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NCBI C++ ToolKit: src/objtools/blast/seqdb_writer/unit_test/writedb_unit_test.cpp Source File

sequence.assign(

, slength);

vector<int> & layout,

BOOST_REQUIRE(layout.size());

(

= 0;

< (

)raw.size();

+= width) {

width = layout[layout_i];

BOOST_REQUIRE(width);

>>= (64 - 8*width);

left = raw.size() -

;

width1 = (left < width) ? left : width;

sub(raw,

, width1);

(

by = 0; by < (

)sub.size(); by++) {

x = (x << 8) + (sub[by] & 0xFF);

layout_i = (layout_i + 1) % layout.size();

layout.push_back(per);

vector<int> & layout,

ifstream

(fname.c_str());

(

&& !

.eof()) {

.read(

, 1024);

amt =

.gcount();

raw.append(

, amt);

layout.push_back(per);

BOOST_REQUIRE(found);

(seqid->

()) {

BOOST_REQUIRE(found);

BOOST_REQUIRE(! seq.empty());

BOOST_REQUIRE(

.empty() || is_nucl);

<

ASNOBJ>

<

ASNOBJ>

<

ASNOBJ>

BOOST_REQUIRE_EQUAL(s1, s2);

& title)

rv1 = dst.

(oid, gi);

rv2 = src.

(gi, src_oid);

BOOST_REQUIRE_EQUAL(dst.

(), title);

(

= 0;

< files.size();

++) {

(s.size() == 0)

;

BOOST_REQUIRE(s2 <= s);

pos =

.rfind(delim);

(pos == string::npos)

.size()-(pos + delim.size()));

need_hash =

)

found_hash =

;

(

= 0;

< files.size();

++) {

(ext ==

|| ext ==

) {

(ext ==

|| ext ==

) {

BOOST_REQUIRE(found_hash);

vector<string> files;

& src_name,

& dst_name,

& title,

+= (is_protein ?

:

);

* ext[] = {

,

,

,

,

};

(

= 0;

< (

(ext)/

(*ext));

++) {

fname(

+

(ext[

]));

vector<string> files;

unique_ptr<CObjectIStream> ois

(

* ptr = gis; *ptr !=

; ptr ++) {

(

** ptr = gis; *ptr; ptr ++) {

BOOST_REQUIRE(!

->AtEOF());

BOOST_REQUIRE(! entry.

());

BOOST_REQUIRE(entry->

());

78883515, 78883517,

24431485, 19110479, 15054463,

15054465, 15054467, 15054469, 15054471, 19570808, 18916476,

1669608, 1669610, 1669612, 1669614, 1669616, 10944307,

10944309, 10944311, 19909844, 19909846, 19909860, 19911180,

19911220, 19911222, 19911224, 57472140, 20126670, 20387092,

57639630, 57639632, 7670507, 2394289, 21280378, 21327938,

6518520, 20086356, 20086357, 21392391, 20086359, 19110509,

21623739, 21623761, 38303844, 38197377, 56788779, 57032781,

57870443, 56789136, 0

srcname(

);

dstname(

);

title(

);

dstname2(

);

title2(

);

1477444, 1669609, 1669611, 1669615, 1669617, 7544146,

22652804,

3114354, 3891778, 3891779, 81294290,

81294330, 49089974, 62798905, 3041810, 7684357, 7684359,

7684361, 7684363, 7544148, 3452560, 3452564, 6681587,

6681590, 6729087, 7259315, 2326257, 3786310, 3845607,

13516469, 2575863, 4049591, 3192363, 1871126, 2723484,

6723181, 11125717, 2815400, 1816433, 3668177, 6552408,

13365559, 8096667, 3721768, 9857600, 2190043, 3219276,

10799943, 10799945, 0

,

);

,

);

BOOST_REQUIRE(bytes.size() == sv.

());

bs1->

().ResetSeq_data();

nm =

;

vector<string> files;

rv1 = db2.

(oid, pig);

db2.

(oid, gis,

);

found_gi =

;

(

= 0;

< gis.size();

++) {

(gis[

] == 129295 + oid) {

BOOST_REQUIRE(found_gi);

BOOST_REQUIRE_EQUAL(pig-oid, 101);

BOOST_REQUIRE_EQUAL(oid, 3);

gis[] = { 129295, 129296, 129297, 129299, 0 };

letter_count = 0;

(

= 0; gis[

];

++) {

BOOST_REQUIRE_EQUAL(3, (

) v.size());

BOOST_REQUIRE_EQUAL(v[0],

(

));

BOOST_REQUIRE_EQUAL(v[1],

(

));

BOOST_REQUIRE_EQUAL(v[2],

(

));

BOOST_REQUIRE_EQUAL(25, (

)

.size());

BOOST_REQUIRE_EQUAL(oids, 4);

BOOST_REQUIRE_EQUAL(letter_count, letters);

vector<string> files;

bdls->

().push_back(dl);

dl->SetTitle(

);

dl->SetSeqid().push_back(seqid);

dl->SetTaxid(12345);

BOOST_REQUIRE(files.size() != 0);

found = seqdb.

