| /dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/dbi/sequence/ |
| H A D | SequenceDbiUnitTests.cpp | 42 U2SequenceDbi *SequenceTestData::sequenceDbi = nullptr; member in U2::SequenceTestData
69 sequenceDbi = dbi->getSequenceDbi(); in init()
77 if (sequenceDbi == nullptr) { in getSequenceDbi()
80 return sequenceDbi; in getSequenceDbi()
84 if (sequenceDbi != nullptr) { in shutdown()
87 sequenceDbi = nullptr; in shutdown()
101 U2SequenceDbi *sequenceDbi = SequenceTestData::getSequenceDbi(); in checkUpdateSequence() local
127 sequenceDbi->updateSequenceData(id, in checkUpdateSequence()
232 sequenceDbi->createSequenceObject(seq, "/", os); in Test()
338 sequenceDbi->createSequenceObject(seq, "/", os); in Test()
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| H A D | SequenceDbiUnitTests.h | 58 static U2SequenceDbi *sequenceDbi;
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| /dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/dbi/msa/ |
| H A D | MsaDbiUnitTests.cpp | 37 U2SequenceDbi *MsaTestData::sequenceDbi = nullptr; member in U2::MsaTestData
50 sequenceDbi = dbi->getSequenceDbi(); in init()
61 sequenceDbi = nullptr; in shutdown()
74 if (nullptr == sequenceDbi) { in getSequenceDbi()
77 return sequenceDbi; in getSequenceDbi()
110 U2SequenceDbi *sequenceDbi = MsaTestData::getSequenceDbi(); in IMPLEMENT_TEST() local
113 sequenceDbi->createSequenceObject(seq1, "", os); in IMPLEMENT_TEST()
115 sequenceDbi->createSequenceObject(seq2, "", os); in IMPLEMENT_TEST()
185 sequenceDbi->createSequenceObject(seq1, "", os); in IMPLEMENT_TEST()
187 sequenceDbi->createSequenceObject(seq2, "", os); in IMPLEMENT_TEST()
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| H A D | MsaDbiUnitTests.h | 46 static U2SequenceDbi *sequenceDbi; variable
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| /dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/dbi/features/ |
| H A D | FeatureDbiUnitTests.cpp | 40 U2SequenceDbi *FeatureTestData::sequenceDbi = nullptr; member in U2::FeatureTestData
52 sequenceDbi = dbi->getSequenceDbi(); in init()
72 sequenceDbi = nullptr; in shutdown()
99 if (nullptr == sequenceDbi) { in getSequenceDbi()
102 return sequenceDbi; in getSequenceDbi()
177 sequenceDbi->createSequenceObject(seq, "", os); in IMPLEMENT_TEST()
203 sequenceDbi->createSequenceObject(seq, "", os); in IMPLEMENT_TEST()
232 sequenceDbi->createSequenceObject(seq1, "", os); in IMPLEMENT_TEST()
235 sequenceDbi->createSequenceObject(seq2, "", os); in IMPLEMENT_TEST()
382 sequenceDbi->createSequenceObject(seq, "", os); in IMPLEMENT_TEST()
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| H A D | FeatureDbiUnitTests.h | 59 static U2SequenceDbi *sequenceDbi; variable
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_sequence/sequence_info/ |
| H A D | DinuclOccurTask.cpp | 55 U2SequenceDbi *sequenceDbi = dbiConnection.dbi->getSequenceDbi(); in run() local
63 qint64 seqLength = sequenceDbi->getSequenceObject(seqRef.entityId, os).length; in run()
77 QByteArray sequence = sequenceDbi->getSequenceData(seqRef.entityId, block, os); in run()
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| H A D | DNAStatisticsTask.cpp | 358 U2SequenceDbi *sequenceDbi = dbiConnection.dbi->getSequenceDbi(); in computeStats() local
359 CHECK(sequenceDbi != nullptr, ); in computeStats()
376 const QByteArray seqBlock = sequenceDbi->getSequenceData(seqRef.entityId, block, os); in computeStats()
511 result.isoelectricPoint = calcPi(sequenceDbi); in computeStats()
515 double DNAStatisticsTask::calcPi(U2SequenceDbi *sequenceDbi) { in calcPi() argument
524 QByteArray seqBlock = sequenceDbi->getSequenceData(seqRef.entityId, block, os); in calcPi()
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| H A D | CharOccurTask.cpp | 58 U2SequenceDbi *sequenceDbi = dbiConnection.dbi->getSequenceDbi(); in run() local
73 QByteArray sequence = sequenceDbi->getSequenceData(seqRef.entityId, block, os); in run()
