(
"enable_TestTimeout",
73 "Run TestTimeout test, which is artificially disabled by default in" 74 "order to avoid unwanted failure during the daily automated builds.");
88list<CRef<CSeq_id> >& seqid_list = defline->SetSeqid();
90defline->SetTitle(title);
99vector<CRef<CBlast_def_line> > defline_v;
100 for(
size_t i=0;
i<array_size; ++
i)
106 for(
size_t i=0;
i<array_size; ++
i)
108 swap(defline_v[
i], defline_v[
rnd.GetRand(0, defline_v.size()-1)]);
112 for(
size_tindex=0; index<array_size; index++)
114 const stringfasta_str = defline_v[index]->GetSeqid().back()->AsFastaString();
116defline_set->
Set().push_back(defline_v[index]);
127 const char*
consttheIds[] = {
128 "gi|289223532|ref|WP_003131952.1|",
129 "gi|15674171|ref|NP_268346.1|",
130 "gi|116513137|ref|YP_812044.1|",
131 "gi|125625229|ref|YP_001033712.1|",
132 "gi|281492845|ref|YP_003354825.1|",
133 "gi|385831755|ref|YP_005869568.1|",
134 "gi|13878750|sp|Q9CDN0.1|RS18_LACLA",
135 "gi|122939895|sp|Q02VU1.1|RS18_LACLS",
136 "gi|166220956|sp|A2RNZ2.1|RS18_LACLM",
137 "gi|12725253|gb|AAK06287.1|AE006448_5",
138 "gi|116108791|gb|ABJ73931.1|",
139 "gi|124494037|emb|CAL99037.1|",
140 "gi|281376497|gb|ADA65983.1|",
141 "gi|300072039|gb|ADJ61439.1|",
142 "gi|326407763|gb|ADZ64834.1|" 152 const stringfasta_str = (*itr)->GetSeqid().back()->AsFastaString();
154 stringstartId(theIds[index]);
155BOOST_CHECK_MESSAGE(startId.find(fasta_str) != string::npos,
"Error for "<< fasta_str);
163 const char*
consttheIds[] = {
164 "gi|446057344|ref|WP_000135199.1|",
165 "gi|443615715|ref|YP_007379571.1|",
166 "gi|444353545|ref|YP_007389689.1|",
167 "gi|448240163|ref|YP_007404216.1|",
168 "gi|449306713|ref|YP_007439069.1|",
169 "gi|67472372|sp|P0A7T7.2|RS18_ECOLI",
170 "gi|67472373|sp|P0A7T8.2|RS18_ECOL6",
171 "gi|67472374|sp|P0A7T9.2|RS18_ECO57",
181 const stringfasta_str = (*itr)->GetSeqid().back()->AsFastaString();
183 stringstartId(theIds[index]);
185BOOST_CHECK_MESSAGE(startId.find(fasta_str) != string::npos,
"Error for "<< fasta_str);
194 const char*
consttheIds[] = {
195 "gi|4757812|ref|NP_004880.1|",
196 "gi|114614837|ref|XP_001139040.1|",
197 "gi|426357086|ref|XP_004045879.1|",
198 "gi|7404340|sp|P56134.3|ATPK_HUMAN",
199 "gi|3335128|gb|AAC39887.1|",
200 "gi|3552030|gb|AAC34895.1|",
201 "gi|48145899|emb|CAG33172.1|",
202 "gi|49457306|emb|CAG46952.1|",
203 "gi|51094625|gb|EAL23877.1|",
204 "gi|119597067|gb|EAW76661.1|" 214 const stringfasta_str = (*itr)->GetSeqid().back()->AsFastaString();
216 stringstartId(theIds[index]);
217BOOST_CHECK_MESSAGE(startId.find(fasta_str) != string::npos,
"Error for "<< fasta_str);
226 const char*
consttheIds[] = {
227 "gi|9626178|ref|NP_040526.1|",
228 "gi|56160501|ref|AP_000176.1|",
229 "gi|56160855|ref|AP_000513.1|" 230 "gi|139364|sp|P03252.1|PRO_ADE02",
231 "gi|34810217|pdb|1NLN|A",
232 "gi|33330456|gb|AAQ10554.1|" 242 const stringfasta_str = (*itr)->GetSeqid().back()->AsFastaString();
244 stringstartId(theIds[index]);
245BOOST_CHECK_MESSAGE(startId.find(fasta_str) != string::npos,
"Error for "<< fasta_str);
254 const char*
consttheIds[] = {
255 "gi|133922597|ref|NM_001083308.1|",
256 "gi|55621735|ref|XM_526424.1|",
257 "gi|397465444|ref|XM_003804458.1|",
258 "gi|61741314|gb|AY858112.1|" 268 const stringfasta_str = (*itr)->GetSeqid().back()->AsFastaString();
270 stringstartId(theIds[index]);
271BOOST_CHECK_MESSAGE(startId.find(fasta_str) != string::npos,
"Error for "<< fasta_str);
283BOOST_CHECK_EQUAL(taxids.
size(), 0);
285list<int> taxid_list;
288taxid_list.push_back(200003);
289taxid_list.push_back(200002);
290taxid_list.push_back(200001);
294BOOST_CHECK_EQUAL(taxids.
size(), 3);
306BOOST_CHECK_EQUAL(taxids.
size(), 0);
312taxid_set.
insert(100002);
313taxid_set.
insert(100003);
314taxid_set.
insert(100004);
315taxid_set.
insert(100005);
318BOOST_CHECK_EQUAL(taxid_set.
size(), taxids.
size());
User-defined methods of the data storage class.
User-defined methods of the data storage class.
void SortBySeqIdRank(bool is_protein, bool useBlastRank=false)
Sort the deflines according to the toolkit established ranking of Seq-ids.
TTaxIds GetLeafTaxIds() const
void SetLeafTaxIds(const TTaxIds &t)
iterator_bool insert(const value_type &val)
NCBITEST_INIT_CMDLINE(arg_desc)
CRef< CBlast_def_line_set > s_MakeRandomDeflineSet(const char *const theIds[], size_t array_size)
BOOST_AUTO_TEST_CASE(SortRefSeqProteinSet1)
static CRef< CBlast_def_line > s_MakeDefline(const string &id, const string &title)
constexpr size_t ArraySize(const Element(&)[Size])
#define ITERATE(Type, Var, Cont)
ITERATE macro to sequence through container elements.
void swap(NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair1, NCBI_NS_NCBI::pair_base_member< T1, T2 > &pair2)
static SIZE_TYPE ParseFastaIds(CBioseq::TId &ids, const CTempString &s, bool allow_partial_failure=false)
Parse an entire set of |-delimited FASTA-style IDs, appending the results to IDS.
bool IsSetLinks(void) const
Check if a value has been assigned to Links data member.
void ResetLinks(void)
Reset Links data member.
Tdata & Set(void)
Assign a value to data member.
const Tdata & Get(void) const
Get the member data.
list< CRef< CBlast_def_line > > Tdata
TLinks & SetLinks(void)
Assign a value to Links data member.
void ResetTaxid(void)
Reset Taxid data member.
static size_t rnd(size_t minimal, size_t maximal)
Defines the CNcbiApplication and CAppException classes for creating NCBI applications.
Utility stuff for more convenient using of Boost.Test library.
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