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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/
H A DSQLiteMsaDbi.cpp370 QList<qint64> SQLiteMsaDbi::getOrderedRowIds(const U2DataId &msaId, U2OpStatus &os) { in getOrderedRowIds()
382 U2AlphabetId SQLiteMsaDbi::getMsaAlphabet(const U2DataId &msaId, U2OpStatus &os) { in getMsaAlphabet()
449 void SQLiteMsaDbi::removeRow(const U2DataId &msaId, qint64 rowId, U2OpStatus &os) { in removeRow()
522 void SQLiteMsaDbi::deleteRowsData(const U2DataId &msaId, U2OpStatus &os) { in deleteRowsData()
529 U2Msa SQLiteMsaDbi::getMsaObject(const U2DataId &msaId, U2OpStatus &os) { in getMsaObject()
547 int SQLiteMsaDbi::getNumOfRows(const U2DataId &msaId, U2OpStatus &os) { in getNumOfRows()
562 void SQLiteMsaDbi::recalculateRowsPositions(const U2DataId &msaId, U2OpStatus &os) { in recalculateRowsPositions()
580 qint64 SQLiteMsaDbi::getMaximumRowId(const U2DataId &msaId, U2OpStatus &os) { in getMaximumRowId()
594 QList<U2MsaRow> SQLiteMsaDbi::getRows(const U2DataId &msaId, U2OpStatus &os) { in getRows()
625 U2MsaRow SQLiteMsaDbi::getRow(const U2DataId &msaId, qint64 rowId, U2OpStatus &os) { in getRow()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/
H A DMysqlMsaDbi.cpp94 U2Msa MysqlMsaDbi::getMsaObject(const U2DataId &msaId, U2OpStatus &os) { in getMsaObject()
115 int MysqlMsaDbi::getNumOfRows(const U2DataId &msaId, U2OpStatus &os) { in getNumOfRows()
131 QList<U2MsaRow> MysqlMsaDbi::getRows(const U2DataId &msaId, U2OpStatus &os) { in getRows()
167 U2MsaRow MysqlMsaDbi::getRow(const U2DataId &msaId, qint64 rowId, U2OpStatus &os) { in getRow()
201 QList<qint64> MysqlMsaDbi::getOrderedRowIds(const U2DataId &msaId, U2OpStatus &os) { in getOrderedRowIds()
214 U2AlphabetId MysqlMsaDbi::getMsaAlphabet(const U2DataId &msaId, U2OpStatus &os) { in getMsaAlphabet()
414 void MysqlMsaDbi::removeRow(const U2DataId &msaId, qint64 rowId, U2OpStatus &os) { in removeRow()
441 void MysqlMsaDbi::deleteRowsData(const U2DataId &msaId, U2OpStatus &os) { in deleteRowsData()
621 qint64 MysqlMsaDbi::getMsaLength(const U2DataId &msaId, U2OpStatus &os) { in getMsaLength()
754 void MysqlMsaDbi::recalculateRowsPositions(const U2DataId &msaId, U2OpStatus &os) { in recalculateRowsPositions()
[all …]
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/util/
H A DMultipleSequenceAlignmentExporter.cpp39 …leSequenceAlignmentExporter::getAlignment(const U2DbiRef &dbiRef, const U2DataId &msaId, U2OpStatu… in getAlignment() argument
77 …enceAlignmentExporter::getAlignmentObject(const U2DbiRef &dbiRef, const U2DataId &msaId, U2OpStatu… in getAlignmentObject() argument
88 … const U2DataId &msaId, in getAlignmentRows()
109 QList<U2MsaRow> MultipleSequenceAlignmentExporter::exportRows(const U2DataId &msaId, U2OpStatus &os… in exportRows() argument
116 QList<U2MsaRow> MultipleSequenceAlignmentExporter::exportRows(const U2DataId &msaId, const QList<qi… in exportRows() argument
152 QVariantMap MultipleSequenceAlignmentExporter::exportAlignmentInfo(const U2DataId &msaId, U2OpStatu… in exportAlignmentInfo() argument
174 U2Msa MultipleSequenceAlignmentExporter::exportAlignmentObject(const U2DataId &msaId, U2OpStatus &o… in exportAlignmentObject() argument
H A DMultipleSequenceAlignmentImporter.cpp55 U2DataId msaId = createEmptyMsaObject(con, folder, al->getName(), al->getAlphabet(), os); in createAlignment() local
133 …equenceAlignmentImporter::importMsaInfo(const DbiConnection &con, const U2DataId &msaId, const QVa… in importMsaInfo()
210 …portRows(const DbiConnection &con, MultipleSequenceAlignment &al, const U2DataId &msaId, const QLi… in importRows()
/dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/format/sqlite_object_dbi/
H A DSQLiteObjectDbiUnitTests.cpp391 U2DataId msaId = SQLiteObjectDbiTestData::createTestMsa(false, os); in IMPLEMENT_TEST() local
412 U2DataId msaId = SQLiteObjectDbiTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
429 U2DataId msaId = SQLiteObjectDbiTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
