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

vector<string> format_tokens;

(vector<string>, iter, format_tokens) {

(m_FieldMap.count(*iter) > 0);

x_AddFieldToShow(m_FieldMap[*iter]);

vector<string> format_tokens;

(format_tokens.empty())

(vector<string>, iter, format_tokens) {

((*iter)[0] ==

) {

field = (*iter).substr(1);

(resolved.empty())

(

<<

);

parse_local_ids)

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

(; iter != defline.end(); ++iter)

(iter != defline.begin())

((*iter)->IsSetTitle())

((*iter)->GetTitle().empty())

(defline.front()->IsSetTitle())

(defline.front()->GetTitle().empty())

<< defline.front()->GetTitle();

vector<string> title_tokens;

(title_tokens.empty()){

id_token = title_tokens[0];

(obj_id.

())

id_token = obj_id.

();

obj_id->

(id_token);

retval->

(*sid_in);

vector<CConstRef<objects::CSeq_id> > subject_id_list;

subject_id_list.push_back(next_id);

vector< CConstRef<CSeq_id> > original_seqids;

original_seqids.clear();

original_seqids.push_back(*

);

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

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

subject_id_list.push_back(next_id);

(name ==

)

((*itr)->IsSetTaxid()) {

(;desc_s; ++desc_s) {

(; desc; ++desc) {

(align.

(

, pct))

= 100.0 *

/(double) query_len;

kQueryRow = 0;

kSubjectRow = 1;

score = 0, sum_n = 0;

bit_score = .0, evalue = .0;

list<TGi> use_this_gi;

num_ident, use_this_gi);

bioseqs_found =

;

list<CRef<CSeq_id> > query_ids;

query_ids.push_back(

);

bioseqs_found =

;

(setSubjectIds || setSubjectTaxInfo || setSubjectTaxInfoAll || setSubjectTitle ||

(setSubjectIds || setSubjectTaxInfo || setSubjectTitle || setSubjectTaxInfoAll) {

(setSubjectTaxInfoAll) {

(setSubjectTaxInfo) {

(setSubjectTitle) {

list<CRef<CSeq_id> > subject_ids;

subject_ids.push_back(

);

bioseqs_found =

;

(query_is_na && subject_is_na) {

finalAln = densegAln;

reversed_ds->

(ds);

align_length = 0, num_gaps = 0, num_gap_opens = 0;

num_positives = 0;

btop_string =

;

(

= 0;

(num_matches > 0) {

(matrix && !matrix->

().empty() &&

(num_matches > 0) {

q_start = 0, q_end = 0, s_start = 0, s_end = 0;

q_start = alnVec->

(kQueryRow) + 1;

s_start = alnVec->

(kSubjectRow) + 1;

s_end = alnVec->

(kSubjectRow) + 1;

query_frame = 1, subject_frame = 1;

((s_start - s_end) > 0 ) {

(num_ident, align_length, num_gaps, num_gap_opens, num_positives,

query_frame, subject_frame);

<<

;

;

<<

;

;

<<

;

;

<<

;

;

<<

;

;

<<

;

;

<<

;

;

<<

;

;

<<

;

;

<<

;

;

<<

;

;

<<

;

;

<<

;

;

<<

;

;

<<

;

;

& rid

,

iteration

,

num_hits = align_set->

().size();

(num_hits != 0) {

<<

<< num_hits <<

<<

;

iteration,

<<

<< iteration <<

;

kLineLength(0);

kHtmlFormat(

);

kTabularFormat(

);

kTabularFormat, rid);

kHtmlFormat, kTabularFormat);

<<

<< num_queries <<

;

total_bit_string, raw_score_string;

, total_bit_string, raw_score_string);

((evalue >= 1.0e-180) && (evalue < 0.0009)){

positives,

query_frame,

subject_frame)

list<string> field_names;

field_names.push_back((*iter).first);

list<ETabularField>::iterator iter;

& program_version,

& domain_sys,

& rid

,

iteration

,

<<

<< domain_sys << endl;

<<

<< endl;

num_hits = align_set->

().size();

(num_hits != 0) {

<<

<< num_hits <<

<<

;

& junction_seq,

& query_seq) {

(right_start <= left_stop) {

np_len = left_stop - right_start + 1;

np_start = right_start;

junction_seq =

+ query_seq.substr(np_start, np_len) +

;

np_len = right_start - left_stop - 1;

junction_len = np_len;

np_start = left_stop + 1;

junction_seq = query_seq.substr(np_start, np_len);

((

)qrange.

() < query_len) {

((

)srange.

() < subject_len) {

(

=0;

< starts.size();

+=2) {

(starts[

] >= 0 && starts[

+ 1] >= 0) {

(starts[

] < 0) {

(lens[

/2] < 10) {

((

)qrange.

() < query_len) {

((

)srange.