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| H A D | DNAStatisticsTask.h | 93 double calcPi(U2SequenceDbi *sequenceDbi);
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/util/ |
| H A D | McaDbiUtils.cpp | 51 U2SequenceDbi *sequenceDbi = connection.dbi->getSequenceDbi(); in updateMca() local
52 SAFE_POINT_EXT(nullptr != sequenceDbi, os.setError("NULL Sequence Dbi"), ); in updateMca()
249 U2SequenceDbi *sequenceDbi = con->dbi->getSequenceDbi(); in removeCharacters() local
260 QByteArray seq = sequenceDbi->getSequenceData(row.sequenceId, seqReg, os); in removeCharacters()
288 U2SequenceDbi *sequenceDbi = con->dbi->getSequenceDbi(); in replaceCharactersInRow() local
298 QByteArray sequence = sequenceDbi->getSequenceData(row.sequenceId, {0, row.length}, os); in replaceCharactersInRow()
331 U2SequenceDbi *sequenceDbi = con->dbi->getSequenceDbi(); in replaceCharactersInRow() local
342 QByteArray seq = sequenceDbi->getSequenceData(row.sequenceId, seqReg, os); in replaceCharactersInRow()
385 U2SequenceDbi *sequenceDbi = con->dbi->getSequenceDbi(); in removeRegion() local
393 QByteArray seq = sequenceDbi->getSequenceData(row.sequenceId, seqReg, os); in removeRegion()
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| H A D | MultipleSequenceAlignmentExporter.cpp | 128 U2SequenceDbi *sequenceDbi = con.dbi->getSequenceDbi(); in exportSequencesOfRows() local
129 …SAFE_POINT(nullptr != sequenceDbi, "NULL Sequence Dbi during exporting rows sequences!", QList<DNA… in exportSequencesOfRows()
139 QByteArray seqData = sequenceDbi->getSequenceData(sequenceId, regionInSequence, os); in exportSequencesOfRows()
142 U2Sequence seqObj = sequenceDbi->getSequenceObject(sequenceId, os); in exportSequencesOfRows()
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| H A D | MultipleChromatogramAlignmentExporter.cpp | 134 U2SequenceDbi *sequenceDbi = connection.dbi->getSequenceDbi(); in exportSequence() local
135 …SAFE_POINT_EXT(nullptr != sequenceDbi, os.setError("NULL Sequence Dbi during exporting rows sequen… in exportSequence()
137 U2Sequence dbSequence = sequenceDbi->getSequenceObject(sequenceId, os); in exportSequence()
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| H A D | MsaDbiUtils.cpp | 937 U2SequenceDbi *sequenceDbi = con->dbi->getSequenceDbi(); in removeRegion() local
957 QByteArray seq = sequenceDbi->getSequenceData(row.sequenceId, seqReg, os); in removeRegion()
978 U2SequenceDbi *sequenceDbi = con->dbi->getSequenceDbi(); in replaceCharactersInRow() local
994 QByteArray sequence = sequenceDbi->getSequenceData(row.sequenceId, sequenceRange, os); in replaceCharactersInRow()
1012 U2SequenceDbi *sequenceDbi = con->dbi->getSequenceDbi(); in replaceNonGapCharacter() local
1020 … QByteArray sequenceData = sequenceDbi->getSequenceData(msaRow.sequenceId, sequenceRegion, os); in replaceNonGapCharacter()
1040 U2SequenceDbi *sequenceDbi = con->dbi->getSequenceDbi(); in keepOnlyAlphabetChars() local
1051 … QByteArray sequenceData = sequenceDbi->getSequenceData(msaRow.sequenceId, sequenceRegion, os); in keepOnlyAlphabetChars()
1074 U2SequenceDbi *sequenceDbi = con->dbi->getSequenceDbi(); in removeEmptyRows() local
1084 U2Sequence seq = sequenceDbi->getSequenceObject(row.sequenceId, os); in removeEmptyRows()
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| H A D | MultipleChromatogramAlignmentImporter.cpp | 126 U2SequenceDbi *sequenceDbi = connection.dbi->getSequenceDbi(); in importRowChildObjects() local
127 …SAFE_POINT_EXT(nullptr != sequenceDbi, os.setError("NULL Sequence Dbi during importing an alignmen… in importRowChildObjects()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/ |
| H A D | SQLiteDbi.cpp | 57 sequenceDbi = new SQLiteSequenceDbi(this); in SQLiteDbi()
77 delete sequenceDbi; in ~SQLiteDbi()
97 return sequenceDbi; in getSequenceDbi()
145 return sequenceDbi; in getSQLiteSequenceDbi()
