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NCBI C++ ToolKit: src/algo/blast/unit_tests/seqdb_reader/seqdb_unit_test.cpp Source File

<

A,

B,

C,

D,

E>

oss <<

<<

<< c << d << e;

* slice (0);

*

(0);

(

, begin,

, end,

);

BOOST_REQUIRE_MESSAGE(0 == memcmp(slice,

+ begin, sliceL), op);

success = db.

(nt_gi, oid);

oss <<

<< nt_gi <<

;

BOOST_REQUIRE_MESSAGE(success,

);

(

= 1;

<length;

*= 2) {

(

j = 0; j<length; j +=

) {

(oid & 1) != 0;

(oid & 1) == 0;

(

d = 2; d < oid; d++) {

exp_count(0);

BOOST_REQUIRE_EQUAL(

, lowest);

BOOST_REQUIRE_EQUAL(

, highest);

BOOST_REQUIRE_EQUAL(

, exp_count);

<

NUM,

DIF>

cout <<

<<

*

= (

*) buf_in;

(

< length) {

<

ASNOBJ>

num1(0), num2(0);

BOOST_REQUIRE(num1 >= 1);

BOOST_REQUIRE_EQUAL(num1, num2);

num1(0), num2(0);

BOOST_REQUIRE(num1 >= 1);

BOOST_REQUIRE_EQUAL(num1, num2);

caught_exception =

;

num1(0), num2(0);

BOOST_REQUIRE(num1 >= 1);

BOOST_REQUIRE_EQUAL(num1, num2);

caught_exception =

;

(! caught_exception) {

BOOST_ERROR(

);

caught_exception =

;

caught_exception =

;

(! caught_exception) {

BOOST_ERROR(

);

BOOST_REQUIRE(num1 >= 1);

caught_exception =

;

BOOST_REQUIRE(num1 >= 1);

caught_exception =

;

(! caught_exception) {

BOOST_ERROR(

);

BOOST_REQUIRE_EQUAL(

(100), nseqs);

BOOST_REQUIRE_EQUAL(

(51718), vlength);

BOOST_REQUIRE_EQUAL(

(

),

oid_values[] = { 0, 100000 };

(

end_oid : oid_values) {

BOOST_REQUIRE(vol2 < vol1);

BOOST_REQUIRE_EQUAL(seq2, seq1 - 1);

BOOST_REQUIRE(vol3 < vol2);

BOOST_REQUIRE_EQUAL(seq3, seq2 - 1);

BOOST_CHECK_EQUAL(0

, vol4);

BOOST_CHECK_EQUAL(0, seq4);

BOOST_CHECK_EQUAL(10, seq4);

BOOST_CHECK(vol4 > 0);

nseqs(0), noids(0);

vlength(0), tlength(0);

BOOST_REQUIRE_EQUAL(

(100), nseqs);

BOOST_REQUIRE_EQUAL(

(100), noids);

BOOST_REQUIRE_EQUAL(

(26945), tlength);

BOOST_REQUIRE_EQUAL(

(26945), vlength);

BOOST_REQUIRE_EQUAL(

(

),

* bufp_blst = 0;

* bufp_ncbi = 0;

BOOST_REQUIRE_EQUAL(

(30118382ul), hashval_blst);

BOOST_REQUIRE_EQUAL(

(3084382219ul), hashval_ncbi);

* bufp_blst = 0;

* bufp_ncbi = 0;

BOOST_REQUIRE_EQUAL(

(3219499033ul), hashval_blst);

BOOST_REQUIRE_EQUAL(

(3219499033ul), hashval_ncbi);

* bufp1 = 0;

* bufp2 = 0;

BOOST_REQUIRE_EQUAL(

(30118382ul), hashval1);

BOOST_REQUIRE_EQUAL(

(3084382219ul), hashval2);

* bufp1 = 0;

* bufp2 = 0;

BOOST_REQUIRE_EQUAL(

(3219499033ul), hashval1);

BOOST_REQUIRE_EQUAL(

(3219499033ul), hashval2);

BOOST_REQUIRE_EQUAL(

, got);

BOOST_REQUIRE_EQUAL(

, got);

= (

BOOST_REQUIRE_EQUAL(

, got);

= (

BOOST_REQUIRE_EQUAL(

, got);

list< CRef< CSeq_id > > seqids =

BOOST_REQUIRE_EQUAL(

(136774894ul), h);

list< CRef< CSeq_id > > seqids =

BOOST_REQUIRE_EQUAL(

(2942938647ul), h);

BOOST_REQUIRE_EQUAL( (

) 330, dbp.

(13) );

BOOST_REQUIRE_EQUAL( (

) 422, dbp.

(19) );

BOOST_REQUIRE_EQUAL( (

) 67, dbp.

(26) );

BOOST_REQUIRE_EQUAL( (

) 104, dbp.

(27) );

BOOST_REQUIRE_EQUAL( (

) 282, dbp.

(38) );

BOOST_REQUIRE_EQUAL( (

) 158, dbp.

(43) );

BOOST_REQUIRE_EQUAL( (

) 472, dbp.

(54) );

BOOST_REQUIRE_EQUAL( (

) 207, dbp.

(93) );

BOOST_REQUIRE_EQUAL( (

) 833, dbn.

(9) );

BOOST_REQUIRE_EQUAL( (

) 250, dbn.

(26) );

BOOST_REQUIRE_EQUAL( (

) 708, dbn.

(39) );

BOOST_REQUIRE_EQUAL( (

) 472, dbn.

(43) );

BOOST_REQUIRE_EQUAL( (

) 708, dbn.

(39) );

BOOST_REQUIRE_EQUAL( (

) 448, dbn.

(47) );

BOOST_REQUIRE_EQUAL( (

) 825, dbn.

(61) );

BOOST_REQUIRE_EQUAL( (

) 371, dbn.

(70) );

plen(0), nlen(0);

(

= 0;

< plen;

++) {

(

= 0;

< nlen;

++) {

BOOST_REQUIRE_EQUAL(

(100), nlen);

BOOST_REQUIRE_EQUAL(

(100), plen);

BOOST_REQUIRE_EQUAL(

(26945), ptot);

BOOST_REQUIRE_EQUAL(

(51718), ex_tot);

BOOST_REQUIRE_EQUAL(

(51726), ap_tot);

* bufp = 0;

BOOST_REQUIRE_EQUAL(

(1128126064ul), hashval);

* bufp = 0;

BOOST_REQUIRE_EQUAL(

(3219499033ul), hashval);

nr_seqs(0), nr_oids(0), sp_seqs(0), sp_oids(0);

nr_tlen(0), nr_vlen(0), sp_tlen(0), sp_vlen(0);

BOOST_REQUIRE_EQUAL(nr_seqs, nr_oids);

BOOST_REQUIRE_EQUAL(nr_tlen, nr_vlen);

BOOST_REQUIRE_GT(nr_seqs, sp_seqs);

BOOST_REQUIRE_NE(nr_oids, sp_oids);

BOOST_REQUIRE_GT(nr_tlen, sp_tlen);

BOOST_REQUIRE_NE(nr_vlen, sp_vlen);

* seqid_list[] = {

,

,

,

,

,

,

,

,

,

,

,

,

,

1153908, 507276, 851580, 200775, 1028308, 939134,

199107, 511756, 27645, 429124, 575812, 648744,

199, 233, 186, 441, 96, 206,

277, 205, 110, 206, 510, 293,

BOOST_REQUIRE((L_seqid == L_len) && (L_len == L_pig));

(

= 0;

<L_seqid;

++) {

arr_seqid(seqid_list[

]);

arr_pig(pig_list[

]), arr_len(len_list[

]);

vector<int> seqid2oid;

pig2oid = 0, oid2pig=0, oid2len =0;

.AccessionToOids(arr_seqid, seqid2oid);

BOOST_REQUIRE(

.PigToOid(arr_pig, pig2oid));

BOOST_CHECK_EQUAL(pig2oid, seqid2oid[0]);

BOOST_REQUIRE(pig2oid !=

(-1));

oid2len =

.GetSeqLength(pig2oid);

BOOST_REQUIRE(

.OidToPig (pig2oid, oid2pig));

BOOST_REQUIRE_EQUAL(arr_len, oid2len);

BOOST_REQUIRE_EQUAL(arr_pig, oid2pig);

(

);

NUM_ITEMS = 6;

** str_list[NUM_ITEMS];

{

,

,

,

,

, 0 };

{

,

,

, 0 };

{

,

, 0 };

{

,

,

, 0 };

* len_list[NUM_ITEMS];

l0[] = { 261, 0 };

l1[] = { 232, 0 };

l2[] = { 17, 90, 0 };

l3[] = { 17, 90, 0 };

l4[] = { 333, 0 };

l5[] = { 281, 0 };

BOOST_REQUIRE_EQUAL(NUM_ITEMS, L_str);

BOOST_REQUIRE_EQUAL(NUM_ITEMS, L_len);

(

= 0;

< NUM_ITEMS;

++) {

(

** strp = str_list[

]; *strp; strp++) {

.AccessionToOids(*strp, oids);

BOOST_REQUIRE_MESSAGE(! oids.empty(),

<< *strp <<

<<

);

(vector<int>, iter, oids) {

str_iter = str_oids.