() < subject_len) {

(

& nuc_without_gap,

& nuc,

& prot,

gap_char) {

new_prot (new_prot_size,

);

total_inserted_gap = 0;

(

= 0;

< (

)

.size();

++) {

(

[

] == gap_char) {

index_new_prot = (

+1)/3 - 1;

index_original_prot = index_new_prot - total_inserted_gap;

(num_gaps == 3) {

(index_new_prot < (

)new_prot.size()) {

total_inserted_gap ++;

(num_bases == 0) {

new_prot[index_new_prot] = gap_char;

}

(num_bases == 3) {

index_new_prot -= gap_hold;

(index_new_prot < (

)new_prot.size() && index_original_prot < (

)

.size()) {

new_prot[index_new_prot] =

[index_original_prot];

(

j = 0; j < gap_hold; j++) {

position = index_new_prot + 1 + j;

(position < (

) new_prot.size()) {

new_prot[position] = gap_char;

((

)nuc_without_gap.size()%3 > 0) {

(

.size() > nuc_without_gap.size()/3) {

new_prot[new_prot.size() - 1] =

[

.size() - 1];

}

(new_prot[new_prot.size() - 1] ==

) {

new_prot.pop_back();

& aligned_query_string,

& aligned_germline_string,

& query_translation_string,

& germline_translation_string){

(annot->m_FrameInfo[0] >=0) {

query_trans_offset = ((alnvec.

(0) + 3) - annot->m_FrameInfo[0])%3;

query_trans_start = query_trans_offset > 0?(3 - query_trans_offset):0;

gap_str.push_back(gap_char);

(

= query_trans_start;

< (

)aligned_vdj_query.size();

=

+ 3) {

(query_aln_pos < (

)aligned_germline_string.size() &&

query_aln_pos< (

)aligned_query_string.size() &&

aligned_germline_string[query_aln_pos] != gap_char &&

aligned_query_string[query_aln_pos] != gap_char){

query_translation_template = aligned_query_string.substr(query_aln_pos);

query_translation_string,

query_translation_string =

(final_query_translation_template, query_translation_template, query_translation_string, gap_char);

germline_translation_template = aligned_germline_string.substr(query_aln_pos);

germline_translation_string,

germline_translation_string =

(final_germline_translation_template, germline_translation_template, germline_translation_string, gap_char);

identity = 0;

identity = ((double)num_ident)/length;

v_query_alignment =

;

v_germline_alignment =

;

airr_data[

], airr_data[

]);

identity = 0;

identity = ((double)num_ident)/length;

d_query_alignment =

;

d_germline_alignment =

;

airr_data[

], airr_data[

]);

identity = 0;

identity = ((double)num_ident)/length;

j_query_alignment =

;

j_germline_alignment =

;

airr_data[

], airr_data[

]);

airr_data[

] = v_identity_str;

airr_data[

] = d_identity_str;

airr_data[

] = j_identity_str;

airr_data[

] = v_query_alignment;

airr_data[

] = d_query_alignment;

airr_data[

] = j_query_alignment;

airr_data[

] = v_germline_alignment;

airr_data[

] = d_germline_alignment;

airr_data[

] = j_germline_alignment;

airr_data[

] = whole_query_alignment;

airr_data[

] +=

;

airr_data[

] += seq.substr(start_pos);

airr_data[

] +=

;

airr_data[

] += seq.substr(start_pos);

airr_data[

] +=

;

airr_data[

] += seq .substr(start_pos);

identity = 0;

identity = ((double)num_ident)/length;

c_query_alignment =

;

c_germline_alignment =

;

airr_data[

], airr_data[

]);

airr_data[

] = c_identity_str;

airr_data[

] = c_query_alignment;

airr_data[

] = c_germline_alignment;

(align_d && align_j) {

}

(align_j) {

(align_d && align_j) {

}

(align_j) {

airr_data[

], airr_data[

]);

locus_name = {{

,

}, {

,

}, {

,

}, {

,

},

{

,

}, {

,

}, {

,

}};

found_v =

;

found_d =

;

found_j =

;

found_c =

;

(align_result && !align_result.

() && align_result->

() && align_result->

()) {

(annot->m_ChainType[index] ==

&& !found_v) {

(annot->m_ChainType[index] ==

&& !found_d) {

temp_align->

(**iter);

(annot->m_ChainType[index] ==

&& !found_j) {

(annot->m_ChainType[index] ==

&& !found_c) {

(list<string>, iter, ig_opts->m_AirrField) {

(align_result && !align_result.

() && align_result->

() && align_result->

() && !(align_result->

().empty())) {

list<CRef<CSeq_id> > query_seqid =

();

(annot->m_FrameInfo[0] >= 0) {

seq_data(

, annot->m_FrameInfo[0],

.length() - annot->m_FrameInfo[0]);

(locus_name.

(annot->m_ChainTypeToShow) != locus_name.