450 U2DataId msaId = SQLiteObjectDbiTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
473 U2DataId msaId = SQLiteObjectDbiTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
499 U2DataId msaId = SQLiteObjectDbiTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
541 U2DataId msaId = SQLiteObjectDbiTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
629 U2DataId msaId = SQLiteObjectDbiTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
716 U2DataId msaId = SQLiteObjectDbiTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
790 U2DataId msaId = SQLiteObjectDbiTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
[all …]
/dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/format/sqlite_msa_dbi/
H A DMsaDbiSQLiteSpecificUnitTests.cpp204 U2DataId msaId = MsaSQLiteSpecificTestData::createTestMsa(false, os); in IMPLEMENT_TEST() local
236 U2DataId msaId = MsaSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
282 U2DataId msaId = MsaSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
314 U2DataId msaId = MsaSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
372 U2DataId msaId = MsaSQLiteSpecificTestData::createTestMsa(false, os); in IMPLEMENT_TEST() local
404 U2DataId msaId = MsaSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
451 U2DataId msaId = MsaSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
484 U2DataId msaId = MsaSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
583 U2DataId msaId = MsaSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
656 U2DataId msaId = MsaSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
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/dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/format/sqlite_mod_dbi/
H A DModDbiSQLiteSpecificUnitTests.cpp270 U2DataId msaId = ModSQLiteSpecificTestData::createTestMsa(false, os); in IMPLEMENT_TEST() local
288 U2DataId msaId = ModSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
366 U2DataId msaId = ModSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
458 U2DataId msaId = ModSQLiteSpecificTestData::createTestMsa(false, os); in IMPLEMENT_TEST() local
476 U2DataId msaId = ModSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
555 U2DataId msaId = ModSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
650 U2DataId msaId = ModSQLiteSpecificTestData::createTestMsa(false, os); in IMPLEMENT_TEST() local
674 U2DataId msaId = ModSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
777 U2DataId msaId = ModSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
939 U2DataId msaId = ModSQLiteSpecificTestData::createTestMsa(true, os); in IMPLEMENT_TEST() local
[all …]
/dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/dbi/msa/
H A DMsaDbiUnitTests.cpp86 U2DataId msaId = msaDbi->createMsaObject("", "Test name", testAlphabet, os); in IMPLEMENT_TEST() local
106 U2DataId msaId = msaDbi->createMsaObject("", "Test name", alphabet, os); in IMPLEMENT_TEST() local
177 …U2DataId msaId = msaDbi->createMsaObject("", "Test name", BaseDNAAlphabetIds::NUCL_DNA_DEFAULT(), … in IMPLEMENT_TEST() local
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/kalign/src/
H A DKalignWorker.cpp162 …SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDb… in tick() local
204 SharedDbiDataHandler msaId = context->getDataStorage()->putAlignment(msa); in send() local
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/tcoffee/
H A DTCoffeeWorker.cpp172 …SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDb… in tick() local
206 SharedDbiDataHandler msaId = context->getDataStorage()->putAlignment(t->resultMA); in sl_taskFinished() local
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/mafft/
H A DMAFFTWorker.cpp173 …SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDb… in tick() local
216 SharedDbiDataHandler msaId = context->getDataStorage()->putAlignment(msa); in send() local
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/
H A DMuscleWorker.cpp176 …SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDb… in tick() local
