/dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/dbi/assembly/ |
H A D | AssemblyDbiTestUtil.h | 33 static bool compareReads(const U2AssemblyRead &r1, const U2AssemblyRead &r2); 35 static bool findRead(const U2AssemblyRead &subj, QList<U2AssemblyRead> &reads); 37 …static bool compareReadLists(U2DbiIterator<U2AssemblyRead> *iter, QList<U2AssemblyRead> &expectedR… 39 static void var2readList(const QVariantList &varList, QList<U2AssemblyRead> &reads); 47 Q_DECLARE_METATYPE(U2::U2AssemblyRead);
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H A D | AssemblyDbiTestUtil.cpp | 44 bool AssemblyDbiTestUtil::compareReads(const U2AssemblyRead &r1, const U2AssemblyRead &r2) { in compareReads() 80 bool AssemblyDbiTestUtil::findRead(const U2AssemblyRead &subj, QList<U2AssemblyRead> &reads) { in findRead() 82 const U2AssemblyRead &curRead = reads.at(i); in findRead() 91 …ol AssemblyDbiTestUtil::compareReadLists(U2DbiIterator<U2AssemblyRead> *iter, QList<U2AssemblyRead… in compareReadLists() 93 const U2AssemblyRead &read = iter->next(); in compareReadLists() 104 void AssemblyDbiTestUtil::var2readList(const QVariantList &varList, QList<U2AssemblyRead> &reads) { in var2readList() 106 U2AssemblyRead read = var.value<U2AssemblyRead>(); in var2readList()
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H A D | AssemblyDbiUnitTests.cpp | 192 U2AssemblyRead read1(new U2AssemblyReadData()); in Test() 233 QList<U2AssemblyRead> expectedReads; in Test() 296 QList<U2AssemblyRead> expectedReads; in Test() 329 U2AssemblyRead read(new U2AssemblyReadData()); in Test() 345 QList<U2AssemblyRead> reads; in Test() 501 QList<U2AssemblyRead> reads; in Test() 503 const U2AssemblyRead read = var.value<U2AssemblyRead>(); in Test() 508 BufferedDbiIterator<U2AssemblyRead> it(reads); in Test() 514 foreach (U2AssemblyRead read, reads) { in Test() 537 QList<U2AssemblyRead> reads; in Test() [all …]
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/ |
H A D | SQLiteAssemblyDbi.h | 54 …virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2DataId &assemblyId, const U2Region &r, U2O… 66 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByName(const U2DataId &assemblyId, const QByteArray… 113 …virtual void addReads(const U2DataId &assemblyId, U2DbiIterator<U2AssemblyRead> *it, U2OpStatus &o… 130 …virtual void addReads(AssemblyAdapter *a, U2DbiIterator<U2AssemblyRead> *it, U2AssemblyReadsImport… 160 …static QByteArray packData(SQLiteAssemblyDataMethod method, const U2AssemblyRead &read, U2OpStatus… 162 static void unpackData(const QByteArray &packed, U2AssemblyRead &read, U2OpStatus &os); 166 static void addToCoverage(U2AssemblyCoverageImportInfo &cii, const U2AssemblyRead &read); 169 class SQLiteAssemblyNameFilter : public SQLiteResultSetFilter<U2AssemblyRead> { 174 virtual bool filter(const U2AssemblyRead &r) { in filter() 182 class SimpleAssemblyReadLoader : public SQLiteResultSetLoader<U2AssemblyRead> { [all …]
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H A D | SQLiteAssemblyDbi.cpp | 153 U2DbiIterator<U2AssemblyRead> *res = a->getReadsByRow(r, minRow, maxRow, os); in getReadsByRow() 344 static QByteArray getQuality(const U2AssemblyRead &read) { in getQuality() 427 U2AssemblyRead tmp(new U2AssemblyReadData()); in packData() 444 void SQLiteAssemblyUtils::unpackData(const QByteArray &packedData, U2AssemblyRead &read, U2OpStatus… in unpackData() 561 U2AssemblyRead read(new U2AssemblyReadData()); in calculateCoverage() 605 void SQLiteAssemblyUtils::addToCoverage(U2AssemblyCoverageImportInfo &ii, const U2AssemblyRead &rea… in addToCoverage() 644 U2AssemblyRead SimpleAssemblyReadLoader::load(SQLiteQuery *q) { in load() 645 U2AssemblyRead read(new U2AssemblyReadData()); in load() 650 return U2AssemblyRead(); in load() 658 return U2AssemblyRead(); in load() [all …]