();

* llp = len_list[

];

oid_len.

(

.GetSeqLength(*iter));

oid_iter = oid_len.

();

exp_iter = exp_len.

();

(oid_iter != oid_len.

()) {

BOOST_REQUIRE(exp_iter != exp_len.

());

BOOST_REQUIRE_EQUAL(*oid_iter, *exp_iter);

*

=

;

is_prot =

;

oss_fn <<

<<

<<

<< gi;

vector<char> seqdb_data;

vector<char> expected_data;

gi_trans = db.

(gi, oid);

BOOST_REQUIRE(gi_trans);

BOOST_REQUIRE(! bs.

());

BOOST_REQUIRE_EQUAL(

(seqdb_data.size()), 872);

expected_bs =

;

expected_data.assign(data_str.data(),

data_str.data() + data_str.size());

vector<char> seqdb_tmp;

seqdb_tmp.swap(seqdb_data);

BOOST_REQUIRE_EQUAL(expected_bs, seqdb_bs);

BOOST_REQUIRE_EQUAL(expected_data.size(), seqdb_data.size());

num_diffs = 0;

(

= 0;

< expected_data.size();

++) {

= unsigned(expected_data[

]) & 0xFF;

= unsigned(seqdb_data[

]) & 0xFF;

cout <<

<< dec <<

<<

<<

<<

(

) <<

<<

<<

(

);

cout <<

<< (

-

) <<

;

cout <<

<< (

-

) <<

;

cout <<

<< dec << num_diffs << endl;

BOOST_REQUIRE_EQUAL((

) 0, (

)num_diffs);

caught_exception =

;

BOOST_REQUIRE_EQUAL((

) 11112222,

);

caught_exception =

;

(! caught_exception) {

BOOST_ERROR(

);

caught_exception =

;

BOOST_REQUIRE_EQUAL((

) 11112222,

);

caught_exception =

;

(! caught_exception) {

BOOST_ERROR(

);

caught_exception =

;

BOOST_REQUIRE_EQUAL((

) 11112222,

);

caught_exception =

;

(! caught_exception) {

BOOST_ERROR(

);

caught_exception =

;

BOOST_REQUIRE_EQUAL((

) 11112222,

);

caught_exception =

;

(! caught_exception) {

BOOST_ERROR(

);

caught_exception =

;

.GetOidAtOffset(0, vlength + 1);

caught_exception =

;

(! caught_exception) {

BOOST_ERROR(

);

caught_exception =

;

.GetOidAtOffset(noids + 1, 0);

caught_exception =

;

(! caught_exception) {

BOOST_ERROR(

);

segments = 1000;

((

== 0) ?

:

);

vol_length(0);

(

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

range_target = (vol_length * j) / segments;

range_ratio = double(range_target) / vol_length;

oid_ratio = double(oid_here) / num_oids;

percent_diff = 100.0 *

(oid_ratio - range_ratio);

BOOST_REQUIRE(prev_oid <= oid_here);

BOOST_REQUIRE(percent_diff <= 30.0);

prev_oid = oid_here;

vector<string>

;

.push_back(

);

.push_back(

);

.push_back(

);

.push_back(

);

.push_back(

);

BOOST_REQUIRE(s->length() > 2);

prot_nucl = (*s)[0];

(*s, 2, s->length()-2);

* mask_name[] = {

,

,

,

,

(

= 0; ranges[

];

+= 2) {

= ranges[

];

second = ranges[

+1];

obegin(0), oend(0);

lowest(INT_MAX);

num_found(0);

num_found = (

) oids.size();

(vector<int>, iter, oids) {

((*iter) > highest) {

((*iter) < lowest) {

num_found = oend-obegin;

(oend > highest) {

(obegin < lowest) {

(

v = obegin; v < oend; v++) {

(obegin == oend) {

low_gi = 20*1000*1000;

high_gi = 30*1000*1000;

dbs.push_back(

);

dbs.push_back(

);

dbs.push_back(

);

dbs.push_back(

);

(

dbnum = 0; dbnum < dbs.size(); dbnum++) {

all_gis_in_range =

;

all_oids_in_range =

;

(! (all_oids_in_range || all_gis_in_range)) {

(all_oids_in_range) {

((oid < (low_oid-1)) || ((high_oid-1)) < oid) {

all_oids_in_range =

;

(all_gis_in_range) {

list< CRef<CSeq_id> > ids = db.

(oid);

gi_in_range =

;

((**seqid).IsGi()) {

gi = (**seqid).GetGi();

((gi > low_gi) && (gi < high_gi)) {

gi_in_range =

;

(! gi_in_range) {

all_gis_in_range =

;

gis_confined (

);

oids_confined(

);

gis_confined =

;

oids_confined =

;

gis_confined =

;

oids_confined =

;

gis_confined =

;

oids_confined =

;

gis_confined =

;

oids_confined =

;

BOOST_REQUIRE_EQUAL(oids_confined, all_oids_in_range);

BOOST_REQUIRE_EQUAL(gis_confined, all_gis_in_range);

caught_exception =

;

caught_exception =

;

(! caught_exception) {

BOOST_ERROR(

);

BOOST_REQUIRE_EQUAL(29, found);

BOOST_REQUIRE_EQUAL(29, found);

BOOST_REQUIRE_EQUAL(58, found);

(

);

BOOST_REQUIRE_EQUAL((

) seqdbgifile.

(), gis.size());

(gis.begin(), gis.end());

ifstream gifile(fn.c_str());

BOOST_REQUIRE(gifile);

vector<TGi> reference;

reference.reserve(gis.size());

( !gifile.eof() ) {

(tgi == -1)

;

(reference.begin(), reference.end());

BOOST_REQUIRE_EQUAL(reference.size(), gis.size());

(

= 0;

< reference.size();

++) {

BOOST_REQUIRE_MESSAGE(reference[

] == gis[

],

);

dbs.push_back(

);

dbs.push_back(

);

dbs.push_back(dbs[0] +

+ dbs[1]);

vector< vector<TGi> > gis(dbs.size());

vector< vector<string> > volumes(dbs.size());

(

= 0;

< (

)dbs.size();

++) {

BOOST_REQUIRE_NO_THROW(db.

(

(dbs[

],

db->

(oid, gis[

],

);

BOOST_REQUIRE(volumes[0] == volumes[1]);

BOOST_REQUIRE(volumes[0] == volumes[2]);

BOOST_REQUIRE_EQUAL(gis[0].

() + gis[1].

(), gis[2].

());

vector<TGi> zero_one(gis[0]);

zero_one.insert(zero_one.end(), gis[1].begin(), gis[1].end());

(zero_one.begin(), zero_one.end());

(gis[2].begin(), gis[2].end());

BOOST_REQUIRE(zero_one == gis[2]);

gi1a = 446106212;

gi2a = 494110381;

gi2b = 30172867;

success = db.

(gi1a, oid1);

BOOST_REQUIRE(success);

success = db.

(gi2a, oid2);

BOOST_REQUIRE(success);

BOOST_REQUIRE(oid1 != oid2);

BOOST_REQUIRE_EQUAL((

)gi2taxid.

