

1140  if

(m_MaxTotalScoreLen < sci->total_bit_string.size()){

1147  if

(m_MaxEvalueLen < sci->evalue_string.size()){

1154

hit.

Set

().clear();

1188  out

<<

"(Click headers to sort columns)\n"

;

1192  out

<<

"<div id=\"desctbl\">"

<<

"<table id=\"descs\">"

<<

"\n"

<<

"<thead>"

<<

"\n"

;

1193  out

<<

"<tr class=\"first\">"

<<

"\n"

<<

"<th>Accession</th>"

<<

"\n"

<<

"<th>Description</th>"

<<

"\n"

;

1203

parameters_to_change,

1206

parameters_to_change.

clear

();

1224  out

<<

"<th>"

<<

kN

<<

"</th>"

<<

"\n"

;

1228  out

<<

"<th>Links</th>\n"

;

1230  out

<<

"</thead>\n"

;

1235  out

<<

"<tbody>\n"

;

1241  out

<<

"</tbody>\n</table></div>\n"

;

1247  int

percent_identity = 0;

1249  bool

first_new =

true

;

1250  int

prev_database_type = 0, cur_database_type = 0;

1251  bool

is_first =

true

;

1253  bool

is_mixed_database =

false

;

1263

parameters_to_change,

1269  string

line_component;

1271  if

(is_mixed_database) {

1274  out

<<

"<tr>\n<th colspan=\""

<< tableColNumber<<

"\" class=\"l sp\">"

;

1276  if

(cur_database_type) {

1277  out

<<

"Genomic sequences"

;

1279  out

<<

"Transcripts"

;

1285  out

<<

"</th></tr>\n"

;

1287

}

else if

(prev_database_type != cur_database_type) {

1289  out

<<

"<tr>\n<th colspan=\""

<< tableColNumber<<

"\" class=\"l sp\">"

;

1291  if

(cur_database_type) {

1292  out

<<

"Genomic sequences"

;

1294  out

<<

"Transcripts"

;

1297  out

<<

"<span class=\"slink\">" 1298

<<

" [<a href=\"Blast.cgi?CMD=Get&" 1300

<<

"&DATABASE_SORT="

;

1301  if

(cur_database_type) {

1306  out

<<

"#sort_mark\">show first</a>]</span>"

;

1312  out

<<

"</th></tr>\n"

;

1316

prev_database_type = cur_database_type;

1320  out

<<

"<td class=\"l\">\n"

;

1355  out

<< line_component;

1360  if

(!(sdl->

id

->AsFastaString().find(

"gnl|BL_ORD_ID"

) != string::npos ||

1361

sdl->

id

->AsFastaString().find(

"lcl|Subject_"

) != string::npos)){

1372  out

<<

"</td><td class=\"lim l\"><div class=\"lim\">"

;

1374

line_component =

" "

+ sdl->

defline

;

1375  string

actual_line_component;

1376

actual_line_component = line_component;

1380  out

<<

"</div></td><td>"

;

1382  out

<< actual_line_component;

1388  out

<< (*iter)->bit_string;

1394  out

<<

"<td>"

<< (*iter)->total_bit_string <<

"</td>"

;

1401

(*iter)->total_bit_string.size());

1404  int

percent_coverage = 100*(*iter)->master_covered_length/

m_QueryLength

;

1406  out

<<

"<td>"

<< percent_coverage <<

"%</td>"

;

1417  out

<<

"<td>"

<< (*iter)->evalue_string <<

"</td>"

;

1426  out

<<

"<td>"

<< percent_identity <<

"%</td>"

;

1452  bool

first_time =

true

;

1456

first_time =

false

;

1458  out

<< *iter_linkout;

1485  string

evalue_buf, bit_score_buf, total_bit_score_buf, raw_score_buf;

1491

list<string> use_this_seq;

1493

use_this_seq.clear();

1495

num_ident, use_this_seq);

1498

evalue_buf, bit_score_buf, total_bit_score_buf,

1501

unique_ptr<SScoreInfo> score_info(

new SScoreInfo

);

1502

score_info->sum_n = sum_n == -1 ? 1:sum_n ;

1505

score_info->use_this_seqid = use_this_seq;

1507

score_info->bit_string = bit_score_buf;

1508

score_info->raw_score_string = raw_score_buf;

1509

score_info->evalue_string = evalue_buf;

1511

score_info->blast_rank = blast_rank+1;

1513

score_info->flip =

false

;

1514  return

score_info.release();

1520  string

evalue_buf, bit_score_buf, total_bit_score_buf, raw_score_buf;

1522  if

(aln.