()) {

[

] = locus_name[annot->m_ChainTypeToShow];

v_evalue = 0;

d_evalue = 0;

j_evalue = 0;

c_evalue = 0;

(annot->m_DframeStart > 0 && annot->m_FrameInfo[2] > 0) {

(annot->m_FrameInfo[2] >= query_d_start) {

d_frame_used = ((annot->m_FrameInfo[2] - query_d_start)%3 + query_d_frame_start)%3;

query_length > query_J_stop + 1))) {

(

[

]->name.find(

) != string::npos) {

(

[

]->name.find(

) != string::npos) {

(

[

]->name.find(

) != string::npos) {

(

[

]->name.find(

) != string::npos) {

(

[

]->name.find(

) != string::npos && annot->m_DomainInfo[9] >=0) {

list<CRef<CSeq_id> > query_seqid =

();

& program_version,

& domain_sys,

iteration,

print_airr_format_header,

(print_airr_format_header) {

(list<string>, iter, ig_opts->m_AirrField) {

(list<string>, iter, ig_opts->m_AirrField) {

& chain_type,

& master_chain_type_to_show,

retval =

(align, scope, chain_type, master_chain_type_to_show, matrix);

& chain_type,

& master_chain_type_to_show,

coding_frame_offset = (

- annot->m_FrameInfo[0])%3;

fwr4_seq_for_translatioin =

.substr(coding_frame_offset>0?(3-coding_frame_offset):0);

coding_frame_offset = (

- annot->m_FrameInfo[0])%3;

cdr3_seq_for_translatioin =

.substr(coding_frame_offset>0?(3-coding_frame_offset):0);

(

)(query_length - airrcdr3start)));

airr_cdr3_seq_for_translatioin =

.substr(coding_frame_offset>0?(3-coding_frame_offset):0);

(

& nuc_seq,

& translated_seq,

is_first_domain,

region_start,

frame_start,

& next_trans_addition,

& next_trans_substract,

extra_from_next_region) {

(is_first_domain) {

coding_frame_offset = ((region_start%3 + 3) - frame_start%3)%3;;

start_pos = coding_frame_offset>0?(3-coding_frame_offset):0;

(start_pos < (

)nuc_seq.size()){

seq_for_translatioin = nuc_seq.substr(start_pos);

seq_for_translatioin = next_trans_addition + nuc_seq;

(next_trans_substract) {

seq_for_translatioin.erase(0, 1);

next_trans_substract =

;

next_trans_offset = seq_for_translatioin.length()%3;

(next_trans_offset == 2) {

seq_for_translatioin = seq_for_translatioin + extra_from_next_region;;

next_trans_substract =

;

}

(next_trans_offset == 1) {

next_trans_addition = seq_for_translatioin.substr(seq_for_translatioin.length() - next_trans_offset);

seq_for_translatioin = seq_for_translatioin.substr(0, seq_for_translatioin.length() - next_trans_offset);

(align_result && !align_result.

() && align_result->

() && align_result->

()) {

(annot->m_ChainType[index] ==

|| annot->m_ChainType[index] ==

|| annot->m_ChainType[index] ==

) {

is_protein = ig_opts->m_IsProtein;

(annot->m_TopGeneIds[0], annot->m_GeneInfo[0], annot->m_GeneInfo[1]);

(annot->m_TopGeneIds[1], annot->m_GeneInfo[2], annot->m_GeneInfo[3]);

(annot->m_TopGeneIds[2], annot->m_GeneInfo[4], annot->m_GeneInfo[5]);

(annot->m_TopGeneIds[3], annot->m_GeneInfo[6], annot->m_GeneInfo[7]);

(annot->m_FrameInfo[1] >= 0 && annot->m_FrameInfo[2] >= 0) {

off = annot->m_FrameInfo[1];

= annot->m_FrameInfo[2] - off;

(annot->m_FrameInfo[0] >= 0) {

= (annot->m_FrameInfo[1] - annot->m_FrameInfo[0])%3 == 0 ?

:

;

(

% 3 == 0) {

(seq_trans.find(

) != string::npos) {

(annot->m_FrameInfo[0] >= 0) {

v_start = annot->m_FrameInfo[0];

v_j_length =

(

(annot->m_GeneInfo[5], annot->m_GeneInfo[3]), annot->m_GeneInfo[1]) - annot->m_FrameInfo[0];

seq_data(

, v_start, v_j_length);

(seq_trans.find(

) == string::npos) {

((ig_opts->m_DomainSystem ==

)?

:

,

annot->m_DomainInfo[0], annot->m_DomainInfo[1]+1,

annot->m_DomainInfo_S[0], annot->m_DomainInfo_S[1]+1);

((ig_opts->m_DomainSystem ==

)?

:

,

annot->m_DomainInfo[2], annot->m_DomainInfo[3]+1,

annot->m_DomainInfo_S[2], annot->m_DomainInfo_S[3]+1);

((ig_opts->m_DomainSystem ==

)?

:

,

annot->m_DomainInfo[4], annot->m_DomainInfo[5]+1,

annot->m_DomainInfo_S[4], annot->m_DomainInfo_S[5]+1);

((ig_opts->m_DomainSystem ==

)?

:

,

annot->m_DomainInfo[6], annot->m_DomainInfo[7]+1,

annot->m_DomainInfo_S[6], annot->m_DomainInfo_S[7]+1);

((ig_opts->m_DomainSystem ==

)?

:

,

annot->m_DomainInfo[8], annot->m_DomainInfo[9]+1,

annot->m_DomainInfo_S[8], annot->m_DomainInfo_S[9]+1);

((ig_opts->m_DomainSystem ==

)?