(), 44);

BOOST_REQUIRE_EQUAL(gi2taxid[gi1a],

);

BOOST_REQUIRE_EQUAL((

)gi2taxid.

(), 23);

BOOST_REQUIRE_EQUAL(gi2taxid[gi2a], tax2a);

BOOST_REQUIRE_EQUAL(gi2taxid[gi2b], tax2b);

BOOST_REQUIRE_EQUAL((

)gi2taxid.

(), 67);

BOOST_REQUIRE_EQUAL(gi2taxid[gi1a],

);

BOOST_REQUIRE_EQUAL(gi2taxid[gi2a], tax2a);

BOOST_REQUIRE_EQUAL(gi2taxid[gi2b], tax2b);

gi1a = 446106212;

gi2a = 494110381;

success = db.

(gi1a, oid1);

BOOST_REQUIRE(success);

success = db.

(gi2a, oid2);

BOOST_REQUIRE(success);

BOOST_REQUIRE(oid1 != oid2);

BOOST_REQUIRE(gi2taxids.

());

BOOST_REQUIRE_EQUAL((

) gi2taxids.

(), 44);

BOOST_REQUIRE_EQUAL((

) gi2taxids[gi1a].

(), 5);

BOOST_REQUIRE_EQUAL_COLLECTIONS(

gi2taxids[gi1a].begin(), gi2taxids[gi1a].end(),

expected1.

(), expected1.

()

BOOST_REQUIRE(!gi2taxids.

());

BOOST_REQUIRE_EQUAL((

) gi2taxids.

(), 23);

BOOST_REQUIRE_EQUAL((

) gi2taxids[gi2a].

(), 4);

BOOST_REQUIRE_EQUAL_COLLECTIONS(

gi2taxids[gi2a].begin(), gi2taxids[gi2a].end(),

expected2a.

(), expected2a.

()

BOOST_REQUIRE(!gi2taxids.

());

BOOST_REQUIRE_EQUAL((

) gi2taxids.

(), 67);

BOOST_REQUIRE_EQUAL((

) gi2taxids[gi1a].

(), 5);

BOOST_REQUIRE_EQUAL((

) gi2taxids[gi2a].

(), 4);

BOOST_REQUIRE_EQUAL_COLLECTIONS(

gi2taxids[gi1a].begin(), gi2taxids[gi1a].end(),

expected1.

(), expected1.

()

BOOST_REQUIRE_EQUAL_COLLECTIONS(

gi2taxids[gi2a].begin(), gi2taxids[gi2a].end(),

expected2a.

(), expected2a.

()

gi1a = 446106212;

gi2a = 494110381;

vector<int> expected1;

(expected1.begin(), expected1.end());

vector<int> expected2a;

expected2a.assign(

(tax2a),

(tax2a));

(expected2a.begin(), expected2a.end());

success = db.

(gi1a, oid1);

BOOST_REQUIRE(success);

success = db.

(gi2a, oid2);

BOOST_REQUIRE(success);

BOOST_REQUIRE(oid1 != oid2);

vector<TTaxId> taxids;

(taxids.begin(), taxids.end());

BOOST_REQUIRE_EQUAL((

) taxids.size(), (

) expected1.size());

BOOST_REQUIRE_EQUAL_COLLECTIONS(

taxids.begin(), taxids.end(),

expected1.begin(), expected1.end()

(taxids.begin(), taxids.end());

BOOST_REQUIRE_EQUAL((

) taxids.size(), (

) expected2a.size());

BOOST_REQUIRE_EQUAL_COLLECTIONS(

taxids.begin(), taxids.end(),

expected2a.begin(), expected2a.end()

(expected2a.begin(), expected2a.end());

(taxids.begin(), taxids.end());

BOOST_REQUIRE_EQUAL((

) taxids.size(), (

) expected2a.size());

BOOST_REQUIRE_EQUAL_COLLECTIONS(

taxids.begin(), taxids.end(),

expected2a.begin(), expected2a.end()

gi1a = 446106212;

1386, 1392, 1396, 1428, 1234146

gi2a = 494110381;

1678, 216816, 469594, 1263059

vector<int> expected1;

(expected1.begin(), expected1.end());

vector<int> expected2a;

expected2a.assign(

(tax2a),

(tax2a));

(expected2a.begin(), expected2a.end());

success = db.

(gi1a, oid1);

BOOST_REQUIRE(success);

success = db.

(gi2a, oid2);

BOOST_REQUIRE(success);

BOOST_REQUIRE(oid1 != oid2);

vector<TTaxId> taxids;

(taxids.begin(), taxids.end());

BOOST_REQUIRE_EQUAL((

) taxids.size(), (

) expected1.size());

BOOST_REQUIRE_EQUAL_COLLECTIONS(

taxids.begin(), taxids.end(),

expected1.begin(), expected1.end()

(taxids.begin(), taxids.end());

BOOST_REQUIRE_EQUAL((

) taxids.size(), (

) expected2a.size());

BOOST_REQUIRE_EQUAL_COLLECTIONS(

taxids.begin(), taxids.end(),

expected2a.begin(), expected2a.end()

(expected2a.begin(), expected2a.end());

(taxids.begin(), taxids.end());

BOOST_REQUIRE_EQUAL((

) taxids.size(), (

) expected2a.size());

BOOST_REQUIRE_EQUAL_COLLECTIONS(

taxids.begin(), taxids.end(),

expected2a.begin(), expected2a.end()

kNumTestGis = 3;

kGiOids[kNumTestGis] = { 15, 51, 84 };

vector<int> oid_list;

BOOST_REQUIRE_EQUAL(1, (

)oid_list.size());

BOOST_REQUIRE_EQUAL(1, (

)oid_list.size());

BOOST_REQUIRE_EQUAL(1, (

)oid_list.size());

oids1.push_back(oid);

BOOST_REQUIRE(! oids2.empty());

(vector<int>, iter, oids1) {

BOOST_REQUIRE(*iter == oids2[0]);

kFirstOid(0);

kLastOid(100);

vector<int> oid_list;

BOOST_REQUIRE_EQUAL(kFirstOid, start);

BOOST_REQUIRE_EQUAL(kLastOid, end);

BOOST_REQUIRE_EQUAL(kFirstOid, start);

BOOST_REQUIRE_EQUAL(kFirstOid, end);

BOOST_REQUIRE_EQUAL(kFirstOid, start);

BOOST_REQUIRE_EQUAL(kLastOid, end);

BOOST_REQUIRE_EQUAL(

.taxid, 57176);

BOOST_REQUIRE_EQUAL((

)

.scientific_name,

(

));

BOOST_REQUIRE_EQUAL((

)

.common_name,

(

));

BOOST_REQUIRE_EQUAL((

)

.blast_name,

(

));

BOOST_REQUIRE_EQUAL((

)

.s_kingdom,

(

));

BOOST_REQUIRE_EQUAL(

.taxid, 562);

slen(0),alen(0);

exp_hash = 705445389u;

BOOST_REQUIRE_EQUAL((290/4) + 1, slen);

BOOST_REQUIRE_EQUAL(20, alen);

BOOST_REQUIRE_EQUAL(exp_hash, h);

(vector<int>, oid, oids) {

slen(0),alen(0);

(

+ slen, alen);

BOOST_REQUIRE_EQUAL((

)

.size(), 0);

BOOST_REQUIRE_EQUAL((

)

.size(),

);

BOOST_REQUIRE_EQUAL((

) *(

-1), 0);

BOOST_REQUIRE_EQUAL((

) *(

+slen), 0);

slen(0),alen(0);

BOOST_REQUIRE_EQUAL((290/4) + 1, slen);

BOOST_REQUIRE_EQUAL(20, alen);

low(0), high(0),

(0);

.GetPigBounds(& low, & high, &

);

BOOST_REQUIRE(low < high);

BOOST_REQUIRE(

);

caught_exception =

;

BOOST_REQUIRE(low < high);

BOOST_REQUIRE(

);

low(0), high(0),

(0);

BOOST_REQUIRE(low < high);

BOOST_REQUIRE(

);

caught_exception =

;

(! caught_exception) {

BOOST_ERROR(

);

pair<bool, string> TStringBool;

vector< TStringBool > TStringBoolVec;

TStringBoolVec paths;

paths.push_back(TStringBool(

,

));

paths.push_back(TStringBool(

,

));

paths.push_back(TStringBool(

,

));

paths.push_back(TStringBool(

,

));

paths.push_back(TStringBool(

,

));

(TStringBoolVec, iter, paths) {

filename = iter->second;

found = ! resolved.empty();

position = resolved.find(filename);

BOOST_REQUIRE(found);

BOOST_REQUIRE(resolved.size() > filename.size());

BOOST_REQUIRE_EQUAL(position + filename.size(), resolved.size());

BOOST_REQUIRE(! found);

(

= 0;

< gis.size();

++) {

a3.push_back(special);

(

= 0; (

*3) < 500;

++) {

a5.push_back(special);

(

= 0;

< 500;

++) {

(((

% 15) == 0) || (gi == special)) {

BOOST_REQUIRE(

== both.

