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

*

[]={

,

,

};

*

=

;

*

=

;

* k_GetSeqSubmitForm[] = {

,

* k_GetSeqSelectForm =

;

* k_GetTreeViewForm =

;

list <FeatureInfo*>* external_feature,

* matrix_name

)

: m_SeqalignSetRef(&seqalign),

m_Seqloc(mask_seqloc),

m_QueryFeature(external_feature),

m_UseLongSeqIds(

)

m_SeqLocColor = eBlack;

m_CanRetrieveSeq =

;

m_NumAlignToShow = 1000000;

m_MidLineStyle = eBar;

m_ConfigFile =

;

m_DynamicFeature =

;

m_MasterGeneticCode = 1;

m_SlaveGeneticCode = 1;

m_AlignTemplates =

;

m_DomainInfo =

;

m_SeqPropertyLabel.reset(

vector<string>);

m_TranslatedFrameForLocalSeq = eFirst;

m_ResultPositionIndex = -1;

m_currAlignSeqListIndex = 1;

m_QueryAnchoredSetIndex = -1;

(

.GetData().empty()) {

( !

.GetData().empty() )

m_Matrix =

*[

.GetRows()];

(

= 0;

<

.GetRows(); ++

) {

m_Matrix[

] =

[

.GetCols()];

(

= 0;

<

.GetRows(); ++

) {

(

j = 0; j <

.GetCols(); j++) {

m_Matrix[

][j] =

(

, j);

aln_stop = (

)

->GetAlnStop();

master_strand =

->StrandSign(0);

slave_strand =

->StrandSign(1);

alignParams = alignInfo;

alignParams =

(alignParams,

,(master_strand==1 ?

:

)+ (

)

+ (slave_strand==1?

:

));

(master_frame != 0 && slave_frame != 0) {

+ (

)

+((slave_frame > 0) ?

:

) +

(slave_frame));

}

(master_frame != 0){

}

(slave_frame != 0){

gap,

master_strand,

slave_strand,

master_frame,

slave_frame,

aln_is_prot)

<<

<<

<<

<<(aln_stop+1)<<

<<identity<<

<<

;

<<

<<gap<<

<<(aln_stop+1)

<<

<<(master_strand==1 ?

:

)

<<

<<(slave_strand==1?

:

)<<

;

(master_frame != 0 && slave_frame != 0) {

<<

<< ((master_frame > 0) ?

:

)

<< master_frame <<

<<((slave_frame > 0) ?

:

)

<< slave_frame<<

;

}

(master_frame != 0){

<<

<< ((master_frame > 0) ?

:

)

<< master_frame <<

;

}

(slave_frame != 0){

<<

<< ((slave_frame > 0) ?

:

)

<< slave_frame <<

;

line_len = 60;

do_wrap =

;

length = (

)

.size();

(length > line_len) {

(

= 0;

< length;

++){

(

> 0 &&

% line_len == 0){

(do_wrap &&

((

)

[

])){

isStyled =

;

(startStyledOutput || (!styledSeqStr.empty() && !stopStyledOutput)){

styledSeqStr += seq[currIndex];

(!styledSeqStr.empty() && (stopStyledOutput || currIndex == (

)seq.size() - 1) ) {

(

= 0;

< (

)seq.size();

++){

(!isStyled)

<< seq[

];

frame = (start % 3) + 1;

*(ss.

().front()), scope);

& raw_cdr_product,

frame_adj)

concat_exon(total_coding_len,

);

coding_start_base = total_coding_len - 1 - (frame -1) - frame_adj;

num_base = total_coding_len - 1;

coding_start_base = 0;

coding_start_base += frame - 1 + frame_adj;

(

= 0;

< iter->GetLength();

++){

((

)num_base >= coding_start_base){

(num_coding_base % 3 == 2){

(num_coding_base / 3 < raw_cdr_product.size()){

concat_exon[num_base]

= raw_cdr_product[num_coding_base / 3];

(

= 0;

< iter->GetLength() &&

num_base >= 0;

++){

((

)num_base <= coding_start_base){

(num_coding_base % 3 == 2){

(num_coding_base / 3 <

raw_cdr_product.size() &&

coding_start_base >= num_coding_base){

concat_exon[num_base]

= raw_cdr_product[num_coding_base / 3];

list<CSeq_loc_CI::TRange>& slave_feat_range,

trans_frame += frame_adj;

is_first_in_range =

;

list<CSeq_loc_CI::TRange> acutal_slave_feat_range = slave_feat_range;

(list<CSeq_loc_CI::TRange>, iter_temp,

acutal_slave_feat_range){

IntersectionWith(*iter_temp);

(!actual_feat_seq_range.

()){

slave_aln_from = 0, slave_aln_to = 0;

curr_exon_leading_len = 0;

(is_first_in_range) {

curr_exon_leading_len

= actual_feat_seq_range.

() - iter_temp->GetFrom();

curr_exon_leading_len

= iter_temp->GetTo() - actual_feat_seq_range.

();

is_first_in_range =

;

frame_offset = (3 - (prev_exon_len + curr_exon_leading_len)%3

+ (trans_frame - 1)) % 3;

actual_feat_seq_range.

() +

master_feat_range.push_back(master_range);

prev_exon_len += iter_temp->GetLength();

frame_adj,

mix_loc)

GetBioseqLength(), raw_cdr_product);

from = iter->GetFrom();

(genetic_code > 0) {

ce->SetId(genetic_code);

gc.

().push_back(ce);

raw_cdr_product, &gc);

raw_cdr_product;

length_per_line,

feat_aln_start_totalexon,

list<TSeqPos>& start)

actual_line_len = 0;

aln_len = line.size();

previous_num_letter = 0;

(

= 0;

<= feat_aln_start_totalexon;

++){

pos = concat_exon.size() -1 -

;

(pos >= 0 &&

((

) concat_exon[pos])){

previous_num_letter ++;

(

((

) concat_exon[

])){

previous_num_letter ++;

(

= 0;

< aln_len;

+= actual_line_len){

(aln_len -

< length_per_line) {

actual_line_len = aln_len -

;

actual_line_len = length_per_line;

has_intron =

;

(

j =

; j < actual_line_len +

; j ++){

(

((

) line[j])){

start.push_back(previous_num_letter - prev_num);

start.push_back(previous_num_letter + prev_num);

start.push_back(previous_num_letter + prev_num);

start.push_back(previous_num_letter - prev_num);

}

(has_intron) {

list<ENa_strand>& feat_seq_strand,

seq_feat->

(*feat_data);

feat_seq_strand.front())));

.push_back(seq_feat);

feat_seq_strand.pop_front();

anot_list.push_back(anot);

color_feat_mismatch,

((

)feat_line.size() > start){

actual_feat = feat_line.substr(start,

);

actual_reference_feat = reference_feat_line.substr(start,

);

(color_feat_mismatch

styledSequenceStr;

(

= 0;

< (

)actual_feat.size() &&

< (

)actual_reference_feat.size();

++){

styledOutput = actual_feat[

] != actual_reference_feat[

] &&

stopStyledOutput = (actual_feat[

] == actual_reference_feat[

]) && actual_feat[

] !=

;

(!isStyled)

<< actual_feat[

];

& master_feat_str,

id_length = alnRoInfo->

;

substr(aln_start, line_length)) &&

<<(*iter)->feature->feature_id;

((*iter)->feature_start.empty()){

-(*iter)->feature->feature_id.size());

feat_start = (*iter)->feature_start.front();

-(*iter)->feature->feature_id.size());

-(*iter)->feature->feature_id.size());

(*iter)->feature_start.pop_front();

color_cds_mismatch =

;

color_cds_mismatch =

;

color_cds_mismatch =

;

(*iter)->feature_string,

color_cds_mismatch, aln_start,

master_feat_str = (*iter)->feature_string;

seqUrlInfo->

= sequence::CDeflineGenerator().GenerateDefline(bsp_handle);

idString =

->GetSeqId(1).GetSeqIdString();

(bdl_list.size() > 0) {

&

= sequence_masks->front()->GetSeqId();

first_encoding_base,

align_length,

& translation,

& sequence,

feat(align_length,

);

(

= first_encoding_base;

< (

) feat.size() &&

j < (

)translation.size();

++) {

(sequence[

] != gap_char) {

(num_base%3 == 2) {

feat[

] = translation[j];

vector<string>& sequence)

{

(

->IsPositiveStrand(0) &&

->IsPositiveStrand(1)) {

non_gap_aln_pos = 0;

num_consecutive = 0;

(

=0;

< (

) sequence[0].