:

,

annot->m_DomainInfo[10], annot->m_DomainInfo[11]+1);

is_first_domain =

;

next_trans_substract =

;

(

[

]->name.find(

) != string::npos) {

next_trans_addition, next_trans_substract,

is_first_domain =

;

(

[

]->name.find(

) != string::npos) {

next_trans_addition, next_trans_substract,

is_first_domain =

;

(

[

]->name.find(

) != string::npos) {

next_trans_addition, next_trans_substract,

is_first_domain =

;

(

[

]->name.find(

) != string::npos) {

next_trans_addition, next_trans_substract,

is_first_domain =

;

(

[

]->name.find(

) != string::npos) {

(annot->m_DomainInfo[9] >=0) {

<< header <<

<<

<<

<< endl << endl;

<< header <<

;

(ig_opts->m_Db[4]) {

<<

;

<<

;

<<

<< endl;

(ig_opts->m_Db[4]) {

(!length)

;

<< header <<

;

<<

<< endl;

num_mismatch = 0;

<<

<<

<<

;

<<

;

<<

;

<<

;

<<

;

(ig_opts->m_Db[4]) {

<<

;

<<

<<

<<

<<

<<

;

(ig_opts->m_Db[4]) {

<<

;

(!length)

;

<<

;

<<

<<

<<

;

num_mismatch = 0;

<<

<< length

<<

<< num_match

<<

<< num_mismatch

<<

<< num_gap

<<

<< std::setprecision(3) << num_match*100.0/length

isOverlap = (start > end);

(start <0 || end <0 || start==end) {

(

pos = start; pos < end; ++pos) {

b0, b1, b2, b3, b4, b5;

<<

;

<<

;

<<

<<

;

<<

;

<< header <<

;

<<

<<

<< endl;

<<

<<

<<

<<

;

<<

;

<<

;

<< header <<

<< endl;

q_pos = 0, s_pos = 0;

(domain.

> 0) {

<< std::setprecision(3)

<<

<< domain.

+1 <<

<<

<< domain.

<<

;

(domain.

> 0) {

<<

<< domain.

<<

<<

<< domain.

<<

<<

<< std::setprecision(3)

<<

;

User-defined methods of the data storage class.

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

Formatting of pairwise sequence alignments in tabular form.

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

Create denseseg representation for densediag seqalign.

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 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 string GetTitle(const objects::CBioseq_Handle &bh)

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.

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

TSignedSeqPos GetSeqAlnStart(TNumrow row) const

TSeqPos GetSeqStop(TNumrow row) const

TSignedSeqPos GetSeqAlnStop(TNumrow row) const

TSeqPos GetSeqStart(TNumrow row) const

void Add(const CDense_seg &ds, TAddFlags flags=0)

void Merge(TMergeFlags flags=0)

const CDense_seg & GetDenseg(void) const

TResidue GetGapChar(TNumrow row) const

string & GetSeqString(string &buffer, TNumrow row, TSeqPos seq_from, TSeqPos seq_to) const

void SetGapChar(TResidue gap_char)

string & GetWholeAlnSeqString(TNumrow row, string &buffer, TSeqPosList *insert_aln_starts=0, TSeqPosList *insert_starts=0, TSeqPosList *insert_lens=0, unsigned int scrn_width=0, TSeqPosList *scrn_lefts=0, TSeqPosList *scrn_rights=0) const

void SetAaCoding(TCoding coding)

CSeqVector::TResidue TResidue

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

Class containing information needed for tabular formatting of BLAST results.

ESeqIdType

In what form should the sequence identifiers be shown?

@ eAccession

Show only best accession.

@ eFullId

Show full seq-id, with multiple ids concatenated.

@ eAccVersion

Show only best accession.version.

list< CRef< objects::CSeq_id > > m_QueryId

List of query ids for this HSP.

string m_BitScore

Bit score of this HSP, in appropriate format.

void x_PrintSubjectTaxIds()

Print subject tax info.

void x_PrintSubjectAccessionVersion(void)

Print subject accession.version.

void x_PrintSubjectBlastName()

void SetParseSubjectDefline(bool val)

Should subject deflien be parsed for id or not?

void x_PrintSubjectSeq(void)

Print aligned part of subject sequence.

void x_PrintQueryLength()

Print the query sequence length.

void x_PrintSubjectCommonName()

void x_PrintSubjectAllAccessions(void)

Print all accessions associated with this subject, separated by ';'.

void x_PrintSubjectSciName()

void x_PrintNumIdentical(void)

Print number of identical matches.

map< string, ETabularField > m_FieldMap

Map of field enum values to field names.

void x_SetTaxInfo(const objects::CBioseq_Handle &handle, const CRef< objects::CBlast_def_line_set > &bdlRef)

void x_PrintSubjectEnd(void)

Print subject end.

pair< string, int > m_QueryCovUniqSubject

void x_PrintSeqalignCoverage()

void x_PrintSubjectTitle()

void x_PrintGapOpenings(void)

Print number of gap openings.

void SetBTOP(string btop_string)

Sets the Blast-traceback-operations string.

void PrintNumProcessed(int num_queries)

Prints number of queries processed.

set< string > m_SubjectSuperKingdoms

void x_PrintSubjectAllSeqIds(void)

Print all Seq-ids associated with this subject, separated by ';'.

int m_AlignLength

Alignment length of this HSP.

set< string > m_SubjectBlastNames

bool m_ParseSubjectDefline

Parse subejct defline?

void x_AddFieldToShow(ETabularField field)

Add a field to the list of fields to show, if it is not yet present in the list of fields.

void x_PrintSubjectTaxId()

void x_PrintSubjectSuperKingdom()

string m_SubjectBlastName

EFieldDelimiter

What delimiter to use between fields in each row of the tabular output.

int m_SubjectStart

Starting offset in subject.

void PrintFieldSpecs(void)

Print field specifiers of all requested fields.

void x_PrintPercentIdentical(void)

Print percent of identical matches.