Get

().empty())

1525

unique_ptr<SScoreInfo> score_info(

new SScoreInfo

);

1528  if

(seqSetInfo->hspNum == 0) {

1533

evalue_buf, bit_score_buf, total_bit_score_buf,

1535

score_info->id = seqSetInfo->id;

1537

score_info->total_bit_string = total_bit_score_buf;

1538

score_info->bit_string = bit_score_buf;

1539

score_info->evalue_string = evalue_buf;

1540

score_info->percent_coverage = seqSetInfo->percent_coverage;

1541

score_info->percent_identity = seqSetInfo->percent_identity;

1542

score_info->hspNum = seqSetInfo->hspNum;

1543

score_info->totalLen = seqSetInfo->totalLen;

1545

score_info->use_this_seqid = seqSetInfo->use_this_seq;

1546

score_info->sum_n = seqSetInfo->sum_n == -1 ? 1:seqSetInfo->sum_n ;

1548

score_info->raw_score_string = raw_score_buf;

1549

score_info->match = seqSetInfo->match;

1550

score_info->align_length = seqSetInfo->align_length;

1551

score_info->master_covered_length = seqSetInfo->master_covered_length;

1554

score_info->subjRange = seqSetInfo->subjRange;

1555

score_info->flip = seqSetInfo->flip;

1557

score_info->blast_rank = blast_rank+1;

1559  return

score_info.release();

1562

vector <CShowBlastDefline::SDeflineInfo*>

1565

vector <CShowBlastDefline::SDeflineInfo*> sdlVec;

1566  for

(

size_t i

= 0;

i

< seqIds.size();

i

++) {

1567

list<string> use_this_seq;

1569

sdlVec.push_back(sdl);

1597

sdl->

gi

= (*id).GetGi();

1621  bool

first_new =

true

;

1622  int

prev_database_type = 0, cur_database_type = 0;

1623  bool

is_first =

true

;

1627  string

rowType =

"odd"

;

1633  bool

formatHeaderSort = !is_first && (prev_database_type != cur_database_type);

1634  if

(is_mixed_database && (is_first || formatHeaderSort)) {

1636

subHeaderID = cur_database_type ?

"GnmSeq"

:

"Transcr"

;

1640

prev_database_type = cur_database_type;

1647  string

firstSeq = (is_first) ?

"firstSeq"

:

""

;

1651

rowType = (rowType ==

"odd"

) ?

"even"

:

"odd"

;

1653  if

(!subHeader.empty()) {

1654

defLine = subHeader + defLine;

1667  if

(sdl->

taxid

> 0) {

1690  string

allClustRows;

1697

allClustRows += clustRow;

1701  string

clustMemDiff, clustSizeShow;

1704

clustSizeShow =

"shown"

;

1716  string

allClustRows;

1723

allClustRows += descrHeader;

1730

allClustRows += clustRow;

1740  bool

first_new =

true

;

1749  string

firstSeq = (is_first) ?

"firstSeq"

:

""

;

1771

defLine = descrHeader + defLine;

1788  if

(!(sdl->

id

->AsFastaString().find(

"gnl|BL_ORD_ID"

) != string::npos ||sdl->

id

->AsFastaString().find(

"lcl|Subject_"

) != string::npos)) {

1802  string

descr = (!sdl->

defline

.empty()) ? sdl->

defline

:

"None provided"

;

1805

descr =

"\""

+ descr +

"\""

;

1849  if

(!(sdl->

id

->AsFastaString().find(

"gnl|BL_ORD_ID"

) != string::npos ||sdl->

id

->AsFastaString().find(

"lcl|Subject_"

) != string::npos)) {

1854  string

descr = (!sdl->

defline

.empty()) ? sdl->

defline

:

"None provided"

;

1934  string

seqSetType = isGenomicSeq ?