();

++) {

(sequence[0][

] != gap_char &&

sequence[1][

] != gap_char) {

(num_consecutive >=3) {

non_gap_aln_pos =

- 2;

num_consecutive = 0;

master_frame_extra =

->GetSeqPosFromAlnPos(0, non_gap_aln_pos)%3;

master_frame_start;

master_frame_start =

->GetSeqPosFromAlnPos(0, non_gap_aln_pos) +

->GetSeqStop(0)));

master_translation;

master_translation);

master_first_encoding_base =

->GetAlnPosFromSeqPos(0, master_frame_start);

master_first_encoding_base,

->GetAlnStop() + 1,

sequence[0], gap_char);

->GetAlnStop(),

,

, master_feat, -1);

retval[0].push_back(master_featInfo);

subject_frame_start =

->GetSeqPosFromSeqPos(1, 0, master_frame_start);

subject_translation;

subject_translation);

subject_first_encoding_base =

->GetAlnPosFromSeqPos(1, subject_frame_start);

subject_first_encoding_base,

->GetAlnStop() + 1,

subject_translation,

sequence[1], gap_char);

->GetAlnStop(),

,

, subject_feat, -1);

retval[1].push_back(subject_featInfo);

& sequence ,

gap_char,

&

,

& align_length){

end = (

)sequence.size() - 1;

(

= 0;

< (

)sequence.size();

++){

(sequence[

] != gap_char){

(

= (

)sequence.size() - 1;

> 0;

--){

(sequence[

] != gap_char){

(

= start;

<= end &&

< (

)sequence.size() &&

< (

)sequence_standard.size();

++){

(sequence[

] == gap_char && sequence_standard[

] == gap_char) {

(sequence_standard[

]==sequence[

]){

maxIdLen=0, maxStartLen=0;

rowNum=

->GetNumRows();

->SetAnchor(0);

->SetGapChar(

);

->SetEndChar(

);

->SetEndChar(

);

vector<string> sequence(rowNum);

vector<CAlnMap::TSeqPosList> seqStarts(rowNum);

vector<CAlnMap::TSeqPosList> seqStops(rowNum);

vector<CAlnMap::TSeqPosList> insertStart(rowNum);

vector<CAlnMap::TSeqPosList> insertAlnStart(rowNum);

vector<CAlnMap::TSeqPosList> insertLength(rowNum);

vector<string> seqidArray(rowNum);

vector<CAlnMap::TSignedRange> rowRng(rowNum);

vector<int> frame(rowNum);

vector<TTaxId> taxid(rowNum);

max_feature_num = 0;

vector<int>

(rowNum-1);

vector<double> percent_ident(rowNum-1);

vector<int> align_length(rowNum-1);

vector<string> align_stats(rowNum-1);

vector<string> seq_property_label(rowNum-1);

max_align_stats = 0;

max_seq_property_label = 0;

vector<TSAlnFeatureInfoList> bioseqFeature;

((

)bioseqFeature.size() == rowNum);

vector<TSAlnSeqlocInfoList> masked_regions(rowNum);

(

= 1;

< rowNum;

++) {

list<list<CRange<TSeqPos> > > feat_seq_range;

list<ENa_strand> feat_seq_strand;

(

=0;

<rowNum;

++) {

type_temp ==

|| type_temp ==

){

rowRng[

] =

->GetSeqAlnRange(

);

frame[

] = (

->GetWidth(

) == 3 ?

->IsPositiveStrand(

) ?

->GetWholeAlnSeqString(

, sequence[

], &insertAlnStart[

],

&insertStart[

], &insertLength[

],

(align_length[

-1] > 0 ){

percent_ident[

-1] = ((double)

[

-1])/align_length[

-1]*100;

percent_ident[

- 1] = 0;

align_stats[

-1] =

;

max_align_stats =

(max_align_stats,

(

)align_stats[

-1].

());

seq_property_label[

-1] = (*m_SeqPropertyLabel)[

];

max_seq_property_label =

(max_seq_property_label,

(

)seq_property_label[

-1].

());

&&

->GetWidth(

) != 3

GetBioseqCore()->

());

feat_seq_range, feat_seq_strand,

== 1 && !(master_gi >

) ?

:

);

(!(feat_seq_range.empty()) &&

== 1) {

->GetBioseqHandle(0));

custom_genetic_code = -1;

((*iter_feat)->genetic_code > 0) {

custom_genetic_code = (*iter_feat)->genetic_code;

list<list<CRange<TSeqPos> > > temp_holder;

(bioseqFeature[0], custom_genetic_code, *master_scope_with_feat,

temp_holder, feat_seq_strand,

);

feat_seq_range, feat_seq_strand,

);

maxIdLen=max<size_t>(seqidArray[

].

(), maxIdLen);

maxCood=max<size_t>(

->GetSeqStart(

),

->GetSeqStop(

));

(

= 0;

< rowNum;

++){

num_feature = 0;

maxIdLen=max<size_t>((*iter)->feature->feature_id.size(), maxIdLen);

(num_feature > max_feature_num){

max_feature_num = num_feature;

alnRoInfo->

= rowRng;

alnRoInfo->

= frame;

alnRoInfo->

= taxid;

alnRoInfo->

= rowNum;

aln_stop=

->GetAlnStop();

rowNum = alnRoInfo->

;

vector<int> prev_stop(rowNum);

->GetWidth(0) != 3 &&

->GetWidth(1) != 3) ?

:

;

->GetWidth(0) != 3 &&

->GetWidth(1) != 3) ?

:

;

formattedString;

formattedString += rowdata;

formattedString;

aln_stop=

->GetAlnStop();

rowNum = alnRoInfo->

;

vector<int> prev_stop(rowNum);

->GetWidth(0) != 3 &&

->GetWidth(1) != 3) ?

:

;

->GetWidth(0) != 3 &&

->GetWidth(1) != 3) ?

:

;

rowSetsCount = 1;

actualLineLen=0;

aln_stop=

->GetAlnStop();

rowNum = alnRoInfo->

;

actualLineLen=aln_stop-aln_start+1;

(

=0;

<rowNum;

++) {

hasSequence =

;

end = alnRoInfo->

[

].front() + 1;

has_mismatch =

;

(

index = aln_start; index < aln_start + (

)actualLineLen &&

index < (

)alnRoInfo->

[

].size(); index ++){

}

(!has_mismatch) {

has_mismatch =

;

prev_stop[

] = end;

formattedString;

actualLineLen=0;

aln_stop=

->GetAlnStop();

rowNum = alnRoInfo->

;

actualLineLen=aln_stop-aln_start+1;

(

=0;

<rowNum;

++) {

hasSequence =

;

end = alnRoInfo->

[

].front() + 1;

prev_stop[

] = end;

end = alnRoInfo->

[

].front() + 1;

((j > 0 && end == prev_stop)

|| (j == 0 && start == 1 && end == 1)) {

(

)actualLineLen, alnRoInfo->

[

],

,

(!(j > 0 && end == prev_stop)

&& !(j == 0 && start == 1 && end == 1)) {

list<string> inserts;

insertPosString;

insertAlready =

;

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

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

(!insertAlready){

<< insertPosString<<

;

<<*iter<<

;

insertAlready =

;

gi =

->GetSeqId(

).GetGi();

GetBioseqCore()->

());

anchorTmpl,checkBoxTmpl,id_lbl;

id_lbl =

+ id_lbl;

(showCheckbox || showAnchor) {

(!urlLink.empty()) {

aln_stop=

->GetAlnStop();

aln_vec_info->

= 0;

aln_vec_info->

= 0;

aln_vec_info->

,

finalAln = densegAln;

finalAln = densegAln;

);

((ds->IsSetStrands()

&& !(ds->IsSetWidths() && ds->GetWidths()[0] == 3)){

finalDenseg->

(*ds);

feat_file =

->

(

,

);

feat_file_index =

->

(

,

);

(actual_aln_list.

().empty()){

(CSeq_align_set::Tdata::const_iterator

iter = actual_aln_list.

().begin();

iter != actual_aln_list.

().end()

(!(avRef.

())){

alnvecInfo->use_this_seqid,

alnvecInfo->comp_adj_method);

alnvecInfo->alnvec = avRef;

showDefLine = previousId.

() || !subid->

(*previousId);

<<

<<

;

vector<CRef<CSeq_align_set> > alnVector(

);

(CSeq_align_set::Tdata::const_iterator

alnIter = actual_aln_list.

().begin();

alnIter != actual_aln_list.

().end()

.GetBioseqHandle((*alnIter)->GetSeq_id(1));

alnVector[0]->Set().push_back(convertedDs);

alnVector[1]->Set().push_back(convertedDs);

alnVector[2]->Set().push_back(convertedDs);

alnVector[3]->Set().push_back(convertedDs);

alnVector[4]->Set().push_back(convertedDs);

alnVector[5]->Set().push_back(convertedDs);

alnVector[0]->Set().push_back(convertedDs);

alnVector[0]->Set().push_back(*alnIter);

);

(

= 0;

< (

)alnVector.size();

++){

hasAln =

;

alnRef =

(*alnVector[

]); alnRef; ++alnRef){

(ds->IsSetWidths() &&

ds->GetWidths()[0] == 3 &&

ds->IsSetStrands() &&

numDistinctFrames = 0;

(

= 0;

< (

)alnVector.size();

++){

(!alnVector[

]->

().empty()){

numDistinctFrames ++;

(numDistinctFrames > 1){

<<

;

<<

;

& sequence ,

& middle_line)

min_length=min<int>((

)sequence_standard.size(), (

)sequence.size());

middle_line = sequence;

(

=0;

<min_length;

++){

(sequence_standard[

]==sequence[

]){

middle_line[

] =

;

middle_line[

] = sequence[

];

&&

[(

)sequence_standard[

]][(

)sequence[

]] > 0){

middle_line[

] =

;

middle_line[

] =

;

cerr <<

<< e.

() << endl;

list<string> &use_this_seqid,

SAlnDispParams *alnDispParams =

;

kMaxDeflineNum = 10;

list<CRef<CSeq_id> > ids = bdl->GetSeqid();

isGiList =

;

(

&& isGiList) gi_in_use_this_gi = gi;

(use_this_seqid.empty() ||

) {

firstGi = (firstGi ==

) ? gi_in_use_this_gi : firstGi;

alnDispParams =

SAlnDispParams();

alnDispParams->gi = gi;

(bdl->IsSetTaxid() && bdl->CanGetTaxid()){

taxid = bdl->GetTaxid();

alnDispParams->seqUrlInfo =

(gi_in_use_this_gi,alnDispParams->label,taxid,ids);

(alnDispParams->hasTextSeqID) {

alnDispParams->gi) : 0;

(list<string>, iter_linkout, linkout_url){

alnDispParams->linkoutStr += *iter_linkout;

(bdl->IsSetTitle()){

alnDispParams->title = bdl->GetTitle();

(alnDispParams->title.empty()) {

alnDispParams;

SAlnDispParams *alnDispParams =

SAlnDispParams();

alnDispParams->seqUrlInfo =

(alnDispParams->gi,alnDispParams->label,

,alnDispParams->ids);

alnDispParams;

kLengthString(

);

value_set =

;

(getenv(

)) {

kLengthString.assign(

);

isFirst =

;

aln_vec_info->id_label = (alnDispParams->gi !=

) ?

