Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/align__format__util_8cpp_source.html below:

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

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

{

,

},

<

container>

list<TGi>& use_this_gi,

& comp_adj_method)

k_GiPrefix =

;

hasScore =

;

(

container, iter, scoreList) {

(

.GetStr()==

){

score = (*iter)->GetValue().GetInt();

}

(

.GetStr()==

){

bits = (*iter)->GetValue().GetReal();

}

(

.GetStr()==

||

.GetStr()==

) {

evalue = (*iter)->GetValue().GetReal();

}

(

.GetStr()==

){

gi_v = (

)((*iter)->GetValue().GetInt());

}

(

.GetStr()==

){

sum_n = (*iter)->GetValue().GetInt();

}

(

.GetStr()==

){

num_ident = (*iter)->GetValue().GetInt();

}

(

.GetStr()==

) {

comp_adj_method = (*iter)->GetValue().GetInt();

strGi =

(

.GetStr(),k_GiPrefix,

);

gi = NStr::StringToNumeric<TGi>(strGi);

use_this_gi.push_back(gi);

list<string> string_l;

list<string>::iterator iter = string_l.begin();

(iter != string_l.end())

errsevmsg[] = {

,

,

,

,

(iter->level > 5){

(iter->level == 4){

iter->level = iter->level;

<< errsevmsg[iter->level] <<

<< iter->message <<

;

vector<string> split_line;

(vector<string>, iter, split_line) {

s_FillDbInfoRemotely(

&

,

blastdb->SetName(

);

blastdb->SetType() =

.is_protein

.definition = dbinfo->GetDescription();

(

.definition.empty())

.total_length = dbinfo->GetTotal_length();

.number_seqs =

(dbinfo->GetNum_sequences());

dbfilt_algorithm)

(

.definition.empty())

.filt_algorithm_name.clear();

.filt_algorithm_options.clear();

(dbfilt_algorithm == -1) {

filtering_algorithm;

.filt_algorithm_name,

.filt_algorithm_options);

is_protein,

numSeqs,

numLetters,

&

)

.is_protein = is_protein;

.definition =

(

);

.definition =

(

) +

.number_seqs = numSeqs;

.total_length = numLetters;

retval.push_back(

);

& blastdb_names,

is_protein,

dbfilt_algorithm

,

found_all =

;

vector<string> missing_names;

vector< CRef<objects::CBlast4_database_info> > all_db_info =

rmt_blast_services.

(blastdb_names,is_protein,&found_all,&missing_names);

( !missing_names.empty() ){

(

ndx=0 ; ndx < missing_names.size(); ndx++){

+= missing_names[ndx];

+=

(

);

(

ndx=0 ; ndx < all_db_info.size(); ndx++){

objects::CBlast4_database_info &dbinfo = *all_db_info[ndx];

.name = dbinfo.GetDatabase().GetName();

.definition = dbinfo.GetDescription();

(

.definition.empty())

.total_length = dbinfo.GetTotal_length();

.number_seqs =

(dbinfo.GetNum_sequences());

(

.total_length < 0) {

+=

(

);

retval.push_back(

);

vector<CTempString> dbs;

retval.reserve(dbs.size());

(vector<CTempString>,

, dbs) {

.is_protein = is_protein;

success =

;

retval.push_back(

);

+=

(

);

<<

;

(

= 1;

< dbinfo_list.size();

++) {

db_titles +=

+ dbinfo_list[

].definition;

tot_num_seqs +=

(dbinfo_list[

].number_seqs);

tot_length += dbinfo_list[

].total_length;

;

(vector<SDbInfo>, dbinfo, dbinfo_list) {

(dbinfo->subset ==

) {

<<

;

( !dbinfo->filt_algorithm_name.empty() ) {

<<

<< dbinfo->filt_algorithm_name <<

;

( !dbinfo->filt_algorithm_options.empty() ) {

<<

<< dbinfo->filt_algorithm_options <<

;

<<

;

<< dbinfo->date <<

;

<<

;

<<

;

<<

<<

;

<<

;

<<

;

<<

<<

;

<<

;

<<

;

sprintf(

,

, k);

sprintf(

,

, h);

sprintf(

,

, gbp->

);

use_long_seqids =

;

use_long_seqids = (

.

(

,

) ==

);

(!use_long_seqids) {

((*iter)->IsTitle()) {

all_descr_str += (*iter)->GetTitle();

all_descr_str;

(

);

, tabular, rid);

(

);

&

,

}

(tabular) {

<<

<<

<< rid;

<<

<<

<< rid <<

;

& pattern,

<< num_patterns <<

<<

<< pattern <<

;

(vector<int>::iterator it =

.begin();

<<

<<

;

<<

<<

<<

;

list<TGi>& use_this_gi)

comp_adj_method = 0;

num_ident, use_this_gi, comp_adj_method);

list<string>& use_this_seq)

comp_adj_method = 0;

num_ident, use_this_seq, comp_adj_method);

list<TGi>& use_this_gi,

& comp_adj_method)

hasScore =

;

sum_n, num_ident, use_this_gi, comp_adj_method);

score, bits, evalue, sum_n, num_ident, use_this_gi, comp_adj_method);

score, bits, evalue, sum_n, num_ident, use_this_gi, comp_adj_method);

score, bits, evalue, sum_n, num_ident, use_this_gi, comp_adj_method);

(use_this_gi.size() == 0) {

k_GiPrefix =

;

list<string> use_this_seq;

(list<TGi>, iter_gi, use_this_gi){

use_this_seq.push_back(strSeq);

list<string>& use_this_seq,

& comp_adj_method)

hasScore =

;

list<TGi> use_this_gi;

sum_n, num_ident, use_this_gi, comp_adj_method);

score, bits, evalue, sum_n, num_ident, use_this_gi, comp_adj_method);

score, bits, evalue, sum_n, num_ident, use_this_gi, comp_adj_method);

score, bits, evalue, sum_n, num_ident, use_this_gi, comp_adj_method);

(use_this_gi.size() == 0) {

& dtg =

->GetGeneral();

retval =

->GetSeqIdString(with_version);

total_bit_score,

& bit_score_str,

& total_bit_score_str,

& raw_score_str)

evalue_buf[100], bit_score_buf[100], total_bit_score_buf[100];

kBitScoreFormat(

);

ctoolkit_compatible =

;

value_set =

;

(getenv(

)) {

kBitScoreFormat.assign(

);

ctoolkit_compatible =

;

(evalue < 1.0e-180) {

snprintf(evalue_buf,

(evalue_buf),

);

}

(evalue < 1.0e-99) {

snprintf(evalue_buf,

(evalue_buf),

, evalue);

(ctoolkit_compatible) {

strncpy(evalue_buf, evalue_buf+1,

(evalue_buf-1));

}

(evalue < 0.0009) {

snprintf(evalue_buf,

(evalue_buf),

, evalue);

}

(evalue < 0.1) {

snprintf(evalue_buf,

(evalue_buf),

, evalue);

}

(evalue < 1.0) {

snprintf(evalue_buf,

(evalue_buf),

, evalue);

}

(evalue < 10.0) {

snprintf(evalue_buf,

(evalue_buf),

, evalue);

snprintf(evalue_buf,

(evalue_buf),

, evalue);

(bit_score > 99999){

snprintf(bit_score_buf,

(bit_score_buf),

, bit_score);

}

(bit_score > 99.9){

snprintf(bit_score_buf,

(bit_score_buf),

,

snprintf(bit_score_buf,

(bit_score_buf), kBitScoreFormat.c_str(),

(total_bit_score > 99999){

snprintf(total_bit_score_buf,

(total_bit_score_buf),

,

}

(total_bit_score > 99.9){

snprintf(total_bit_score_buf,

(total_bit_score_buf),

,

(

)total_bit_score);

snprintf(total_bit_score_buf,

(total_bit_score_buf),

,

evalue_str = evalue_buf;

bit_score_str = bit_score_buf;

total_bit_score_str = total_bit_score_buf;

is_first_aln =

;

num_align = 0;

((*iter)->GetSegs().IsDisc()) {

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

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

(*previous_id))){

(num_align >

) {

is_first_aln =

;

previous_id = subid;

new_aln.

().push_back(*iter);

is_first_aln =

;

num_align = 0;

((*iter)->GetSegs().IsDisc()) {

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

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

(*previous_id))){

(num_align >=

) {

is_first_aln =

;

previous_id = subid;

is_first_aln =

;

num_align = 0;

finishCurrent =

;

((*iter)->GetSegs().IsDisc()) {

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

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

(*previous_id))){

finishCurrent = (num_align + 1 ==

) ?

:

;

is_first_aln =

;

previous_id = subid;

(num_align >

&& !finishCurrent) {

new_aln.

().push_back(*iter);

& num_gaps,

& num_gap_opens)

num_gaps = num_gap_opens = align_length = 0;

(

=0;

<chunk_vec->size();

++) {

chunk_length = chunk->GetAlnRange().GetLength();

(chunk->IsGap()) {

num_gaps += chunk_length;

align_length += chunk_length;

(CSeq_align_set::Tdata::const_iterator iter =

.Get().begin();

iter !=

.Get().end(); iter++) {

((*iter)->IsSetSegs()){

(CSeq_align_set::Tdata::const_iterator iter2 =

target.

().push_back(*iter2);

target.

().push_back(*iter);

((*iter)->IsSetDim()){

ds.

((*iter)->GetDim());

((*iter)->IsSetIds()){

ds.

() = (*iter)->GetIds();

((*iter)->IsSetStarts()){

ds.

().push_back(*iterStarts);

((*iter)->IsSetLen()){

ds.

().push_back((*iter)->GetLen());

((*iter)->IsSetStrands()){

((*iter)->IsSetScores()){

ds.