236 SharedDbiDataHandler msaId = context->getDataStorage()->putAlignment(t->resultMA); in sl_taskFinished() local
H A DProfileToProfileWorker.cpp108 SharedDbiDataHandler msaId = context->getDataStorage()->putAlignment(resultAl); in sl_taskFinished() local
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/clustalo/
H A DClustalOWorker.cpp179 …SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDb… in tick() local
213 …SharedDbiDataHandler msaId = context->getDataStorage()->putAlignment(clustalOTask->getResultAlignm… in sl_taskFinished() local
/dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/util/
H A DMsaDbiUtilsUnitTests.cpp91 …U2DataId msaId = msaDbi->createMsaObject("", MsaDbiUtilsTestUtils::alignmentName, BaseDNAAlphabetI… in initTestAlignment() local
126 …U2DataId msaId = msaDbi->createMsaObject("", MsaDbiUtilsTestUtils::alignmentName, BaseDNAAlphabetI… in initTestAlignment() local
171 …U2DataId msaId = msaDbi->createMsaObject("", MsaDbiUtilsTestUtils::alignmentName, BaseDNAAlphabetI… in initTestAlignment() local
228 …U2DataId msaId = msaDbi->createMsaObject("", MsaDbiUtilsTestUtils::alignmentName, BaseDNAAlphabetI… in removeRegionTestAlignment() local
1412 …U2DataId msaId = msaDbi->createMsaObject("", MsaDbiUtilsTestUtils::alignmentName, BaseDNAAlphabetI… in IMPLEMENT_TEST() local
1467 …U2DataId msaId = msaDbi->createMsaObject("", MsaDbiUtilsTestUtils::alignmentName, BaseDNAAlphabetI… in IMPLEMENT_TEST() local
1526 …U2DataId msaId = msaDbi->createMsaObject("", MsaDbiUtilsTestUtils::alignmentName, BaseDNAAlphabetI… in IMPLEMENT_TEST() local
1588 …U2DataId msaId = msaDbi->createMsaObject("", MsaDbiUtilsTestUtils::alignmentName, BaseDNAAlphabetI… in IMPLEMENT_TEST() local
1650 …U2DataId msaId = msaDbi->createMsaObject("", MsaDbiUtilsTestUtils::alignmentName, BaseDNAAlphabetI… in IMPLEMENT_TEST() local
1713 …U2DataId msaId = msaDbi->createMsaObject("", MsaDbiUtilsTestUtils::alignmentName, BaseDNAAlphabetI… in IMPLEMENT_TEST() local
[all …]
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/clustalw/
H A DClustalWWorker.cpp257 …SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDb… in tick() local
300 SharedDbiDataHandler msaId = context->getDataStorage()->putAlignment(msa); in send() local
/dports/biology/ugene/ugene-40.1/src/plugins/workflow_designer/src/library/
H A DSequencesToMSAWorker.cpp97 SharedDbiDataHandler msaId = context->getDataStorage()->putAlignment(ma); in sl_onTaskFinished() local
H A DMSA2SequenceWorker.cpp67 …SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDb… in tick() local
H A DExternalProcessWorker.cpp128 SharedDbiDataHandler msaId = data[slot].value<SharedDbiDataHandler>(); in toAlignment() local
523 SharedDbiDataHandler msaId = getAlignment(d.data(), context, os); in sl_onTaskFinishied() local
/dports/biology/ugene/ugene-40.1/src/plugins/weight_matrix/src/
H A DWeightMatrixBuildWorker.cpp137 …SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDb… in tick() local
224 …SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDb… in tick() local
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/sitecon/src/
H A DSiteconBuildWorker.cpp157 …SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDb… in tick() local
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/hmmer/
H A DHmmerBuildWorker.cpp167 …SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDb… in tick() local
/dports/biology/ugene/ugene-40.1/src/plugins/workflow_designer/src/util/
H A DGrouperActionUtils.cpp312 SharedDbiDataHandler msaId = context->getDataStorage()->putAlignment(result); in finishAction() local
359 SharedDbiDataHandler msaId = context->getDataStorage()->putAlignment(result); in finishAction() local
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/hmm2/src/u_build/
H A DHMMBuildWorker.cpp278 …SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDb… in tick() local
/dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/gobjects/
H A DMsaObjectUnitTests.cpp79 const U2DataId msaId = it->next(); in getTestAlignmentRef() local

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