<<alnDispParams->id_url;

!alnDispParams->seqID->IsGi()){

<<

<<alnDispParams->gi<<

;

(!((alnDispParams->seqID->AsFastaString().find(

) != string::npos) ||

alnDispParams->seqID->AsFastaString().find(

) != string::npos)){

(

(alnDispParams->seqID->AsFastaString().c_str(),

, 4) == 0)

<< alnDispParams->label;

alnDispParams->gi >

)) {

alnDispParams->seqID->WriteAsFasta(

);

(alnDispParams->gi !=

){

<<

<<alnDispParams->gi<<

;

<<

<<alnDispParams->seqID->GetSeqIdString()<<

;

alnDispParams->title);

bMultipleDeflines =

;

maxNumBdl = (aln_vec_info->use_this_seqid.empty()) ? bdl.size() : aln_vec_info->use_this_seqid.size();

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

aln_vec_info->use_this_seqid,

(alnDispParams) {

mdlTag = aln_vec_info->id_label;

<<

<<

mdlTag <<

<< maxNumBdl -

<<

<<

;

<<

<<

<< mdlTag <<

;

bMultipleDeflines =

;

firstGi = alnDispParams->gi;

<< alnDispParams->id_url;

!alnDispParams->seqID->IsGi()){

<<

<<alnDispParams->gi<<

;

(!(alnDispParams->seqID->AsFastaString().find(

) != string::npos) ||

alnDispParams->seqID->AsFastaString().find(

) != string::npos){

(

(alnDispParams->seqID->AsFastaString().c_str(),

, 4) == 0) {

<< alnDispParams->label;

alnDispParams->gi >

)) {

alnDispParams->seqID->WriteAsFasta(

);

*alnDispParams->seqID);

(alnDispParams->gi !=

){

<<

<<alnDispParams->gi<<

;

<<

<<alnDispParams->seqID->GetSeqIdString(

)<<

;

aln_vec_info->id_label = alnDispParams->label;

<< alnDispParams->linkoutStr;

(!alnDispParams->dumpGnlUrl.empty()) {

<<alnDispParams->dumpGnlUrl;

(

.tellp() > 1L) {

(!alnDispParams->title.empty()) {

HTMLEncode(alnDispParams->title) :

alnDispParams->title);

formattedString;

color_mismatch,

((

)sequence.size() > start);

list<CRange<int> > actualSeqloc;

actualSeq = sequence.substr(start,

);

from=(*iter)->aln_range.GetFrom();

to=(*iter)->aln_range.GetTo();

locFrame = (*iter)->seqloc->GetFrame();

(

.Match((*iter)->seqloc->GetInterval().GetId())

&& locFrame == frame){

isFirstChar =

;

(

=max<int>(from, start);

i<=min<int>(to, start+

-1);

++){

isFirstChar =

;

eachSeqloc.

(

, eachSeqloc.

());

(

((

) actualSeq[

-start])){

actualSeq[

-start]=

;

actualSeq[

-start]=

;

actualSeq[

-start]=

((

) actualSeq[

-start]);

&&

== min<int>(to, start+

)){

(!(eachSeqloc.

()==0&&eachSeqloc.

()==0)){

actualSeqloc.push_back(eachSeqloc);

(actualSeqloc.empty()){

endTag =

;

frontTag =

;

(

= 0;

< (

)actualSeq.size();

++){

startStyledOutput =

,stopStyledOutput =

;

(list<

>::iterator iter=actualSeqloc.begin();

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

from = (*iter).GetFrom() - start;

to = (*iter).GetTo() - start;

(to ==

&& to > 0){

startStyledOutput = frontTag;

stopStyledOutput = endTag && frontTag;

(!isStyled)

<<actualSeq[

];

(endTag && frontTag){

=

->GetAlnChunks(

,

->GetSeqAlnRange(antirow));

(

=0;

<chunk_vec->size();

++) {

(chunk->IsGap()) {

gap += (chunk->GetAlnRange().GetTo()

- chunk->GetAlnRange().GetFrom() + 1);

=

->GetAlnChunks(

,

->GetSeqAlnRange(0));

(

=0;

<chunk_vec->size();

++) {

(chunk->IsGap()) {

gap += (chunk->GetAlnRange().GetTo()

- chunk->GetAlnRange().GetFrom() + 1);

custom_genetic_code,

,

& sequence,

list<ENa_strand>& feat_seq_strand,

fill_feat_range )

gi_temp =

(

->GetBioseqHandle(

).GetBioseqCore()->GetId());

GetRangeSeq_loc(

(seq_start, seq_stop),

(seq_start, seq_stop));

(

feat(scope, *loc_ref, sel); feat; ++feat) {

& loc = feat->GetLocation();

has_id =

;

list<CSeq_loc_CI::TRange> isolated_range;

first_loc =

, mixed_strand =

, mix_loc =

;

other_seqloc_length = 0;

& id_it = loc_it.GetSeq_id();

isolated_range.push_back(loc_it.GetRange());

feat_seq_range = loc_it.GetRange();

feat_seq_range += loc_it.GetRange();

(loc_it.IsSetStrand()){

feat_strand = loc_it.GetStrand();

(!first_loc && prev_strand != feat_strand){

mixed_strand =

;

prev_strand = feat_strand;

other_seqloc_length += loc_it.GetRange().GetLength();

(!has_id || mixed_strand){

feat_char =

;

actual_feat_seq_start = 0, actual_feat_seq_stop = 0;

(

->IsPositiveStrand(

)){

actual_feat_seq_start =

actual_feat_seq_stop =

(feat_seq_range.

(), seq_stop);

actual_feat_seq_start =

(feat_seq_range.

(), seq_start);

actual_feat_seq_stop =

genetic_code = -1;

->GetAlnPosFromSeqPos(

, actual_feat_seq_start);

->GetAlnPosFromSeqPos(

, actual_feat_seq_stop);

raw_cdr_product =

isolated_range, handle, feat_strand,

featId, other_seqloc_length%3 == 0 ?

0 : 3 - other_seqloc_length%3,

(feat->IsSetData() && feat->GetData().IsCdregion() && feat->GetData().GetCdregion().IsSetCode()) {

genetic_code = feat->GetData().GetCdregion().GetCode().GetId();

line(aln_stop+1,

);

(

= feat_aln_from;

<= feat_aln_to;

++){

(list<CSeq_loc_CI::TRange>, iter, isolated_range){

total_coding_len += iter->GetLength();

gap_char =

->GetGapChar(

);

concat_exon =

other_seqloc_length%3 == 0 ?

0 : 3 - other_seqloc_length%3);

(fill_feat_range) {

list<CRange<TSeqPos> > master_feat_range;

feat, isolated_range,

other_seqloc_length%3 == 0 ?

3 - other_seqloc_length%3);

(!(master_feat_range.empty())) {

feat_range_list.push_back(master_feat_range);

feat_seq_strand.push_back(master_strand);

feat_aln_start_totalexon = 0;

prev_feat_aln_start_totalexon = 0;

prev_feat_seq_stop = 0;

is_first =

;

is_first_exon_start =

;

isolated_range.reverse();

(list<CSeq_loc_CI::TRange>, iter, isolated_range){

intron_size += iter->GetFrom()

- prev_feat_seq_stop - 1;

IntersectionWith(*iter);

(!actual_feat_seq_range.

()){

(

->IsPositiveStrand(

)){

=

->GetAlnPosFromSeqPos

(

, actual_feat_seq_range.

());

(

, actual_feat_seq_range.

());

=

->GetAlnPosFromSeqPos

<= feat_aln_stop;

++){

(sequence[

] != gap_char){

=

->GetSeqPosFromAlnPos(

,

) -

intron_size - feat_seq_range.

();

(product_adj_seq_pos <

concat_exon.size()){

concat_exon[product_adj_seq_pos];

(

->IsPositiveStrand(

)){

(is_first_exon_start &&

((

) line[

])){

feat_aln_start_totalexon =

- product_adj_seq_pos + 1;

is_first_exon_start =

;

feat_aln_start_totalexon =

product_adj_seq_pos;

is_first_exon_start =

;

(is_first_exon_start &&

((

) line[

])){

feat_aln_start_totalexon =

- product_adj_seq_pos + 1;

is_first_exon_start =

;

prev_feat_aln_start_totalexon =

feat_aln_start_totalexon;

(!is_first_exon_start){

feat_aln_start_totalexon =

- product_adj_seq_pos + 1),

prev_feat_aln_start_totalexon);

prev_feat_aln_start_totalexon =

feat_aln_start_totalexon;

feat_aln_start_totalexon =

(prev_feat_aln_start_totalexon,

product_adj_seq_pos);

prev_feat_aln_start_totalexon =

feat_aln_start_totalexon;

prev_feat_seq_stop = iter->GetTo();

alternativeFeatStr = line;

feat_aln_start_totalexon,

->IsPositiveStrand(

) ?

feat_strand, featInfo->feature_start);

feat_aln_from, feat_aln_to, aln_stop,

feat_char, featId, alternativeFeatStr, genetic_code);

feature.push_back(featInfo);

aln_to,

aln_stop,

pattern_char,

pattern_id,

& alternative_feat_str,

genetic_code)

feat->seqloc = &seqloc;

feat->feature_char = pattern_char;

feat->feature_id = pattern_id;

feat_info->feature_string = alternative_feat_str;

line(aln_stop+1,

);

(

j = aln_from; j <= aln_to; j++){

line[j] = feat->feature_char;

feat_info->feature_string = line;

feat_info->genetic_code = genetic_code;

feat_info->aln_range.Set(aln_from, aln_to);

feat_info->feature = feat;

(

& seq,

insert_alnpos,

aln_start){

end = (

)seq.size() -1 ;

barPos = insert_alnpos - aln_start + 1;

(barPos - end > 1){

spacer(barPos - end - 1,

);

addOn += spacer +

;

}

(barPos - end == 1){

max<int>((barPos - end), 0);

(

& cur_insert,

& new_insert,

insert_alnpos,

aln_start)

curInsertSize = (

)cur_insert.size();

insertLeftSpace = insert_alnpos - aln_start - curInsertSize + 2;

(curInsertSize > 0){

(insertLeftSpace >= 2);

newInsertSize = (

)new_insert.size();

(insertLeftSpace - newInsertSize >= 1){

spacer(insertLeftSpace - newInsertSize,

);

cur_insert += spacer + new_insert;

(curInsertSize > 0){

cur_insert +=

+ new_insert;

cur_insert += new_insert;

insertEnd = aln_start + (

)cur_insert.size() -1 ;

list<string>& inserts)

{

(!insert_list.empty()){

bar(aln_range.