250 sequenceDbi->initSqlSchema(os); in populateDefaultSchema()
420 sequenceDbi->shutdown(os); in shutdown()
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| H A D | SQLiteDbi.h | 178 SQLiteSequenceDbi *sequenceDbi; variable
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| /dports/biology/ugene/ugene-40.1/src/plugins/pcr/src/ |
| H A D | ExtractProductTask.cpp | 85 U2SequenceDbi *sequenceDbi = connection.dbi->getSequenceDbi(); in extractTargetSequence() local
86 … SAFE_POINT_EXT(nullptr != sequenceDbi, setError(L10N::nullPointerError("Sequence DBI")), result); in extractTargetSequence()
88 U2Sequence sequence = sequenceDbi->getSequenceObject(settings.sequenceRef.entityId, stateInfo); in extractTargetSequence()
92 …result.seq = sequenceDbi->getSequenceData(settings.sequenceRef.entityId, product.region, stateInfo… in extractTargetSequence()
103 … result.seq += sequenceDbi->getSequenceData(settings.sequenceRef.entityId, tail, stateInfo); in extractTargetSequence()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/ |
| H A D | MysqlDbi.cpp | 67 sequenceDbi = new MysqlSequenceDbi(this); in MysqlDbi()
81 delete sequenceDbi; in ~MysqlDbi()
128 return sequenceDbi; in getSequenceDbi()
168 return sequenceDbi; in getMysqlSequenceDbi()
334 sequenceDbi->initSqlSchema(os); in populateDefaultSchema()
545 sequenceDbi->shutdown(os); in shutdown()
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| H A D | MysqlDbi.h | 157 MysqlSequenceDbi *sequenceDbi; variable
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| /dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/format/sqlite_object_dbi/ |
| H A D | SQLiteObjectDbiUnitTests.cpp | 43 U2SequenceDbi *SQLiteObjectDbiTestData::sequenceDbi = nullptr; member in U2::SQLiteObjectDbiTestData
75 sequenceDbi = sqliteDbi->getSequenceDbi(); in init()
76 SAFE_POINT(nullptr != sequenceDbi, "Failed to get sequenceDbi!", ); in init()
87 sequenceDbi = nullptr; in shutdown()
120 if (nullptr == sequenceDbi) { in getSequenceDbi()
123 return sequenceDbi; in getSequenceDbi()
175 U2SequenceDbi *sequenceDbi = SQLiteObjectDbiTestData::getSequenceDbi(); in IMPLEMENT_TEST() local
178 sequenceDbi->createSequenceObject(seq1, "", os); in IMPLEMENT_TEST()
180 sequenceDbi->createSequenceObject(seq2, "", os); in IMPLEMENT_TEST()
227 sequenceDbi->createSequenceObject(al2Seq, "", os); in IMPLEMENT_TEST()
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| H A D | SQLiteObjectDbiUnitTests.h | 57 static U2SequenceDbi *sequenceDbi; variable
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| /dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/util/ |
| H A D | MsaDbiUtilsUnitTests.cpp | 40 U2SequenceDbi *MsaDbiUtilsTestUtils::sequenceDbi = nullptr; member in U2::MsaDbiUtilsTestUtils
53 sequenceDbi = dbi->getSequenceDbi(); in init()
54 SAFE_POINT(nullptr != sequenceDbi, "Failed to get sequenceDbi!", ); in init()
64 sequenceDbi = nullptr; in shutdown()
77 if (nullptr == sequenceDbi) { in getSequenceDbi()
80 return sequenceDbi; in getSequenceDbi()
88 SAFE_POINT(nullptr != sequenceDbi, "SequenceDbi is NULL", U2EntityRef()); in initTestAlignment()
99 sequenceDbi->createSequenceObject(sequence, "", os); in initTestAlignment()
141 sequenceDbi->createSequenceObject(sequence, "", os); in initTestAlignment()
206 sequenceDbi->createSequenceObject(sequence, "", os); in addRow()
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| H A D | MsaDbiUtilsUnitTests.h | 63 static U2SequenceDbi *sequenceDbi; variable
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| /dports/biology/ugene/ugene-40.1/src/plugins/dna_export/src/ |
| H A D | DNASequenceGenerator.cpp | 298 U2SequenceDbi *sequenceDbi = con.dbi->getSequenceDbi(); in onGenerateTaskFinished() local
299 …QByteArray seqContent = sequenceDbi->getSequenceData(seqs[sequenceIndex].id, U2_REGION_MAX, stateI… in onGenerateTaskFinished()
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