().push_back(*iterScores);

(bdl_id && bdl_id->

(

) &&

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

taxid = (*iter_bdl)->GetTaxid();

frame = (start % 3) + 1;

score1, sum_n1, num_ident1;

bits1, evalue1;

list<TGi> use_this_gi1;

score2, sum_n2, num_ident2;

bits2, evalue2;

list<TGi> use_this_gi2;

(*info1, score1, bits1, evalue1, sum_n1, num_ident1, use_this_gi1);

(*info2, score2, bits2, evalue2, sum_n2, num_ident2, use_this_gi2);

retval =

;

(length1 > 0 && length2 > 0 && num_ident1 > 0 &&num_ident2 > 0 ) {

(((

)num_ident1)/length1 == ((

)num_ident2)/length2) {

retval = evalue1 < evalue2;

retval = ((double)num_ident1)/length1 >= ((double)num_ident2)/length2;

retval = evalue1 < evalue2;

score1, sum_n1, num_ident1;

bits1, evalue1;

list<TGi> use_this_gi1;

score2, sum_n2, num_ident2;

bits2, evalue2;

list<TGi> use_this_gi2;

(*(info1->

().front()), score1, bits1, evalue1, sum_n1, num_ident1, use_this_gi1);

(*(info2->

().front()), score2, bits2, evalue2, sum_n2, num_ident2, use_this_gi2);

bits1 > bits2;

retval =

;

retval = cov1 > cov2;

}

(cov1 == cov2) {

score1, sum_n1, num_ident1;

bits1, evalue1;

list<TGi> use_this_gi1;

score2, sum_n2, num_ident2;

bits2, evalue2;

list<TGi> use_this_gi2;

(*(info1->

().front()), score1, bits1, evalue1, sum_n1, num_ident1, use_this_gi1);

(*(info2->

().front()), score2, bits2, evalue2, sum_n2, num_ident2, use_this_gi2);

retval = evalue1 < evalue2;

start1 = 0, start2 = 0;

start1 =

(info1->

().front()->GetSeqStart(0),

info1->

().front()->GetSeqStop(0));

start2 =

(info2->

().front()->GetSeqStart(0),

info2->

().front()->GetSeqStop(0));

(start1 == start2) {

score1, sum_n1, num_ident1;

bits1, evalue1;

list<TGi> use_this_gi1;

score2, sum_n2, num_ident2;

bits2, evalue2;

list<TGi> use_this_gi2;

(*(info1->

().front()), score1, bits1, evalue1, sum_n1, num_ident1, use_this_gi1);

(*(info1->

().front()), score2, bits2, evalue2, sum_n2, num_ident2, use_this_gi2);

evalue1 < evalue2;

start1 < start2;

score1, sum_n1, num_ident1;

bits1, evalue1;

list<TGi> use_this_gi1;

score2, sum_n2, num_ident2;

bits2, evalue2;

list<TGi> use_this_gi2;

(*info1, score1, bits1, evalue1, sum_n1, num_ident1, use_this_gi1);

(*info2, score2, bits2, evalue2, sum_n2, num_ident2, use_this_gi2);

bits1 > bits2;

start1 = 0, start2 = 0;

(start1 == start2) {

score1, sum_n1, num_ident1;

bits1, evalue1;

list<TGi> use_this_gi1;

score2, sum_n2, num_ident2;

bits2, evalue2;

list<TGi> use_this_gi2;

(*info1, score1, bits1, evalue1, sum_n1, num_ident1, use_this_gi1);

(*info2, score2, bits2, evalue2, sum_n2, num_ident2, use_this_gi2);

evalue1 < evalue2;

start1 < start2;

start1 = 0, start2 = 0;

(start1 == start2) {

score1, sum_n1, num_ident1;

bits1, evalue1;

list<TGi> use_this_gi1;

score2, sum_n2, num_ident2;

bits2, evalue2;

list<TGi> use_this_gi2;

(*info1, score1, bits1, evalue1, sum_n1, num_ident1, use_this_gi1);

(*info2, score2, bits2, evalue2, sum_n2, num_ident2, use_this_gi2);

evalue1 < evalue2;

start1 < start2;

(do_translation) {

final_aln = denseg_aln;

do_translation) {

identity = 0;

(do_translation) {

final_aln = denseg_aln;

alnvec.GetWholeAlnSeqString(0,

);

alnvec.GetWholeAlnSeqString(1,

);

(

= 0;

< length; ++

) {

identity = ((double)num_ident)/length;

&percentIdent1,

&percentIdent2)

evalue1 = seqSetInfo1->evalue;

evalue2 = seqSetInfo2->evalue;

percentIdent1 = seqSetInfo1->percent_identity;

percentIdent2 = seqSetInfo2->percent_identity;

retval =

;

(percentIdent1 < 0 || percentIdent2 < 0) {

(percentIdent1 > 0 &&percentIdent2 > 0) {

(percentIdent1 == percentIdent2) {

retval = evalue1 < evalue2;

retval = percentIdent1 >= percentIdent2;

retval = evalue1 < evalue2;

score1, score2, sum_n, num_ident;

bits, evalue;

list<TGi> use_this_gi;

total_bits1 = 0, total_bits2 = 0;

sum_n, num_ident, use_this_gi);

total_bits1 += bits;

sum_n, num_ident, use_this_gi);

total_bits2 += bits;

total_bits1 >= total_bits2;

& mv_build_name)

id1 = &(info1->

().front()->GetSeq_id(1));

id2 = &(info2->

().front()->GetSeq_id(1));

linkout1 = 0, linkout2 = 0;

& mv_build_name)

do_translation,

& scope,

& mv_build_name)

(sort_method == 1) {

}

(sort_method == 2) {

}

(sort_method == 3) {

& mv_build_name)

linkoutPrev = 0;

&

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

(prevSubjectId.

() || !

.Match(*prevSubjectId)){

prevSubjectId = &id;

linkout = linkoutdb ? linkoutdb->

(

, mv_build_name): 0;

linkoutPrev = linkout;

linkout = linkoutPrev;

(sort_method == 1) {

target[1]->Set().push_back(*iter);

}

(sort_method == 2){

target[0]->Set().push_back(*iter);

target[1]->Set().push_back(*iter);

(sort_method == 1) {

target[0]->Set().push_back(*iter);

}

(sort_method == 2) {

target[1]->Set().push_back(*iter);

target[0]->Set().push_back(*iter);

target[0]->Set().push_back(*iter);

target[0]->Set().push_back(*iter);

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

(previous_id.

()) {

temp->

().push_back(*iter);

target.push_back(temp);

}

(cur_id.

(*previous_id)){

temp->

().push_back(*iter);

temp->

().push_back(*iter);

target.push_back(temp);

previous_id = &cur_id;

align_set->

().push_back(*iter2);

(

= 0;

< seqIdList.size();

++) {

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

(previous_id.

() || !cur_id.

(*previous_id)) {

(

>= seqIdList.size()) {

(hitsMap.

(idString) != hitsMap.

()) {

temp->

().push_back(*iter);

hitsMap[idString] = temp;

(cur_id.

(*previous_id)){

(!temp.

()) {

temp->

().push_back(*iter);

previous_id = &cur_id;

vector <string> seqIds;

list< CRef<CSeq_align_set> > orderedSet;

(

= 0;

< seqIds.size();

++) {

(hitsMap.

(seqIds[

]) != hitsMap.

()) {

orderedSet.push_back(hitsMap[seqIds[

]]);

success =

;

(!seqId.

())

(!strTag.empty())

vector<string> vecInfo;

(vecInfo.size() != 3)

strRun = vecInfo[0];

strSpotId = vecInfo[1];

strReadIndex = vecInfo[2];

strRun, strSpotId,strReadIndex;

link +=

+ strRun;

link +=

+ strSpotId;

link +=

+ strReadIndex;

(!id_general.

() && id_general->

().find(

) != string::npos){

(id_general.

()){

(id_other.

()){

bestid = id_accession;

bestid = id_general;

db_is_na,

rid,

query_number,

for_alignment) {

(!id_general.

()

&& id_general->

().find(

) != string::npos){

nodb_path =

;

(user_url.find(

) ==string::npos){

*chptr, *dbtmp;

*

=

[

(char)*length + 2];

dbtmp =

[

(char)*length + 2];

memset(dbtmp,

,

(

)*length + 2);

(

= 0;

< length;

++) {

(!

((

)

[

]) && j < 256 &&

< length) {

((chptr = strrchr(tmpbuff,

)) !=

) {

(dbtmp, (

*)(chptr+1));

(!bestID.empty()){

strcpy(gnl, bestID.c_str());

(user_url.find(

) == string::npos){

link += user_url +

+

+

+

+ (db_is_na?

:

);

(user_url.find(

) != string::npos) {

link += user_url +

+

+

+ (db_is_na?

:

);

(gnl[0] !=

){

link +=

+ rid;

(query_number > 0){

(user_url.find(

) ==string::npos){

link +=

;

link +=

;

(

,

));

is_first =

;

parameter = it->first;

(parameters_to_change.count(

(parameter)) > 0 ||

parameters_to_change.count(

(parameter)) > 0) {

it->first +

+ parameters_to_change[it->first];

cgi_query += it->first +

+ it->second;

format_type =

.GetRequestValue(

).GetValue();

ridstr =

.GetRequestValue(

).GetValue();

align_view =

.GetRequestValue(

).GetValue();

cgi_query +=

+ ridstr;

cgi_query +=

+ format_type;

cgi_query +=

+ align_view;

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

GetRequestValue(

).

cgi_query +=

+

GetRequestValue(

).

cgi_query +=

+

GetRequestValue(

).

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

cgi_query +=

+

.GetRequestValue(

).GetValue();

& mv_build_name)

is_mixed =

;

is_first =

;

prev_database = 0;

&

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

linkout = linkoutdb

? linkoutdb->

(

, mv_build_name)

(!is_first && cur_database != prev_database) {

prev_database = cur_database;

formatAsMixedDbs =

;

mixedDbs =

.GetRequestValue(

).GetValue();

(!mixedDbs.empty()) {

formatAsMixedDbs = (mixedDbs ==

|| mixedDbs ==

|| mixedDbs ==

) ?

:

;

formatAsMixedDbs;

lnk_tl_info =

,

lnk_title =

)

kLinkTitle=

;

kLinkTarget=

+ rid +

;

lnkTitle = (lnk_title.empty()) ? kLinkTitle : lnk_title;

lnkTarget =

(lnk_displ,

) ?

: kLinkTarget;

textLink =

)

list<string> linkout_list;

url_link,lnk_displ,lnk_title,lnkTitleInfo;

vector<string> accs;

firstAcc = (accs.size() > 0)? accs[0] : labelList;

lnkTitleInfo =

;

uid = !linkoutInfo.

?

:

;

linkout_list.push_back(url_link);

linkTitle =

;

linkTitle =

;

molID,chainID;

linkout_list.push_back(url_link);

(linkout &

){

lnkTitleInfo =

;

linkout_list.push_back(url_link);

(linkout &

){

lnk_displ =

;

lnkTitleInfo =

;

uid = !linkoutInfo.

?