(*seqid, oid);

BOOST_REQUIRE_EQUAL(found,

);

BOOST_REQUIRE_EQUAL(oid, 0);

* accs[] = {

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

);

* accs[] = {

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

),

prot_gis[] = { 129295, 129296, 129297, 0 };

nucl_gis[] = { 555, 556, 405832, 0 };

,

,

vector<string> files;

title =

;

I1(

), T1(

);

=

+ I1 +

+ T1 +

+

;

vector<string> files;

title =

;

I1(

), T1(

);

=

+ I1 +

+ T1 +

+

;

BOOST_REQUIRE(oids.size() == 1);

vector<string> files;

title =

;

I1(

), T1(

),

I2(

), T2(

);

+ I1 +

+ T1 +

+ I2 +

+ T2 +

+

BOOST_REQUIRE_EQUAL(bdls->

().size(), 1);

BOOST_REQUIRE_EQUAL(bdls->

().front()->GetTitle(), T1);

BOOST_REQUIRE_EQUAL(bdls->

().front()->GetSeqid().size(), 1);

BOOST_REQUIRE_EQUAL(bdls->

().front()->GetSeqid().front()->AsFastaString(), I1);

fn4(

), fn8(

);

(

= 0;

<10;

++) {

);

);

pair<string, string>

;

vector< TPair > ids48;

a4(1234), b4(2), a8(1234), b8(1000);

prefix =

;

(

= 0;

< 5;

++) {

p4(a4), p8(a8);

BOOST_REQUIRE(a4 > p4);

BOOST_REQUIRE(a8 > p8);

BOOST_REQUIRE((a4 >> 32) == 0);

BOOST_REQUIRE((a8 >> 32) != 0);

dbname4 =

;

dbname8 =

;

dbname4 +

,

dbname8 +

,

iupac =

;

(vector< TPair >, iter, ids48) {

f4 =

(

) + iter->first +

+ iupac +

;

f8 =

(

) + iter->second +

+ iupac +

;

i4(

),

i8(

),

d4(

),

d8(

);

BOOST_REQUIRE(index4 == i4);

BOOST_REQUIRE(index8 == i8);

vector<int> overlay;

overlay.push_back(8);

overlay.push_back(4);

data8 =

(dbname8 +

, overlay, 10);

BOOST_REQUIRE(

== d4);

BOOST_REQUIRE(data8 == d8);

vector<string> files;

meta_data[

] =

;

meta_data[

] =

;

meta_data[

] =

;

vector<string> column_data;

column_data.push_back(

);

column_data.push_back(

);

column_data.push_back(

);

column_data.push_back(

);

column_data.push_back(

);

column_data.push_back(

);

column_data.back()[5] = (char) 0;

fname(

);

vname(

);

title(

);

);

col_id =

.CreateUserColumn(title);

(TMeta, iter, meta_data) {

.AddMetaData(iter->first, iter->second);

.AddColumnMetaData(col_id, iter->first, iter->second);

(vector<string>, iter, column_data) {

.AddSequence(*

.GetBioseq(

++));

vector<int> algo_ids;

(vector<int>,

, algo_ids) {

BOOST_REQUIRE_EQUAL(

,

.IsRegistered(*

));

BOOST_REQUIRE_EQUAL(id1+1, id2);

kMaxNumSupportedAlgorithmVariants)

vector<int> algo_ids;

(

= 0;

< kMaxNumSupportedAlgorithmVariants*2;

++) {

options.assign(

);

(

>= kMaxNumSupportedAlgorithmVariants) {

BOOST_REQUIRE_THROW(algo_id =

.Add(masking_algo, options),

algo_id =

.Add(masking_algo, options);

(algo_id != -1) {

algo_ids.push_back(algo_id);

BOOST_REQUIRE_EQUAL(kMaxNumSupportedAlgorithmVariants, algo_ids.size());

(

= 0;

< algo_ids.size();

++) {

BOOST_REQUIRE_EQUAL((

)(masking_algo +

), algo_ids[

]);

(

= 0;

< kMaxNumSupportedAlgorithmVariants*2;

++) {

algo_id = masking_algo +

;

(

>= kMaxNumSupportedAlgorithmVariants) {

BOOST_REQUIRE_EQUAL(

,

.IsRegistered(algo_id));

BOOST_REQUIRE_EQUAL(

,

.IsRegistered(algo_id));

kNumSeqs = 3;

(

= 0;

< kNumSeqs;

++) {

L =

.GetSeqLength(next_oid);

L =

.GetSeqLength(next_oid);

oids.push_back(next_oid++);

);

(

= 0;

< kNumSeqs;

++) {

oid = oids[

];

.AddSequence(*

.GetBioseq(oid));

ranges.back().algorithm_id = seg_id;

