* kDataFile =
"data/nt.555.mfsa";
120boost::test_tools::output_test_stream
out(
"data/sample_parse_seqids_fasta.out");
121 const boolkParseSeqids(
true);
123writer->Print(m_BioseqHandleWithGi, m_Masks, kParseSeqids);
124BOOST_CHECK(
out.match_pattern());
132boost::test_tools::output_test_stream
out(
"data/sample_fasta.out");
133 const boolkParseSeqids(
false);
135writer->Print(m_BioseqHandleWithLocalId, m_Masks, kParseSeqids);
136BOOST_CHECK(
out.match_pattern());
143boost::test_tools::output_test_stream
out(
"data/sample_parse_seqids_acclist.out");
144 const boolkParseSeqids(
true);
146writer->Print(m_BioseqHandleWithGi, m_Masks, kParseSeqids);
147BOOST_CHECK(
out.match_pattern());
155boost::test_tools::output_test_stream
out(
"data/sample_acclist.out");
156 const boolkParseSeqids(
false);
158writer->Print(m_BioseqHandleWithLocalId, m_Masks, kParseSeqids);
159BOOST_CHECK(
out.match_pattern());
167boost::test_tools::output_test_stream
out(
"data/sample_parse_seqids_interval.out");
168 const boolkParseSeqids(
true);
170writer->Print(m_BioseqHandleWithGi, m_Masks, kParseSeqids);
171BOOST_CHECK(
out.match_pattern());
179boost::test_tools::output_test_stream
out(
"data/sample_interval.out");
180 const boolkParseSeqids(
false);
182writer->Print(m_BioseqHandleWithLocalId, m_Masks, kParseSeqids);
183BOOST_CHECK(
out.match_pattern());
194boost::test_tools::output_test_stream
out(
"data/sample_parse_seqids_maskinfo_asn1_text.out");
195 const boolkParseSeqids(
true);
197 "maskinfo_asn1_text",
201writer->Print(m_BioseqHandleWithGi, m_Masks, kParseSeqids);
202BOOST_CHECK(
out.match_pattern());
207boost::test_tools::output_test_stream
out(
"data/sample_maskinfo_asn1_text.out");
208 const boolkParseSeqids(
false);
210 "maskinfo_asn1_text",
214writer->Print(m_BioseqHandleWithLocalId, m_Masks, kParseSeqids);
215BOOST_CHECK(
out.match_pattern());
220 const boolkMatchOrSave(
true);
221 const boolkTextOrBin(
false);
222boost::test_tools::output_test_stream
223 out(
"data/sample_parse_seqids_maskinfo_asn1_bin.out",
224kMatchOrSave, kTextOrBin);
225 const boolkParseSeqids(
true);
227 "maskinfo_asn1_bin",
231writer->Print(m_BioseqHandleWithGi, m_Masks, kParseSeqids);
232BOOST_CHECK(
out.match_pattern());
237 const boolkMatchOrSave(
true);
238 const boolkTextOrBin(
false);
239boost::test_tools::output_test_stream
out(
"data/sample_maskinfo_asn1_bin.out",
240kMatchOrSave, kTextOrBin);
241 const boolkParseSeqids(
false);
243 "maskinfo_asn1_bin",
247writer->Print(m_BioseqHandleWithLocalId, m_Masks, kParseSeqids);
248BOOST_CHECK(
out.match_pattern());
253boost::test_tools::output_test_stream
out(
"data/sample_parse_seqids_maskinfo_xml.out");
254 const boolkParseSeqids(
true);
260writer->Print(m_BioseqHandleWithGi, m_Masks, kParseSeqids);
261BOOST_CHECK(
out.match_pattern());
266boost::test_tools::output_test_stream
out(
"data/sample_maskinfo_xml.out");
267 const boolkParseSeqids(
false);
273writer->Print(m_BioseqHandleWithLocalId, m_Masks, kParseSeqids);
274BOOST_CHECK(
out.match_pattern());
279boost::test_tools::output_test_stream
out(
281 "data/sample_prefacc_parse_seqids_seqloc_asn1_text.out":
282 "data/sample_parse_seqids_seqloc_asn1_text.out");
283 const boolkParseSeqids(
true);
285writer->Print(m_BioseqHandleWithGi, m_Masks, kParseSeqids);
286BOOST_CHECK(
out.match_pattern());
291boost::test_tools::output_test_stream
out(
"data/sample_seqloc_asn1_text.out");
292 const boolkParseSeqids(
false);
294writer->Print(m_BioseqHandleWithLocalId, m_Masks, kParseSeqids);
295BOOST_CHECK(
out.match_pattern());
296BOOST_REQUIRE_EQUAL(GetExpectedNumberOfMasks(), m_Masks.size());
297BOOST_CHECK_EQUAL(GetMaskStart(), m_Masks[0].