CBlastTabularInfo(CNcbiOstream &ostr, const string &format=kDfltArgTabularOutputFmt, EFieldDelimiter delim=eTab, bool parse_local_ids=false)

Constructor.

void x_PrintScore(void)

Print raw score.

void x_PrintQueryStart(void)

Print query start.

void x_PrintBitScore(void)

Print bit score.

TSeqPos m_SubjectLength

Length of subject sequence.

void x_PrintGaps(void)

Print total number of gaps.

void x_PrintNumPositives(void)

Print number of positive matches.

int m_SubjectEnd

Ending offset in subject.

string m_SubjectSuperKingdom

string m_SubjectSeq

Aligned part of the subject sequence.

void x_SetTaxInfoAll(const objects::CBioseq_Handle &handle, const CRef< objects::CBlast_def_line_set > &bdlRef)

void SetEndpoints(int q_start, int q_end, int s_start, int s_end)

Set the HSP endpoints.

void SetSubjectId(list< CRef< objects::CSeq_id > > &id)

Set subject id from a objects::CSeq_id.

void x_PrintQuerySeqId(void) const

Print query Seq-id.

void x_SetQueryCovUniqSubject(const objects::CSeq_align &align)

CNcbiOstream & m_Ostream

Stream to write output to.

CRef< CBlast_def_line_set > m_SubjectDefline

void PrintFieldNames(bool is_csv=false)

Print the names of all supported fields.

void SetParseLocalIds(bool val)

Should local IDs be parsed or not?

void x_PrintSubjectStart(void)

Print subject start.

int m_QueryEnd

Ending offset in query.

int m_SubjectFrame

subject frame

int m_NumGapOpens

Number of gap openings in this HSP.

vector< string > m_SubjectCommonNames

pair< string, int > m_QueryCovSubject

void x_PrintSubjectLength()

Print the subject sequence length.

list< ETabularField > m_FieldsToShow

Which fields to show?

void x_PrintSubjectCommonNames()

virtual void Print(void)

Print one line of tabular output.

void x_PrintSubjectCoverage()

int SetFields(const objects::CSeq_align &sal, objects::CScope &scope, CNcbiMatrix< int > *matrix=0)

Set all member fields, given a Seq-align.

bool m_ParseLocalIds

Should the query deflines be parsed for local IDs?

void x_PrintUniqSubjectCoverage()

void x_PrintEvalue(void)

Print e-value.

void x_PrintMismatches(void)

Print number of mismatches.

void x_PrintSubjectStrand()

void SetNoFetch(bool nofetch)

Avoid fetching sequence (if possible) If the sequence is needed (e.g., will be formatted,...

void x_PrintSubjectAccession(void)

Print subject accession.

list< string > GetAllFieldNames(void)

Return all field names supported in the format string.

void x_PrintPercentPositives()

Print percent positives.

void x_PrintSubjectSeqId(void)

Print subject Seq-id.

vector< list< CRef< objects::CSeq_id > > > m_SubjectIds

All subject sequence ids for this HSP.

string m_FieldDelimiter

Delimiter character for fields to print.

bool GetNoFetch()

Avoid fetch of sequence if true returned.

const list< CRef< CSeq_id > > & GetQueryId() const

Get query seqid list.

set< TTaxId > m_SubjectTaxIds

Blast-traceback-operations.

void x_PrintSubjectSciNames()

bool x_IsFieldRequested(ETabularField field)

int m_NumPositives

Number of positives in this HSP.

void x_PrintField(ETabularField field)

Print the value of a given field.

void x_PrintSubjectSuperKingdoms()

bool x_IsCsv() const

Convenience method to determine if this object is dealing with CSV output formats.

void x_AddDefaultFieldsToShow(void)

Add a default set of fields to show.

void x_PrintSubjectAllGis(void)

Print all gis associated with this subject, separated by ';'.

int m_QueryStart

Starting offset in query.