:

;

linkout_list.push_back(url_link);

lnk_displ =

;

lnkTitleInfo =

+ linkoutInfo.

+

;

user_url = (linkoutInfo.

.empty()) ? mapviewBlastHitUrl : linkoutInfo.

;

linkout_list.push_back(url_link);

linkTitle =

+ linkoutInfo.

+

;

linkout_list.push_back(url_link);

linkTitle =

;

giList =

(giList,

,

);

linkout_list.push_back(url_link);

lnkTitleInfo =

;

linkTitle =

;

linkout_list.push_back(url_link);

lnkTitleInfo =

;

uid = !linkoutInfo.

?

:

;

linkout_list.push_back(url_link);

urlTag =

;

lnkTitleInfo =

;

urlTag = linkoutInfo.

?

:

;

lnkTitleInfo = linkoutInfo.

?

;

seqFrom = (seqFrom == 0) ? seqFrom : seqFrom - 1;

seqTo = (seqTo == 0) ? seqTo : seqTo - 1;

linkout_list.push_back(url_link);

linkout_list;

& cdd_rid,

& entrez_term,

structure_linkout_as_group,

for_alignment,

cur_align,

preComputedResID)

list<string> linkout_list;

first_gi = (first_gi ==

) ? gi : first_gi;

linkoutInfo.

(rid,

structure_linkout_as_group,

linkout_list;

(linkLetter ==

) {

(linkLetter ==

) {

(linkLetter ==

) {

(linkLetter ==

) {

(linkLetter ==

) {

(linkLetter ==

) {

(linkLetter ==

) {

(linkLetter ==

) {

(linkLetter ==

) {

(linkLetter ==

) {

(linkout_map.count(linkout) > 0){

linkout_map[linkout].push_back(cur_id);

vector <CBioseq::TId > idList;

idList.push_back(cur_id);

linkout_map.

(

<

, vector <CBioseq::TId > >::

(linkout,idList));

& mv_build_name,

linkout = (*linkoutdb)->GetLinkout(gi, mv_build_name);

linkout = (*linkoutdb)->GetLinkout(*seqID, mv_build_name);

linkoutWithoutVersion = (*linkoutdb)->GetLinkout(*seqIDNew, mv_build_name);

(linkoutWithoutVersion && (linkoutWithoutVersion |

)) {

linkout = linkout | linkoutWithoutVersion;

cerr <<

<< e.

() << endl;

<

, vector <CBioseq::TId > > &linkout_map,

& mv_build_name)

(!linkoutdb)

;

(linkout &

){

(linkout &

){

<

, vector <CBioseq::TId > > &linkout_map,

& mv_build_name)

kMaxDeflineNum = 10;

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

(num > kMaxDeflineNum)

;

taxName =

.common_name;

list<string> &linkout_list)

lnk_displ =

;

linkout_list.push_back(url_link);

<

, vector < CBioseq::TId > > &linkout_map,

getIdentProteins)

list<string> linkout_list;

vector<string> linkLetters;

(

= 0;

< linkLetters.size();

++) {

vector < CBioseq::TId > idList;

linkoutInfo.

.clear();

(linkout_map.

(linkout) != linkout_map.

()) {

idList = linkout_map[linkout];

disableLink = (linkout == 0 || idList.size() == 0);

giList,labelList;

(

= 0;

< idList.size();

++) {

(first_gi ==

) first_gi = gi;

(!labelList.empty()) labelList +=

;

labelList +=

;

(!giList.empty() && (linkout &

) && !linkoutInfo.

)

;

(!giList.empty()) giList +=

;

linkoutInfo.

.clear();

(one_linkout.size() > 0) {

list<string>::iterator iter = one_linkout.begin();

linkout_list.push_back(*iter);

(getIdentProteins) {

linkout_list;

list<string> linkout_list;

(bdl.size() > 0) {

list< CRef< CBlast_def_line > >::const_iterator iter = bdl.begin();

!linkoutInfo.

&& bdl.size() > 1);

linkout_list;

& cdd_rid,

& entrez_term,

structure_linkout_as_group,

& linkoutOrder,

&preComputedResID,

& mv_build_name)

list<string> linkout_list;

(bdl.size() > 0) {

list< CRef< CBlast_def_line > >::const_iterator iter = bdl.begin();

SLinkoutInfo linkoutInfo;

linkoutInfo.

(rid,

structure_linkout_as_group,

linkoutInfo.cur_align = cur_align;

linkoutInfo.taxid = taxid;

!is_na && bdl.size() > 1);

linkout_list;

getIdentProteins)

list<string> linkout_list;

linkout_list;

& cdd_rid,

& entrez_term,

structure_linkout_as_group,

& linkoutOrder,

&preComputedResID,

& mv_build_name,

getIdentProteins)

list<string> linkout_list;

SLinkoutInfo linkoutInfo;

linkoutInfo.

(rid,

structure_linkout_as_group,

linkoutInfo.cur_align = cur_align;

linkoutInfo.taxid = taxid;

linkout_list;

oppositeStrands =

;

isFirst =

;

query_list.push_back(query_range);

(subject_range.

() > subject_range.

()){

subject_range.

(subject_range.

(), subject_range.

());

subject_list.push_back(subject_range);

oppositeStrands = (!isFirst) ? (*iter)->GetSeqStrand(0) != (*iter)->GetSeqStrand(1) : oppositeStrands;

oppositeStrands;

list<CRange<TSeqPos> > merge_list;

is_first =

;

merge_list.push_back(*iter);

merge_list.pop_back();

merge_list.push_back(temp_range);

prev_range = temp_range;

merge_list.push_back(*iter);

list<CRange<TSeqPos> > merge_list;

list<CRange<TSeqPos> > temp;

temp.push_back(seq_range);

master_covered_lenghth = 0;

master_covered_lenghth += iter->GetLength();

master_covered_lenghth;

list<CRange<TSeqPos> > query_list;

list<CRange<TSeqPos> > subject_list;

*master_covered_lenghth = 0;

*master_covered_lenghth += iter->GetLength();

from = (from == 0) ? iter->GetFrom() :

(from,iter->GetFrom());

to =

(to,iter->GetTo());

subjectRange;

nuc_to_nuc_translation,

& mv_build_name) {

(db_sort == 0 && hit_sort < 1 && hsp_sort < 1)

list< CRef<CSeq_align_set> > seqalign_hit_total_list;

vector< CRef<CSeq_align_set> > seqalign_vec(2);

linkoutdb, mv_build_name);

nuc_to_nuc_translation,

seqalign_hit_total_list.splice(seqalign_hit_total_list.end(),one_seqalign_hit_total_list);

list< CRef<CSeq_align_set> >

nuc_to_nuc_translation,

list< CRef<CSeq_align_set> > seqalign_hit_total_list;

list< CRef<CSeq_align_set> > seqalign_hit_list;

nuc_to_nuc_translation);

}

(hsp_sort ==

) {

seqalign_hit_total_list.push_back(temp);

seqalign_hit_total_list;

nuc_to_nuc_translation,

nuc_to_nuc_translation,

score, sum_n, num_ident;

bits, evalue;

list<TGi> use_this_gi;

sum_n, num_ident, use_this_gi);

(evalue >= evalueLow && evalue <= evalueHigh) {

new_aln->

().push_back(*iter);

(numerator == denominator)

retval =(

) (0.5 + 100.0*((

)numerator)/((double)denominator));

retval =

(99, retval);

(numerator == denominator)

retval =100*(double)numerator/(

)denominator;

percentIdentLow,

percentIdentHigh)

score, sum_n, num_ident;

bits, evalue;

list<TGi> use_this_gi;

sum_n, num_ident, use_this_gi);

(seqAlnLength > 0 && num_ident > 0) {

(alnPercentIdent >= percentIdentLow && alnPercentIdent <= percentIdentHigh) {

new_aln->

().push_back(*iter);

percentIdentLow,

percentIdentHigh)

score, sum_n, num_ident;

bits, evalue;

list<TGi> use_this_gi;

sum_n, num_ident, use_this_gi);

(seqAlnLength > 0 && num_ident > 0) {

( (evalue >= evalueLow && evalue <= evalueHigh) &&

(alnPercentIdent >= percentIdentLow && alnPercentIdent <= percentIdentHigh)) {

new_aln->Set().push_back(*iter);

percentIdent,

percentIdentLow,

percentIdentHigh,

isInRange =

;

evalue_buf, bit_score_buf, total_bit_buf, raw_score_buf;

(evalueLow >= 0 && percentIdentLow >= 0 && queryCoverLow >= 0) {

isInRange = (evalue >= evalueLow && evalue <= evalueHigh) &&

(percentIdent >= percentIdentLow && percentIdent <= percentIdentHigh) &&

(queryCover >= queryCoverLow && queryCover <= queryCoverHigh);

(evalueLow >= 0 && percentIdentLow >= 0) {

isInRange = (evalue >= evalueLow && evalue <= evalueHigh) &&

(percentIdent >= percentIdentLow && percentIdent <= percentIdentHigh);

(evalueLow >= 0 && queryCoverLow >= 0) {

isInRange = (evalue >= evalueLow && evalue <= evalueHigh) &&

(queryCover >= queryCoverLow && queryCover <= queryCoverHigh);

(queryCoverLow >= 0 && percentIdentLow >= 0) {

isInRange = (queryCover >= queryCoverLow && queryCover <= queryCoverHigh) &&

(percentIdent >= percentIdentLow && percentIdent <= percentIdentHigh);

(evalueLow >= 0) {

isInRange = (evalue >= evalueLow && evalue <= evalueHigh);

(percentIdentLow >= 0) {

isInRange = (percentIdent >= percentIdentLow && percentIdent <= percentIdentHigh);

(queryCoverLow >= 0) {

isInRange = (queryCover >= queryCoverLow && queryCover <= queryCoverHigh);

percentIdentLow,

percentIdentHigh,

list< CRef<CSeq_align_set> > seqalign_hit_total_list;

list< CRef<CSeq_align_set> > seqalign_hit_list;

seqalign_hit_total_list.push_back(temp);

alignCount = 0,hspCount = 0;

& newQueryId = (*iter)->GetSeq_id(0);

(prevQueryId.

() || !newQueryId.

(*prevQueryId)){

(hspCount >= maxHsps) {

prevQueryId = &newQueryId;

(alignCount < maxAligns) {

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

(prevSubjectId.

() || !newSubjectId.