"Genomic sequences"

:

"Transcripts"

;

1936  if

(formatHeaderSort) {

1954  if

(!(sdl->

id

->AsFastaString().find(

"gnl|BL_ORD_ID"

) != string::npos ||

1955

sdl->

id

->AsFastaString().find(

"lcl|Subject_"

) != string::npos)) {

1972  string

descr = (!sdl->

defline

.empty()) ? sdl->

defline

:

"None provided"

;

1989  string

deflId,deflFrmID,deflFastaSeq,deflAccs,deflFastaDwnld;

1994

deflAccs = sdl->

id

->AsFastaString();

2058

links += *iter_linkout;

2068  string

show_new,psi_new,psi_new_accesible,show_checked,replaceBy,psiNewSeq;

2071

first_new = (sdl->

is_new

&& first_new) ?

false

: first_new;

2073

show_new =

"hidden"

;

2076

psi_new =

"psi_new"

;

2077

psi_new_accesible =

"psiNw"

;

2085

show_checked =

"hidden"

;

2087  string

psiUsedToBuildPssm = (sdl->

was_checked

) ?

"on"

:

"off"

;

2126  if

(!(sdl->

id

->AsFastaString().find(

"gnl|BL_ORD_ID"

) != string::npos || sdl->

id

->AsFastaString().find(

"lcl|Subject_"

) != string::npos)) {

2134

sdlFormatInfo->

dfln_gi

= dflGi;

2138  string

descr = (!sdl->

defline

.empty()) ? sdl->

defline

:

"None provided"

;

2149  string

deflId,deflFrmID,deflFastaSeq,deflAccs;

2154

deflAccs = sdl->

id

->AsFastaString();

2163

sdlFormatInfo->

dfln_id

= deflId;

2166

sdlFormatInfo->

dflnAccs

=deflAccs;

2185  bool

is_first_aln =

true

;

2186  size_t

num_align = 0;

2195  for

(CSeq_align_set::Tdata::const_iterator iter =

m_AlnSetRef

->Get().begin();

2204

subid = &((*iter)->GetSeq_id(1));

2206  if

(!is_first_aln && !(subid->

Match

(*previous_id))) {

2211

hit.

Set

().clear();

2217

hit.

Set

().push_back(*iter);

2219

is_first_aln =

false

;

2220

previous_id = subid;

2227

hit.

Set

().clear();

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

User-defined methods of the data storage class.

Declares class to display one-line descriptions at the top of the BLAST report.

static CAlignFormatUtil::SSeqAlignSetCalcParams * GetSeqAlignSetCalcParamsFromASN(const objects::CSeq_align_set &alnSet)

static string GetIDUrl(SSeqURLInfo *seqUrlInfo, const objects::CSeq_id &id, objects::CScope &scope)

Create URL for seqid.

static CAlignFormatUtil::SSeqAlignSetCalcParams * GetSeqAlignSetCalcParams(const objects::CSeq_align_set &aln, int queryLength, bool do_translation)

static bool IsMixedDatabase(const objects::CSeq_align_set &alnset, objects::CScope &scope, ILinkoutDB *linkoutdb, const string &mv_build_name)

static list< string > GetFullLinkoutUrl(const list< CRef< objects::CBlast_def_line > > &bdl, const string &rid, const string &cdd_rid, const string &entrez_term, bool is_na, bool structure_linkout_as_group, bool for_alignment, int cur_align, string &linkoutOrder, TTaxId taxid, string &database, int query_number, string &user_url, string &preComputedResID, ILinkoutDB *linkoutdb, const string &mv_build_name)

Get linkout membership for for the list of blast deflines.

static void GetAlnScores(const objects::CSeq_align &aln, int &score, double &bits, double &evalue, int &sum_n, int &num_ident, list< TGi > &use_this_gi)