(gi));

BOOST_REQUIRE(

== both.

(gi));

a3.push_back(special);

(

= 0; (

*3) < 500;

++) {

a5.push_back(special);

(

= 0;

< (

)a5.size();

++) {

BOOST_REQUIRE(

== both.

(a5[

]));

BOOST_REQUIRE(

== both.

(a5[

]));

BOOST_REQUIRE(std::find(a5.begin(), a5.end(), gi) != a5.end());

a3.push_back(special);

(

= 0; (

*3) < 500;

++) {

a3.push_back(

*3);

a5.push_back(

*5);

a5.push_back(special);

BOOST_REQUIRE(calc->IsPositive());

(

= 0;

< 500;

++) {

is_3 = ((

% 3) == 0) || (

== special);

is_5 = ((

% 5) == 0) || (

== special);

(is_3 && (! is_5)) {

BOOST_REQUIRE(

== and_not->

(

));

BOOST_REQUIRE(

== and_not->

(

));

m2.push_back(special);

m3.push_back(special);

m5.push_back(special);

m7.push_back(special);

(

= 0;

< 1000;

++) {

m2.push_back(special);

m3.push_back(special);

m5.push_back(special);

m7.push_back(special);

BOOST_REQUIRE(! not_m5_ornot_m7.

());

(

= 0;

< 1000;

++) {

d2(!(

%2)), d3(!(

%3)), d5(!(

%5)), d7(!(

%7));

(

== special) {

d2 = d3 = d5 = d7 =

;

in_c1 = ( d2 && !d3) || ( d5 && !d7);

in_c2 = (!d2 || d3) && ( d5 != d7);

in_c3 = ( d2 || !d3) && (!d5 || !d7);

BOOST_REQUIRE_EQUAL(in_c1, c1p->

(

));

BOOST_REQUIRE_EQUAL(in_c2, c2p->

(

));

BOOST_REQUIRE_EQUAL(in_c3, ! c3n->

(

));

46071115, 46071116, 46071117, 46071118, 46071119,

46071120, 46071121, 46071122, 46071123, 46071124,

46071125, 46071126, 46071127, 46071128, 46071129,

46071130, 46071131, 46071132, 46071133, 46071134 };

BOOST_REQUIRE((

(v1)/

(

)) == 20);

vector<int>

(v1, v1 + 20);

vector<int> mid(v1 + 5, v1 + 15);

nm =

;

db_A(nm, ty, All);

db_M(nm, ty, Mid);

db_N(nm, ty, Neg);

db_TB(nm, ty, TopBot);

db_NTB(nm, ty, NotTopBot);

A_have =

(db_A, A_count, oid);

M_have =

(db_M, M_count, oid);

N_have =

(db_N, N_count, oid);

TB_have =

(db_TB, TB_count, oid);

NTB_have =

(db_NTB, NTB_count, oid);

BOOST_REQUIRE((! M_have) || A_have);

BOOST_REQUIRE(A_have != N_have);

BOOST_REQUIRE((! TB_have) || A_have);

BOOST_REQUIRE((!M_have) || (!N_have));

BOOST_REQUIRE((!M_have) || (!TB_have));

BOOST_REQUIRE((!M_have) || NTB_have);

BOOST_REQUIRE((!N_have) || (!TB_have));

BOOST_REQUIRE((!N_have) || NTB_have);

BOOST_REQUIRE(TB_have != NTB_have);

BOOST_REQUIRE_EQUAL(

, 100);

BOOST_REQUIRE_EQUAL(A_count, 20);

BOOST_REQUIRE_EQUAL(M_count, 10);

BOOST_REQUIRE_EQUAL(N_count,

-A_count);

BOOST_REQUIRE_EQUAL(TB_count, A_count - M_count);

BOOST_REQUIRE_EQUAL(NTB_count + TB_count, 100);

BOOST_REQUIRE(! idset_TB.

());

*s1 = 0, *s2 = 0;

BOOST_REQUIRE(

(s1) ==

(s2));

(

** p =

; *p; p++) {

((*p)[0] ==

) {

*

[] =

BOOST_REQUIRE_EQUAL((

)ids->GetNumSis(), 9);

(

= 0;

< ids->GetNumSis();

++) {

BOOST_REQUIRE(ids->GetSiOid(

).oid == -1);

(

= 0;

< ids->GetNumSis();

++) {

BOOST_CHECK_MESSAGE(ids->GetSiOid(

).oid != -1,

<< ids->GetSiOid(

).si <<

);

BOOST_REQUIRE_EQUAL(k, ids->GetNumSis());

BOOST_REQUIRE( dbp.

(gi, the_oid));

BOOST_REQUIRE_EQUAL(oid, the_oid);

BOOST_REQUIRE( dbp.

(gi, the_oid));

BOOST_REQUIRE_EQUAL(oid, the_oid);

*

[] = {

,

,

,

,

BOOST_REQUIRE_EQUAL((

)ids->GetNumSis(), 12);

BOOST_REQUIRE_EQUAL((

)ids->GetNumGis(), 13);

(

= 0;

< ids->GetNumSis();

++) {

BOOST_REQUIRE(ids->GetSiOid(

).oid == -1);

(

= 0;

< ids->GetNumGis();

++) {

BOOST_REQUIRE(ids->GetGiOid(

).oid == -1);

(

= 0;

[

];

++) {

found =

;

(

[

][0] ==

) {

gi = atoi(

[

] + 1);

found = ids->GiToOid(gi, oid);

found = ids->SiToOid(str_id, oid);

BOOST_REQUIRE_EQUAL(found,

);

(

>= 0 &&

< 4) {

BOOST_REQUIRE_EQUAL(oid, -1);

}

(

>= 15 &&

< 25) {

cout <<

<<

[

] << endl;

BOOST_REQUIRE(oid != -1);

* inter[] = {

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

,

(

** p = inter; *p; p++)

list< CRef<CSeq_id> > TIds;

(TIds, iter, the_ids) {

BOOST_REQUIRE(itr != need.

());

BOOST_REQUIRE(need.

());

BOOST_REQUIRE_EQUAL((

)db.

(),

(

));

vector<TTaxId> taxids;

* ncbuffer = 0;

BOOST_REQUIRE_EQUAL((

)db.

(),

(

));

BOOST_REQUIRE_EQUAL((

)db.

(),

(

));

seq_total = 0;

BOOST_REQUIRE_EQUAL(oid_count, 0);

BOOST_REQUIRE_EQUAL(seq_total,

(0));

BOOST_REQUIRE_NO_THROW(db.

());

begin(0), end(0);

BOOST_REQUIRE_EQUAL(

(0), oids.size());

BOOST_REQUIRE_EQUAL(begin, end);

BOOST_REQUIRE_EQUAL((

)db.

(),

(

));

acc(

);

seqid(

);

BOOST_REQUIRE_EQUAL(

, db.

(pig, oid));

BOOST_REQUIRE_EQUAL(

, db.

(gi, oid));

BOOST_REQUIRE_EQUAL(

, db.

(gi, pig));

BOOST_REQUIRE_EQUAL(

, db.

(pig, gi));

BOOST_REQUIRE(oids.size() == 0);

BOOST_REQUIRE_NO_THROW(db.

(seqid, oids));

BOOST_REQUIRE(oids.size() == 0);

BOOST_REQUIRE_EQUAL(

, db.