(*prevSubjectId)){

prevSubjectId = &newSubjectId;

new_aln->

().push_back(*iter);

(queryNumber == 0) {

currQueryNum = 0;

& newQueryId = (*iter)->GetSeq_id(0);

(prevQueryId.

() || !newQueryId.

(*prevQueryId)){

prevQueryId = &newQueryId;

(currQueryNum == queryNumber) {

(new_aln.

()) {

new_aln->

().push_back(*iter);

(currQueryNum > queryNumber) {

l_cfg_file_name;

cfgExists =

;

l_fmtcfg_env;

(

!= getenv(

) ) l_ncbi_env = getenv(

);

(

!= getenv(

) ) l_fmtcfg_env = getenv(

);

( l_fmtcfg_env.empty() )

l_cfg_file_name =

;

l_cfg_file_name = l_fmtcfg_env;

l_fchecker( l_cfg_file_name );

cfgExists = l_fchecker.

();

( (!cfgExists) && (!l_ncbi_env.empty()) ) {

( l_ncbi_env.rfind(

) != (l_ncbi_env.length() -1 ))

l_ncbi_env.append(

);

l_cfg_file_name = l_ncbi_env + l_cfg_file_name;

l_fchecker2( l_cfg_file_name );

cfgExists = l_fchecker2.

();

( l_dbg ) fprintf(stderr,

,l_cfg_file_name.c_str());

l_key, l_host_port, l_format;

l_secion_name =

;

l_fmt_suffix =

;

l_host_port_suffix =

;

l_subst_pattern;

l_base_dir =

->Get(l_secion_name,

);

( !l_base_dir.empty() && ( l_base_dir.rfind(

) != (l_base_dir.length()-1)) ) {

l_base_dir.append(

);

default_host_port;

l_subst_pattern=

+l_key_ndx+

;

l_host_port =

->Get(l_secion_name, l_key_ndx);

( l_host_port.empty()){

l_key = url_name + l_host_port_suffix; l_subst_pattern=

+l_key+

;

l_host_port =

->Get(l_secion_name, l_key);

( l_host_port.empty())

(url_name,index);

l_key = url_name + l_fmt_suffix ;

l_format =

->Get(l_secion_name, l_key_ndx);

( l_format.empty() ) l_format =

->Get(l_secion_name, l_key);

( l_format.empty())

(url_name,index);

l_format_file = l_base_dir + l_format;

l_fchecker( l_format_file );

file_name_mode = l_fchecker.

();

( file_name_mode ) {

l_inc_file_name = l_format_file;

*l_mem =

[ (size_t) l_inc_size + 1];

memset( l_mem,0, (

) l_inc_size + 1 ) ;

l_file.seekg( 0, ios::beg );

l_file.read(l_mem, l_inc_size);

l_format.erase(); l_format.reserve( (

)l_inc_size + 1 );

result_url =

(l_format,l_subst_pattern,l_host_port);

( result_url.empty())

(url_name,index);

search_name = url_name;

(url_link.empty()) {

cit = kMapTagToURL.find(tag_name);

( cit != kMapTagToURL.end()) {

cit = kMapTagToHTML.find(tag_name);

( cit != kMapTagToHTML.end()) {

mappedStr = cit->second;

cit = kMapTagToString.find(tag_name);

( cit != kMapTagToString.end()) {

mappedStr = cit->second;

retval.

(0, 0, -1);

(matrix_name ==

||

(packed_mtx ==

) {

retval(

,

) = 1;

retval(

,

) = retval(

,

);

retval(

,

) = retval(

,

);

retval(

,

) = retval(

,

);

tmplParam =

+ tmplParamName +

;

tmplParam =

+ tmplParamName +

;

(inpString,tmplParam,templParamVal,outString);

templParamVal =

(templParamVal, maxParamValLength, spacesFormatFlag);

outString =

(inpString,tmplParamName,templParamVal);

(maxParamValLength >= paramVal.size()) {

numSpaces = maxParamValLength - paramVal.size() + 1;

numSpaces = numSpaces/2;

spaceString.assign(numSpaces,

);

paramVal = paramVal.substr(0, maxParamValLength - 3) +

;

spaceString +=

;

paramVal = paramVal + spaceString;

paramVal = spaceString + paramVal + spaceString;

paramVal = spaceString + paramVal;

httpProt =

;

(!config_reg.

()) {

(config_reg.

(

,

)) {

httpProt = config_reg.

(

,

);

db,logstr_moltype;

(seqUrlInfo->

) {

logstr_moltype =

;

logstr_moltype =

;

logstr_location = (seqUrlInfo->

) ?

:

;

url_link = urlTemplate;

(seqUrlInfo->

.find(

) != string::npos) {

strRun, strSpotId,strReadIndex;

kWgsProjLength = 4;

kWgsProjIDLengthMin = 8;

kWgsProjIDLengthMax = 10;

(wgsAccession.size() < 6) {

wgsProj = wgsAccession.substr(0,kWgsProjLength);

(

= 0;

< wgsProj.length();

++){

(!

(wgsProj[

]&0xff)) {

wgsId = wgsAccession.substr(kWgsProjLength);

(wgsId.length() >= kWgsProjIDLengthMin && wgsId.length() <= kWgsProjIDLengthMax) {

(

= 0;

< wgsId.length();

++){

kWgsProgNameLength = 6;

wgsProjName = wgsAccession.substr(0,kWgsProgNameLength);

title =

+ seqUrlInfo->accession +

;

temp_class_info = classInfo; temp_class_info +=

;

wgsAccession = seqUrlInfo->accession;

isWGS =

;

(isWGS && seqUrlInfo->useTemplates) {

(hasTextSeqID) {

(!seqUrlInfo->useTemplates) {

(seqUrlInfo->useTemplates) {

url_link = l_TraceUrl + (

)

+ actual_id +

+ seqUrlInfo->rid;

temp_class_info = (!seqUrlInfo->defline.empty())?

(temp_class_info,

,seqUrlInfo->defline):temp_class_info;

user_url = (seqUrlInfo->addCssInfo) ?

->Get(

,

) :

->Get(

,

);

temp_class_info = (!seqUrlInfo->defline.empty())?

(temp_class_info,

,seqUrlInfo->defline):temp_class_info;

seqUrlInfo->seqUrl = url_link;

title =

+ seqUrlInfo->accession +

;

!((seqUrlInfo->user_url.find(

) != string::npos && seqUrlInfo->gi >

) ||

(seqUrlInfo->user_url.find(

) != string::npos))) {

url_with_parameters,toolURLParams;

(

&& !seqUrlInfo->blastType.empty() && seqUrlInfo->blastType !=

) {

toolURLParams =

->Get(seqUrlInfo->blastType,

);

(!toolURLParams.empty()) {

urlLinkTemplate = seqUrlInfo->user_url + toolURLParams;

url_with_parameters =

(urlLinkTemplate, seqUrlInfo, *ids);

(seqUrlInfo->user_url.find(

) != string::npos) {

seqUrlInfo->database,

seqUrlInfo->isDbNa, seqUrlInfo->rid,

seqUrlInfo->queryNumber,

seqUrlInfo->isAlignLink);

(!seqUrlInfo->useTemplates) {

(seqUrlInfo->addCssInfo) {

url_link +=

+ title + deflineInfo +

;

url_link += url_with_parameters;

(!seqUrlInfo->useTemplates) url_link +=

;

seqUrlInfo->seqUrl = url_link;

((seqUrlInfo->advancedView || seqUrlInfo->blastType ==

|| seqUrlInfo->blastType ==

) ||

seqUrlInfo->blastType ==

|| seqUrlInfo->blastType ==

) {

url_link =

(seqUrlInfo,ids);

linkURL =

(seqUrlInfo,ids);

(!linkURL.empty()) {

linkTmpl = (seqUrlInfo->

) ? genericLinkMouseoverTmpl : genericLinkTemplate;

(

linkUrl,

reportType,

accession,

linkText,

linktrg,

linkTitle =

,

linkCls =

)

(linkTitle.empty()) {

list<string> customLinksList;

linkUrl,link,linkTiltle = customLinkTitle;

linkUrl = seqUrlInfo->

;

linkText = (seqUrlInfo->

) ?

:

;

linkUrl +=

;

linkTiltle =

;

customLinksList.push_back(link);

customLinksList;

dbtype = (seqUrlInfo->

) ?

:

;

seqViewUrl = (seqUrlInfo->

>

)?seqViewerUrl:seqViewerUrlNonGi;

seqViewerParams;

seqViewerParams =

->Get(seqUrlInfo->

,

);

seqViewerParams = seqViewerParams.empty() ? seqViewerParamsDefault : seqViewerParams;

linkTitle =

;

link_loc =

;

link_loc =

;

linkTitle +=

;

title = (seqUrlInfo->

) ?

:

;

list<string> customLinksList =

(seqUrlInfo,hspRange);

(!graphicLink.empty()) {

customLinksList.push_back(graphicLink);

customLinksList;

customLinkTypes = customLinkTypesInp;

(seqUrlInfo->

==

) {

(seqUrlInfo->

==

) {

(seqUrlInfo->

==

) {

customLinkTypes;

objects::CScope &scope,

customLinkTypes)

list<string> customLinksList;

linkUrl,link;

linkUrl = seqUrlInfo->

;

customLinksList.push_back(link);

customLinksList.push_back(link);

customLinksList.push_back(link);

customLinksList.push_back(link);

linkUrl = seqUrlInfo->

;

customLinksList.push_back(link);

linkUrl = seqUrlInfo->

;

customLinksList.push_back(link);

linkUrl = seqUrlInfo->

+ rs +

;

customLinksList.push_back(link);

customLinksList.push_back(link);

customLinksList.push_back(link);

linkUrl = seqUrlInfo->

;

customLinksList.push_back(link);

customLinksList;

objects::CScope &scope)

linkUrl,link;

(!linkUrl.empty()) {

linkUrl +=

+ seqUrlInfo->

;

objects::CScope &scope)

linkUrl = seqUrlInfo->

;

linkUrl = seqUrlInfo->

;

vector<string> parts;

(parts.size() > 1) {

linkUrl = seqUrlInfo->

+ rs +

;

& dtg = subject_id.GetGeneral();

& dbName = dtg.

();

list<TGi> use_this_gi;

use_this_gi.clear();

num_ident, use_this_gi);

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

seqSetInfo->use_this_gi = use_this_gi;

seqSetInfo->bit_score = bits;

seqSetInfo->raw_score = score;

seqSetInfo->evalue = evalue;

seqSetInfo->match = num_ident;

seqSetInfo->flip =

;

seqSetInfo.release();

(aln.