(),

);

isFirstInsert =

;

curInsertAlnStart = 0;

prvsInsertAlnEnd = 0;

curInsertAlnStart = (*iter)->aln_start;

(isFirstInsert || curInsertAlnStart - prvsInsertAlnEnd >= 1){

bar[curInsertAlnStart-aln_start+1] =

;

seqStart = (*iter)->seq_start;

seqEnd = seqStart + (*iter)->insert_len - 1;

newInsert =

->GetSeqString(newInsert,

, seqStart,

curInsertAlnStart, aln_start);

isFirstInsert =

;

bar[curInsertAlnStart-aln_start+1] =

;

prvsInsertAlnEnd +=

(seq, curInsertAlnStart, aln_start);

leftOverInsertList.push_back(*iter);

inserts.push_back(bar);

inserts.push_back(seq);

(

, aln_range, aln_start, leftOverInsertList, inserts);

aln_start, list<string>& inserts,

& insert_pos_string,

line(aln_range.

(),

);

from = (*iter)->aln_start;

line[from - aln_start + 1] =

;

insert_pos_string = line;

(

, aln_range, aln_start, insert_list, inserts);

(!insert_aln_start.empty()

&& (

)insert_aln_start.front() < line_aln_stop){

insert->aln_start = insert_aln_start.front() - 1;

insert->seq_start = insert_seq_start.front();

insert->insert_len = insert_length.front();

insert_list.push_back(insert);

insert_aln_start.pop_front();

insert_seq_start.pop_front();

insert_length.pop_front();

idString =

->GetSeqId(1).GetSeqIdString();

segs = iter->second.segs;

(seg.

().size() > 1){

((*iterStdseg)->IsSetScores()){

aln->

() = (*iterStdseg)->GetScores();

aln->

().SetStd().push_back(*iterStdseg);

alnSetRef->

().push_back(aln);

alnSetRef->

().push_back(*iter);

((*iterDendiag)->IsSetScores()){

aln->

() = (*iterDendiag)->GetScores();

aln->

().SetDendiag().push_back(*iterDendiag);

((*iter)->IsSetType() && (*iter)->CanGetType()){

aln->

((*iter)->GetType());

alnSetRef->

().push_back(aln);

alnSetRef->

().push_back(*iter);

alnSetRef->

().push_back(*iter);

((*iterStdseg)->IsSetScores()){

aln->

() = (*iterStdseg)->GetScores();

aln->

().SetStd().push_back(*iterStdseg);

alnSetRef->

().push_back(aln);

((*iterDendiag)->IsSetScores()){

aln->

() = (*iterDendiag)->GetScores();

aln->

().SetDendiag().push_back(*iterDendiag);

alnSetRef->

().push_back(aln);

alnSetRef->

().push_back(*iter);

first_align =

;

((*iterStdseg)->IsSetScores()){

aln->

() = (*iterStdseg)->GetScores();

first_align =

;

std::vector< CRef< CScore > >& scores_in = (*iter)->SetScore();

((*it_in)->IsSetId()) {

found =

;

std::vector< CRef< CScore > >& scores_out = aln->

();

((*it_out)->IsSetId()) {

(score_id.

((*it_out)->GetId())) {

scores_out.push_back (*it_in);

aln->

().SetStd().push_back(*iterStdseg);

alnSetRef->

().push_back(aln);

((*iterDendiag)->IsSetScores()){

aln->

() = (*iterDendiag)->GetScores();

first_align =

;

std::vector< CRef< CScore > >& scores_in = (*iter)->SetScore();

((*it_in)->IsSetId()) {

found =

;

std::vector< CRef< CScore > >& scores_out = aln->

();

((*it_out)->IsSetId()) {

(score_id.

((*it_out)->GetId())) {

scores_out.push_back (*it_in);

aln->

().SetDendiag().push_back(*iterDendiag);

alnSetRef->

().push_back(aln);

alnSetRef->

().push_back(*iter);

(

[strGeneLinkUrl.size() + 1024]);

sprintf(

.get(), strGeneLinkUrl.c_str(),

strGeneLinkUrl.assign(

.get());

strGeneLinkUrl;

<<

;

<<

<< query_buf

<<

<< id_label <<

;

<<

<< query_buf

<<

<< id_label <<

;

<<

<< query_buf

<<

<< id_label <<

;

<<

;

<<

<< query_buf

<<

<< id_label <<

;

<<

;

<<

<< query_buf

<<

<< id_label <<

;

<<

;

(

= 0;

< 5;

++) {

(hsp_sort ==

) {

<< url_link <<

;

(type_temp.find(

) != string::npos ||

type_temp ==

||

type_temp ==

||

type_temp ==

|| type_temp ==

)){

master_start =

->GetSeqStart(0) + 1;

master_stop =

->GetSeqStop(0) + 1;

subject_start =

->GetSeqStart(1) + 1;

subject_stop =

->GetSeqStop(1) + 1;

sprintf(

,

,

subj_id_str.c_str(), aln_vec_info->score,

(master_start, master_stop),

(master_start, master_stop),

(subject_start, subject_stop),

(subject_start, subject_stop));

evalue_buf, bit_score_buf, total_bit_buf, raw_score_buf;

aln_vec_info->bits, 0, 0, evalue_buf,

bit_score_buf, total_bit_buf, raw_score_buf);

hidePrevNaviagtion,hideNextNaviagtion, hideFirstNavigation;

hidePrevNaviagtion =

;

hideFirstNavigation =

;

hideNextNaviagtion =

;

(aln_vec_info->sum_n > 0) {

(aln_vec_info->comp_adj_method == 1){

(aln_vec_info->comp_adj_method == 2){

evalue_buf, bit_score_buf, total_bit_buf, raw_score_buf;

aln_vec_info->

, 0, 0, evalue_buf,

bit_score_buf, total_bit_buf, raw_score_buf);

<<

<< aln_vec_info->

;

<<

<<aln_vec_info->

<<

;

<<

<<bit_score_buf<<

;

<<

<<aln_vec_info->

<<

<<

;

(aln_vec_info->

> 0) {

<<

<< aln_vec_info->

<<

;

<<

<< evalue_buf;

<<

;

<<

;

showSortControls =

;

showSortControls =

;

(!(alnDispParams->seqID->AsFastaString().find(

) != string::npos) ||

alnDispParams->seqID->AsFastaString().find(

) != string::npos){

seqid = alnDispParams->seqID->AsFastaString();

hspNum,isFirstDflAttr;

isFirstDflAttr =

;

alnIdLbl = (alnDispParams->gi !=

) ?

linkoutStr, dnldLinkStr;

linkoutStr = (!alnDispParams->linkoutStr.empty()) ? alnDispParams->linkoutStr :

;

dnldLinkStr = alnDispParams->dumpGnlUrl;

firstDefline;

list<string>& use_this_seqid = aln_vec_info->use_this_seqid;

isFirst =

;

alnDefLine =

(alnDispParams,isFirst,

,

,seqLength);

*alnDispParams->

);

alnDispParams;

firstDefline = alnDefLine;

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

(alnDispParams) {

hideDefline = (numBdl > 1)?

:

;

alnDispParams->

= dispId;

alnDispParams->

->AsFastaString();

*alnDispParams->

);

vector <string> parts;

(parts.size() > 0) {

( (isFirst && firstGi ==

) || (alnDispParams->

== firstGi && firstGi !=

) ) {

firstDefline = alnDefLine;

deflines += alnDefLine;

alnDispParams;

deflines = firstDefline;

deflines = firstDefline + alnTitleslnk + alnTitles;

deflines, linkOutStr,customLinkStr;

list<string> linkoutStr;

customLinkStr += *iter_custList;

linkOutStr += *iter_List;

isGenbankAttr = (

(customLinkStr,

) ==

&&

(customLinkStr,

) ==

)?

:

;

hideDndl = (

==

)?

:

;

(sortOneAln.empty()) {

showSortControls)

(aln_vec_info->

.size() > 0 || aln_vec_info->

|| aln_vec_info->

){

(

)

->GetAlnStop(),

aln_vec_info->

,

aln_vec_info->

,

->StrandSign(0),

->StrandSign(1),

addToRange = (

)((to - from) * 0.05);

fromAdjust =

(0,(

)from - addToRange);

toAdjust = to + addToRange;

customLinkStr;

hspLinks += singleLink;

multiHSP = (hspLinks.empty()) ?

