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Searched refs:CFormatGuess (Results 1 – 25 of 60) sorted by relevance

123

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/formatguess/
H A Dformatguess.cpp172 format_name = CFormatGuess::GetFormatName(uFormat); in Run()
178 FormatStrings[ CFormatGuess::eTextASN ] = "Text ASN.1"; in Run()
180 FormatStrings[ CFormatGuess::eXml ] = "XML"; in Run()
188 FormatStrings[ CFormatGuess::eFiveColFeatureTable ] = in Run()
190 FormatStrings[ CFormatGuess::eTaxplot ] = "Tax plot"; in Run()
193 FormatStrings[ CFormatGuess::eFlatFileSequence ] = in Run()
197 FormatStrings[ CFormatGuess::eBed ] = "UCSC BED file"; in Run()
220 case CFormatGuess::eTextASN: in Run()
221 case CFormatGuess::eBinaryASN: in Run()
222 case CFormatGuess::eJSON: in Run()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/
H A Dformat_guess_ex.cpp91 m_Guesser(new CFormatGuess), in CFormatGuessEx()
121 CFormatGuess::EFormat Guess; in GuessFormat()
132 CFormatGuess::eAgp, in GuessFormat()
135 CFormatGuess::eBed, in GuessFormat()
139 CFormatGuess::eGtf, in GuessFormat()
140 CFormatGuess::eGff3, in GuessFormat()
466 case CFormatGuess::eXml: in xGuessGenbankObjectType()
469 case CFormatGuess::eJSON: in xGuessGenbankObjectType()
500 case CFormatGuess::eXml: in GuessFormatAndContent()
501 case CFormatGuess::eJSON: in GuessFormatAndContent()
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H A Dreader_base.cpp118 CFormatGuess::EFormat format, in GetReader()
126 case CFormatGuess::eBed: in GetReader()
128 case CFormatGuess::eBed15: in GetReader()
130 case CFormatGuess::eWiggle: in GetReader()
132 case CFormatGuess::eGtf: in GetReader()
135 case CFormatGuess::eGff3: in GetReader()
137 case CFormatGuess::eGvf: in GetReader()
139 case CFormatGuess::eVcf: in GetReader()
141 case CFormatGuess::eRmo: in GetReader()
143 case CFormatGuess::eFasta: in GetReader()
[all …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/readers/
H A Dformat_guess_ex.cpp89 m_Guesser(new CFormatGuess), in CFormatGuessEx()
119 CFormatGuess::EFormat Guess; in GuessFormat()
130 CFormatGuess::eAgp, in GuessFormat()
133 CFormatGuess::eBed, in GuessFormat()
137 CFormatGuess::eGtf, in GuessFormat()
138 CFormatGuess::eGff3, in GuessFormat()
464 case CFormatGuess::eXml: in xGuessGenbankObjectType()
467 case CFormatGuess::eJSON: in xGuessGenbankObjectType()
498 case CFormatGuess::eXml: in GuessFormatAndContent()
499 case CFormatGuess::eJSON: in GuessFormatAndContent()
[all …]
H A Dreader_base.cpp118 CFormatGuess::EFormat format, in GetReader()
126 case CFormatGuess::eBed: in GetReader()
128 case CFormatGuess::eBed15: in GetReader()
130 case CFormatGuess::eWiggle: in GetReader()
132 case CFormatGuess::eGtf: in GetReader()
135 case CFormatGuess::eGff3: in GetReader()
137 case CFormatGuess::eGvf: in GetReader()
139 case CFormatGuess::eVcf: in GetReader()
141 case CFormatGuess::eRmo: in GetReader()
143 case CFormatGuess::eFasta: in GetReader()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/util/
H A Dformat_guess.cpp203 const CFormatGuess::NAME_MAP CFormatGuess::sm_FormatNames = {
292 CFormatGuess::ESequenceType
370 CFormatGuess::EFormat CFormatGuess::Format(CNcbiIstream& input, EOnError onerror) in Format()