~CBlastTabularInfo()

Destructor.

void SetQueryId(list< CRef< objects::CSeq_id > > &id)

Set query id from a objects::CSeq_id.

void x_PrintQuerySeq(void)

Print aligned part of query sequence.

void x_PrintSubjectFrame()

void x_PrintFrames()

Print frames.

void x_ResetFields(void)

Reset values of all fields.

void x_PrintQueryAndDbNames(const string &program, const objects::CBioseq &bioseq, const string &dbname, const string &rid, unsigned int iteration, CConstRef< objects::CBioseq > subj_bioseq)

Print query and database names.

void x_PrintAlignmentLength(void)

Print alignment length.

int m_Score

Raw score of this HSP.

void x_SetFieldsToShow(const string &format)

Set fields to show, given an output format string.

void PrintHeader(const string &program, const objects::CBioseq &bioseq, const string &dbname, const string &rid=kEmptyStr, unsigned int iteration=numeric_limits< unsigned int >::max(), const objects::CSeq_align_set *align_set=0, CConstRef< objects::CBioseq > subj_bioseq=CConstRef< objects::CBioseq >(), bool is_csv=false)

Print the tabular output header.

vector< string > m_SubjectSciNames

void x_PrintQueryGi(void)

Print query gi.

void x_DeleteFieldToShow(ETabularField field)

Delete a field from the list of fields to show.

void x_SetFieldDelimiter(EFieldDelimiter delim, string customDelim="")

Set the tabular fields delimiter.

void x_PrintQueryAccession(void)

Print query accession.

int m_QueryFrame

query frame

void x_PrintSubjectAllTitles()

void x_PrintSubjectBlastNames()

list< CRef< objects::CSeq_id > > m_SubjectId

string m_SubjectCommonName

void x_PrintQueryAccessionVersion(void)

Print query accession.version.

void x_SetQueryCovSeqalign(const CSeq_align &align, int query_len)

void SetScores(int score, double bit_score, double evalue)

Set the HSP scores.

void x_PrintQueryEnd(void)

Print query end.

void x_PrintSubjectGi(void)

Print subject gi.

int m_NumGaps

Total number of gaps in this HSP.

int m_NumIdent

Number of identities in this HSP.

void SetCounts(int num_ident, int length, int gaps, int gap_opens, int positives=0, int query_frame=1, int subject_frame=1)

Set various counts/lengths.

void x_SetSubjectIds(const objects::CBioseq_Handle &bh, const CRef< objects::CBlast_def_line_set > &bdlRef)

void x_SetQueryCovSubject(const objects::CSeq_align &align)

string m_QuerySeq

Aligned part of the query sequence.

string m_Evalue

E-value of this HSP, in appropriate format.

TSeqPos m_QueryLength

Length of query sequence.

ENa_strand GetSeqStrand(TDim row) const

void Reverse(void)

Reverse the segments' orientation.

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

overloaded Assign()

void x_ComputeIgDomain(SIgDomain &domain)

void PrintMasterAlign(const CConstRef< blast::CIgBlastOptions > &ig_opts, const string &header="# ") const

Print domain information.

void SetMinusStrand(bool minus=true)

Set strand information.

vector< SIgDomain * > m_IgDomains

string m_OtherInfo[num_otherinfo]

map< string, string > m_AirrData

CRef< CSeq_align > m_TopAlign_V

void x_PrintIgDomain(const SIgDomain &domain) const

void SetSeqType(bool isNucl)

Set sequence type.

void SetJGene(const string &id, int s, int e)

Set gene info.

int SetFields(const objects::CSeq_align &align, objects::CScope &scope, const string &chain_type, const string &master_chain_type_to_show, CNcbiMatrix< int > *matrix=0)

Set fields for all other alignments.

void SetDGene(const string &id, int s, int e)

Set gene info.

void x_PrintIgGenes(bool isHtml=false, const string &header="# ") const

void PrintHeader(const CConstRef< blast::CIgBlastOptions > &ig_opts, const string &program, const objects::CBioseq &bioseq, const string &dbname, const string &domain_sys, const string &rid=kEmptyStr, unsigned int iteration=numeric_limits< unsigned int >::max(), const objects::CSeq_align_set *align_set=0, CConstRef< objects::CBioseq > subj_bioseq=CConstRef< objects::CBioseq >())

virtual void Print(void)

Override the print method.

void AddIgDomain(const string &name, int start, int end, int s_start=-1, int s_end=-1)

Set domain info.

void SetFrame(const string &frame="N/A")

Set out-of-frame information.

void SetCGene(const string &id, int s, int e)

Set gene info.

CRef< CSeq_align > m_TopAlign_J

void SetIgAnnotation(const CRef< blast::CIgAnnotation > &annot, const CConstRef< blast::CIgBlastOptions > &ig_opts, CConstRef< CSeq_align_set > &align_result, CScope &scope)

One method to set all annotation information.

void SetIgCDR3FWR4Annotation(const CRef< blast::CIgAnnotation > &annot)

method to set cdr3 and fwr4 annotation information

CRef< CSeq_align > m_TopAlign_D

int SetMasterFields(const objects::CSeq_align &align, objects::CScope &scope, const string &chain_type, const string &master_chain_type_to_show, CNcbiMatrix< int > *matrix=0)

Set fields for master alignment.