:

;

alignInfo += alignRows;

aln_vec_info->feat5 =

;

aln_vec_info->feat3 =

;

aln_vec_info->feat_list.clear();

&& (

)

->GetBioseqHandle(1).GetBioseqLength()

aln_vec_info->actual_range = range;

aln_vec_info->feat_list =

->GetFeatInfo(id_str, aln_vec_info->actual_range, aln_vec_info->feat5, aln_vec_info->feat3, 2);

(

?

:

),

alignFeature;

alignParams = alignInfo;

allAlnFeatures =

;

(aln_vec_info->feat_list.size() > 0) {

(vector<SFeatInfo*>, iter, aln_vec_info->feat_list){

aln_vec_info->subject_gi,

(*iter)->range.GetFrom(),

(*iter)->range.GetTo(),

allAlnFeatures += alignFeature;

(aln_vec_info->feat5 || aln_vec_info->feat3){

(aln_vec_info->feat5){

aln_vec_info->subject_gi,

aln_vec_info->feat5->range.GetFrom(),

aln_vec_info->feat5->range.GetTo(),

(aln_vec_info->actual_range.GetFrom() - aln_vec_info->feat5->range.GetTo()) + (

)

+ aln_vec_info->feat5->feat_str);

allAlnFeatures += alignFeature;

(aln_vec_info->feat3){

aln_vec_info->subject_gi,

aln_vec_info->feat3->range.GetFrom(),

aln_vec_info->feat3->range.GetTo(),

(aln_vec_info->feat3->range.GetFrom() - aln_vec_info->actual_range.GetTo()) + (

)

+ aln_vec_info->feat3->feat_str);

allAlnFeatures += alignFeature;

(!allAlnFeatures.empty()) {

(aln_vec_info->feat_list.size() > 0) {

<<

<<

;

(vector<SFeatInfo*>, iter, aln_vec_info->feat_list){

?

:

,

(*iter)->range.GetFrom() +1 ,

(*iter)->range.GetTo() + 1,

<< (*iter)->feat_str;

(aln_vec_info->feat5 || aln_vec_info->feat3){

<<

<<

;

(aln_vec_info->feat5){

?

:

,

aln_vec_info->feat5->range.GetFrom() + 1 ,

aln_vec_info->feat5->range.GetTo() + 1,

<< aln_vec_info->actual_range.GetFrom() - aln_vec_info->feat5->range.GetTo()

<<

<< aln_vec_info->feat5->feat_str;

(aln_vec_info->feat3){

?

:

,

aln_vec_info->feat3->range.GetFrom() + 1 ,

aln_vec_info->feat3->range.GetTo() + 1,

<< aln_vec_info->feat3->range.GetFrom() - aln_vec_info->actual_range.GetTo()

<<

<< aln_vec_info->feat3->feat_str;

(aln_vec_info->feat_list.size() > 0 || aln_vec_info->feat5 || aln_vec_info->feat3 ){

has_valid_loc =

;

(

=0;

<

->GetNumRows();

++){

->GetSeqRange(

).IntersectingWith(loc_range)){

actualAlnStart = 0, actualAlnStop = 0;

(

->IsPositiveStrand(

)){

->GetAlnPosFromSeqPos(

,

->GetAlnPosFromSeqPos(

,

->GetAlnPosFromSeqPos(

,

->GetAlnPosFromSeqPos(

,

alnloc->aln_range.Set(actualAlnStart, actualAlnStop);

has_valid_loc =

;

(has_valid_loc) {

alnloc->seqloc = *iter;

loc_list.push_back(alnloc);

vector<TSAlnFeatureInfoList>& retval)

retval.resize(row_num);

(list<FeatureInfo*>::iterator iter=

->begin();

(

= 0;

< row_num;

++){

((*iter)->seqloc->GetInt().GetId().Match(

->GetSeqId(

))){

actualSeqStart = 0, actualSeqStop = 0;

(

->IsPositiveStrand(

)){

((*iter)->seqloc->GetInt().GetFrom()

<

->GetSeqStart(

)){

actualSeqStart =

->GetSeqStart(

);

actualSeqStart = (*iter)->seqloc->GetInt().GetFrom();

((*iter)->seqloc->GetInt().GetTo() >

->GetSeqStop(

)){

actualSeqStop =

->GetSeqStop(

);

actualSeqStop = (*iter)->seqloc->GetInt().GetTo();

((*iter)->seqloc->GetInt().GetFrom()

<

->GetSeqStart(

)){

actualSeqStart = (*iter)->seqloc->GetInt().GetFrom();

actualSeqStart =

->GetSeqStart(

);

((*iter)->seqloc->GetInt().GetTo() >

->GetSeqStop(

)){

actualSeqStop = (*iter)->seqloc->GetInt().GetTo();

actualSeqStop =

->GetSeqStop(

);

alnFrom =

->GetAlnPosFromSeqPos(

, actualSeqStart);

alnTo =

->GetAlnPosFromSeqPos(

, actualSeqStop);

(alnTo - alnFrom >= 0){

alnTo, aln_stop, (*iter)->feature_char,

(*iter)->feature_id, tempFeat, -1);

retval[

].push_back(featInfo);

(

aln_from,

aln_to,

& domain_name,

& final_domain) {

domain_string(aln_to - aln_from + 1,

);

(domain_string.size() > 2){

(

= 0;

< (

)domain_string.size();

++){

domain_string[

] =

;

domain_string[0] =

;

domain_string[domain_string.size()-1] =

;

midpoint = ((

)domain_string.size())/2;

first_possible_pos = 1;

actual_first_pos =

(first_possible_pos, midpoint - ((

)domain_name.size())/2);

(

= actual_first_pos, j = 0;

< domain_string.size() - 1 && j < domain_name.size();

++, j ++){

domain_string[

] = domain_name[j];

(

= 0;

< domain_string.size();

++){

final_domain[

+ aln_from] = domain_string[

];

vector<TSAlnFeatureInfoList>& retval)

final_domain (

->GetAlnStop() + 1,

);

last_aln_to =

->GetAlnStop();

((*iter)->seqloc->GetInt().GetId().Match(

->GetSeqId(0))){

actualSeqStart = 0, actualSeqStop = 0;

(

->IsPositiveStrand(0)){

actualSeqStart =

((

)

->GetSeqStart(0),

(

)(*iter)->seqloc->GetInt().GetFrom());

actualSeqStop =

((

)

->GetSeqStop(0),

(

)(*iter)->seqloc->GetInt().GetTo());

alnFrom =

->GetAlnPosFromSeqPos(0, actualSeqStart);

(actualSeqStart > 0 && (*iter)->is_subject_start_valid) {

->GetAlnPosFromSeqPos(0, actualSeqStart - 1) > 1) {

subj_aln_from =

->GetAlnPosFromSeqPos(1,

(

)(*iter)->subject_seqloc->GetInt().GetFrom());

(subj_aln_from >= 0) {

alnFrom = subj_aln_from;

alnTo =

->GetAlnPosFromSeqPos(0, actualSeqStop);

(actualSeqStop < (

)

->GetSeqStop(0) &&

(*iter)->is_subject_stop_valid) {

(

->GetAlnPosFromSeqPos(0, actualSeqStop + 1) - alnTo > 1) {

subj_aln_to =

->GetAlnPosFromSeqPos(1,

(

)(*iter)->subject_seqloc->GetInt().GetTo());

(subj_aln_to >= 0) {

alnTo = subj_aln_to;

actual_aln_from =

(alnFrom,last_aln_to +1);

(actual_aln_from > alnTo) {

last_aln_to = alnTo;

aln_stop, aln_stop,

,

, final_domain, -1);

retval[0].push_back(featInfo);

(

);

(

);

value_set =

;

(getenv(

)) {

gi =

->GetSeqId(

).GetGi();

gi =

->GetSeqId(

).GetGi();

(toolUrl.find(

) != string::npos

idString, prevIdString,prevIdStringWithVersion,idStringWithVersion;

(CSeq_align_set::Tdata::const_iterator

iter = actual_aln_list.

().begin();

iter != actual_aln_list.

().end()

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

(!prevIdString.empty() && !prevIdStringWithVersion.empty() && prevIdString == idString && prevIdStringWithVersion != idStringWithVersion) {

prevIdStringWithVersion = idStringWithVersion;

prevIdString = idString;

SAlnLinksParams *alnLinksParam =

?

SAlnLinksParams : &

[idString];

alnLinksParam->segs +=

;

currFrom = alnLinksParam->subjRange->GetFrom();

currTo = alnLinksParam->subjRange->GetTo();

alnLinksParam->subjRange->SetFrom(

(from,currFrom));

alnLinksParam->subjRange->SetTo(

(to,currTo));

alnLinksParam->hspNumber = (!

) ? alnLinksParam->hspNumber + 1 : 1;

idString, prevIdString;

(CSeq_align_set::Tdata::const_iterator

iter = currSeqAlignIter;

iter != actual_aln_list.

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

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

(prevIdString.empty() || prevIdString == idString) {

prevIdString = idString;

unordered_set <string> :: const_iterator idsIter;

(actual_aln_list.

().empty()){

showBlastDefline =

;

(CSeq_align_set::Tdata::const_iterator

iter = actual_aln_list.

().begin();

iter != actual_aln_list.

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

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

idsIter = selectedIDs.find(currID);

(idsIter == selectedIDs.end() && idCount < (

)selectedIDs.size())

;

(idsIter == selectedIDs.end() && idCount >= (

)selectedIDs.size())

;

(previousId.

() ||

!subid->

(*previousId)){

showBlastDefline =

;

showBlastDefline =

;

(!previousId.

() &&

!subid->

(*previousId)){

.RemoveFromHistory(

.GetBioseqHandle(*previousId));

(!(avRef.