382 CFormatGuess::CFormatGuess() in CFormatGuess() function in CFormatGuess
391 CFormatGuess::CFormatGuess( in CFormatGuess() function in CFormatGuess
400 CFormatGuess::CFormatGuess( in CFormatGuess() function in CFormatGuess
409 CFormatGuess::~CFormatGuess() in ~CFormatGuess()
426 CFormatGuess::EFormat
433 CFormatGuess::EFormat
434 CFormatGuess::GuessFormat( in GuessFormat()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/util/
H A Dformat_guess.cpp203 const CFormatGuess::NAME_MAP CFormatGuess::sm_FormatNames = {
292 CFormatGuess::ESequenceType
370 CFormatGuess::EFormat CFormatGuess::Format(CNcbiIstream& input, EOnError onerror) in Format()
382 CFormatGuess::CFormatGuess() in CFormatGuess() function in CFormatGuess
391 CFormatGuess::CFormatGuess( in CFormatGuess() function in CFormatGuess
400 CFormatGuess::CFormatGuess( in CFormatGuess() function in CFormatGuess
409 CFormatGuess::~CFormatGuess() in ~CFormatGuess()
426 CFormatGuess::EFormat
433 CFormatGuess::EFormat
434 CFormatGuess::GuessFormat( in GuessFormat()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/util/
H A Dformat_guess.hpp49 class NCBI_XUTIL_EXPORT CFormatGuess class
174 typedef CFormatGuess::EFormat TFormat;
234 CFormatGuess();
236 CFormatGuess(const string& fname);
241 CFormatGuess(CNcbiIstream& input);
243 ~CFormatGuess();
411 inline CFormatGuess::CFormatHints&
420 inline CFormatGuess::CFormatHints&
428 inline CFormatGuess::CFormatHints&
441 inline CFormatGuess::CFormatHints&
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/util/
H A Dformat_guess.hpp49 class NCBI_XUTIL_EXPORT CFormatGuess class
174 typedef CFormatGuess::EFormat TFormat;
234 CFormatGuess();
236 CFormatGuess(const string& fname);
241 CFormatGuess(CNcbiIstream& input);
243 ~CFormatGuess();
411 inline CFormatGuess::CFormatHints&
420 inline CFormatGuess::CFormatHints&
428 inline CFormatGuess::CFormatHints&
441 inline CFormatGuess::CFormatHints&
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/table2asn/
H A Dmultireader.cpp430 CFormatGuess FG(istr); in xAnnotGetFormat()
789 … LOG_POST("Recognized input file as format: " << CFormatGuess::GetFormatName(CFormatGuess::eGff3)); in LoadGFF3Fasta()
802 CFormatGuess::EFormat format; in OpenFile()
815 case CFormatGuess::eTextASN: in OpenFile()
819 case CFormatGuess::eGff3: in OpenFile()
982 case CFormatGuess::eUnknown: in xCreateASNStream()
986 case CFormatGuess::eXml: in xCreateASNStream()
1121 case CFormatGuess::eTextASN: in xGetAnnotLoader()
1133 case CFormatGuess::eGff2: in xGetAnnotLoader()
1134 case CFormatGuess::eGff3: in xGetAnnotLoader()
[all …]
H A Dhuge_file.cpp111 FG.GetFormatHints().AddPreferredFormat(CFormatGuess::eBinaryASN); in RecognizeContent()
112 FG.GetFormatHints().AddPreferredFormat(CFormatGuess::eTextASN); in RecognizeContent()
113 FG.GetFormatHints().AddPreferredFormat(CFormatGuess::eFasta); in RecognizeContent()
114 FG.GetFormatHints().AddPreferredFormat(CFormatGuess::eGff3); in RecognizeContent()
123 case CFormatGuess::eBinaryASN: in RecognizeContent()
126 case CFormatGuess::eTextASN: in RecognizeContent()
129 case CFormatGuess::eFasta: in RecognizeContent()
130 case CFormatGuess::eGff3: in RecognizeContent()
H A Dmultireader.hpp40 …CFormatGuess::EFormat OpenFile(const string& filename, CRef<CSerialObject>& input_sequence, TAnnot…