().empty())

total_bits = 0;

highest_bits = 0;

lowest_evalue = 0;

highest_length = 1;

highest_ident = 0;

totalLen = 0;

list<TGi> use_this_gi;

totalLen += align_length;

num_ident, use_this_gi);

use_this_gi.clear();

(bits > highest_bits) {

highest_length = align_length;

highest_ident = num_ident;

(bits > highest_bits) {

highest_bits = bits;

lowest_evalue = evalue;

seqSetInfo->

= highest_ident;

seqSetInfo->

= lowest_evalue;

seqSetInfo->

=

(aln.

());

(aln.

().empty())

highest_bits = 0;

highest_length = 1;

highest_ident = 0;

list<TGi> use_this_gi;

num_ident, use_this_gi);

(bits > highest_bits) {

highest_length = align_length;

highest_ident = num_ident;

highest_bits = bits;

percent_identity;

<

container>

& totalBitScore,

& percentCoverage,

& percentIdent,

list<TGi>& use_this_gi)

k_GiPrefix =

;

hasScore =

;

(

container, iter, scoreList) {

(

.GetStr()==

) {

evalue = (*iter)->GetValue().GetReal();

}

(

.GetStr()==

){

bitScore = (*iter)->GetValue().GetReal();

}

(

.GetStr()==

){

totalBitScore = (*iter)->GetValue().GetReal();

}

(

.GetStr()==

){

percentCoverage = (*iter)->GetValue().GetInt();

}

(

.GetStr()==

&& (*iter)->GetValue().IsInt()){

percentIdent = (*iter)->GetValue().GetInt();

}

(

.GetStr()==

&& (*iter)->GetValue().IsReal()){

percentIdent = (*iter)->GetValue().GetReal();

}

(

.GetStr()==

){

hspNum = (*iter)->GetValue().GetInt();

}

(

.GetStr()==

){

totalLen = (*iter)->GetValue().GetReal();

}

(

.GetStr()==

){

rawScore = (*iter)->GetValue().GetInt();

}

(

.GetStr()==

){

gi_v = (

) ((*iter)->GetValue().GetInt());

}

(

.GetStr()==

){

sum_n = (*iter)->GetValue().GetInt();

strGi =

(

.GetStr(),k_GiPrefix,

);

gi = NStr::StringToNumeric<TGi>(strGi);

use_this_gi.push_back(gi);

k_GiPrefix =

;

(CUser_object::TData::const_iterator fit = fields.begin(); fit != fields.end(); ++fit) {

gi = NStr::StringToNumeric<TGi>(strGi);

use_this_gi.push_back(gi);

(CUser_object::TData::const_iterator fit = fields.begin(); fit != fields.end(); ++fit) {

use_this_seq.push_back(*acc_iter);

hasScore =

;

bitScore = -1;

totalBitScore = -1;

percentCoverage = -1;

percentIdent = -1;

totalLen = 0;

list<TGi> use_this_gi;

list<string> use_this_seq;

hasScore =

(aln.

(),evalue,bitScore, totalBitScore,percentCoverage,percentIdent,hspNum,totalLen,rawScore,sum_n,use_this_gi);

evalue,bitScore, totalBitScore,percentCoverage,percentIdent,hspNum,totalLen,rawScore,sum_n,use_this_gi);

evalue,bitScore, totalBitScore,percentCoverage,percentIdent,hspNum,totalLen,rawScore,sum_n,use_this_gi);

evalue,bitScore, totalBitScore,percentCoverage,percentIdent,hspNum,totalLen,rawScore,sum_n,use_this_gi);

(use_this_gi.size() == 0) {

seqSetInfo->evalue = evalue;

seqSetInfo->bit_score = bitScore;

seqSetInfo->total_bit_score = totalBitScore;

seqSetInfo->percent_coverage = percentCoverage;

seqSetInfo->percent_identity = percentIdent;

seqSetInfo->hspNum = hspNum;

seqSetInfo->totalLen = (

)totalLen;

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

seqSetInfo->use_this_seq = use_this_seq;

seqSetInfo->raw_score = rawScore;

seqSetInfo->flip =

;

seqSetInfo.release();

list<TGi>& use_this_gi,

list<TGi>& use_this_gi,

found =

;

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

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

taxid = (*iter)->GetTaxid();

(!use_this_gi.empty()) {

(list<TGi>, iter_gi, use_this_gi){

(cur_gi == *iter_gi){

((*iter_id)->Match(aln_id)

(*iter_id)->IsGeneral() && (*iter_id)->GetGeneral().CanGetDb() &&

aln_id.

().

() == (*iter_id)->GetGeneral().GetDb())) {

k_GiPrefix =

;

k_SeqIDPrefix =

;

textSeqid =

(use_this_seqid,k_SeqIDPrefix,

);

(list<string>, iter_seq, use_this_seq){

list<TGi> use_this_gi;

(list<string>, iter_seq, use_this_seq){

(isGi) use_this_gi.push_back(NStr::StringToNumeric<TGi>(strGI));

found =

;

(list<string>, iter_seq, use_this_seq){

((isGi && cur_gi == NStr::StringToNumeric<TGi>((useThisSeq))) || (!isGi && curSeqID == useThisSeq)){

(isGiList) *isGiList = isGi;

(alnSeqID->

()) {

found = std::find(seqList.begin(), seqList.end(), curSeqID) != seqList.end();

(list<string>, iter_seq, use_this_seq){

found = std::find(seqList.begin(), seqList.end(), useThisSeq) != seqList.end();

has_match =

;

(list<string>, iter_seq, use_this_seq) {

(useThisSeq == textSeqIDToMatch) {

list<string> new_use_this_seq;

hasAccType =

;

(list<string>, iter_seq, use_this_seq) {

(useThisSeqAccType != accessionType) {

new_use_this_seq.push_back(useThisSeq);

use_this_seq = new_use_this_seq;

list<string>& use_this_seq,

(gi) *gi =

(*ids);

(textSeqID) *textSeqID =

(wid,

);

found =

;

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

curSeqID =

(wid,

);

(taxid && (*iter)->IsSetTaxid() && (*iter)->CanGetTaxid()){

*taxid = (*iter)->GetTaxid();

(!use_this_seq.empty()) {

(list<string>, iter_seq, use_this_seq){

((isGi && cur_gi == NStr::StringToNumeric<TGi>((useThisSeq))) || (!isGi && curSeqID == useThisSeq)){

((*iter_id)->Match(aln_id)

(*iter_id)->IsGeneral() && (*iter_id)->GetGeneral().CanGetDb() &&

aln_id.

().

() == (*iter_id)->GetGeneral().GetDb())) {

(gi) *gi = cur_gi;

(textSeqID) *textSeqID = curSeqID;

list<TGi>& use_this_gi)

found =

;

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

(!use_this_gi.empty()) {

(list<TGi>, iter_gi, use_this_gi){

(cur_gi == *iter_gi){

((*iter_id)->Match(aln_id)

(*iter_id)->IsGeneral() && (*iter_id)->GetGeneral().CanGetDb() &&

aln_id.

().

() == (*iter_id)->GetGeneral().GetDb())) {

list<CRef<CSeq_align> >::iterator mItr=alnset.

().begin();

(;mItr != alnset.

().end(); ++mItr) {

(coll[0] == align_subj_rng) {

subj_rng_coll += align_subj_rng;

query_rng.

(

.GetSeqPosFromAlnPos(0,subj_aln_start));

query_rng.

(

.GetSeqPosFromAlnPos(0,subj_aln_end));

subj_rng_coll += subj_rng;

(CBioseq::TId::const_iterator iter = ids.begin(); iter != ids.end();

((*iter)->Which() == choice){

(!(

.

())){

->GetGi();

(;desc_t; ++desc_t) {

(

.IsGi() ||

.IsPrf() ||

.IsPir()) {

retval =

.AsFastaString();

retval =

.GetSeqIdString(

);

hasTextSeqID =

;

hasTextSeqID =

;

(hasTextSeqID && textSeqID) {

hasTextSeqID;

hasTextSeqID =

;

(seqID.

()) {

(seqID.

()) {

(!seqID.

()) {

hasTextSeqID =

;

hasTextSeqID;

vector <string> &seqList)

list<string> use_this_seq;

=

;

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

(previous_id.

() || !subid->

(*previous_id)){

use_this_seq.clear();

previous_id = subid;

new_aln->

().push_back(*iter);

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.

static void s_CalcAlnPercentIdent(const CRef< CSeq_align_set > &info1, const CRef< CSeq_align_set > &info2, double &percentIdent1, double &percentIdent2)

static string s_GetTaxName(TTaxId taxid)

static bool s_ProcessAlignSet(const CSeq_align_set &alnset, list< CRange< TSeqPos > > &query_list, list< CRange< TSeqPos > > &subject_list)

static CRef< CSeq_id > s_GetSeqIdByType(const list< CRef< CSeq_id > > &ids, CSeq_id::E_Choice choice)

return id type specified or null ref

static string s_MapURLLink(string urlTemplate, CAlignFormatUtil::SSeqURLInfo *seqUrlInfo, const CBioseq::TId &ids)

static list< CRange< TSeqPos > > s_MergeRangeList(list< CRange< TSeqPos > > &source)