Extract score info from blast alingment.

static void BuildFormatQueryString(CCgiContext &ctx, string &cgi_query)

static void GetScoreString(double evalue, double bit_score, double total_bit_score, int raw_score, string &evalue_str, string &bit_score_str, string &total_bit_score_str, string &raw_score_str)

format evalue and bit_score

static string GetBareId(const objects::CSeq_id &id)

Get sequence id with no database source (bare accession)

static string MapTemplate(string inpString, string tmplParamName, Int8 templParamVal)

Replace template tags by real data.

static bool MatchSeqInSeqList(TGi cur_gi, CRef< objects::CSeq_id > &seqID, list< string > &use_this_seq, bool *isGiList=NULL)

Matches text seqID or gi with the list of seqIds or gis.

static int GetSeqLinkoutInfo(objects::CBioseq::TId &cur_id, ILinkoutDB **linkoutdb, const string &mv_build_name, TGi gi=INVALID_GI)

static CRef< objects::CSeq_id > GetDisplayIds(const objects::CBioseq_Handle &handle, const objects::CSeq_id &aln_id, list< TGi > &use_this_gi, TGi &gi, TTaxId &taxid)

Scan the the list of blast deflines and find seqID to be use in display.

static list< string > GetLinkoutUrl(int linkout, const objects::CBioseq::TId &ids, const string &rid, const string &cdd_rid, const string &entrez_term, bool is_na, TGi first_gi, bool structure_linkout_as_group, bool for_alignment, int cur_align, string preComputedResID)

Get the list of urls for linkouts.

static int GetPercentMatch(int numerator, int denominator)

function for calculating percent match for an alignment.

static string MapTagToConstString(const string tag_name, EMapConstString flag=eMapToURL)

static void AddSpace(CNcbiOstream &out, size_t number)

Add the specified white space.

static string MapSpaceTemplate(string inpString, string tmplParamName, string templParamVal, unsigned int maxParamLength, int spacesFormatFlag=eSpacePosAtLineEnd)

Replace template tags by real data and calculate and add spaces dependent on maxParamLength and space...

static string GetLabel(CConstRef< objects::CSeq_id > id, bool with_version=false)

Return a label for an ID Tries to recreate behavior of GetLabel before a change that prepends "ti|" t...

static string MapTagToHTML(const string tag_name)

void PutTargetGiFirst(TGi gi)

Place the CBlast_def_line object which contains the requested gi as the first in the list (if found)

Class for computing sequences' titles ("definitions").

static void GetTaxInfo(TTaxId taxid, SSeqDBTaxInfo &info)

Get taxonomy information.

static CRef< CBlast_def_line_set > ExtractBlastDefline(const CBioseq &bioseq)

Extract a Blast-def-line-set object from a Bioseq retrieved by CSeqDB.

const CSeq_id & GetSeq_id(TDim row) const

Get seq-id (the first one if segments have different ids).

size_t m_MaxEvalueLen

Eval header size.

int m_StartIndex

The start index of defline for PSI blast description table.

void x_InitLinkOutInfo(SDeflineInfo *sdl, objects::CBioseq::TId &cur_id, int blast_rank, bool getIdentProteins)

string m_MapViewerBuildName

mapviewer build name associated with the sequences in the BLAST database out of which the results are...

void x_FillDeflineAndId(const objects::CBioseq_Handle &handle, const objects::CSeq_id &aln_id, list< string > &use_this_seqid, SDeflineInfo *sdl, int blast_rank)

Internal function to fill defline info.

CShowBlastDefline(const objects::CSeq_align_set &seqalign, objects::CScope &scope, size_t line_length=65, size_t deflines_to_show=kDfltArgNumDescriptions, bool translated_nuc_alignment=false, CRange< TSeqPos > *master_range=NULL)

Constructors.