(seqid, oid));

residue(12345);

vector<string> paths1;

vector<string> paths2;

BOOST_REQUIRE_EQUAL(paths1.size(),

(1));

BOOST_REQUIRE_EQUAL(paths2.size(),

(1));

BOOST_REQUIRE_EQUAL((

)paths1[0], (

)paths2[0]);

BOOST_REQUIRE(!sd.

());

BOOST_REQUIRE(!sd.

());

(

di = 0; di < 2; di++) {

& db = di ? db65 : db56;

(

oi = 0; oi < 2; oi++) {

list< CRef<CSeq_id> > ids = db.

(oi);

(! ids.empty()) {

&

= *ids.front();

.GetGeneral().GetDb() ==

) {

BOOST_REQUIRE(

== 1);

BOOST_REQUIRE(oid == oi);

nucl_gi = 46071107;

nucl_str = (

prot_gi = 43914529;

prot_str =

;

nucl_oid(-1), prot_oid(-1);

.GiToOid(nucl_gi, nucl_oid);

.GiToOid(prot_gi, prot_oid);

.GetSequenceAsString(nucl_oid, nstr);

.GetSequenceAsString(prot_oid, pstr);

BOOST_REQUIRE_EQUAL((

)nstr, (

)nucl_str);

BOOST_REQUIRE_EQUAL((

)pstr, (

)prot_str);

BOOST_REQUIRE_EQUAL((

)

.GetTotalLength(), 12345);

BOOST_REQUIRE_EQUAL((

)

.GetTotalLengthStats(), 23456);

BOOST_REQUIRE_EQUAL((

)

.GetNumSeqs(), 123);

BOOST_REQUIRE_EQUAL((

)

.GetNumSeqsStats(), 234);

.push_back(*ids);

.push_back(*ids);

& amt = m[

];

db.

(oid, gis,

);

(vector<TGi>, iter, gis) {

BOOST_REQUIRE_EQUAL((

)have_got.

(), 100);

BOOST_REQUIRE_EQUAL((

)have_not.

(), 89);

(

* idp = gis; *idp; ++idp) {

BOOST_REQUIRE_EQUAL((

) id_pop.

(), nlist_gis);

BOOST_REQUIRE_EQUAL(total, nlist_gis);

BOOST_REQUIRE_EQUAL((

) id_pop.

(), seqp_gis);

BOOST_REQUIRE_EQUAL(total, seqp_gis-nlist_gis);

BOOST_REQUIRE_EQUAL((

) id_pop.

(), 0);

BOOST_REQUIRE_EQUAL(total, -seqp_gis);

= have_got.

(gi1, oid1);

BOOST_REQUIRE(

);

list< CRef<CSeq_id> > got_ids = have_got.

(oid1);

list< CRef<CSeq_id> > not_ids = have_not.

(oid1);

BOOST_REQUIRE_EQUAL(diff, 2);

found = have_got.

(gis[0], oid);

BOOST_REQUIRE(found);

vector<TGi> gis_w, gis_wo;

have_got.

(oid, gis_w);

have_not.

(oid, gis_wo);

count_w = (

) gis_w.size();

count_wo = (

) gis_wo.size();

BOOST_REQUIRE_EQUAL(count_w, (count_wo+1));

vector<unsigned int> pigs;

pigs.push_back(281224);

db =

;

= 134;

found = have_got.

(pigs[0], oid);

BOOST_REQUIRE(found);

BOOST_REQUIRE_EQUAL((

)pig_w, pigs[0]);

found =

;

(vector<int>, iter, oids) {

BOOST_REQUIRE(found);

found =

;

(vector<int>, iter, oids) {

BOOST_REQUIRE(found);

NStr::Tokenize(

,

sides(

);

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

(

= 0;

< ids.size();

++) {

is4(

), is8(

);

(sides[

]) {

idstr = ids[

];

have = db4.TiToOid(idnum, oid);

BOOST_REQUIRE_EQUAL(is4, have);

BOOST_REQUIRE_EQUAL(is4, (oid >= 0));

have = db8.TiToOid(idnum, oid);

BOOST_REQUIRE_EQUAL(is8, have);

BOOST_REQUIRE_EQUAL(is8, (oid >= 0));

seqid(

(

) + idstr);

db4.SeqidToOids(seqid, oids);

BOOST_REQUIRE_EQUAL(is4, (oids.size() == 1));

db8.SeqidToOids(seqid, oids);

BOOST_REQUIRE_EQUAL(is8, (oids.size() == 1));

oid1(-1), oid2(-1);

okay1 = p1.

(pig, oid1);

okay2 = p2.

(pig, oid2);

BOOST_REQUIRE(okay1);

BOOST_REQUIRE(okay2);

BOOST_REQUIRE(oid1 > 0);

BOOST_REQUIRE(oid2 > 0);

BOOST_REQUIRE(oid1 == oid2);

size1 = p1.

(oid1)->

().size();

size2 = p2.

(oid2)->

().size();

BOOST_CHECK_NE(0, size1);

BOOST_CHECK_NE(0, size2);

BOOST_CHECK_GE(size1, 14);

BOOST_CHECK_GT(size1, (size2 + 5));

ostringstream fasta;

(list<string>, iter, ids) {

vector<int> tmp_oids;

BOOST_REQUIRE_MESSAGE(tmp_oids.size(),

(

)+(*iter));

oids.insert(oids.end(), tmp_oids.begin(), tmp_oids.end());

(oids.begin(), oids.end());

oids.erase(unique(oids.begin(), oids.end()), oids.end());

(vector<int>, iter, oids) {

all_fasta = fasta.str();

=

(

) + acc;

BOOST_REQUIRE_MESSAGE(all_fasta.size() == exp_size,

);

BOOST_REQUIRE_MESSAGE(exp_oids == oids.size(),

);

(db,

, 4, 5411);

(db,

, 4, 5411);

acc(

);

.AccessionToOids(acc, oids);

BOOST_REQUIRE(oids.size());

fname(

);

vname(

);

title(

);

BOOST_REQUIRE_EQUAL(

.GetTitle(), title);

BOOST_REQUIRE_EQUAL((

)

.size(), 1);

BOOST_REQUIRE_EQUAL(title,

[0]);

BOOST_REQUIRE(comedy_column >= 0);

BOOST_REQUIRE_EQUAL((

)metadata_db.

(), 3);

BOOST_REQUIRE_EQUAL(metadata_db.

(

)->second,

(

));

BOOST_REQUIRE_EQUAL(metadata_db.

(

)->second,

(

));

BOOST_REQUIRE_EQUAL(metadata_db.

(

)->second,

(

));

BOOST_REQUIRE(metadata_db == metadata_user);

BOOST_REQUIRE(db.

(comedy_column,

) ==

);

BOOST_REQUIRE(db.

(comedy_column,

) ==

);

BOOST_REQUIRE(

.GetValue(

) ==

);

BOOST_REQUIRE(

.GetValue(

) ==

);

vector<string> volumes;

BOOST_REQUIRE(meta_vol0.

(

) != meta_vol0.

());

BOOST_REQUIRE(meta_vol0.

(

)->second ==

);

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;

BOOST_REQUIRE_EQUAL((

) column_data.size(), db.

());

BOOST_REQUIRE_EQUAL((

) column_data.size(),

.GetNumOIDs());

(

oid = 0; oid <

; oid++) {

.GetBlob(oid, cr_blob);

BOOST_REQUIRE(db_blob.

() == column_data[oid]);

BOOST_REQUIRE(cr_blob.

() == column_data[oid]);

good(

);

bad (

);

both(

);

vector<int> o1, o2, o3;

BOOST_REQUIRE(o1.size() == 1);

BOOST_REQUIRE(o2.size() == 0);

BOOST_REQUIRE(o3.size() == 1);

BOOST_REQUIRE_EQUAL((

)algos.size(), 2);

algo_opts, algo_name;

filtering_algo, algo_name, algo_opts);

BOOST_REQUIRE_EQUAL(algo_opts,

);

filtering_algo, algo_name, algo_opts);

BOOST_REQUIRE_EQUAL(algo_opts,

(

));

BOOST_REQUIRE_EQUAL(algos.size(), 1U);

BOOST_REQUIRE_EQUAL(11, algos.front());

BOOST_REQUIRE(ranges.