MAKE_CONST_MAP(kMapTagToURL, ct::tagStrNocase, ct::tagStrNocase, { { "BL2SEQ_WBLAST_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi" }, { "CBLAST_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/Structure/cblast/cblast.cgi" }, { "DOWNLOAD_CGI","/blast/dumpgnl.cgi"}, { "ENTREZ_QUERY_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/entrez/query.fcgi" }, { "ENTREZ_SITES_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/sites/entrez" }, { "ENTREZ_SUBSEQ_TM", "<@protocol@>//www.ncbi.nlm.nih.gov/<@db@>/<@gi@>?report=gbwithparts&from=<@from@>&to=<@to@>&RID=<@rid@>" }, { "ENTREZ_TM", "<@protocol@>//www.ncbi.nlm.nih.gov/<@db@>/<@acc@>?report=genbank&log$=<@log@>&blast_rank=<@blast_rank@>&RID=<@rid@>" }, { "ENTREZ_VIEWER_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/entrez/viewer.fcgi" }, { "GENE_INFO", "<@protocol@>//www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=%d&RID=%s&log$=geneexplicit%s&blast_rank=%d" }, { "MAP_SEARCH_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/mapview/map_search.cgi" }, { "MAPVIEWER_CGI", "https://www.ncbi.nlm.nih.gov/mapview/maps.cgi?maps=blast_set" }, {"SEQVIEW_URL","https://www.ncbi.nlm.nih.gov/<@dbtype@>/<@seqid@>?report=graph&rid=<@rid@>[<@seqid@>]&"}, {"SEQVIEW_URL_NON_GI","https://www.ncbi.nlm.nih.gov/projects/sviewer/?RID=<@rid@>&id=<@firstSeqID@>&"}, { "TRACE_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/Traces/trace.cgi" }, { "TREEVIEW_CGI", "<@protocol@>//www.ncbi.nlm.nih.gov/blast/treeview/blast_tree_view.cgi"}, { "WGS", "<@protocol@>//www.ncbi.nlm.nih.gov/nuccore/<@wgsacc@>" }, })

static void s_AddLinkoutInfo(map< int, vector< CBioseq::TId > > &linkout_map, int linkout, CBioseq::TId &cur_id)

static string s_MapCustomLink(string linkUrl, string reportType, string accession, string linkText, string linktrg, string linkTitle="", string linkCls="")

static bool s_GetSRASeqMetadata(const CBioseq::TId &ids, string &strRun, string &strSpotId, string &strReadIndex)

void s_AddOtherRelatedInfoLinks(CBioseq::TId &cur_id, const string &rid, bool is_na, bool for_alignment, int cur_align, list< string > &linkout_list)

static list< string > s_NumGiToStringGiList(list< TGi > use_this_gi)

static CRange< TSeqPos > & s_FixMinusStrandRange(CRange< TSeqPos > &rng)

static bool s_FillDbInfoLocally(const string &dbname, CAlignFormatUtil::SDbInfo &info, int dbfilt_algorithm)

Initialize database statistics with data obtained from local BLAST databases.

static CRef< CScope > kScope

bool s_GetBlastScore(const container &scoreList, int &score, double &bits, double &evalue, int &sum_n, int &num_ident, list< TGi > &use_this_gi, int &comp_adj_method)

Get blast score information.

static list< string > s_GetLinkoutUrl(int linkout, string giList, string labelList, TGi first_gi, CAlignFormatUtil::SLinkoutInfo &linkoutInfo, bool textLink=true)

string s_GetBestIDForURL(CBioseq::TId &ids)

static bool s_isAlnInFilteringRange(double evalue, double percentIdent, int queryCover, double evalueLow, double evalueHigh, double percentIdentLow, double percentIdentHigh, int queryCoverLow, int queryCoverHigh)

static string s_MapCommonUrlParams(string urlTemplate, CAlignFormatUtil::SSeqURLInfo *seqUrlInfo)

static int s_LinkLetterToType(string linkLetter)

static double adjustPercentIdentToDisplayValue(double value)

const char k_PSymbol[ePMatrixSize+1]

Residues.

static string s_UseThisSeqToTextSeqID(string use_this_seqid, bool &isGi)

static string s_MapLinkoutGenParam(string &url_link_tmpl, const string &rid, string giList, bool for_alignment, int cur_align, string &label, string &lnk_displ, string lnk_tl_info="", string lnk_title="")

static list< string > s_GetFullLinkoutUrl(CBioseq::TId &cur_id, CAlignFormatUtil::SLinkoutInfo &linkoutInfo, map< int, vector< CBioseq::TId > > &linkout_map, bool getIdentProteins)

static bool FromRangeAscendingSort(CRange< TSeqPos > const &info1, CRange< TSeqPos > const &info2)

const int k_NumAsciiChar

Number of ASCII characters for populating matrix columns.

Declares the CBlastServices class.

static string GetProtocol(void)

static const char * kNoHitsFound

The string containing the message that no hits were found.

static CRef< objects::CSeq_align_set > FilterSeqalignBySeqList(objects::CSeq_align_set &source_aln, vector< string > &seqList)

function for Filtering seqalign by specific subjects

static void PrintPhiInfo(int num_patterns, const string &pattern, double prob, vector< int > &offsets, CNcbiOstream &out)

Prints out PHI-BLAST info for header (or footer)

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 int GetAlignmentLength(const objects::CSeq_align &aln, bool do_translation)

get the alignment length

static bool IsWGSAccession(string &accession, string &wgsProj)

Check if accession is WGS.

static void PruneSeqalign(const objects::CSeq_align_set &source_aln, objects::CSeq_align_set &new_aln, unsigned int num=static_cast< unsigned int >(kDfltArgNumAlignments))

Fill new alignset containing the specified number of alignments with unique slave seqids.

static int GetUniqSeqCoverage(objects::CSeq_align_set &alnset)

Calculate the uniq subject query coverage range (blastn only)

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

static void SortHitByMolecularType(list< CRef< objects::CSeq_align_set > > &seqalign_hit_list, objects::CScope &scope, ILinkoutDB *linkoutdb, const string &mv_build_name)

sort a list of seqalign set by molecular type

static void AcknowledgeBlastQuery(const objects::CBioseq &cbs, size_t line_len, CNcbiOstream &out, bool believe_query, bool html, bool tabular=false, const string &rid=kEmptyStr)

Print out blast query info.

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

static list< CRef< objects::CSeq_align_set > > SortOneSeqalignForSortableFormat(const objects::CSeq_align_set &source, bool nuc_to_nuc_translation, int hit_sort, int hsp_sort)

static void GetAsciiProteinMatrix(const char *matrix_name, CNcbiMatrix< int > &retval)

Retrieve a scoring matrix for the provided matrix 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 x_AcknowledgeBlastSequence(const objects::CBioseq &cbs, size_t line_len, CNcbiOstream &out, bool believe_query, bool html, const string &label, bool tabular, const string &rid)

static void PrintDbReport(const vector< SDbInfo > &dbinfo_list, size_t line_length, CNcbiOstream &out, bool top=false)

Print out blast database information.

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 string GetSeqDescrString(const objects::CBioseq &cbs)

Returns a full description for a Bioseq, concatenating all available titles.

@ eAddEOLAtLineEnd

add EOL at the beginning of the string

@ eAddEOLAtLineStart

add spaces at the end of the string

@ eSpacePosAtLineEnd

add spaces at the begining of the string

static list< TGi > StringGiToNumGiList(list< string > &use_this_seq)

Convert if string gi list to TGi list.

static string AddSpaces(string paramVal, size_t maxParamLength, int spacesFormatFlag=eSpacePosToCenter)

Calculate the number of spaces and add them to paramVal.

static CRef< objects::CSeq_align_set > FilterSeqalignByPercentIdent(objects::CSeq_align_set &source_aln, double percentIdentLow, double percentIdentHigh)

function for Filtering seqalign by percent identity

static bool RemoveSeqsOfAccessionTypeFromSeqInUse(list< string > &use_this_seq, objects::CSeq_id::EAccessionInfo accesionType)

function to remove sequences of accesionType from use_this_seq list

static bool SortHitByMasterStartAscending(CRef< objects::CSeq_align_set > &info1, CRef< objects::CSeq_align_set > &info2)

sorting function for sorting a list of seqalign set by ascending mater start position

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 map< string, CRef< objects::CSeq_align_set > > HspListToHitMap(vector< string > seqIdList, const objects::CSeq_align_set &source)

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

Get sequence id with no database source (bare accession)

static string GetGnlID(const objects::CDbtag &dtg)

Return ID for GNL label.

static bool m_geturl_debug_flag

static void SortHit(list< CRef< objects::CSeq_align_set > > &seqalign_hit_list, bool do_translation, objects::CScope &scope, int sort_method, ILinkoutDB *linkoutdb, const string &mv_build_name)

actual sorting function for SortHitByMolecularType

static void FillScanModeBlastDbInfo(vector< SDbInfo > &retval, bool is_protein, int numSeqs, Int8 numLetters, string &tag)

Fills one BLAST dbinfo structure.

static bool SortHitByTotalScoreDescending(CRef< objects::CSeq_align_set > const &info1, CRef< objects::CSeq_align_set > const &info2)

return the comparison result: 1st >= 2nd => true, false otherwise

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

Create URL for seqid that goes to entrez or trace.

static bool SortHspBySubjectStartAscending(const CRef< objects::CSeq_align > &info1, const CRef< objects::CSeq_align > &info2)

static CAlignFormatUtil::DbType GetDbType(const objects::CSeq_align_set &actual_aln_list, objects::CScope &scope)

Set the database as gi type.

static void PruneSeqalignAll(const objects::CSeq_align_set &source_aln, objects::CSeq_align_set &new_aln, unsigned int number)

Fill new alignset containing the specified number of alignments plus the rest of alignments for the l...

static void PrintTildeSepLines(string str, size_t line_len, CNcbiOstream &out)

Print out misc information separated by "~".

static string BuildUserUrl(const objects::CBioseq::TId &ids, TTaxId taxid, string user_url, string database, bool db_is_na, string rid, int query_number, bool for_alignment)

return the custom url (such as mapview)

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

Replace template tags by real data.

static CAlignFormatUtil::SSeqAlignSetCalcParams * GetSeqAlignCalcParams(const objects::CSeq_align &aln)

static string GetURLFromRegistry(const string url_name, int index=-1)

retrieve URL from .ncbirc file combining host/port and format strings values.

static bool IsGiList(list< string > &use_this_seq)

Check if use_this_seq conatins gi list.

static double GetSeqAlignSetCalcPercentIdent(const objects::CSeq_align_set &aln, bool do_translation)

static string GetGraphiscLink(SSeqURLInfo *seqUrlInfo, bool hspRange=false)

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 void PrintKAParameters(double lambda, double k, double h, size_t line_len, CNcbiOstream &out, bool gapped, const Blast_GumbelBlk *gbp=NULL)

Print out kappa, lamda blast parameters.

static CRef< objects::CSeq_align > CreateDensegFromDendiag(const objects::CSeq_align &aln)

Create denseseg representation for densediag seqalign.

static list< string > GetCustomLinksList(SSeqURLInfo *seqUrlInfo, const objects::CSeq_id &id, objects::CScope &scope, int customLinkTypes=eLinkTypeDefault)

Create the list of string links for seqid that go.

static string GetURLDefault(const string url_name, int index=-1)

settings are not complete.