(

j = 0; j < (

+5); j++) {

pair<TSeqPos, TSeqPos> rng;

rng.first =

* 13 + j * 7 + 2;

rng.second = rng.first + 3 + (

+j) % 11;

ranges.back().offsets.push_back(rng);

ranges.back().algorithm_id = repeat_id;

(

j = 0; j < (

+5); j++) {

pair<TSeqPos, TSeqPos> rng;

rng.first =

* 10 + j * 5 + 2;

rng.second = rng.first + 20;

ranges.back().offsets.push_back(rng);

.SetMaskData(ranges, gis);

seg_repeated_id;

BOOST_REQUIRE_THROW( seg_repeated_id =

(void)seg_repeated_id;

vector<int> algo_ids;

kMaxNumSupportedAlgorithmVariants =

(

= 0;

< kMaxNumSupportedAlgorithmVariants*2;

++) {

(

>= kMaxNumSupportedAlgorithmVariants) {

BOOST_REQUIRE_THROW(

algo_id =

.RegisterMaskAlgorithm(masking_algorithm, options),

algo_id =

.RegisterMaskAlgorithm(masking_algorithm, options);

(algo_id != -1) {

algo_ids.push_back(algo_id);

BOOST_REQUIRE_EQUAL(kMaxNumSupportedAlgorithmVariants, algo_ids.size());

(

= 0;

< algo_ids.size();

++) {

BOOST_REQUIRE_EQUAL((

)(masking_algorithm +

), (

)algo_ids[

]);

);

);

L =

.GetSeqLength(oid);

.AddSequence(*

.GetBioseq(oid));

pair<TSeqPos, TSeqPos> rng;

ranges.back().offsets.push_back(rng);

);

);

L =

.GetSeqLength(oid);

.AddSequence(*

.GetBioseq(oid));

pair<TSeqPos, TSeqPos> rng;

ranges.back().offsets.push_back(rng);

(

& v) {

retval =

;

line = line.erase(0,

.GetKey().size()+1);

ifstream alias_file(fname.c_str());

( ! alias_file ) {

; }

(getline(alias_file, line)) {

kCurrentYear =

tmp_aliasfile, tmp_gifile;

kDbName(

);

(

);

kAliasFileName(tmp_aliasfile.

());

ofstream gifile(tmp_gifile.

().c_str());

gifile <<

<< endl;

gifile <<

<< endl;

gifile <<

<< endl;

kAliasFileName +=

;

BOOST_REQUIRE(

(kAliasFileName).Exists());

BOOST_CHECK_EQUAL(

, alias_file_data.

.

());

BOOST_CHECK_EQUAL(

, alias_file_data.

.

());

BOOST_CHECK(alias_file_data.

.

() ==

);

tmp_aliasfile, tmp_gifile;

kDbName(

);

(

);

kAliasFileName(tmp_aliasfile.

());

ofstream gifile(tmp_gifile.

().c_str());

gifile <<

<< endl;

gifile <<

<< endl;

kAliasFileName +=

;

BOOST_REQUIRE(

(kAliasFileName).Exists());

BOOST_CHECK_EQUAL(

, alias_file_data.

.

());

BOOST_CHECK_EQUAL(

, alias_file_data.

.

());

BOOST_CHECK(alias_file_data.

.

() ==

);

BOOST_CHECK(alias_file_data.

.

() ==

);

(

);

kNumVols(3);

kMyAliasDb(

);

kAliasFileName(kMyAliasDb +

);

BOOST_REQUIRE(

(kAliasFileName).Exists());

BOOST_CHECK(alias_file_data.

.

() ==

);

BOOST_CHECK(alias_file_data.

.

() ==

);

kDbName(

);

(

);

kAliasFileName(tmp_aliasfile.

());

kAliasFileName +=

;

BOOST_REQUIRE(

(kAliasFileName).Exists());

BOOST_CHECK(alias_file_data.

.

() ==

);

BOOST_CHECK(alias_file_data.

.

() ==

);

(

);

kMyAliasDb(

);

kAliasFileName(kMyAliasDb +

);

vector<string> dbs2aggregate;

dbs2aggregate.push_back(

);

dbs2aggregate.push_back(

);

dbs2aggregate.push_back(

);

BOOST_REQUIRE(

(kAliasFileName).Exists());

(vector<string>, itr, dbs2aggregate) {

BOOST_CHECK(alias_file_data.

.

() ==

);

BOOST_CHECK(alias_file_data.

.

() ==

);

(

);

kAliasFileName(kMyAliasDb +

);

(

(kAliasFileName).Exists()) {

BOOST_REQUIRE(

(kAliasFileName).Exists() ==

);

BOOST_REQUIRE(

(kAliasFileName).Exists() ==

);

(

);

kAliasFileName(kMyAliasDb +

);

(

(kAliasFileName).Exists()) {

BOOST_REQUIRE(

(kAliasFileName).Exists() ==

);

vector<string> dbs2aggregate;

dbs2aggregate.push_back(

);

dbs2aggregate.push_back(

);

dbs2aggregate.push_back(

);

dbs2aggregate.push_back(

);

dbs2aggregate.push_back(

);

BOOST_REQUIRE(

(kAliasFileName).Exists() ==

);

(

);

kBlastDb(

);

kAliasFileName(kBlastDb +

);

(

(kAliasFileName).Exists()) {

BOOST_REQUIRE(

(kAliasFileName).Exists() ==

);

BOOST_REQUIRE(

(kAliasFileName).Exists() ==

);

tmp_aliasfile, tmp_gifile;

kDbName(

);

(

);

kAliasFileName(tmp_aliasfile.