());

BOOST_CHECK_EQUAL((

) nr_sum.

(),

);

BOOST_CHECK_EQUAL((

) sp_sum.

(),

);

BOOST_CHECK_EQUAL((

) ac_sum.

(),

);

BOOST_CHECK_EQUAL((

) sc_sum.

(),

);

BOOST_CHECK_EQUAL((

) nr_sum.

(sp_sum),

);

BOOST_CHECK_EQUAL((

) nr_sum.

(ac_sum),

);

BOOST_CHECK_EQUAL((

) nr_sum.

(sc_sum),

);

BOOST_CHECK_EQUAL((

) sp_sum.

(sc_sum),

);

BOOST_CHECK_EQUAL((

) ac_sum.

(sc_sum),

);

path =

(

) + ch +

;

ifstream

(path.c_str());

BOOST_REQUIRE_EQUAL(h1, h2);

BOOST_REQUIRE(db.

(555, oid));

BOOST_REQUIRE(deflines.

());

BOOST_REQUIRE(deflines.

());

kExpectedSize = 1420;

BOOST_REQUIRE_EQUAL(kExpectedSize, db.

());

vector<string> gnomon_ids;

gnomon_ids.push_back(

);

gnomon_ids.push_back(

);

gnomon_ids.push_back(

);

gnomon_ids.push_back(

);

gnomon_ids.push_back(

);

(

= 0;

< gnomon_ids.size();

++) {

BOOST_REQUIRE( !oids.empty() );

BOOST_REQUIRE_EQUAL(

, (

)oids.front());

BOOST_REQUIRE( !oids.empty() );

BOOST_REQUIRE_EQUAL(

, (

)oids.front());

BOOST_REQUIRE(found);

BOOST_REQUIRE_EQUAL(

, (

)oid);

seqidlist_name = seqidlist_tmpfile.

();

blastdb_name = alias_file_tmpfile.

() +

;

kSeqIdIncluded =

;

ofstream stream(seqidlist_name.c_str());

stream << kSeqIdIncluded << endl;

ofstream stream(blastdb_name.c_str());

stream <<

<< endl;

stream <<

<< endl;

stream <<

<< seqidlist_name << endl;

BOOST_REQUIRE_EQUAL(1U, oids.size());

seqid2search =

;

BOOST_CHECK_EQUAL(0

, oids.size());

rv = system(

);

BOOST_REQUIRE_EQUAL(0, rv);

db_name =

;

BOOST_REQUIRE_EQUAL((

) dbs_sum.

(),

);

BOOST_REQUIRE_EQUAL_COLLECTIONS(taxids.

(), taxids.

(),

returned.

(), returned.

());

returned.

(), returned.

());

oids[] = {

0x7acee466, 0x4cbc1ab0,

0x7d219922, 0x7e096431,

0x276283ea, 0x13cee382,

0x51f8b267, 0x37183674,

0x03559cd6, 0x6bdcfbb7

nrecs = (

) (

oids /

oids[0]);

uint4_gi = 0xFFFFFFFF;

big_gi = 0xC0000000;

(

= 0;

< nrecs; ++

) {

BOOST_REQUIRE(oid == oids[

]);

BOOST_FAIL(

);

BOOST_REQUIRE_EQUAL(55, found);

list< CRef<CSeq_id> > ids = db.

(1);

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

fasta_id = (*itr)->AsFastaString();

BOOST_REQUIRE_EQUAL(1 , num_acc);

BOOST_REQUIRE_EQUAL(fasta_id ,

);

BOOST_REQUIRE_EQUAL(63, found);

BOOST_REQUIRE_EQUAL(1, found);

BOOST_REQUIRE_EQUAL(3, oid);

BOOST_REQUIRE_EQUAL(2, found);

num_pigs = 5;

pigs[num_pigs] = {4377482, 1287445, 2, 6066974, 5303747};

num_valid_pig = 4;

(

=0;

< num_pigs;

++) {

pig_list->

(pigs[

]);

db_name =

;

BOOST_REQUIRE_EQUAL(pig_db.

(), 4);

BOOST_REQUIRE_EQUAL(negative_pig_db.

(), (

) (total_num_seqs - num_valid_pig));

vector<string> seq_ids;

list< CRef<CSeq_id> > ids = pig_db.

(oid);

seq_ids.push_back(ids.front()->GetSeqIdString());

BOOST_REQUIRE_EQUAL(oid_found, oid);

BOOST_REQUIRE_EQUAL(seq_ids.size(), num_valid_pig);

(

=0;

< seq_ids.size();

++){

BOOST_REQUIRE_EQUAL(

.size(), (

) 0);

num_pigs = 5;

pigs[num_pigs] = {2, 355704, 863725, 1727116, 24036443};

db_name =

;

(

=0;

< num_pigs;

++) {

pos_list->

(pigs[

]);

BOOST_REQUIRE_EQUAL(total_num_seqs, 1);

check_oids[1] = {12};

BOOST_REQUIRE_EQUAL(oid, check_oids[c]);

(

=0;

< num_pigs;

++) {

pos_list->

(pigs[

]);

BOOST_REQUIRE_EQUAL(total_num_seqs, 3);

check_oids[3] = {2, 6, 8};

BOOST_REQUIRE_EQUAL(oid, check_oids[c]);

(

=0;

< num_pigs;

++) {

p.push_back(pigs[

]);

BOOST_REQUIRE_EQUAL(total_num_seqs, 5);

check_oids[5] = {0, 1, 3, 5, 7};

BOOST_REQUIRE_EQUAL(oid, check_oids[c]);

(

=0;

< num_pigs;

++) {

p.push_back(pigs[

]);

check_oids[2] = {1, 3 };

BOOST_REQUIRE_EQUAL(oid, check_oids[c]);

db_name =

;

total_num_seqs = 0;

total_length = 0;

BOOST_REQUIRE(total_num_seqs > 0);

BOOST_REQUIRE(total_length > 0);

(

=0;

< MAX_FD_COUNT;

++) {

(

=0;

< 10000;

++) {

kNumThreads=64;

vector<CTestThread*> threads;

(

=0;

< kNumThreads;

++) {

(

=0;

< kNumThreads;

++) {

threads[

]->Run();

(

=0;

< kNumThreads;

++) {

threads[

]->Join();

db_name =

;

acc =

;

vector<TTaxId> tax_ids;

BOOST_REQUIRE_EQUAL(tax_ids.size(), 4U);

BOOST_REQUIRE_EQUAL(tax_ids[0], 1678);

BOOST_REQUIRE_EQUAL(tax_ids[3], 1263059);

vector<TTaxId> tax_ids;

BOOST_REQUIRE_EQUAL(tax_ids.size(), 1U);

BOOST_REQUIRE_EQUAL(tax_ids[0], 1205679);

acc =

;

vector<TTaxId> tax_ids;

BOOST_REQUIRE_EQUAL(tax_ids.size(), 0

);

db_name =

;

acc =

;

vector<TTaxId> tax_ids;

BOOST_REQUIRE_EQUAL(tax_ids.size(), 1U);

BOOST_REQUIRE_EQUAL(tax_ids[0], 0);

acc =

;

vector<TTaxId> tax_ids;

BOOST_REQUIRE_EQUAL(tax_ids.size(), 0

);

test_list.

(689972625);

test_list.

(689972107);

test_list.

(689971919);

test_list.

(689971844);

test_list.

(689971914);

test_list.

(123);

db_name =

;

vector<CSeqDBGiList::SGiOid> gilist = test_list.

();

(

=0;

< test_list.

();

++){

BOOST_REQUIRE_EQUAL( gilist[

].oid, oids[

]);

alias_db_name =

;

vector<CSeqDBGiList::SGiOid> gilist = test_list.

();

(

=0;

< test_list.

();

++){

BOOST_REQUIRE_EQUAL( gilist[

].oid, oids[

]);

gi = 1492455000;

giless_protein =

;

BOOST_REQUIRE_EQUAL(db_giless.