first);
298BOOST_CHECK_EQUAL(GetMaskStop(), m_Masks[0].second);
306 const boolkMatchOrSave(
true);
307 const boolkTextOrBin(
false);
308boost::test_tools::output_test_stream
311 "data/sample_prefacc_parse_seqids_seqloc_asn1_bin.out":
312 "data/sample_parse_seqids_seqloc_asn1_bin.out",
315 const boolkParseSeqids(
true);
317writer->Print(m_BioseqHandleWithGi, m_Masks, kParseSeqids);
318BOOST_CHECK(
out.match_pattern());
323 const boolkMatchOrSave(
true);
324 const boolkTextOrBin(
false);
325boost::test_tools::output_test_stream
326 out(
"data/sample_seqloc_asn1_bin.out", kMatchOrSave, kTextOrBin);
327 const boolkParseSeqids(
false);
329writer->Print(m_BioseqHandleWithLocalId, m_Masks, kParseSeqids);
330BOOST_CHECK(
out.match_pattern());
335boost::test_tools::output_test_stream
out(
337 "data/sample_prefacc_parse_seqids_seqloc_xml.out":
338 "data/sample_parse_seqids_seqloc_xml.out");
339 const boolkParseSeqids(
true);
341writer->Print(m_BioseqHandleWithGi, m_Masks, kParseSeqids);
342BOOST_CHECK(
out.match_pattern());
347boost::test_tools::output_test_stream
out(
"data/sample_seqloc_xml.out");
348 const boolkParseSeqids(
false);
350writer->Print(m_BioseqHandleWithLocalId, m_Masks, kParseSeqids);
351BOOST_CHECK(
out.match_pattern());
@ eExtreme_Positional
numerical value
BOOST_AUTO_TEST_SUITE_END() static int s_GetSegmentFlags(const CBioseq &bioseq)
ncbi::TMaskedQueryRegions mask
Base class for reading FASTA sequences.
Output filter to print masked sequence locations as Blast-db-mask-info objects.
Output filter to write masked data in fasta format.
Output filter to print masked sequences as sets of intervals.
Output filter to print masked sequence locations as NCBI Seq-loc objects.
Output filter to print masked sequences as sets of intervals one per line.
pair< TSeqPos, TSeqPos > TMaskedInterval
Type representing a masked interval within a sequence.
vector< TMaskedInterval > TMaskList
A type representing the total of masking information about a sequence.
Template class for iteration on objects of class C (non-medifiable version)
std::ofstream out("events_result.xml")
main entry point for tests
Operators to edit gaps in sequences.
static DLIST_TYPE *DLIST_NAME() first(DLIST_LIST_TYPE *list)
unsigned int TSeqPos
Type for sequence locations and lengths.
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
CRef< CSeq_loc > SaveMask(void)
Directs the *following* call to ReadOneSeq to note the locations of lowercase letters.
const CSeq_id & GetBestID(void) const
@ fNoParseID
Generate an ID (whole defline -> title)
@ fUniqueIDs
Forbid duplicate IDs.
@ fAssumeNuc
Assume nucs unless accns indicate otherwise.
static bool PreferAccessionOverGi(void)
Check if the option to prefer accession.version over GI is enabled (SeqId/PreferAccessionOverGi or SE...
CConstBeginInfo ConstBegin(const C &obj)
Get starting point of non-modifiable object hierarchy.
static CRef< CObjectManager > GetInstance(void)
Return the existing object manager or create one.
CSeq_entry_Handle AddTopLevelSeqEntry(CSeq_entry &top_entry, TPriority pri=kPriority_Default, EExist action=eExist_Default)
Add seq_entry, default priority is higher than for defaults or loaders Add object to the score with p...
CBioseq_Handle GetBioseqHandle(const CSeq_id &id)
Get bioseq handle by seq-id.
void AddDefaults(TPriority pri=kPriority_Default)
Add default data loaders from object manager.
IO_PREFIX::ifstream CNcbiIfstream
Portable alias for ifstream.
@ eBlast_filter_program_dust
bool IsSeq(void) const
Check if variant Seq is selected.
std::istream & in(std::istream &in_, double &x_)
static const int kAlgoId(2)
BOOST_AUTO_TEST_CASE(WriteFastaParseSeqids)
static const string kAlgoOptions("window=64; level=20; linker=1")
CBioseq_Handle m_BioseqHandleWithLocalId
CBioseq_Handle m_BioseqHandleWithGi
TSeqPos GetMaskStop() const
CMaskWriter::TMaskList m_Masks
void x_LoadMaskedBioseqGi555()
CBioseq_Handle x_LoadMaskedBioseq(bool parse_seqids)
void x_LoadMaskedBioseqLocalId()
size_t GetExpectedNumberOfMasks() const
TSeqPos GetMaskStart() const
void x_ConvertMasks(CRef< CSeq_loc > mask)
Utility stuff for more convenient using of Boost.Test library.
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