());

ofstream gifile(tmp_gifile.

().c_str());

gifile <<

<< endl;

gifile <<

<< endl;

BOOST_REQUIRE_THROW(

kAliasFileName +=

;

BOOST_REQUIRE(!

(kAliasFileName).Exists());

(

);

BOOST_REQUIRE_THROW(

BOOST_REQUIRE(bd.

());

(

);

BOOST_REQUIRE_THROW(

BOOST_REQUIRE(bd.

());

BOOST_REQUIRE(f1.Exists() ==

);

BOOST_REQUIRE(f2.

() ==

);

kDbName(

);

(!reader.

()) {

BOOST_REQUIRE(se->

());

(

oid=0; oid<total; oid++)

vector<TTaxId> taxids;

BOOST_REQUIRE(taxids.size() == 1);

BOOST_REQUIRE_EQUAL(

, taxids.front());

kDbName(

);

(!reader.

()) {

BOOST_REQUIRE(se->

());

(

oid=0; oid<total; oid++)

vector<TTaxId> taxids;

BOOST_REQUIRE(taxids.size() == 1);

BOOST_REQUIRE_EQUAL(

, taxids.front());

kDbName(

);

(!reader.

()) {

BOOST_REQUIRE(se->

());

(

oid=0; oid<total; oid++)

vector<TTaxId> taxids;

BOOST_REQUIRE(taxids.size() == 1);

BOOST_REQUIRE_EQUAL(

, taxids.front());

(

);

vector<string> ids(1,

);

BOOST_REQUIRE(f1.

() ==

);

BOOST_REQUIRE(f1.

() ==

);

vector<string> ids(1,

);

BOOST_REQUIRE(f1.

() ==

);

BOOST_REQUIRE(f1.

() ==

);

title(

);

ids.push_back(

);

ids.push_back(

);

success = bd->

(ids, &fasta_file);

BOOST_REQUIRE(success);

BOOST_REQUIRE(f1.

() ==

);

BOOST_REQUIRE(f1.

() ==

);

(

);

title(

);

success = bd->

(ids, &fasta_file);

BOOST_REQUIRE(success);

BOOST_REQUIRE(f1.

() ==

);

BOOST_REQUIRE(f1.

() ==

);

unique_ptr<CObjectIStream> ois

BOOST_REQUIRE(status ==

);

BOOST_REQUIRE(f1.

() ==

);

big_gi = 0xC0000000;

nrecs = 10;

(

= 0;

< nrecs; ++

) {

tidlist.push_back(seqid);

wdb.AddIds(

, tidlist);

BOOST_FAIL(

);

(

= 0;

< nrecs; ++

) {

rdb->IdToOid(

(

, seqid->GetGi()), oid);

BOOST_REQUIRE(oid ==

);

BOOST_FAIL(

);

sequence =

;

std::unordered_map<string, CSeq_id::E_Choice> fasta_ids = {

(

it: fasta_ids) {

ostr <<

<< it.first << endl << sequence << endl;

BOOST_REQUIRE(istr);

=

;

title =

;

(

it: fasta_ids) {

list< CRef<CSeq_id> > ids = seqdb.

(index++);

BOOST_REQUIRE_MESSAGE(ids.front()->Which() == it.second,

(

)

+

BOOST_REQUIRE_EQUAL(index, (

)fasta_ids.size());

sequence =

;

std::unordered_map<string, CSeq_id::E_Choice> fasta_ids = {

it = fasta_ids.begin();

ostr <<

<< it->first <<

;

(; it != fasta_ids.end(); ++it) {

ostr <<

<< it->first <<

;

ostr << endl << sequence << endl;

BOOST_REQUIRE(istr);

=

;

title =

;

list< CRef<CSeq_id> > ids = seqdb.

(0);

BOOST_REQUIRE_EQUAL(ids.size(), fasta_ids.size());

seqdb_id = ids.begin();

(

it: fasta_ids) {

BOOST_REQUIRE_MESSAGE((*seqdb_id)->Which() == it.second,

(

)

+

BOOST_REQUIRE(seqdb_id == ids.end());

sequence =

;

std::unordered_map<string, CSeq_id::E_Choice> fasta_ids = {

(

it: fasta_ids) {

ostr <<

<< it.first << endl << sequence << endl;

BOOST_REQUIRE(istr);

=

;

title =

;

(

it: fasta_ids) {

list< CRef<CSeq_id> > ids = seqdb.