())){

alnvecInfo->use_this_seqid,

alnvecInfo->comp_adj_method);

alnvecInfo->alnvec = avRef;

<<

<<

;

static CRef< CScope > m_Scope

User-defined methods of the data storage class.

User-defined methods of the data storage class.

@ eExtreme_Biological

5' and 3'

User-defined methods of the data storage class.

Sequence alignment display tool.

const int k_NumAsciiChar

Number of ASCII characters for populating matrix columns.

bool GetSeqData(ParserPtr pp, const DataBlk &entry, CBioseq &bioseq, Int4 nodetype, unsigned char *seqconv, Uint1 seq_data_type)

#define BLAST_DEFAULT_MATRIX

Default matrix name: BLOSUM62.

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

Create URL for seqid.

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

Set the database as gi type.

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

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

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 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 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 int GetPercentMatch(int numerator, int denominator)

function for calculating percent match for an alignment.

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

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

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

return gi from id list

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

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)

list< TSeqPos > TSeqPosList

TSignedSeqPos GetAlnPosFromSeqPos(TNumrow row, TSeqPos seq_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

const CSeq_id & GetSeqId(TNumrow row) const

bool IsPositiveStrand(TNumrow row) const

TSignedSeqPos GetSeqPosFromAlnPos(TNumrow for_row, TSeqPos aln_pos, ESearchDirection dir=eNone, bool try_reverse_dir=true) const

bool IsNegativeStrand(TNumrow row) const

TRange GetSeqRange(TNumrow row) const

TSeqPos GetSeqStop(TNumrow row) const

int StrandSign(TNumrow row) const

TSeqPos GetSeqStart(TNumrow row) const

const CBioseq_Handle & GetBioseqHandle(TNumrow row) const

void SetAaCoding(TCoding coding)

CSeqVector::TResidue TResidue

void SetGenCode(int gen_code, TNumrow row=-1)

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

void Reverse(void)

Reverse the segments' orientation.

bool IsSetWidths(void) const

void Assign(const CSerialObject &obj, ESerialRecursionMode how=eRecursive)

overloaded Assign()

const TWidths & GetWidths(void) const

void x_FillSeqid(string &id, int row) const

make the appropriate seqid

@ eShowSequencePropertyLabel

@ eTranslateNucToNucAlignment

@ eShowInfoOnMouseOverSeqid

@ eShowTranslationForLocalSeq

@ eShowAlignStatsForMultiAlignView

void x_DisplayAlnvec(CNcbiOstream &out)

Display the current alnvec.

void x_DisplayAlignInfo(CNcbiOstream &out, SAlnInfo *aln_vec_info)

Display score,bits,expect,method.

list< string > m_HSPLinksList

void x_GetDomainInfo(int row_num, int aln_stop, vector< TSAlnFeatureInfoList > &retval) const

static CRef< objects::CSeq_align_set > PrepareBlastUngappedSeqalignEx(const objects::CSeq_align_set &alnset)

static functions same as PrepareBlastUngappedSeqalign, but process seg scores uniformly even if there...

string x_FormatOneDynamicFeature(string viewerURL, TGi subjectGi, int fromRange, int toRange, string featText)

list< CRef< DomainInfo > > * m_DomainInfo

void x_DisplaySequenceIDForPairwise(SAlnRowInfo *alnRoInfo, int row, bool has_mismatch, CNcbiOstrstream &out)

objects::CGetFeature * m_DynamicFeature

list< FeatureInfo * > * m_QueryFeature

external feature such as phiblast

CNcbiIfstream * m_ConfigFile

string m_CurrAlnID_Lbl

gi(if exists) that is used for html formatting otherwise id without db part

int m_currAlignHsp

Current HSP number for single alignmnet.

string x_GetDumpgnlLink(const list< CRef< objects::CSeq_id > > &ids) const

get dumpgnl url to sequence record

SeqLocColorOption m_SeqLocColor

ILinkoutDB * m_LinkoutDB

Reference to LinkoutDB implementation. Not owned by this class.

virtual string x_DisplayRowData(SAlnRowInfo *alnRoInfo)

Display pairwise alignment.

void x_FillIdentityInfo(const string &sequence_standard, const string &sequence, int &match, int &positive, string &middle_line)

compute number of identical and positive residues and set middle line accordingly

string x_PrintDefLine(const objects::CBioseq_Handle &bsp_handle, SAlnInfo *aln_vec_info)

print defline

void x_DisplaySequenceLine(SAlnRowInfo *alnRoInfo, int row, int prev_stop, CNcbiOstrstream &out)

TSubjectMaskMap m_SubjectMasks

Map of subject masks.

void x_DisplayAlignSortInfo(CNcbiOstream &out, string id_label)

Display Sorting controls.

void x_ShowAlnvecInfoTemplate(CNcbiOstream &out, SAlnInfo *aln_vec_info, bool show_defline)

list< string > m_CustomLinksList

void x_ProcessRowDataSet(SAlnRowInfo *alnRoInfo, int aln_start, vector< int > &prev_stop)

string x_MapDefLine(SAlnDispParams *alnDispParams, bool isFisrt, bool linkout, bool hideDefline, int seqLength)

void x_DoFills(int row, objects::CAlnMap::TSignedRange &aln_range, int aln_start, TSInsertInformationList &insert_list, list< string > &inserts) const

recusively fill the insert for anchored view

void x_PreProcessSeqAlign(objects::CSeq_align_set &actual_aln_list)

Sets m_Segs,m_HspNumber.

string x_FormatDefLinesHeader(const objects::CBioseq_Handle &bsp_handle, SAlnInfo *aln_vec_info)

int x_GetLinkout(const objects::CSeq_id &id)

string m_CurrAlnID_DbLbl

gi(if exists) that is used for html formatting otherwise id with db part like ti:xxxxxxx or GNOMON:XX...

void x_InitAlignLinks(SAlnDispParams *alnDispParams, const list< CRef< objects::CBlast_def_line > > &bdl_list, int lnkDispPrarms)

void x_DisplayInsertsForQueryAnchored(SAlnRowInfo *alnRoInfo, int row, CNcbiOstrstream &out)

int m_ResultPositionIndex

result position index for multiple query case

map< string, struct SAlnLinksParams > m_AlnLinksParams

void DisplaySeqalign(CNcbiOstream &out)

call this to display seqalign

void x_SetFeatureInfo(CRef< SAlnFeatureInfo > feat_info, const objects::CSeq_loc &seqloc, int aln_from, int aln_to, int aln_stop, char pattern_char, string pattern_id, string &alternative_feat_str, int genetic_code) const

set feature info

CRef< objects::CObjectManager > m_FeatObj

SeqLocCharOption m_SeqLocChar

string x_GetGeneLinkUrl(int gene_id)

get the URL of the Gene info link.

void x_ShowAlnvecInfo(CNcbiOstream &out, SAlnInfo *aln_vec_info, bool show_defline)

bool m_UseLongSeqIds

print long sequence ids (with gi and accession with database source)

void x_DisplaySingleAlignParams(CNcbiOstream &out, SAlnInfo *aln_vec_info, bool showSortControls)

Display Sorting controls,score,bits,expect,method,features identities,positives,frames etc.

string x_FormatDynamicFeaturesInfo(string alignInfo, SAlnInfo *aln_vec_info)

string x_FormatAlnHSPLinks(string &alignInfo)

objects::CScope & m_Scope

string x_GetSegs(int row) const

segments starts and stops used for map viewer, etc

AutoPtr< const vector< string > > m_SeqPropertyLabel

void x_GetInserts(TSInsertInformationList &insert_list, objects::CAlnMap::TSeqPosList &insert_aln_start, objects::CAlnMap::TSeqPosList &insert_seq_start, objects::CAlnMap::TSeqPosList &insert_length, int line_aln_stop)

get insert information

CRef< objects::CAlnVec > x_GetAlnVecForSeqalign(const objects::CSeq_align &align)

string x_FormatSingleAlign(SAlnInfo *aln_vec_info)

void x_PrepareDynamicFeatureInfo(SAlnInfo *aln_vec_info)

Calculate data for feature display.

list< CRef< SAlnSeqlocInfo > > TSAlnSeqlocInfoList

List of SAlnSeqlocInfo structures.

string m_MapViewerBuildName

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

CAlignFormatUtil::SLinkoutInfo m_LinkoutInfo

int m_cur_align

Gene info reader object, reads Gene info entries from files.

void x_AddTranslationForLocalSeq(vector< TSAlnFeatureInfoList > &retval, vector< string > &sequence) const

void x_DisplayMpvAnchor(CNcbiOstream &out, SAlnInfo *aln_vec_info)

Display anchor for links from mapview.

CDisplaySeqalign(const objects::CSeq_align_set &seqalign, objects::CScope &scope, list< CRef< CSeqLocInfo > > *mask_seqloc=NULL, list< FeatureInfo * > *external_feature=NULL, const char *matrix_name="BLOSUM62")

Constructors.

int m_QueryAnchoredSetIndex

string x_FormatAlignSortInfo()

string x_HTMLSeqIDLink(SAlnRowInfo *alnRoInfo, int row, TGi giToUse)

int x_GetNumGaps()

Count number of total gaps.

void x_DisplayMiddLine(SAlnRowInfo *alnRoInfo, int row, CNcbiOstrstream &out)

string x_PrintDynamicFeatures(void)

void x_DisplayAlnvecInfo(CNcbiOstream &out, SAlnInfo *aln_vec_info, bool show_defline)

display alnvec info

void x_InitAlignParams(objects::CSeq_align_set &actual_aln_list)

Inits align parameters for displaySetup scope for feature fetching and m_DynamicFeature inits m_FeatO...