(gi, pig),

);

BOOST_REQUIRE_EQUAL(pig, -1);

(

=0;

< 200000;

++) {

static const char * kFileName

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

ncbi::TMaskedQueryRegions mask

vector< CRef< CSeq_id > > SeqIdList

`Blob' Class for SeqDB (and WriteDB).

CTempString Str() const

Get blob contents as a CTempString.

TTaxIds GetLeafTaxIds() const

void SetLeafTaxIds(const TTaxIds &t)

FASTA-format output; see also ReadFasta in <objtools/readers/fasta.hpp>

GI list containing the intersection of two other lists of GIs.

CNcbiOstrstreamToString class helps convert CNcbiOstrstream to a string Sample usage:

CNegativeIdList(const int *ids, bool use_tis)

static SIZE_TYPE Convert(const CTempString &src, TCoding src_coding, TSeqPos pos, TSeqPos length, string &dst, TCoding dst_coding)

int ChangeOpenedFilseCount(EFilesCount fc)

int GetOpenedFilseCount(void)

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

Raw Sequence and Ambiguity Data.

void GetPigBounds(int *low_id, int *high_id, int *count)

Get PIG Bounds.

unsigned GetSequenceHash(int oid)

Get the sequence hash for a given OID.

void HashToOids(unsigned hash, vector< int > &oids)

Get the OIDs for a given sequence hash.

void GetGiBounds(TGi *low_id, TGi *high_id, int *count)

Get GI Bounds.

vector< SGiOid > m_GisOids

Pairs of GIs and OIDs.

int GetNumGis() const

Get the number of GIs in the array.

void GetPigList(vector< TPig > &pigs) const

void GetGiList(vector< TGi > &gis) const

Get the gi list.

void AddTaxIds(const set< TTaxId > &tax_ids)

T GetKey(int index) const

void AddGi(TGi gi)

Add a new GI to the list.

bool FindGi(TGi gi) const

Test for existence of a GI.

vector< SSiOid > m_SisOids

Pairs of Seq-ids and OIDs.

SeqDB ID list for performing boolean set operations.

bool Blank() const

Check if an ID list is blank.

void Compute(EOperation op, const vector< int > &ids, bool positive=true)

Perform a logical operation on a list.

bool IsPositive()

Checks whether a positive GI list was produced.

CRef< CSeqDBNegativeList > GetNegativeList()

Retrieve a negative GI list.

CRef< CSeqDBGiList > GetPositiveList()

Retrieve a positive GI list.

bool IdToOid(Int8 id, TOid &oid)

GI or TI translation.

void UnLease()

Return any memory held by this object to the atlas.

void AddTaxIds(const set< TTaxId > &tax_ids)

void SetGiList(const vector< TGi > &new_list)

Set ID set for this negative list.

void SetPigList(const vector< TPig > &new_list)

vector< TTi > m_Tis

TIs to exclude from the SeqDB instance.

bool FindGi(TGi gi)

Test for existence of a GI.

vector< TGi > m_Gis

GIs to exclude from the SeqDB instance.

Reader for BlastDb format column files.

void GetColumnBlob(int col_id, int oid, CBlastDbBlob &blob)

Fetch the data blob for the given column and oid.

int TOID

Sequence type accepted and returned for OID indices.

bool IdsToOids(CSeqDBGiList &id_list) const

Get OIDs from an ID list.

static void FindVolumePaths(const string &dbname, ESeqType seqtype, vector< string > &paths, vector< string > *alias_paths=NULL, bool recursive=true, bool expand_links=true)

Find volume paths.

bool OidToPig(int oid, int &pig) const

Translate an OID to a PIG.

Uint8 GetTotalLength() const

Returns the sum of the lengths of all available sequences.

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

Gets a list of GIs for an OID.

bool PigToOid(int pig, int &oid) const

Translate a PIG to an OID.

void SetIterationRange(int oid_begin, int oid_end)

Set Iteration Range.

int GetNumOIDs() const

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

TGi GetSeqGI(int oid) const

Returns the first Gi (if any) of the sequence.

Uint8 GetVolumeLength() const

Returns the sum of the lengths of all volumes.

void GetAvailableMaskAlgorithms(vector< int > &algorithms)

Get a list of algorithm IDs for which mask data exists.

bool OidToGi(int oid, TGi &gi) const

Translate an OID to a GI.

const string & GetDBNameList() const

Get list of database names.

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

Gets a list of sequence identifiers.

Int8 GetDiskUsage() const

Retrieve the disk usage in bytes for this BLAST database.

void ResetInternalChunkBookmark()

Resets this object's internal chunk bookmark, which is used when the oid_state argument to GetNextOID...

EOidListType

Indicates how block of OIDs was returned.

CRef< CSeq_data > GetSeqData(int oid, TSeqPos begin, TSeqPos end) const

Fetch data as a CSeq_data object.

bool GiToPig(TGi gi, int &pig) const

Translate a GI to a PIG.

void GetAliasFileValues(TAliasFileValues &afv)

Get Name/Value Data From Alias Files.

int GetMaxLength() const

Returns the length of the largest sequence in the database.

int GetSeqLength(int oid) const

Returns the sequence length in base pairs or residues.

bool PigToGi(int pig, TGi &gi) const

Translate a PIG to a GI.

ESeqType GetSequenceType() const

Returns the type of database opened - protein or nucleotide.

const CSeqDBGiList * GetGiList() const

Get GI list attached to this database.

ESeqType

Sequence types (eUnknown tries protein, then nucleotide).

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

Translate a Seq-id to any matching OID.

void RetAmbigSeq(const char **buffer) const

Returns any resources associated with the sequence.

int GetOidAtOffset(int first_seq, Uint8 residue) const

Find the sequence closest to the given offset into the database.

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

Get a CBioseq for a sequence.

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

Get a CBioseq for a sequence without sequence data.

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

Get taxid for an OID.

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

Get information about one type of masking available here.

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

Returns the sum of the sequence lengths.

void RetSequence(const char **buffer) const

Returns any resources associated with the sequence.

string GetTitle() const

Returns the database title.

int GetNumSeqs() const

Returns the number of sequences available.

void GetTaxIdsForSeqId(const CSeq_id &seq_id, vector< TTaxId > &taxids)

Get all tax ids for a seq id.

EOidListType GetNextOIDChunk(int &begin_chunk, int &end_chunk, int oid_size, vector< int > &oid_list, int *oid_state=NULL)

Return a chunk of OIDs, and update the OID bookmark.

int GetSequence(int oid, const char **buffer) const

Get a pointer to raw sequence data.

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

Translate an Accession to a list of OIDs.

void ListColumns(vector< string > &titles)

List columns titles found in this database.

void GetTaxIdsForAccession(const string &accs, vector< TTaxId > &taxids)

Get all tax ids for an accessions.

bool CheckOrFindOID(int &next_oid) const

Find an included OID, incrementing next_oid if necessary.

string GetDate() const

Returns the construction date of the database.

int GetNumSeqsStats() const

Returns the number of sequences available.

@ eUnfilteredAll

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

@ eFilteredRange

Sum of included sequences with OIDs within the iteration range.

@ eFilteredAll

Values from alias files, or summation over all included sequences.

int GetColumnId(const string &title)

Get an ID number for a given column title.

void SeqidToOids(const CSeq_id &seqid, vector< int > &oids) const

Translate a Seq-id to a list of OIDs.

int GetAmbigSeqAlloc(int oid, char **buffer, int nucl_code, ESeqDBAllocType strategy, TSequenceRanges *masks=NULL) const

Get a pointer to sequence data with ambiguities.

CSeqDBIter Begin() const

Returns a sequence iterator.

const string & GetColumnValue(int column_id, const string &key)

Look up the value for a specific column metadata key.

CRef< CBioseq > GiToBioseq(TGi gi) const

Get a CBioseq for a given GI.

static void GetTaxInfo(TTaxId taxid, SSeqDBTaxInfo &info)

Get taxonomy information.

CRef< CBlast_def_line_set > GetHdr(int oid) const

Get the ASN.1 header for the sequence.

Uint8 GetTotalLengthStats() const

Returns the sum of the lengths of all available sequences.

int GetSeqLengthApprox(int oid) const

Returns an unbiased, approximate sequence length.

CRef< CBioseq > SeqidToBioseq(const CSeq_id &seqid) const

Get a CBioseq for a given Seq-id.