(index++);

BOOST_REQUIRE_MESSAGE(ids.front()->Which() == it.second,

(

)

+

BOOST_REQUIRE_EQUAL(index, (

)fasta_ids.size());

sequence =

;

std::unordered_map<string, CSeq_id::E_Choice> fasta_ids = {

(

it: fasta_ids) {

ostr <<

<< it.first << endl << sequence << endl;

BOOST_REQUIRE(istr);

=

;

title =

;

(

it: fasta_ids) {

list< CRef<CSeq_id> > ids = seqdb.

(index++);

BOOST_REQUIRE_MESSAGE(ids.front()->Which() == it.second,

(

)

+

BOOST_REQUIRE_EQUAL(index, (

)fasta_ids.size());

sequence =

;

std::unordered_map<string, CSeq_id::E_Choice> fasta_ids = {

it = fasta_ids.begin();

ostr <<

<< it->first <<

;

(; it != fasta_ids.end(); ++it) {

ostr <<

<< it->first <<

;

ostr << endl << sequence << endl;

BOOST_REQUIRE(istr);

=

;

title =

;

list< CRef<CSeq_id> > ids = seqdb.

(0);

BOOST_REQUIRE_EQUAL(ids.size(), fasta_ids.size());

seqdb_id = ids.begin();

(

it: fasta_ids) {

BOOST_REQUIRE_MESSAGE((*seqdb_id)->Which() == it.second,

(

)

+

BOOST_REQUIRE(seqdb_id == ids.end());

sequence =

;

std::unordered_map<string, CSeq_id::E_Choice> fasta_ids = {

(

it: fasta_ids) {

ostr <<

<< it.first << endl << sequence << endl;

BOOST_REQUIRE(istr);

=

;

title =

;

(

it: fasta_ids) {

list< CRef<CSeq_id> > ids = seqdb.

(index++);

BOOST_REQUIRE_EQUAL(ids.front()->Which(), it.second);

BOOST_REQUIRE_EQUAL(index, (

)fasta_ids.size());

vector<string> idlist;

( !line.empty() ) {

idlist.push_back(line);

(

);

num_of_ids = 12;

vector<CSeqDBGiList::SSiOid> read_idlist;

BOOST_REQUIRE_EQUAL(num_of_ids, list_info.

);

BOOST_REQUIRE_EQUAL(num_of_ids, read_idlist.size());

BOOST_REQUIRE_EQUAL(read_idlist[2].

,

);

BOOST_REQUIRE_EQUAL(read_idlist[7].

,

);

BOOST_REQUIRE_EQUAL(read_idlist[11].

,

);

(

);

num_of_ids = 9;

vector<CSeqDBGiList::SSiOid> read_idlist;

BOOST_REQUIRE_EQUAL(num_of_ids, list_info.

);

BOOST_REQUIRE_EQUAL(num_of_ids, read_idlist.size());

BOOST_REQUIRE_EQUAL(read_idlist[2].

,

);

BOOST_REQUIRE_EQUAL(read_idlist[6].

,

);

(

);

num_of_ids = 12;

vector<string> dup_list;

dup_list.insert(dup_list.begin(), idlist.begin(), idlist.end());

dup_list.insert(dup_list.end(), idlist.begin(), idlist.end());

vector<CSeqDBGiList::SSiOid> read_idlist;

BOOST_REQUIRE_EQUAL(num_of_ids, list_info.

);

BOOST_REQUIRE_EQUAL(num_of_ids, read_idlist.size());

BOOST_REQUIRE_EQUAL(read_idlist[2].

,

);

BOOST_REQUIRE_EQUAL(read_idlist[7].

,

);

BOOST_REQUIRE_EQUAL(read_idlist[11].

,

);

num_ids = 7;

pair <string, CSeq_id::E_Choice> fasta_ids[num_ids] = {

=

;

title =

;

list< CRef<CSeq_id> > ids = seqdb.

(0);

BOOST_REQUIRE_EQUAL(ids.size(), num_ids);

seqdb_id = ids.begin();

(

it: fasta_ids) {

BOOST_REQUIRE_EQUAL((*seqdb_id)->Which(),it.second);

BOOST_REQUIRE_EQUAL((*seqdb_id)->GetSeqIdString(

),it.first);

=

;

title =

;

vector<string> db_ids;

vector<int> db_oids;

list<CRef<CSeq_id> > seq_ids = seqdb.

(oid);

vector<string> ref_ids;

(getline(ref_ids_file, line)) {

ref_ids.push_back(line);

vector<blastdb::TOid> oids;

(vector<blastdb::TOid>, itr, oids){

=

;

title =

;

vector<string> db_ids;

vector<int> db_oids;

list<CRef<CSeq_id> > seq_ids = seqdb.