static CRef< objects::CSeq_align_set > FilterSeqalignByEval(objects::CSeq_align_set &source_aln, double evalueLow, double evalueHigh)

function for Filtering seqalign by expect value

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

Create URL showing aligned regions info.

static bool GetTextSeqID(const list< CRef< objects::CSeq_id > > &ids, string *textSeqID=NULL)

static void GetBlastDbInfo(vector< SDbInfo > &retval, const string &blastdb_names, bool is_protein, int dbfilt_algorithm, bool is_remote=false)

Retrieve BLAST database information for presentation in BLAST report.

static void GetUseThisSequence(const objects::CSeq_align &aln, list< TGi > &use_this_gi)

Extract use_this_gi info from blast alingment.

static bool SortHitByPercentIdentityDescendingEx(const CRef< objects::CSeq_align_set > &info1, const CRef< objects::CSeq_align_set > &info2)

sorting function for sorting a list of seqalign set by descending identity

static void ExtractSeqAlignForSeqList(CRef< objects::CSeq_align_set > &all_aln_set, string alignSeqList)

extract seq_align_set coreesponding to seqid list

static int GetPercentMatch(int numerator, int denominator)

function for calculating percent match for an alignment.

static string GetSeqIdString(const objects::CBioseq &cbs, bool believe_local_id=true)

Returns a full '|'-delimited Seq-id string for a Bioseq.

static bool MatchSeqInUseThisSeqList(list< string > &use_this_seq, string textSeqIDToMatch)

static list< string > GetSeqLinksList(SSeqURLInfo *seqUrlInfo, bool hspRange=false)

static CRef< objects::CSeq_align_set > SortSeqalignForSortableFormat(CCgiContext &ctx, objects::CScope &scope, objects::CSeq_align_set &aln_set, bool nuc_to_nuc_translation, int db_order, int hit_order, int hsp_order, ILinkoutDB *linkoutdb, const string &mv_build_name)

static double GetPercentIdentity(const objects::CSeq_align &aln, objects::CScope &scope, bool do_translation)

calculate the percent identity for a seqalign

static void ExtractSeqalignSetFromDiscSegs(objects::CSeq_align_set &target, const objects::CSeq_align_set &source)

If a Seq-align-set contains Seq-aligns with discontinuous type segments, extract the underlying Seq-a...

static bool IsWGSPattern(string &wgsAccession)

Check if accession is WGS.

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

static bool SortHitByScoreDescending(const CRef< objects::CSeq_align_set > &info1, const CRef< objects::CSeq_align_set > &info2)

static CRef< objects::CSeq_align_set > FilterSeqalignByScoreParams(objects::CSeq_align_set &source_aln, double evalueLow, double evalueHigh, double percentIdentLow, double percentIdentHigh)

function for Filtering seqalign by expect value and percent identity

static void GetAlignLengths(objects::CAlnVec &salv, int &align_length, int &num_gaps, int &num_gap_opens)

Count alignment length, number of gap openings and total number of gaps in a single alignment.

static string BuildSRAUrl(const objects::CBioseq::TId &ids, string user_url)

return the SRA (Short Read Archive) URL

static bool SortHspByMasterStartAscending(const CRef< objects::CSeq_align > &info1, const CRef< objects::CSeq_align > &info2)

sorting function for sorting a list of seqalign by ascending mater start position

static int SetCustomLinksTypes(SSeqURLInfo *seqUrlInfo, int customLinkTypesInp)

Create info indicating what kind of links to display.

static int GetMasterCoverage(const objects::CSeq_align_set &alnset)

static unique_ptr< CNcbiRegistry > m_Reg

static int GetFrame(int start, objects::ENa_strand strand, const objects::CBioseq_Handle &handle)

return the frame for a given strand Note that start is zero bases.

static void GetBdlLinkoutInfo(const list< CRef< objects::CBlast_def_line > > &bdl, map< int, vector< objects::CBioseq::TId > > &linkout_map, ILinkoutDB *linkoutdb, const string &mv_build_name)

Create map that holds all linkouts for the list of blast deflines and corresponding seqIDs.

static bool SortHspByPercentIdentityDescending(const CRef< objects::CSeq_align > &info1, const CRef< objects::CSeq_align > &info2)

sorting function for sorting a list of seqalign by descending identity

static CRef< objects::CSeq_align_set > HitListToHspList(list< CRef< objects::CSeq_align_set > > &source)

extract all nested hsp's into a list

static string GetTitle(const objects::CBioseq_Handle &bh)

static TTaxId GetTaxidForSeqid(const objects::CSeq_id &id, objects::CScope &scope)

return the tax id for a seqid

static void AddSpace(CNcbiOstream &out, size_t number)

Add the specified white space.

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

Create URL to FASTA info.

static list< string > GetGiLinksList(SSeqURLInfo *seqUrlInfo, bool hspRange=false)

static void AcknowledgeBlastSubject(const objects::CBioseq &cbs, size_t line_len, CNcbiOstream &out, bool believe_query, bool html, bool tabular=false)

Print out blast subject info.

static TGi GetGiForSeqIdList(const list< CRef< objects::CSeq_id > > &ids)

return gi from id list

static void SplitSeqalignByMolecularType(vector< CRef< objects::CSeq_align_set > > &target, int sort_method, const objects::CSeq_align_set &source, objects::CScope &scope, ILinkoutDB *linkoutdb, const string &mv_build_name)

static bool SortHitByMasterCoverageDescending(CRef< objects::CSeq_align_set > const &info1, CRef< objects::CSeq_align_set > const &info2)

static void BlastPrintError(list< SBlastError > &error_return, bool error_post, CNcbiOstream &out)

Output blast errors.

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 void HspListToHitList(list< CRef< objects::CSeq_align_set > > &target, const objects::CSeq_align_set &source)

group hsp's with the same id togeter

static void SortHitByPercentIdentityDescending(list< CRef< objects::CSeq_align_set > > &seqalign_hit_list, bool do_translation)

sort a list of seqalign set by alignment identity

static string MapProtocol(string url_link)

static string GetFullIDLink(SSeqURLInfo *seqUrlInfo, const objects::CBioseq::TId *ids)

static bool SortHspByScoreDescending(const CRef< objects::CSeq_align > &info1, const CRef< objects::CSeq_align > &info2)

static CRef< objects::CSeq_align_set > LimitSeqalignByHsps(objects::CSeq_align_set &source_aln, int maxAligns, int maxHsps)

function for Limitting seqalign by hsps number (by default results are not cut off within the query)

static CRef< objects::CSeq_align_set > ExtractQuerySeqAlign(CRef< objects::CSeq_align_set > &source_aln, int queryNumber)

function for extracting seqalign for the query

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)

static void x_WrapOutputLine(string str, size_t line_len, CNcbiOstream &out, bool html=false)

Wrap a string to specified length.

static unsigned int GetSubjectsNumber(const objects::CSeq_align_set &source_aln, unsigned int num)

Calculate number of subject sequnces in alignment limitted by num.

static CRange< TSeqPos > GetSeqAlignCoverageParams(const objects::CSeq_align_set &alnset, int *masterCoverage, bool *flip)

TDim GetNumRows(void) const

TSeqPos GetAlnStop(TNumseg seg) const

TSignedRange GetSeqAlnRange(TNumrow row) const

CRef< CAlnChunkVec > GetAlnChunks(TNumrow row, const TSignedRange &range, TGetChunkFlags flags=fAlnSegsOnly) const

API for Remote Blast Services.

static CNcbiApplication * Instance(void)

Singleton method.

void Resize(size_t i, size_t j, T val=T())

resize this matrix, filling the empty cells with a known value

TThisType & Subtract(const TRange &r)

position_type GetCoveredLength(void) const

Returns total length covered by ranges in this collection, i.e.

Uint8 GetTotalLength() const

Returns the sum of the lengths of all available sequences.

const string & GetDBNameList() const

Get list of database names.

void GetMaskAlgorithmDetails(int algorithm_id, objects::EBlast_filter_program &program, string &program_name, string &algo_opts)

Get information about one type of masking available here.

string GetTitle() const

Returns the database title.

int GetNumSeqs() const

Returns the number of sequences available.

string GetDate() const

Returns the construction date of the database.

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.

Tdata::size_type Size() const

CRef< CSeq_align > CreateTranslatedDensegFromNADenseg(void) const

Create a Dense-seg with widths from Dense-seg of nucleotides Used by AlnMgr to handle translated nucl...

CRef< CSeq_align > CreateDensegFromStdseg(SSeqIdChooser *SeqIdChooser=0) const

---------------------------------------------------------------------------- PRE : the Seq-align has ...

TSeqPos GetSeqStop(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

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

TSeqPos GetSeqStart(TDim row) const

@Seq_descr.hpp User-defined methods of the data storage class.

Class to sort by linkout bit.

string m_MapViewerBuildName

CSortHitByMolecularTypeEx(ILinkoutDB *linkoutdb, const string &mv_build_name)

bool operator()(const CRef< CSeq_align_set > &info1, const CRef< CSeq_align_set > &info2)

virtual int GetLinkout(TGi gi, const string &mv_build_name)=0

Retrieve the Linkout for a given GI.

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

const_iterator end() const

const_iterator begin() const

const_iterator begin() const

const_iterator end() const

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

main entry point for tests

bool Empty(const CNcbiOstrstream &src)

static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)

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

CRef< objects::CBlast4_database_info > GetDatabaseInfo(CRef< objects::CBlast4_database > blastdb)

Retrieve detailed information for one BLAST database If information about multiple databases is neede...

#define GI_FROM(T, value)

const CNcbiRegistry & GetConfig(void) const

Get the application's cached configuration parameters (read-only).

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

int TSignedSeqPos

Type for signed sequence position.

#define TAX_ID_TO(T, tax_id)

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

TCgiEntries::iterator TCgiEntriesI

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

#define ERR_POST_EX(err_code, err_subcode, message)

Error posting with error codes.

@ eDiag_Info

Informational message.

@ eDiag_Fatal

Fatal error – guarantees exit(or abort)

#define NCBI_THROW(exception_class, err_code, message)

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

const string & GetMsg(void) const

Get message string.

virtual bool Exists(void) const

Check existence of file.

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.

static EAccessionInfo IdentifyAccession(const CTempString &accession, TParseFlags flags=fParse_AnyRaw)

Deduces information from a bare accession a la WHICH_db_accession; may report false negatives on prop...

string GetSeqIdString(bool with_version=false) const

Return seqid string with optional version for text seqid type.