CRef< objects::CScope > m_ScopeRef

Scope to fetch sequence.

string x_FormatClusterMemData(SDeflineInfo *sdl, string defline)

size_t m_MaxQueryCoverLen

string x_FormatPsi(SDeflineInfo *sdl, bool &first_new)

Format PSI blat related data.

int m_Option

Display options.

bool x_CheckForStructureLink()

Checks the first X deflines (currently X is 200) for a structure link.

void x_DisplayDefline(CNcbiOstream &out)

Display defline for regular output.

SScoreInfo * x_GetScoreInfoForTable(const objects::CSeq_align_set &aln, int blast_rank)

Internal function to return score info.

static void GetBioseqHandleDeflineAndId(const objects::CBioseq_Handle &handle, list< TGi > &use_this_gi, string &seqid, string &defline, bool show_gi=true, TGi this_gi_first=INVALID_GI)

Returns sequence id and a BLAST defline as strings, given a Bioseq handle and a list of gis.

PsiblastStatus m_PsiblastStatus

string m_BlastType

Blast type.

SScoreInfo * x_GetScoreInfo(const objects::CSeq_align &aln, int blast_rank)

Internal function to return score info.

PsiblastSeqStatus

PSI-BLAST sequence status (applicable in HTML only)

@ eGoodSeq

above the threshold evalue

@ eUnknown

Uninitialized.

@ eCheckedSeq

user checked

@ eRepeatSeq

previously already found

SAppLogInfo * m_AppLogInfo

static void GetSeqIdList(const objects::CBioseq_Handle &bh, list< CRef< objects::CSeq_id > > &ids)

Converts a Bioseq handle's sequence id type into a list of objects::CSeq_id references,...

void DisplayBlastDefline(CNcbiOstream &out)

Display defline.

string m_Database

Database name.

bool m_TranslatedNucAlignment

used to calculate the alignment length

int m_SkipFrom

seq aligns to be skipped

vector< SDeflineFormattingInfo * > m_SdlFormatInfoVec

void DisplayOneDefline(CNcbiOstream &out, SDeflineInfo *sdl, SScoreInfo *iter, bool &is_first)

Display one defline.

SDeflineInfo * x_GetDeflineInfo(CConstRef< objects::CSeq_id > id, list< string > &use_this_seqid, int blast_rank)

Internal function to return defline info.

void x_DisplayDeflineTableBody(CNcbiOstream &out)

Display defline table contents for table output.

void x_DisplayDeflineTableTemplate(CNcbiOstream &out)

Display defline for table output using templates.

static string GetSeqIdListString(const list< CRef< objects::CSeq_id > > &id, bool show_gi)

Creates a '|' delimited string, corresponding to a list of Seq-ids.

string x_FormatDeflineTableLine(SDeflineInfo *sdl, SScoreInfo *iter, bool &first_new)

Format defline.

SDeflineInfo * GetDeflineInfo(CConstRef< objects::CSeq_id > id, list< string > &use_this_seqid, int blast_rank)

Get one defline info.

size_t m_MaxScoreLen

Score header size.

string x_FormatClusterMemDataTxt(SDeflineInfo *sdl, string defline)

ILinkoutDB * m_LinkoutDB

Reference to LinkoutDB implementation. Not owned by this class.

vector< SScoreInfo * > m_ScoreList

List containing score info for all seqalign.

void x_InitDefline(void)

Initialize defline params for regular output.

string m_PreComputedResID

CDD precomputed results ID.

string m_Rid

blast request id

int m_PositionIndex

result position index for multiple query case

void Init(void)

Initialize defline params.

string x_FormatDeflineTableLineCSV(SDeflineInfo *sdl, SScoreInfo *iter)

size_t m_MaxPercentIdentityLen

string m_LinkoutOrder

Linkout order for display.

size_t m_LineLen

Line length.

void DisplayBlastDeflineTable(CNcbiOstream &out)

string x_FormatDeflineTableLineText(SDeflineInfo *sdl, SScoreInfo *iter)

vector< CShowBlastDefline::SDeflineFormattingInfo * > GetFormattingInfo(void)

Get deflines formatting info.

size_t m_NumToShow

Number of seqalign hits to show.