(oid);

BOOST_REQUIRE_EQUAL(oid, num_oids);

vector<string> ref_ids;

(getline(ref_ids_file, line)) {

ref_ids.push_back(line);

vector<blastdb::TOid> oids;

(

=0;

<oids.size();

++){

BOOST_REQUIRE_EQUAL(oids[

],

);

kNumOfDeflines=4;

=

;

seq[9]={1,2,3,4,1,2,3,4,

};

(

=0;

< kNumOfDeflines;

++){

num_taxids[kNumOfDeflines] = {14, 107, 1, 45};

num_deflines[kNumOfDeflines] = {11, 107, 6, 43};

(

=0;

< kNumOfDeflines;

++){

BOOST_REQUIRE_EQUAL(num_taxids[

],

.size());

BOOST_REQUIRE_EQUAL(num_deflines[

], new_set->

().size());

BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &bioseq)

ncbi::TMaskedQueryRegions mask

Code to build a database given various sources of sequence data.

Binary GI or TI List Builder.

void Write(const string &fname)

Write the list to a file.

void AppendId(const Int8 &id)

Add an identifier to the list.

`Blob' Class for SeqDB (and WriteDB).

@ eNone

Write the string as-is.

int WriteString(CTempString str, EStringFormat fmt)

Write string data to the blob.

static int GetSeqidlist(CMemoryFile &file, vector< CSeqDBGiList::SSiOid > &idlist, SBlastSeqIdListInfo &list_info)

Get seqidlist from dbv5 seqidlist file.

Build BlastDB format databases from various data sources.

bool AddSequences(IBioseqSource &src, bool add_pig=false)

Add sequences from an IBioseqSource object.

bool AddFasta(CNcbiIstream &fasta_file)

Add sequences from a file containing FASTA data.

void SetUseRemote(bool use_remote)

Specify whether to use remote fetching for locally absent IDs.

void SetSourceDb(const string &src_db_name)

Specify source database(s) via the database name(s).

void SetTaxids(CTaxIdSet &taxids)

Specify a mapping of sequence ids to taxonomic ids.

bool Build(const vector< string > &ids, CNcbiIstream *fasta_file)

Build the database.

void StartBuild()

Start building a new database.

bool EndBuild(bool erase=false)

Finish building a new database.

bool AddIds(const vector< string > &ids)

Add the specified sequences from the source database.

Base class for reading FASTA sequences.

Registry class for the sequence masking/filtering algorithms used to create masks to be added to a CW...

This represents a set of masks for a given sequence.

static CNcbiApplication * Instance(void)

Singleton method.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

void GetRawSeqAndAmbig(int oid, const char **buffer, int *seq_length, int *ambig_length) const

Raw Sequence and Ambiguity Data.

bool OidToPig(int oid, int &pig) const

Translate an OID to a PIG.

void GetGis(int oid, vector< TGi > &gis, bool append=false) const

Gets a list of GIs for an OID.

int GetNumOIDs() const

Returns the size of the (possibly sparse) OID range.

Uint8 GetVolumeLength() const

Returns the sum of the lengths of all volumes.

bool OidToGi(int oid, TGi &gi) const

Translate an OID to a GI.

list< CRef< CSeq_id > > GetSeqIDs(int oid) const

Gets a list of sequence identifiers.

int GetSeqLength(int oid) const

Returns the sequence length in base pairs or residues.

ESeqType GetSequenceType() const

Returns the type of database opened - protein or nucleotide.

bool SeqidToOid(const CSeq_id &seqid, int &oid) const

Translate a Seq-id to any matching OID.

CRef< CBioseq > GetBioseq(int oid, TGi target_gi=ZERO_GI, const CSeq_id *target_seq_id=NULL) const

Get a CBioseq for a sequence.

void GetTaxIDs(int oid, map< TGi, TTaxId > &gi_to_taxid, bool persist=false) const

Get taxid for an OID.

void GetTotals(ESummaryType sumtype, int *oid_count, Uint8 *total_length, bool use_approx=true) const

Returns the sum of the sequence lengths.

string GetTitle() const

Returns the database title.

int GetNumSeqs() const

Returns the number of sequences available.

void GetAllTaxIDs(int oid, set< TTaxId > &taxids) const

Get all tax ids for an oid.

void AccessionToOids(const string &acc, vector< int > &oids) const

Translate an Accession to a list of OIDs.

bool CheckOrFindOID(int &next_oid) const

Find an included OID, incrementing next_oid if necessary.

@ eUnfilteredAll

Sum of all sequences, ignoring GI and OID lists and alias files.

CRef< CBioseq > GiToBioseq(TGi gi) const

Get a CBioseq for a given GI.

CRef< CBlast_def_line_set > GetHdr(int oid) const

Get the ASN.1 header for the sequence.

void AccessionsToOids(const vector< string > &accs, vector< blastdb::TOid > &oids) const

bool GiToOid(TGi gi, int &oid) const

Translate a GI to an OID.

CSeqEntryGetSource(CRef< CSeq_entry > seq_entry)

CTypeIterator< CBioseq > m_Bioseq

CRef< CSeq_entry > m_entry

CRef< CObjectManager > m_objmgr

virtual CConstRef< CBioseq > GetNext()

Get a Bioseq object if there are any more to get.