61 …CFormatGuess::EFormat xReadFile(CNcbiIstream& in, CRef<objects::CSeq_entry>& entry, CRef<objects::…
68 CRef<objects::CSeq_entry> xReadFlatfile(CFormatGuess::EFormat format, const string& filename);
74 …unique_ptr<CObjectIStream> xCreateASNStream(CFormatGuess::EFormat format, unique_ptr<istream>& ins…
77 CFormatGuess::EFormat xInputGetFormat(CNcbiIstream&, CFileContentInfo* = nullptr) const;
78 CFormatGuess::EFormat xAnnotGetFormat(CNcbiIstream&) const;
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/feat_import/
H A Dfeat_import.cpp225 CFormatGuess fg(istr); in xGetInputFormat()
226 fg.GetFormatHints().AddPreferredFormat(CFormatGuess::eGtf); in xGetInputFormat()
227 fg.GetFormatHints().AddPreferredFormat(CFormatGuess::eGff3); in xGetInputFormat()
228 fg.GetFormatHints().AddPreferredFormat(CFormatGuess::eGffAugustus); in xGetInputFormat()
229 fg.GetFormatHints().AddPreferredFormat(CFormatGuess::eBed); in xGetInputFormat()
230 fg.GetFormatHints().AddPreferredFormat(CFormatGuess::eFiveColFeatureTable); in xGetInputFormat()
236 case CFormatGuess::eGtf: in xGetInputFormat()
237 case CFormatGuess::eGffAugustus: in xGetInputFormat()
239 case CFormatGuess::eGff3: in xGetInputFormat()
241 case CFormatGuess::eBed: in xGetInputFormat()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/multireader/
H A Dmultireader.cpp181 CFormatGuess::EFormat m_uFormat;
778 case CFormatGuess::eBed: in xProcessSingleFile()
789 case CFormatGuess::eGtf: in xProcessSingleFile()
797 case CFormatGuess::eGff3: in xProcessSingleFile()
803 case CFormatGuess::eGvf: in xProcessSingleFile()
806 case CFormatGuess::eAgp: in xProcessSingleFile()
818 case CFormatGuess::eRmo: in xProcessSingleFile()
1359 case CFormatGuess::eWiggle: in xSetFlags()
1376 case CFormatGuess::eBed: in xSetFlags()
1394 case CFormatGuess::eGtf: in xSetFlags()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/readers/
H A Dformat_guess_ex.hpp129 CFormatGuess::EFormat GuessFormat();
130 CFormatGuess::EFormat GuessFormatAndContent(
133 bool TestFormat(CFormatGuess::EFormat );
136 CFormatGuess::CFormatHints& GetFormatHints(void) in GetFormatHints()
140 auto_ptr<CFormatGuess> m_Guesser;
145 bool x_TryFormat(CFormatGuess::EFormat Format);
162 CFormatGuess::EFormat baseFormat);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/readers/
H A Dformat_guess_ex.hpp134 CFormatGuess::EFormat GuessFormat();
135 CFormatGuess::EFormat GuessFormatAndContent(
138 bool TestFormat(CFormatGuess::EFormat );
141 CFormatGuess::CFormatHints& GetFormatHints(void) in GetFormatHints()
145 auto_ptr<CFormatGuess> m_Guesser;
150 bool x_TryFormat(CFormatGuess::EFormat Format);
167 CFormatGuess::EFormat baseFormat);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/
H A Dunit_test_format_guess.cpp44 CFormatGuess Guess; in BOOST_AUTO_TEST_CASE()
45 for (int fmt = 1; fmt < (int)CFormatGuess::eFormat_max; fmt++) { in BOOST_AUTO_TEST_CASE()
46 if ( fmt == CFormatGuess::eGtf_POISENED) continue; in BOOST_AUTO_TEST_CASE()
47 Guess.TestFormat((CFormatGuess::EFormat)fmt, CFormatGuess::eDefault); in BOOST_AUTO_TEST_CASE()
H A Dunit_test_format_guess_ex.cpp61 CFormatGuess::EFormat Guess; in BOOST_AUTO_TEST_CASE()