SAlignTemplates * m_AlignTemplates

string m_AlignedRegionsUrl

void x_GetFeatureInfo(TSAlnFeatureInfoList &feature, int custom_genetic_code, objects::CScope &scope, objects::CSeqFeatData::E_Choice choice, int row, string &sequence, list< list< CRange< TSeqPos > > > &feat_seq_range, list< objects::ENa_strand > &feat_seq_strand, bool fill_feat_range) const

get feature info

string x_FormatAlnBlastInfo(SAlnInfo *aln_vec_info)

string m_PreComputedResID

CDD precomputed results ID.

void x_PrepareIdentityInfo(SAlnInfo *aln_vec_info)

list< CRef< SAlnFeatureInfo > > TSAlnFeatureInfoList

string m_CurrAlnAccession

accession that is displayed

static CRef< objects::CSeq_align_set > PrepareBlastUngappedSeqalign(const objects::CSeq_align_set &alnset)

static functions Need to call this if the seqalign is stdseg or dendiag for ungapped blast alignment ...

CConstRef< objects::CSeq_align_set > m_SeqalignSetRef

reference to seqalign set

string x_FormatIdentityInfo(string alignInfo, SAlnInfo *aln_vec_info)

list< CRef< SInsertInformation > > TSInsertInformationList

void DisplayPairwiseSeqalign(CNcbiOstream &out, unordered_set< string > selectedIDs)

int m_currAlignSeqListIndex

Current subject seq index in descriptions table.

void x_PreProcessSingleAlign(objects::CSeq_align_set::Tdata::const_iterator currSeqAlignIter, objects::CSeq_align_set &actual_aln_list, bool multipleSeqs)

void x_FillLocList(TSAlnSeqlocInfoList &loc_list, const list< CRef< CSeqLocInfo > > *masks) const

convert the passed seqloc list info using alnment coordinates

void x_OutputSeq(string &sequence, const objects::CSeq_id &id, int start, int len, int frame, int row, bool color_mismatch, const TSAlnSeqlocInfoList &loc_list, CNcbiOstream &out) const

display sequence for one row

void x_CalcUrlLinksParams(const objects::CSeq_align &align, string idString, string toolUrl)

string x_DisplayRowDataSet(SAlnRowInfo *alnRoInfo, int aln_start, vector< int > &prev_stop)

void x_FillInserts(int row, objects::CAlnMap::TSignedRange &aln_range, int aln_start, list< string > &inserts, string &insert_pos_string, TSInsertInformationList &insert_list) const

get inserts info

list< string > m_LinkoutList

MiddleLineStyle m_MidLineStyle

TranslatedFrameForLocalSeq m_TranslatedFrameForLocalSeq

void x_DisplaySequenceIDForQueryAnchored(SAlnRowInfo *alnRoInfo, int row, CNcbiOstrstream &out)

void x_PrintFeatures(SAlnRowInfo *alnRoInfo, int row, string &master_feat_str, CNcbiOstream &out)

print out features and fill master_feat_str if applicable

list< CRef< CSeqLocInfo > > * m_Seqloc

display character option for list of seqloc

void x_DisplayBl2SeqLink(CNcbiOstream &out)

Dipslay Bl2seq TBLASTX link.

virtual ~CDisplaySeqalign()

Destructor.

void x_GetQueryFeatureList(int row_num, int aln_stop, vector< TSAlnFeatureInfoList > &features) const

get external query feature info such as phi blast pattern

CRef< objects::CScope > m_featScope

string x_InitDefLinesHeader(const objects::CBioseq_Handle &bsp_handle, SAlnInfo *aln_vec_info)

SAlnDispParams * x_FillAlnDispParams(const CRef< objects::CBlast_def_line > &iter, const objects::CBioseq_Handle &bsp_handle, list< string > &use_this_seqid, TGi firstGi, int numLinkoutReads)

int m_NumBlastDefLines

Number of subject sequence deflines.

CAlignFormatUtil::SSeqURLInfo * x_InitSeqUrl(TGi giToUse, string accession, TTaxId taxid, const list< CRef< objects::CSeq_id > > &ids)

get url to sequence record

void SetSubjectMasks(const TSeqLocInfoVector &masks)

Sets the masks and the masking algorithm used for the subject sequences.

SAlnRowInfo * x_PrepareRowData(void)

Calculate data for pairwise alignment display.

static CRef< objects::CSeq_align_set > PrepareBlastUngappedSeqalignEx2(objects::CSeq_align_set &alnset)

same as PrepareBlastUngappedSeqalign2, but sets aggregate scores.

static string GetLoaderNameFromArgs(CReader *reader=0)

static TRegisterLoaderInfo RegisterInObjectManager(CObjectManager &om, CReader *reader=0, CObjectManager::EIsDefault is_default=CObjectManager::eDefault, CObjectManager::TPriority priority=CObjectManager::kPriority_NotSet)

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

bool Match(const CObject_id &oid2) const

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

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

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 ...

namespace ncbi::objects::

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

Template class for iteration on objects of class C (non-medifiable version)

@ eRight

Towards higher aln coord (always to the right)

@ eLeft

Towards lower aln coord (always to the left)

@ eBackwards

Towards lower seq coord (to the left if plus strand, right if minus)

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

Retrieve the Linkout for a given GI.

Collection of masked regions for a single query sequence.

container_type::const_iterator const_iterator

iterator_bool insert(const value_type &val)

container_type::value_type value_type

string GetSeqIdString(const CSeq_id &id)

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

main entry point for tests

const size_t kDfltLineLength

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

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

unsigned int TSeqPos

Type for sequence locations and lengths.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

#define NON_CONST_ITERATE(Type, Var, Cont)

Non constant version of ITERATE macro.

SStrictId_Tax::TId TTaxId

Taxon id type.

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

const string & GetValue() const

Get the value as a string, (necessarily) prefetching it all if applicable; the result remains availab...

#define ERR_POST(message)

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

#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 const char * what(void) const noexcept

Standard report (includes full backlog).

virtual void Assign(const CSerialObject &source, ESerialRecursionMode how=eRecursive)

Set object to copy of another one.

@ eSerial_AsnText

ASN.1 text.

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

HTML encodes a string. E.g. <.

TGi FindGi(const container &ids)

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

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.

bool Match(const CSeq_id &sid2) const

Match() - TRUE if SeqIds are equivalent.

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

string GetLabel(const CSeq_id &id)

@ eContent

Untagged human-readable accession or the like.

@ eBoth

Type and content, delimited by a vertical bar.

TRange GetTotalRange(void) const

void Add(const CSeq_loc &other)

Simple adding of seq-locs.

void SetPartialStart(bool val, ESeqLocExtremes ext)

set / remove e_Lim fuzz on start or stop (lt/gt - indicating partial interval)

void SetPartialStop(bool val, ESeqLocExtremes ext)

CConstBeginInfo ConstBegin(const C &obj)

Get starting point of non-modifiable object hierarchy.

static CObjectOStream * Open(ESerialDataFormat format, CNcbiOstream &outStream, bool deleteOutStream)

Create serial object writer and attach it to an output stream.

TSeqPos GetStop(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the stop of the location.

const CSeq_id & GetId(const CSeq_loc &loc, CScope *scope)

If all CSeq_ids embedded in CSeq_loc refer to the same CBioseq, returns the first CSeq_id found,...

ENa_strand GetStrand(const CSeq_loc &loc, CScope *scope=0)

Returns eNa_strand_unknown if multiple Bioseqs in loc Returns eNa_strand_other if multiple strands in...

TSeqPos GetStart(const CSeq_loc &loc, CScope *scope, ESeqLocExtremes ext=eExtreme_Positional)

If only one CBioseq is represented by CSeq_loc, returns the position at the start of the location.

bool IsSameBioseq(const CSeq_id &id1, const CSeq_id &id2, CScope *scope, CScope::EGetBioseqFlag get_flag=CScope::eGetBioseq_All)

Determines if two CSeq_ids represent the same CBioseq.

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

Main method.

static void Translate(const string &seq, string &prot, const CGenetic_code *code, bool include_stop=true, bool remove_trailing_X=false, bool *alt_start=NULL, bool is_5prime_complete=true, bool is_3prime_complete=true)

Translate a string using a specified genetic code.

@ eGetId_Best

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

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)

Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

void AddDefaults(TPriority pri=kPriority_Default)

Add default data loaders from object manager.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

TBioseqCore GetBioseqCore(void) const

Get bioseq core structure.

const CSeqFeatData & GetData(void) const

TSeqPos GetBioseqLength(void) const

bool IsSetProduct(void) const

CScope & GetScope(void) const

Get scope this handle belongs to.

CRef< CSeq_loc > GetRangeSeq_loc(TSeqPos start, TSeqPos stop, ENa_strand strand=eNa_strand_unknown) const

Return CSeq_loc referencing the given range and strand on the bioseq If start == 0,...

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

SAnnotSelector & SetResolveAll(void)

SetResolveAll() is equivalent to SetResolveMethod(eResolve_All).

SAnnotSelector & SetAdaptiveDepth(bool value=true)

SetAdaptiveDepth() requests to restrict subsegment resolution depending on annotations found on lower...

const CSeq_loc & GetProduct(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.

position_type GetLength(void) 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.

#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.

NCBI_NS_STD::string::size_type SIZE_TYPE

static string SizetToString(size_t value, TNumToStringFlags flags=0, int base=10)

Convert size_t to string.

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 bool IsBlank(const CTempString str, SIZE_TYPE pos=0)

Check if a string is blank (has no text).

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.

static string & ToLower(string &str)

Convert string to lower case – string& version.

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[]

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.

TId & SetId(void)

Select the variant.

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.