Simple implementation of ILineReader for i(o)streams.

void FixTaxId(CRef< objects::CBlast_def_line_set > deflines)

Check that each defline has the specified taxid; if not, replace the defline and set the taxid.

void SetMappingFromFile(CNcbiIstream &f)

Builder for BlastDb format column files.

void ListFiles(vector< string > &files) const

List Filenames.

vector< CRef< CSeq_id > > TIdList

Type used for lists of sequence identifiers.

@ eProtein

Protein database.

@ eNucleotide

Nucleotide database.

void ListFiles(vector< string > &files)

List Filenames.

void SetPig(int pig)

Set the PIG to be used for the sequence.

void AddSequence(const CBioseq &bs)

Add a sequence as a CBioseq.

void SetMaxVolumeLetters(Uint8 letters)

Set maximum letters for output volumes.

EIndexType

Whether and what kind of indices to build.

@ eFullIndex

Use several forms of each Seq-id in the string index.

@ eAddHash

Add an index from sequence hash to OID.

@ eDefault

Like eFullIndex but also build a numeric Trace ID index.

@ eNoIndex

Build a database without any indices.

@ eFullWithTrace

Like eFullIndex but also build a numeric Trace ID index.

void ListVolumes(vector< string > &vols)

List Volumes.

static CRef< CBlast_def_line_set > ExtractBioseqDeflines(const CBioseq &bs, bool parse_ids=true, bool long_ids=false, bool scan_bioseq_4_cfastareader_usrobj=false)

Extract Deflines From Bioseq.

void SetDeflines(const CBlast_def_line_set &deflines)

Set the deflines to be used for the sequence.

void Close()

Close the Database.

Interface to a source of Bioseq objects.

iterator_bool insert(const value_type &val)

static const char si[8][64]

SStaticPair< const char *, const char * > TPair

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

main entry point for tests

Operators to edit gaps in sequences.

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

#define GI_FROM(T, value)

CNcbiEnvironment & SetEnvironment(void)

Get a non-const copy of the application's cached environment.

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

@ eDiag_Fatal

Fatal error – guarantees exit(or abort)

CNcbiIstream & AsInputFile(EIfExists if_exists, IOS_BASE::openmode mode=IOS_BASE::in)

Create I/O stream on the base of our file.

virtual bool Remove(TRemoveFlags flags=eRecursive) const

Remove a directory entry.

CNcbiOstream & AsOutputFile(EIfExists if_exists, IOS_BASE::openmode mode=IOS_BASE::out)

static void Add(const string &path)

Add the name of a dir entry; it will be deleted on (normal) exit.

Int8 GetFileSize(void) const

Get length of the mapped file.

const string & GetFileName(void) const

Return used file name (generated or given in the constructor).

virtual bool Exists(void) const

Check existence of file.

@ eIfExists_Throw

You can make call of AsInputFile/AsOutputFile only once, on each following call throws CFileException...

@ eIfExists_Reset

Delete previous stream and return reference to new object.

@ eOnlyEmpty

Directory entry only, no other files or subdirectories.

#define MSerial_AsnText

I/O stream manipulators –.

@ eSerial_AsnText

ASN.1 text.

virtual CRef< CSeq_entry > ReadOneSeq(ILineErrorListener *pMessageListener=nullptr)

Read a single effective sequence, which may turn out to be a segmented set.

long TFlags

binary OR of EFlags

EFlags

Note on fAllSeqIds: some databases (notably nr) have merged identical sequences, joining their deflin...

bool AtEOF(void) const

Indicates (negatively) whether there is any more input.

@ fAssumeNuc

Assume nucs unless accns indicate otherwise.

@ fAssumeProt

Assume prots unless accns indicate otherwise.

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.

CBeginInfo Begin(C &obj)

Get starting point of object hierarchy.

static CObjectIStream * Open(ESerialDataFormat format, CNcbiIstream &inStream, bool deleteInStream)

Create serial object reader and attach it to an input stream.

CBioseq_Handle AddBioseq(CBioseq &bioseq, TPriority pri=kPriority_Default, EExist action=eExist_Throw)

Add bioseq, return bioseq handle.

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.

CConstRef< CBioseq > GetCompleteBioseq(void) const

Get the complete bioseq.

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

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

void Reset(void)

Reset reference object.

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 Empty(void) const THROWS_NONE

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

uint32_t Uint4

4-byte (32-bit) unsigned integer

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

position_type GetToOpen(void) const

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::ofstream CNcbiOfstream

Portable alias for ofstream.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

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

Convert size_t to string.

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

Convert Int8 to string.

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

Convert int to string.

static SIZE_TYPE Find(const CTempString str, const CTempString pattern, ECase use_case=eCase, EDirection direction=eForwardSearch, SIZE_TYPE occurrence=0)

Find the pattern in the string.

static string UInt8ToString(Uint8 value, TNumToStringFlags flags=0, int base=10)

Convert UInt8 to string.

@ eCurrent

Use current time. See also CCurrentTime.