65 BOOST_CHECK_EQUAL(Guess, CFormatGuess::eBed); in BOOST_AUTO_TEST_CASE()
77 CFormatGuess::EFormat Guess; in BOOST_AUTO_TEST_CASE()
81 BOOST_CHECK_EQUAL(Guess, CFormatGuess::eGff2); in BOOST_AUTO_TEST_CASE()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/app/blastdb/
H A Dmakeblastdb.cpp76 typedef CFormatGuess::EFormat TFormat;
168 case CFormatGuess::eBinaryASN: in s_ReadObject()
172 case CFormatGuess::eTextASN: in s_ReadObject()
192 CFormatGuess fg(file); in s_ReadObject()
399 typedef CFormatGuess::EFormat TFormat;
792 CFormatGuess fg(input); in x_GuessFileType()
804 case CFormatGuess::eFasta: in x_AddSequenceData()
808 case CFormatGuess::eTextASN: in x_AddSequenceData()
809 case CFormatGuess::eBinaryASN: in x_AddSequenceData()
889 CFormatGuess::EFormat mask_file_format = CFormatGuess::eUnknown; in x_ProcessMaskData()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/blastdb/
H A Dmakeblastdb.cpp76 typedef CFormatGuess::EFormat TFormat;
168 case CFormatGuess::eBinaryASN: in s_ReadObject()
172 case CFormatGuess::eTextASN: in s_ReadObject()
192 CFormatGuess fg(file); in s_ReadObject()
399 typedef CFormatGuess::EFormat TFormat;
792 CFormatGuess fg(input); in x_GuessFileType()
804 case CFormatGuess::eFasta: in x_AddSequenceData()
808 case CFormatGuess::eTextASN: in x_AddSequenceData()
809 case CFormatGuess::eBinaryASN: in x_AddSequenceData()
889 CFormatGuess::EFormat mask_file_format = CFormatGuess::eUnknown; in x_ProcessMaskData()
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objmgr/util/
H A Dobj_sniff.hpp216 inline ESerialDataFormat FormatGuess2Serial(CFormatGuess::EFormat fmt) in FormatGuess2Serial()
220 case CFormatGuess::eBinaryASN: in FormatGuess2Serial()
222 case CFormatGuess::eTextASN: in FormatGuess2Serial()
224 case CFormatGuess::eXml: in FormatGuess2Serial()
226 case CFormatGuess::eFasta: in FormatGuess2Serial()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objmgr/util/
H A Dobj_sniff.hpp216 inline ESerialDataFormat FormatGuess2Serial(CFormatGuess::EFormat fmt) in FormatGuess2Serial()
220 case CFormatGuess::eBinaryASN: in FormatGuess2Serial()
222 case CFormatGuess::eTextASN: in FormatGuess2Serial()
224 case CFormatGuess::eXml: in FormatGuess2Serial()
226 case CFormatGuess::eFasta: in FormatGuess2Serial()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/unit_tests/api/
H A Dblast_test_util.hpp86 switch (ncbi::CFormatGuess().Format(in)) { in ReadObject()
87 case ncbi::CFormatGuess::eTextASN: in ReadObject()
90 case ncbi::CFormatGuess::eBinaryASN: in ReadObject()
93 case ncbi::CFormatGuess::eXml: in ReadObject()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/unit_tests/api/
H A Dblast_test_util.hpp86 switch (ncbi::CFormatGuess().Format(in)) { in ReadObject()
87 case ncbi::CFormatGuess::eTextASN: in ReadObject()
90 case ncbi::CFormatGuess::eBinaryASN: in ReadObject()
93 case ncbi::CFormatGuess::eXml: in ReadObject()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/align_format/unit_test/
H A Dblast_test_util.hpp97 switch (ncbi::CFormatGuess().Format(in)) { in ReadObject()
98 case ncbi::CFormatGuess::eTextASN: in ReadObject()
101 case ncbi::CFormatGuess::eBinaryASN: in ReadObject()
104 case ncbi::CFormatGuess::eXml: in ReadObject()

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