CRef< CSeq_align > m_TopAlign_C

void SetVGene(const string &id, int s, int e)

Set gene info.

void PrintHtmlSummary(const CConstRef< blast::CIgBlastOptions > &ig_opts) const

Print Html style summary.

static const int num_otherinfo

void x_PrintIgDomainHtml(const SIgDomain &domain) const

void SetAirrFormatData(CScope &scope, const CRef< blast::CIgAnnotation > &annot, const CBioseq_Handle &query_handle, CConstRef< CSeq_align_set > align_result, const CConstRef< blast::CIgBlastOptions > &ig_opts)

void x_PrintPartialQuery(int start, int end, bool isHtml=false) const

string m_AirrCdr3SeqTrans

void PrintAirrRearrangement(CScope &scope, const CRef< blast::CIgAnnotation > &annot, const string &program_version, const CBioseq &query_bioseq, const string &dbname, const string &domain_sys, const string &rid, unsigned int iteration, const CSeq_align_set *align_set, CConstRef< CBioseq > subj_bioseq, CNcbiMatrix< int > *matrix, bool print_airr_format_header, const CConstRef< blast::CIgBlastOptions > &ig_opts)

string m_MasterChainTypeToShow

TData & GetData()

retrieve the data associated with this matrix

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

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.

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 ...

void Reverse(void)

Reverse the segments' orientation NOTE: currently *only* works for dense-seg.

CRange< TSeqPos > GetSeqRange(TDim row) const

GetSeqRange NB: On a Spliced-seg, in case the product-type is protein, these only return the amin par...

TSeqPos GetSeqStop(TDim row) const

const CSeq_id & GetSeq_id(TDim row) const

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

bool GetNamedScore(const string &id, int &score) const

Get score.

TSeqPos GetSeqStart(TDim row) const

ENa_strand GetSeqStrand(TDim row) const

Get strand (the first one if segments have different strands).

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

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

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

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

@ eRight

Towards higher aln coord (always to the right)

const_iterator begin() const

const_iterator end() const

iterator_bool insert(const value_type &val)

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator end() const

ETabularField

Enumeration for all fields that are supported in the tabular output.

@ eAlignmentLength

Alignment length.

@ eSubjectEnd

End of alignment in subject.

@ eSubjectAllAccessions

All subject accessions, separated by ';'.

@ eQueryCovSubject

Query Coverage per Subject.

@ ePositives

Number of positive-scoring matches.

@ eSubjectAllGis

All subject gis.

@ eSubjectSciName

Subject Scientific Name.

@ eSubjFrame

Subject frame.

@ eSubjectSeq

Aligned part of subject sequence.

@ eQueryStart

Start of alignment in query.

@ eSubjectTaxIds

Subject Tax IDs.

@ eQueryEnd

End of alignment in query.

@ eSubjectCommonNames

Subject Common Names.

@ eQueryAccession

Query accession.

@ eSubjectLength

Subject sequence length.

@ eSubjectSeqId

Subject Seq-id(s)

@ eQueryAccessionVersion

Query accession.version.

@ eGapOpenings

Number of gap openings.

@ eQuerySeqId

Query Seq-id(s)

@ eSubjectAccession

Subject accession.

@ ePercentPositives

Percentage of positive-scoring matches.

@ eSubjectBlastName

Subject Blast Name.

@ eNumIdentical

Number of identical matches.

@ eSubjectAllSeqIds

If multiple redundant sequences, all sets of subject Seq-ids, separated by ';'.

@ eMismatches

Number of mismatches.

@ eSubjectStrand

Subject Strand.

@ eSubjectBlastNames

Subject Blast Names.

@ eQueryCovUniqSubject

Query Coverage per Subject.

@ ePercentIdentical

Percentage of identical matches.

@ eSubjectSciNames

Subject Scientific Names.

@ eSubjectTitle

Only the first subject defline.

@ eSubjectSuperKingdoms

Subject Super Kingdoms.

@ eQuerySeq

Aligned part of query sequence.

@ eSubjectTaxId

Subject Tax ID.

@ eSubjectStart

Start of alignment in subject.

@ eSubjAccessionVersion

Subject accession.version.

@ eSubjectSuperKingdom

Subject Super Kingdom.

@ eSubjectAllTitles

All subject deflines.

@ eGaps

Total number of gaps.

@ eBTOP

BLAST traceback operations.

@ eQueryFrame

Query frame.

@ eQueryLength

Query sequence length.

@ eQueryCovSeqalign

Query Coverage per Seqalign.

@ eSubjectCommonName

Subject Common Name.

const char * kDfltArgTabularOutputFmtTag

Tag/keyword which is equivalent to using kDfltArgTabularOutputFmt.

const char * kDfltArgTabularOutputFmt

Default value for tabular and comma-separated value output formats.

const size_t kNumTabularOutputFormatSpecifiers

Number of elements in the sc_FormatSpecifiers array.

const SFormatSpec sc_FormatSpecifiers[]

Array containing the supported output formats for tabular output.

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

static SQLCHAR output[256]

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

#define ERR_POST(message)

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

void Warning(CExceptionArgs_Base &args)

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

Set object to copy of another one.

const string AsFastaString(void) const

TGi FindGi(const container &ids)

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

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

Optimized implementation of CSerialObject::Assign, which is not so efficient.

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

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

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

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

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

@ fLabel_Version

Show the version.

@ eContent

Untagged human-readable accession or the like.

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

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

TTaxId GetTaxId(const CBioseq_Handle &handle)

return the tax-id associated with a given sequence.

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.

@ fIs5PrimePartial

= 0x4 Translate first codon even if not start codon (because sequence is 5' partial)

CBioseq_Handle GetBioseqHandle(const CSeq_id &id)

Get bioseq handle by seq-id.