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

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

CConstRef< CSeq_id > GetSeq_idByType(const container &ids, CSeq_id::E_Choice choice)

Search the container of CRef<CSeq_id> for the id of given type.

EAccessionInfo

For IdentifyAccession (below)

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

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

const CTextseq_id * GetTextseq_Id(void) const

Return embedded CTextseq_id, if any.

CConstRef< CSeq_id > FindTextseq_id(const container &ids)

Return text seq-id from id list if exists, return 0 otherwise.

@ eContent

Untagged human-readable accession or the like.

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

TSeqPos GetBioseqLength(void) const

bool Empty(void) const THROWS_NONE

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

void Reset(void)

Reset reference object.

bool Empty(void) const THROWS_NONE

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

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

TThisType CombinationWith(const TThisType &r) const

bool IntersectingWith(const TThisType &r) const

TThisType & Set(position_type from, position_type to)

virtual const string & Get(const string &section, const string &name, TFlags flags=0) const

Get the parameter value.

virtual bool HasEntry(const string &section, const string &name=kEmptyStr, TFlags flags=0) const

bool Empty(TFlags flags=fAllLayers) const

Verify if Registry is empty.

#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 Int8ToString(Int8 value, TNumToStringFlags flags=0, int base=10)

Convert Int8 to string.

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

Truncate whitespace in a string.

static int CompareNocase(const CTempString s1, SIZE_TYPE pos, SIZE_TYPE n, const char *s2)

Case-insensitive compare of a substring with another string.

static Int8 StringToInt8(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to Int8.

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 double StringToDouble(const CTempStringEx str, TStringToNumFlags flags=0)

Convert string to double.

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 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 bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

static string JavaScriptEncode(const CTempString str)

Encode a string for JavaScript.

static bool SplitInTwo(const CTempString str, const CTempString delim, string &str1, string &str2, TSplitFlags flags=0)

Split a string into two pieces using the specified delimiters.

int TWrapFlags

Bitwise OR of "EWrapFlags".

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 string & ToUpper(string &str)

Convert string to upper case – string& version.

static string URLEncode(const CTempString str, EUrlEncode flag=eUrlEnc_SkipMarkChars)

URL-encode string.

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

Truncate whitespace in a string.

static string & ToLower(string &str)

Convert string to lower case – string& version.

@ fConvErr_NoThrow

Do not throw an exception on error.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

@ fWrap_HTMLPre

Wrap as pre-formatted HTML?

@ fWrap_FlatFile

Wrap for flat file use.

@ fWithCommas

Use commas as thousands separator.

string AsString(const CTimeFormat &format=kEmptyStr, TSeconds out_tz=eCurrentTimeZone) const

Transform time to string.

@ fFormat_Simple

Use single characters as format symbols.

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

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

static const char label[]

@ eBlast4_residue_type_nucleotide

@ eBlast4_residue_type_protein

const Tdata & Get(void) const

Get the member data.

void SetFrom(TFrom value)

Assign a value to From data member.

TTo GetTo(void) const

Get the To member data.

TFrom GetFrom(void) const

Get the From member data.

void SetTo(TTo value)

Assign a value to To data member.

bool IsSetData(void) const

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

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 TTag & GetTag(void) const

Get the Tag member data.

bool IsStrs(void) const

Check if variant Strs is selected.

const TStrs & GetStrs(void) const

Get the variant data.

bool IsId(void) const

Check if variant Id is selected.

const TData & GetData(void) const

Get the Data member data.

bool CanGetDb(void) const

Check if it is safe to call GetDb method.

bool CanGetTag(void) const

Check if it is safe to call GetTag method.

const TDb & GetDb(void) const

Get the Db member data.

bool IsSetLabel(void) const

field label Check if a value has been assigned to Label data member.

const TStr & GetStr(void) const

Get the variant data.

const TData & GetData(void) const

Get the Data member data.

const TLabel & GetLabel(void) const

Get the Label member data.

const TType & GetType(void) const

Get the Type member data.

bool IsSetData(void) const

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

vector< CStringUTF8 > TStrs

vector< CRef< CUser_field > > TData

TId GetId(void) const

Get the variant data.

const TDenseg & GetDenseg(void) const

Get the variant data.

Tdata & Set(void)

Assign a value to data member.

TScore & SetScore(void)

Assign a value to Score data member.

TLens & SetLens(void)

Assign a value to Lens data member.

bool IsSetBounds(void) const

regions of sequence over which align was computed Check if a value has been assigned to Bounds data m...

E_Choice Which(void) const

Which variant is currently selected.

TDim GetDim(void) const

Get the Dim member data.

void SetSegs(TSegs &value)

Assign a value to Segs data member.

TScores & SetScores(void)

Assign a value to Scores data member.

void SetDim(TDim value)

Assign a value to Dim data member.

void SetDim(TDim value)

Assign a value to Dim data member.

vector< TSeqPos > TStarts

void SetType(TType value)

Assign a value to Type data member.

bool IsDendiag(void) const

Check if variant Dendiag is selected.

bool IsSetType(void) const

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

const TStd & GetStd(void) const

Get the variant data.

TStarts & SetStarts(void)

Assign a value to Starts data member.

TStrands & SetStrands(void)

Assign a value to Strands data member.

bool CanGetExt(void) const

Check if it is safe to call GetExt method.

const TDendiag & GetDendiag(void) const

Get the variant data.

bool IsStd(void) const

Check if variant Std is selected.

vector< ENa_strand > TStrands

bool IsDisc(void) const

Check if variant Disc is selected.

vector< CRef< CScore > > TScores

TType GetType(void) const

Get the Type member data.

bool IsSetDim(void) const

dimensionality Check if a value has been assigned to Dim data member.

void SetNumseg(TNumseg value)

Assign a value to Numseg data member.

const TExt & GetExt(void) const

Get the Ext member data.

bool IsSetScore(void) const

for whole alignment Check if a value has been assigned to Score data member.

list< CRef< CSeq_align > > Tdata

TIds & SetIds(void)

Assign a value to Ids data member.

const TScore & GetScore(void) const

Get the Score member data.

TBounds & SetBounds(void)

Assign a value to Bounds data member.

const TScores & GetScores(void) const

Get the Scores member data.

const TDisc & GetDisc(void) const

Get the variant data.

list< CRef< CDense_diag > > TDendiag

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

const TBounds & GetBounds(void) const

Get the Bounds member data.

ENa_strand

strand of nucleic acid

bool IsGeneral(void) const

Check if variant General is selected.

E_Choice Which(void) const

Which variant is currently selected.

TGi GetGi(void) const

Get the variant data.

E_Choice

Choice variants.

const TGeneral & GetGeneral(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

list< CRef< CSeqdesc > > Tdata

const TInst & GetInst(void) const

Get the Inst member data.

const TTitle & GetTitle(void) const

Get the variant data.

bool CanGetLength(void) const

Check if it is safe to call GetLength method.

const TId & GetId(void) const

Get the Id member data.

const Tdata & Get(void) const

Get the member data.

bool IsSetInst(void) const

the sequence data Check if a value has been assigned to Inst data member.

TLength GetLength(void) const

Get the Length member data.

list< CRef< CSeq_id > > TId

bool IsSetDescr(void) const

descriptors Check if a value has been assigned to Descr data member.

const TDescr & GetDescr(void) const

Get the Descr member data.

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Title

a title for this sequence

char * dbname(DBPROCESS *dbproc)

Get name of current database.

unsigned int

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

HTML library helper classes and functions.

use only n Cassandra database for the lookups</td > n</tr > n< tr > n< td > yes</td > n< td > do not use tables BIOSEQ_INFO and BLOB_PROP in the Cassandra database

std::false_type tagStrNocase

constexpr bool empty(list< Ts... >) noexcept

const string version

version string

double value_type

The numeric datatype used by the parser.

Magic spell ;-) needed for some weird compilers... very empiric.

const GenericPointer< typename T::ValueType > T2 value

const CharType(& source)[N]

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

#define ASSERT

macro for assert.

Defines NCBI C++ diagnostic APIs, classes, and macros.

Defines classes: CDirEntry, CFile, CDir, CSymLink, CMemoryFile, CFileUtil, CFileLock,...

Portable reference counted smart and weak pointers using CWeakRef, CRef, CObject and CObjectEx.

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_)

double lambda(size_t dimMatrix_, const Int4 *const *scoreMatrix_, const double *q_)

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 PCRE2_SIZE * offsets

const SNCBIPackedScoreMatrix * NCBISM_GetStandardMatrix(const char *name)

void NCBISM_Unpack(const SNCBIPackedScoreMatrix *psm, SNCBIFullScoreMatrix *fsm)

Expand a packed score matrix into an unpacked one, which callers can proceed to index directly by sta...

Defines BLAST database access classes.

Defines exception class and several constants for SeqDB.

void SeqDB_SplitQuoted(const string &dbname, vector< CSeqDB_Substring > &dbs, bool keep_quote=false)

Combine and quote list of database names.

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

#define row(bind, expected)

Structure to hold the Gumbel parameters (for FSC).

double Alpha_un

Ungapped alpha.

double Sigma

cov(L) = sigma y + tau

double a

avg(L) = a y + b

double Alpha

var(L) = alpha y + beta

string filt_algorithm_name

Filtering algorithm ID used in BLAST search.

string filt_algorithm_options

Filtering algorithm options used in BLAST search.

void Init(string rid_in, string cdd_rid_in, string entrez_term_in, bool is_na_in, string database_in, int query_number_in, string user_url_in, string preComputedResID_in, string linkoutOrder_in, bool structure_linkout_as_group_in=false, bool for_alignment_in=true)

CRange< TSeqPos > subjRange

Structure that holds information for all hits of one subject in Seq Align Set.

CRange< TSeqPos > subjRange

int master_covered_length

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

string user_url

user url TOOL_URL from .ncbirc

string blastType

blast type refer to blobj->adm->trace->created_by

CRange< TSeqPos > seqRange

sequence range

string database

name of the database

string defline

sequence defline

bool addCssInfo

bool indicating that css info should be added

int queryNumber

the query number

string accession

accession

string segs

string containing align segments in the the following format seg1Start-seg1End,seg2Start-seg2End

int blast_rank

index of the current alignment

string seqUrl

sequence URL created

bool isAlignLink

bool indicating if link is in alignment section

bool isDbNa

bool indicating if the database is nucleotide or not

string resourcesUrl

URL(s) to other resources from .ncbirc.

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4