void x_DisplayDeflineTableTemplateCSV(CNcbiOstream &out)

string m_EntrezTerm

entrez term

void Display(CNcbiOstream &out)

Display defline.

void x_DisplayDeflineTableTemplateText(CNcbiOstream &out)

void x_DisplayDeflineTable(CNcbiOstream &out)

Display defline for table output.

string x_FormatDeflineTableHeaderText(void)

string m_CddRid

cdd blast request id

SDeflineTemplates * m_DeflineTemplates

blast defline templates

void x_InitFormattingInfo(SScoreInfo *sci)

CConstRef< objects::CSeq_align_set > m_AlnSetRef

Internal data with score information for each defline.

unique_ptr< CNcbiIfstream > m_ConfigFile

Internal configure file, i.e. .ncbirc.

@ eNewPass

Sequences are newly found in current pass.

@ eFirstPass

First pass. Default.

@ eRepeatPass

Sequences were found in previous pass.

void x_InitDeflineTable(void)

Initialize defline params for table output.

size_t m_MaxTotalScoreLen

Total score header size.

int m_QueryNumber

query number

unique_ptr< CNcbiRegistry > m_Reg

bool m_StructureLinkout

Indicates if 'Related structures' link should show.

TIdString2SeqStatus * m_SeqStatus

hash table to track psiblast status for each sequence

string x_FormatSeqSetHeaders(int isGenomic, bool formatHeaderSort)

Format headers for Transcrit/Genomic seq set.

CRange< TSeqPos > * m_MasterRange

blast sub-sequnce query

void x_GetTaxonomyInfoForTaxID(SDeflineInfo *sdl, SSeqDBTaxInfo &taxInfo)

container_type::const_iterator const_iterator

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

std::ofstream out("events_result.xml")

main entry point for tests

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

const CCgiEntry & GetRequestValue(const string &name, bool *is_found=0) const

static string HTMLEncode(const string &str, THTMLEncodeFlags flags=fEncodeAll)

HTML encodes a string. E.g. <.

const string AsFastaString(void) const

TGi FindGi(const container &ids)

Return gi from id list if exists, return 0 otherwise.

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

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

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

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

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

Wrappers for use with FindBestChoice from <corelib/ncbiutil.hpp>

@ eContent

Untagged human-readable accession or the like.

@ eFasta

Tagged ID in NCBI's traditional FASTA style.

TSeqPos GetLength(const CSeq_id &id, CScope *scope)

Get sequence length if scope not null, else return max possible TSeqPos.

string GenerateDefline(const CBioseq_Handle &bsh, TUserFlags flags=0)

Main method.

vector< CSeq_id_Handle > TId

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

bool Empty(void) const THROWS_NONE

Check if CConstRef is empty – not pointing to any object which means having a null value.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

#define NCBI_INT8_FORMAT_SPEC

int64_t Int8

8-byte (64-bit) signed integer

position_type GetLength(void) const

#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.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static string DoubleToString(double value, int precision=-1, TNumToStringFlags flags=0)

Convert double to string.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

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

Truncate whitespace in a string.

@ eReverseSearch

Search in a backward direction.

@ eNocase

Case insensitive compare.

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

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

const Tdata & Get(void) const

Get the member data.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

TStr & SetStr(void)

Select the variant.

Tdata & Set(void)

Assign a value to data member.

const Tdata & Get(void) const

Get the member data.

bool IsLocal(void) const

Check if variant Local is selected.

bool IsGi(void) const

Check if variant Gi is selected.

@ e_Gi

GenInfo Integrated Database.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

unsigned int

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

HTML library helper classes and functions.

double value_type

The numeric datatype used by the parser.

const struct ncbi::grid::netcache::search::fields::SIZE size

const GenericPointer< typename T::ValueType > T2 value

GenericValue< UTF8<> > Value

GenericValue with UTF8 encoding.

int strncmp(const char *str1, const char *str2, size_t count)

Defines NCBI C++ exception handling.