CSeq_inst::TMol GetSequenceType(const CSeq_id &id, TGetFlags flags=0)

Get molecular type of sequence (protein/dna/rna) Return CSeq_inst::eMol_not_set if sequence is not fo...

vector< CSeq_id_Handle > TId

TSeqPos GetBioseqLength(void) const

CConstRef< CSeq_id > GetSeqId(void) const

Get id which can be used to access this bioseq handle Throws an exception if none is available.

const TId & GetId(void) const

CSeqVector GetSeqVector(EVectorCoding coding, ENa_strand strand=eNa_strand_plus) const

Get sequence: Iupacna or Iupacaa if use_iupac_coding is true.

@ eCoding_Iupac

Set coding to printable coding (Iupacna or Iupacaa)

void GetSeqData(TSeqPos start, TSeqPos stop, string &buffer) const

Fill the buffer string with the sequence data for the interval [start, stop).

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 NotEmpty(void) const THROWS_NONE

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

bool NotEmpty(void) const THROWS_NONE

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

position_type GetLength(void) const

bool NotEmpty(void) const

position_type GetToOpen(void) const

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

NCBI_NS_STD::string::size_type SIZE_TYPE

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

Convert Int8 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 string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string Quote(const CTempString str, char quote_char='"', char escape_char = '\\')

Quote string (generic version).

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 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.

@ fDoubleScientific

DoubleToString*(): Use scientific format for double conversions.

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

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

const TOrg & GetOrg(void) const

Get the Org member data.

bool IsSet(void) const

Check if a value has been assigned to data member.

list< CRef< CSeq_id > > TSeqid

bool CanGet(void) const

Check if it is safe to call Get method.

const Tdata & Get(void) const

Get the member data.

list< CRef< CBlast_def_line > > Tdata

TFrom GetFrom(void) const

Get the From member data.

bool IsStr(void) const

Check if variant Str is selected.

const TStr & GetStr(void) const

Get the variant data.

TStr & SetStr(void)

Select the variant.

TId GetId(void) const

Get the variant data.

const TDenseg & GetDenseg(void) const

Get the variant data.

bool CanGet(void) const

Check if it is safe to call Get method.

E_Choice Which(void) const

Which variant is currently selected.

bool IsSetStrands(void) const

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

const TStarts & GetStarts(void) const

Get the Starts member data.

const TLens & GetLens(void) const

Get the Lens member data.

vector< TSignedSeqPos > TStarts

bool IsDendiag(void) const

Check if variant Dendiag is selected.

bool IsStd(void) const

Check if variant Std is selected.

bool IsSet(void) const

Check if a value has been assigned to data member.

list< CRef< CSeq_align > > Tdata

const TStrands & GetStrands(void) const

Get the Strands member data.

const Tdata & Get(void) const

Get the member data.

const TSegs & GetSegs(void) const

Get the Segs member data.

TLocal & SetLocal(void)

Select the variant.

const TLocal & GetLocal(void) const

Get the variant data.

bool IsLocal(void) const

Check if variant Local is selected.

const TSource & GetSource(void) const

Get the variant data.

const TOrg & GetOrg(void) const

Get the variant data.

@ e_Ncbieaa

extended ASCII 1 letter aa codes

@ e_Org

if all from one organism

@ e_Source

source of materials, includes Org-ref

char * dbname(DBPROCESS *dbproc)

Get name of current database.

unsigned int

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

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

string SeqDB_ResolveDbPath(const string &filename)

Resolve a file path using SeqDB's path algorithms.

struct containing annotated domain information

const char * name

Format specification name.

string common_name

Common name, such as "noisy night monkey".

string blast_name

A simple category name, such as "birds".

string s_kingdom

A string of length 1 indicating the "Super Kingdom".

string scientific_name

Scientific name, such as "Aotus vociferans".

static void s_GetCigarString(const CSeq_align &align, string &cigar, int query_len, CScope &scope)

static void SetCdrFwrSeq(const string &nuc_seq, string &translated_seq, bool is_first_domain, int region_start, int frame_start, string &next_trans_addition, bool &next_trans_substract, string extra_from_next_region)

bool s_IsValidName(const string &name)

static string s_GetSeqIdListString(const list< CRef< CSeq_id > > &id, CBlastTabularInfo::ESeqIdType id_type)

CRef< CSeq_id > s_ReplaceLocalId(const CBioseq_Handle &bh, CConstRef< CSeq_id > sid_in, bool parse_local)

static void s_GetGermlineTranslation(const CRef< blast::CIgAnnotation > &annot, CAlnVec &alnvec, const string &aligned_query_string, const string &aligned_germline_string, string &query_translation_string, string &germline_translation_string)

static string s_InsertGap(const string &nuc_without_gap, const string &nuc, const string &prot, char gap_char)

static void s_FillJunctionalInfo(int left_stop, int right_start, int &junction_len, string &junction_seq, const string &query_seq)

static void s_SetAirrAlignmentInfo(const CRef< CSeq_align > &align_v, const CRef< CSeq_align > &align_d, const CRef< CSeq_align > &align_j, const CRef< CSeq_align > &align_c, const CRef< blast::CIgAnnotation > &annot, CScope &scope, map< string, string > &airr_data)

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