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

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

CRef< CBioseq > PigToBioseq(int pig) const

Get a CBioseq for a given PIG.

int GetAmbigSeq(int oid, const char **buffer, int nucl_code) const

Get a pointer to sequence data with ambiguities.

void GetMaskData(int oid, const vector< int > &algo_ids, TSequenceRanges &ranges)

Get masked ranges of a sequence.

bool GiToOid(TGi gi, int &oid) const

Translate a GI to an OID.

const map< string, string > & GetColumnMetaData(int column_id)

Get all metadata for the specified column.

CSeqDBIdSet GetIdSet() const

Get IdSet list attached to this database.

void GetLeafTaxIDs(int oid, map< TGi, set< TTaxId > > &gi_to_taxid_set, bool persist=false) const

Get taxid for an OID.

void Append(const char *p)

CSeqIdList(const char **str)

CSimpleGiList(const vector< TGi > &gis)

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

CRef< CSeqDBIsam > m_Isam

CTestThread(CSeqDBAtlas &atlas)

CTmpEnvironmentSetter(const char *name, const char *value=NULL)

const_iterator end() const

const_iterator find(const key_type &key) const

iterator_bool insert(const value_type &val)

const_iterator begin() const

const_iterator find(const key_type &key) const

const_iterator end() const

Defines column reader class for SeqDB.

int GetSeqLength(const CBioseq &bioseq)

static const unsigned long CR

static const struct name_t names[]

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

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

static const char * expected[]

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

static const column_t columns[]

#define GI_FROM(T, value)

constexpr size_t ArraySize(const Element(&)[Size])

#define ITERATE(Type, Var, Cont)

ITERATE macro to sequence through container elements.

SStrictId_Tax::TId TTaxId

Taxon id type.

void Set(const string &name, const string &value)

Set an environment variable by name.

const string & Get(const string &name, bool *found=NULL) const

Get environment value by name.

static void Add(const string &path)

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

const string & GetFileName(void) const

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

static string ConvertToOSPath(const string &path)

Convert "path" on any OS to the current OS-dependent path.

static char GetPathSeparator(void)

Get path separator symbol specific for the current platform.

const TPrim & Get(void) const

#define MSerial_AsnText

I/O stream manipulators –.

const string AsFastaString(void) const

virtual void Write(const CSeq_entry_Handle &handle, const CSeq_loc *location=0)

Unspecified locations designate complete sequences; non-empty custom titles override the usual title ...

void SetWidth(TSeqPos width)

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.

int32_t Int4

4-byte (32-bit) signed integer

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

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

Convert size_t to string.

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

Convert string to Int8.

static list< string > & Split(const CTempString str, const CTempString delim, list< string > &arr, TSplitFlags flags=0, vector< SIZE_TYPE > *token_pos=NULL)

Split a string using specified delimiters.

@ fSplit_MergeDelimiters

Merge adjacent delimiters.

bool IsSetLinks(void) const

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

TTaxid GetTaxid(void) const

Get the Taxid member data.

bool IsSetTaxid(void) const

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

void SetTaxid(TTaxid value)

Assign a value to Taxid data member.

EBlast_filter_program

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

const Tdata & Get(void) const

Get the member data.

@ eBlast_filter_program_repeat

@ eBlast_filter_program_seg

const TTag & GetTag(void) const

Get the Tag member data.

TId GetId(void) const

Get the variant data.

TGi GetGi(void) const

Get the variant data.

const TGeneral & GetGeneral(void) const

Get the variant data.

@ e_General

for other databases

@ e_Gi

GenInfo Integrated Database.

void ResetDescr(void)

Reset Descr data member.

const TInst & GetInst(void) const

Get the Inst member data.

const TNcbi4na & GetNcbi4na(void) const

Get the variant data.

bool CanGetSeq_data(void) const

Check if it is safe to call GetSeq_data method.

const TSeq_data & GetSeq_data(void) const

Get the Seq_data member data.

char * dbname(DBPROCESS *dbproc)

Get name of current database.

unsigned int

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

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is whole

where boath are integers</td > n< td ></td > n</tr > n< tr > n< td > tse</td > n< td > optional</td > n< td > String</td > n< td class=\"description\"> TSE option controls what blob is smart and slim</td> n<td> orig</td> n</tr> n<tr> n<td> last_modified</td> n<td> optional</td> n<td> Integer</td> n<td class=\"description\"> The blob last modification If provided then the exact match will be requested with n the Cassandra storage corresponding field value</td> n<td> Positive integer Not provided means that the most recent match will be selected</td> n<td></td> n</tr> n<tr> n<td> use_cache</td> n<td> optional</td> n<td> String</td> n<td class=\"description\"> The option controls if the Cassandra LMDB cache and or database should be used It n affects the seq id resolution step and the blob properties lookup step The following n options are BIOSEQ_INFO and BLOB_PROP at all

CBioseq_Info & GetBioseq(CTSE_Info &tse, const CBioObjectId &id)

unique_ptr< CLocalTaxon > tax1

static void hex(unsigned char c)

constexpr auto sort(_Init &&init)

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

const struct ncbi::grid::netcache::search::fields::KEY key

const GenericPointer< typename T::ValueType > T2 value

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

BOOST_AUTO_TEST_SUITE(psiblast_iteration)

static const string kDb("db")

string s_Stringify(CRef< ASNOBJ > a)

static void s_TestMaskingLimits(EMaskingType mask, unsigned first, unsigned last, unsigned lowest, unsigned highest, unsigned count)

static void s_MapAllGis(CSeqDB &db, map< int, int > &m, int change, int &total)

static void s_TestPartialAmbig(CSeqDB &db, TGi nt_gi)

void s_ApproxEqual(NUM a, NUM b, DIF epsilon, int lineno)

BOOST_AUTO_TEST_CASE(ConstructLocal)

static bool s_DbHasOID(CSeqDB &db, int &count, int oid)

BOOST_AUTO_TEST_CASE_TIMEOUT(TestGiToOidTimeout, 15)

static void s_ModifyMap(map< int, int > &m, int key, int c, int &total)

static void s_CheckIdLookup(CSeqDB &db, const string &acc, size_t exp_oids, size_t exp_size)

static void s_TestPartialAmbigRange(CSeqDB &db, int oid, int begin, int end)

static Uint4 s_BufHash(const char *buf_in, Uint4 length, Uint4 start=1)

string s_ToString(const A &a, const B &b, const C &c, const D &d, const E &e)

static bool s_MaskingTest(EMaskingType mask, unsigned oid)

Defines exception class and several constants for SeqDB.

const blastdb::TOid kSeqDBEntryNotFound

Int4 TOid

Ordinal ID in BLAST databases.

const int kSeqDBNuclNcbiNA8

Used to request ambiguities in Ncbi/NA8 format.

ESeqDBIdType SeqDB_SimplifyAccession(const string &acc, Int8 &num_id, string &str_id, bool &simpler)

String id simplification.

bool SeqDB_IsBinaryGiList(const string &fname)

Read a text or binary SeqId list from a file.

unsigned SeqDB_SequenceHash(const char *sequence, int length)

Returns a path minus filename.

const int kSeqDBNuclBlastNA8

Used to request ambiguities in BLAST/NA8 format.

string SeqDB_ResolveDbPath(const string &filename)

Resolve a file path using SeqDB's path algorithms.

Defines `expert' version of CSeqDB interfaces.

ISAM index database access object.

static const char * kTaxid

static SLJIT_INLINE sljit_ins nr(sljit_gpr dst, sljit_gpr src)

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

List of sequence offset ranges.

int measured_oids

Measured oid count should equal filtered if alias files are correct.

int total_oids

Total oid count, sum of all volume oid counts.

Int8 filtered_length

Filtered length, result of all filtering.

void CompareField(Int8 X, Int8 Y, string &sum, char ch)

Int8 total_length

Total length, sum of all volume lengths.

string Compare(SDbSumInfo &other)

int filtered_oids

Filtered oid count, result of all filtering.

Int8 measured_length

Measured length should equal filtered if alias files are correct.

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

int g(Seg_Gsm *spe, Seq_Mtf *psm, Thd_Gsm *tdg)

static string kCount("Count")

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