E_Choice Which(void) const

Which variant is currently selected.

const TLoc & GetLoc(void) const

Get the Loc member data.

list< CRef< CStd_seg > > TStd

void SetSegs(TSegs &value)

Assign a value to Segs data member.

const TIds & GetIds(void) const

Get the Ids member data.

void SetType(TType value)

Assign a value to Type data member.

const TStd & GetStd(void) const

Get the variant data.

const TDendiag & GetDendiag(void) const

Get the variant data.

list< CRef< CSeq_align > > Tdata

list< CRef< CDense_diag > > TDendiag

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

void SetLocation(TLocation &value)

Assign a value to Location data member.

void SetComment(const TComment &value)

Assign a value to Comment data member.

Tdata & Set(void)

Assign a value to data member.

E_Choice

Choice variants.

TFrame GetFrame(void) const

Get the Frame member data.

void SetData(TData &value)

Assign a value to Data data member.

const TCdregion & GetCdregion(void) const

Get the variant data.

bool IsSetFrame(void) const

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

void Select(E_Choice index, EResetVariant reset=eDoResetVariant)

Select the requested variant if needed.

ENa_strand

strand of nucleic acid

const TId & GetId(void) const

Get the Id member data.

const TWhole & GetWhole(void) const

Get the variant data.

TFrom GetFrom(void) const

Get the From member data.

E_Choice Which(void) const

Which variant is currently selected.

TGi GetGi(void) const

Get the variant data.

bool IsLocal(void) const

Check if variant Local is selected.

TTo GetTo(void) const

Get the To member data.

bool IsWhole(void) const

Check if variant Whole is selected.

@ e_Gi

GenInfo Integrated Database.

@ e_not_set

No variant selected.

TSeq & SetSeq(void)

Select the variant.

void SetData(TData &value)

Assign a value to Data data member.

TAnnot & SetAnnot(void)

Assign a value to Annot data member.

const TId & GetId(void) const

Get the Id member data.

list< CRef< CSeq_id > > TId

list< CRef< CSeq_feat > > TFtable

list< CRef< CSeq_annot > > TAnnot

@ e_Ncbieaa

extended ASCII 1 letter aa codes

unsigned int

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

HTML library helper classes and functions.

if(yy_accept[yy_current_state])

CMD5 - class for computing Message Digest version 5 checksums.

const TYPE & Get(const CNamedParameterList *param)

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

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.

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 string kSubject("subject")

Defines BLAST database access classes.

vector< TMaskedQueryRegions > TSeqLocInfoVector

Collection of masked regions for all queries in a BLAST search.

static const char * k_FrameConversion[k_NumFrame]

static void s_OutputFeature(string &reference_feat_line, string &feat_line, bool color_feat_mismatch, int start, int len, CNcbiOstream &out, bool is_html)

void s_CalculateIdentity(const string &sequence_standard, const string &sequence, char gap_char, int &match, int &align_length)

static const char * k_DefaultSpaceMaintainerTempl

static void s_DisplayIdentityInfo(CNcbiOstream &out, int aln_stop, int identity, int positive, int match, int gap, int master_strand, int slave_strand, int master_frame, int slave_frame, bool aln_is_prot)

show blast identity, positive etc.

static const int k_SeqStopMargin

static const char * k_DefaultAnchorWithPosTempl

static const char * k_DefaultFeaturesTempl

static const int k_NumFrame

static const int k_GetSubseqThreshhold

static const char * color[]

static string s_MapFeatureURL(string viewerURL, string textSeqID, string db, int fromRange, int toRange, string rid)

static CRef< CScope > s_MakeNewMasterSeq(list< list< CRange< TSeqPos > > > &feat_range, list< ENa_strand > &feat_seq_strand, const CBioseq_Handle &handle)

make a new copy of master seq with feature info and return the scope that contains this sequence

static const char k_IntronChar

static int x_AddBar(string &seq, int insert_alnpos, int aln_start)

add a "|" to the current insert for insert on next rows and return the insert end position.

static const char k_IdentityChar

static void s_MakeDomainString(int aln_from, int aln_to, const string &domain_name, string &final_domain)

static string s_GetCdsSequence(int genetic_code, CFeat_CI &feat, CScope &scope, list< CRange< TSeqPos > > &range, const CBioseq_Handle &handle, ENa_strand feat_strand, string &feat_id, TSeqPos frame_adj, bool mix_loc)

return cds coded sequence and fill the id if found

static int s_AdjustInsert(string &cur_insert, string &new_insert, int insert_alnpos, int aln_start)

Add new insert seq to the current insert seq and return the end position of the latest insert.

static const int k_MinDeflinesToShow

static const char * k_DefaultAnchorTempl

static void s_WrapOutputLine(CNcbiOstream &out, const string &str)

wrap line

static const char * k_DefaultCheckboxTempl

static const int k_GetDynamicFeatureSeqLength

static int s_GetFrame(int start, ENa_strand strand, const CSeq_id &id, CScope &sp)

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

static const int k_StartSequenceMargin

static int s_GetStdsegMasterFrame(const CStd_seg &ss, CScope &scope)

reture the frame for master seq in stdseg

static const char * k_DefaultPairwiseWithIdntTempl

static const int k_AlignStatsMargin

static const int k_MaxDeflinesToShow

static void s_ColorDifferentBases(string &seq, char identity_char, CNcbiOstream &out)

To add color to bases other than identityChar.

static void s_MapSlaveFeatureToMaster(list< CRange< TSeqPos > > &master_feat_range, ENa_strand &master_feat_strand, CFeat_CI &feat, list< CSeq_loc_CI::TRange > &slave_feat_range, ENa_strand slave_feat_strand, CAlnVec *av, int row, TSeqPos frame_adj)

map slave feature info to master seq

static const char * k_DefaultCheckboxExTempl

static bool s_ProcessStyledContent(string &seq, int currIndex, bool startStyledOutput, bool stopStyledOutput, string tmpl, string &styledSeqStr, CNcbiOstream &out)

To add style to bases for some conditions.

static const int k_FeatureIdLen

static string s_GetConcatenatedExon(CFeat_CI &feat, ENa_strand feat_strand, list< CRange< TSeqPos > > &range, TSeqPos total_coding_len, string &raw_cdr_product, TSeqPos frame_adj)

return concatenated exon sequence

static void s_FillCdsStartPosition(string &line, string &concat_exon, size_t length_per_line, TSeqPos feat_aln_start_totalexon, ENa_strand seq_strand, ENa_strand feat_strand, list< TSeqPos > &start)

fill the cds start positions (1 based)

static const int k_IdStartMargin

static const int k_SequencePropertyLabelMargin

static string s_GetFinalTranslatedString(const CSeq_loc &loc, CScope &scope, int first_encoding_base, int align_length, const string &translation, const string &sequence, char gap_char)

static const int k_ColorMismatchIdentity

threshhold to color mismatch. 98 means 98%

static const char * k_DefaultMaskSeqLocTempl

#define row(bind, expected)

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 needed for creation seqID URL in descriptions and alignments.

CRange< TSeqPos > seqRange

sequence range

string defline

sequence defline

bool useTemplates

bool indicating that templates should be used when contsructing links

string segs

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

bool advancedView

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

string resourcesUrl

URL(s) to other resources from .ncbirc.

structure for store feature display info

string alignRowTmpl

Template for displayin actual pairwise alignment - BLAST_ALIGN_ROWS.

string alnTitlesTmpl

Template for displaying multiple defline titles.

string alignFeatureLinkTmpl

Template for displaying align features link -ALN_FEATURES_LINK.

string alignInfoFrameTmpl

Template for displaying frame data ALIGN_PARAMS_FRAME, part of BLAST_ALIGN_PARAMS.

string alnSeqInfoTmpl

Template for displaying sequnce link in defline.

string alignQueryAnchTempl

Template for displaying one set of query anchored alignment - BLAST_QUERY_ANCH_NAV.

string alnTitlesLinkTmpl

Template for displaying link for more defline titles.

string alignInfoMethodTmpl

Template for displaying frame data ALIGN_PARAMS_METHOD, part of BLAST_ALIGN_PARAMS.

string alignFeatureTmpl

Template for displaying align features -ALN_FEATURES.

string sortInfoTmpl

Template for displaying Sort by header - SORT_ALIGNS_SEQ.

string alnDefLineTmpl

Template for displaying one defline ALN_DEFLINE_ROW.

string alignInfoTmpl

Template for displaying singe align params - BLAST_ALIGN_PARAMS_NUC,BLAST_ALIGN_PARAMS_PROT.

string alignHeaderTmpl

Template for displaying header,deflines and gene info - BLAST_ALIGN_HEADER.

string alignRowTmplLast

Template for displayin actual last pairwise alignment - BLAST_ALIGN_ROWS_LST.

CRef< objects::CSeq_id > seqID

seqID used in defline

CAlignFormatUtil::SSeqURLInfo * seqUrlInfo

list< CRef< objects::CSeq_id > > ids

TGi gi

gi used in defline

string title

sequnce title

store feature information

store alnvec and score info

CRef< objects::CAlnVec > alnvec

vector< objects::SFeatInfo * > feat_list

objects::SFeatInfo * feat5

objects::SFeatInfo * feat3

vector< string > align_stats

vector< objects::CAlnMap::TSignedRange > rowRng

vector< objects::CAlnMap::TSeqPosList > insertLength

bool show_seq_property_label

vector< double > percent_ident

vector< objects::CAlnMap::TSeqPosList > seqStarts

vector< string > seq_property_label

vector< TSAlnSeqlocInfoList > masked_regions

objects::CAlnMap::TSignedRange currRange

vector< objects::CAlnMap::TSeqPosList > insertAlnStart

vector< TSAlnFeatureInfoList > bioseqFeature

vector< objects::CAlnMap::TSeqPosList > insertStart

vector< string > sequence

vector< string > seqidArray

vector< objects::CAlnMap::TSeqPosList > seqStops

int max_seq_property_label

vector< int > align_length

internal insert information aln_start.

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