EBlast_filter_program

This defines the possible sequence filtering algorithms to be used in a BLAST database.

Tdata & Set(void)

Assign a value to data member.

const Tdata & Get(void) const

Get the member data.

@ eBlast_filter_program_dust

@ eBlast_filter_program_max

@ eBlast_filter_program_repeat

@ eBlast_filter_program_seg

@ eBlast_filter_program_windowmasker

@ eBlast_filter_program_other

TFrom GetFrom(void) const

Get the From member data.

TGi GetGi(void) const

Get the variant data.

bool IsGi(void) const

Check if variant Gi is selected.

@ e_Other

for historical reasons, 'other' = 'refseq'

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

bool IsSeq(void) const

Check if variant Seq is selected.

TSeq & SetSeq(void)

Select the variant.

const TId & GetId(void) const

Get the Id member data.

void SetInst(TInst &value)

Assign a value to Inst data member.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

unsigned int

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

const std::string kOutput

Command line flag to specify the output.

static const char * data4[]

BOOST_AUTO_TEST_SUITE(psiblast_iteration)

bool DeleteBlastDb(const string &dbpath, CSeqDB::ESeqType seq_type)

Deletes all files associated with a BLAST database.

const blastdb::TOid kSeqDBEntryNotFound

Defines `expert' version of CSeqDB interfaces.

ISAM index database access object.

int WriteBlastSeqidlistFile(const vector< string > &idlist, CNcbiOstream &os, const string &title, const CSeqDB *seqdb=NULL)

static SLJIT_INLINE sljit_ins lr(sljit_gpr dst, sljit_gpr src)

Encapsulates the alias' file key-value pair.

Value(const string &name)

void Set(const string &v)

Auxiliary class to parse the contents of an alias file.

void x_Parse(const string &fname)

Parse the alias file's contents.

bool x_HasKeyword(string line, Value &data)

SAliasFileData(const string &fname)

Structure describing filtered regions created using a particular sequence filtering algorithm.

Blast DB v5 seqid list info.

Template structure SStaticPair is simlified replacement of STL pair<> Main reason of introducing this...

Utility stuff for more convenient using of Boost.Test library.

static const string kTitle

CTraceGlyph inline method implementation.

static bool ambig(char c)

Defines BLAST database construction classes.

void CWriteDB_CreateAliasFile(const string &file_name, const string &db_name, CWriteDB::ESeqType seq_type, const string &gi_file_name, const string &title=string(), EAliasFileFilterType alias_type=eGiList)

Writes an alias file that restricts a database with a gi list.

@ eSeqIdList

Filter a BLAST database via a Seq-id list.

Code for database isam construction.

string s_HexDumpFile(const string &fname, const vector< int > &layout, int base)

void RegisterTooManyVariantsOfSameMaskingAlgorithm(EBlast_filter_program masking_algo, size_t kMaxNumSupportedAlgorithmVariants)

CRef< CSeq_id > s_GiToSeqId(TGi gi)

static void s_DupIdsBioseq(CWriteDB &w, CSeqDB &s, const TIdList &ids, int cutpoint)

vector< CRef< CSeq_id > > TIdList

void s_Unstringify(const string &s, ASNOBJ &a)

CRef< CBioseq > s_FastaStringToBioseq(const string &str, bool protein)

void s_CheckFiles(const vector< string > &files, bool need_hash=false)

void s_Stringify(const ASNOBJ &a, string &s)

static void s_DupIdsRaw(CWriteDB &w, CSeqDBExpert &seqdb, const TIdList &ids)

void s_WrapUpColumn(CWriteDB_ColumnBuilder &cb)

static CRef< CScope > s_GetScope()

void s_WrapUpDb(CWriteDB &db)

BOOST_AUTO_TEST_CASE(NuclBioseqDupI)

string s_ExtractLast(const string &data, const string &delim)

#define BOOST_REQUIRE_CUTPOINT(X)

void s_RemoveFile(const string &f)

void s_TestDatabase(CSeqDBExpert &src, const string &name, const string &title)

static void s_DupSequencesTest(const TIdList &ids, bool is_protein, bool raw_data, const string &src_name, const string &dst_name, const string &title, int cutpoint=99)

string s_HexDumpText(const string &raw, const vector< int > &layout, int base)

CRef< ASNOBJ > s_Duplicate(const ASNOBJ &a)

void s_RemoveFiles(const vector< string > &files)

void s_CheckSorted(const string &fname)

CRef< CSeq_id > s_AccToSeqId(const char *acc)

void s_TestReadPDBAsn1(CNcbiIfstream &istr, CNcbiIfstream &ref_ids_file, int num_oids)

void s_WrapUpFiles(const vector< string > &files)

static void s_BuildIds(TIdList &ids, TGi *gis)

void s_FetchRawData(CSeqDBExpert &seqdb, int oid, string &sequence, string &ambig)

static void s_NuclBioseqDupSwitch(int cutpoint)

void s_CompareBioseqs(CBioseq &src, CBioseq &dst)

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