Process information in the NCBI Registry, including working with configuration files.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

Useful/utility classes and methods.

std::istream & in(std::istream &in_, double &x_)

static int match(PCRE2_SPTR start_eptr, PCRE2_SPTR start_ecode, uint16_t top_bracket, PCRE2_SIZE frame_size, pcre2_match_data *match_data, match_block *mb)

static const char * kQueryCovLine2

static const char * kScore

static const size_t kBits_size

static const char * kTwoSpaceMargin

static void s_DisplayStructureOverview(CNcbiOstream &out, const string &rid, const string &param, const string &entrez_term)

static const size_t kOneSpaceMargin_size

static const char * kTotal

static const char * kBits

static const char * kHeader

static const char * kPsiblastCheckboxChecked

static const char * kTotalScore

static const char * kPsiblastNewSeqBackgroundGif

static const char * kOneSpaceMargin

static const int kMaxPercentIdentityLen

static const char * kScientific

static const char * kPsiblastEvalueLink

static const char * kDescription

static const char * kNewSeqHeader

static const size_t kCoverage_size

static const int kMaxTaxonomyNameLengthExt

static const char * kCommon

static const int kMaxTaxonomyNameLength

static const char * kAccession

static const char * kIdentLine2

static const char * kIdentity

static const int kMaxAccLength

static const char * kQueryCov

static const char * kPsiblastNewSeqGif

static const char * kPsiblastCheckedBackgroundGif

static const char * kMember

static const char * kEllipsis

static void s_DisplayCheckboxChecked(CNcbiOstream &out, TGi gi)

static const char * kRepeatHeader

static void s_DisplayCheckbox(CNcbiOstream &out, TGi gi)

static const size_t kTwoSpaceMargin_size

static const char * kCluster

static const int kMaxDispNumberLength

static const char * kPsiblastCheckedGif

static const char * kScoreLine2

static const char * kPsiblastCheckbox

static const int kMaxDescrLength

static const char * kMaxScore

static const char * kAncestor

static const char * kTaxid

static const char * kEvalue

static const char * kName

static const char * kTaxa

static const char * kAccAbbr

static const char * kPerc

static const char * kCoverage

static const size_t kScore_size

static void s_DisplayDescrColumnHeader(CNcbiOstream &out, int currDisplaySort, string query_buf, int columnDisplSort, int columnHspSort, string columnText, int max_data_len, bool html)

static const char * kNumOf

static const size_t kTotal_size

static const char * kLenAbbr

static void s_LimitDescrLength(string &descr, size_t maxDescrLength=kMaxDescrLength)

static const size_t kHeader_size

static const char * kValue

static const size_t kIdentity_size

static const size_t kQueryCov_size

static const char * kClusterTitle

static const size_t kValue_size

static SLJIT_INLINE sljit_ins or(sljit_gpr dst, sljit_gpr src)

Structure that holds information needed for creation seqID URL in descriptions and alignments.

bool useTemplates

bool indicating that templates should be used when contsructing links

bool advancedView

bool indicating that advanced view design option should be used when contsructing links

string resourcesUrl

URL(s) to other resources from .ncbirc.

vector< string > queryCoverageVec

vector< string > taxidVec

vector< string > deflIdVec

vector< string > percentIdentityVec

Data Representing each defline.

CConstRef< objects::CSeq_id > id

list< string > linkout_list

vector< SClusterMemberInfo > clustMemList

string psiFirstNewAnchorTmpl

first new seq anchor template (psi blast)

string scoreInfoTmpl

score info template

string seqInfoTmpl

sequence infor template

string psiGoodGiHiddenTmpl

good gi hidden field tewmplate (psi blast)

string defLineTmpl

whole defilne template

string subHeaderSort

subheader sort template for Transcript/Genomic case

string subHeaderTmpl

subheader templates for Transcript/Genomic case

CConstRef< objects::CSeq_id > id

list< string > use_this_seqid

string common_name

Common name, such as "noisy night monkey".

string blast_name

A simple category name, such as "birds".

string scientific_name

Scientific name, such as "Aotus vociferans".

TTaxId taxid

An identifier for this species or taxonomic group.


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