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/util/ |
H A D | MysqlMultiTableAssemblyAdapter.h | 59 …virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2Region ®ion, U2OpStatus &os, bool sorte… 60 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByRow(const U2Region ®ion, qint64 minRow, qint64… 61 virtual U2DbiIterator<U2AssemblyRead> *getReadsByName(const QByteArray &name, U2OpStatus &os); 63 …virtual void addReads(U2DbiIterator<U2AssemblyRead> *it, U2AssemblyReadsImportInfo &ii, U2OpStatus… 95 void initTables(const QList<U2AssemblyRead> &reads, U2OpStatus &os); 171 class MysqlMtaReadsIterator : public U2DbiIterator<U2AssemblyRead> { 173 …MysqlMtaReadsIterator(QVector<U2DbiIterator<U2AssemblyRead> *> &iterators, const QVector<QByteArra… 179 virtual U2AssemblyRead next(); 181 virtual U2AssemblyRead peek(); 184 QVector<U2DbiIterator<U2AssemblyRead> *> iterators;
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H A D | MysqlAssemblyAdapter.cpp | 41 bool MysqlAssemblyNameFilter::filter(const U2AssemblyRead &r) { in filter() 45 U2AssemblyRead MysqlSimpleAssemblyReadLoader::load(U2SqlQuery *q) { in load() 46 U2AssemblyRead read(new U2AssemblyReadData()); in load() 51 return U2AssemblyRead(); in load() 60 return U2AssemblyRead(); in load() 65 return U2AssemblyRead(); in load()
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H A D | MysqlAssemblyAdapter.h | 44 class MysqlAssemblyNameFilter : public MysqlRSFilter<U2AssemblyRead> { 47 virtual bool filter(const U2AssemblyRead &r); 53 class MysqlSimpleAssemblyReadLoader : public MysqlRSLoader<U2AssemblyRead> { 55 U2AssemblyRead load(U2SqlQuery *q);
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H A D | MysqlMultiTableAssemblyAdapter.cpp | 167 QVector<U2DbiIterator<U2AssemblyRead> *> iterators; in getReads() 178 QVector<U2DbiIterator<U2AssemblyRead> *> iterators; in getReadsByRow() 197 QVector<U2DbiIterator<U2AssemblyRead> *> iterators; in getReadsByName() 211 initTables(QList<U2AssemblyRead>(), os); in addReads() 226 U2AssemblyRead read = it->next(); in addReads() 563 initTables(QList<U2AssemblyRead>(), os); in flushTables() 873 U2AssemblyRead MysqlMtaReadsIterator::next() { in next() 874 U2AssemblyRead res; in next() 880 U2AssemblyRead candidate = it->peek(); in next() 914 U2AssemblyRead MysqlMtaReadsIterator::peek() { in peek() [all …]
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H A D | MysqlSingleTableAssemblyAdapter.cpp | 153 U2DbiIterator<U2AssemblyRead> *MysqlSingleTableAssemblyAdapter::getReads(const U2Region &r, U2OpSta… in getReads() 158 …return new MysqlRSIterator<U2AssemblyRead>(q, new MysqlSimpleAssemblyReadLoader(), nullptr, U2Asse… in getReads() 161 U2DbiIterator<U2AssemblyRead> *MysqlSingleTableAssemblyAdapter::getReadsByRow(const U2Region &r, qi… in getReadsByRow() 167 …return new MysqlRSIterator<U2AssemblyRead>(q, new MysqlSimpleAssemblyReadLoader(), nullptr, U2Asse… in getReadsByRow() 170 U2DbiIterator<U2AssemblyRead> *MysqlSingleTableAssemblyAdapter::getReadsByName(const QByteArray &na… in getReadsByName() 175 …urn new MysqlRSIterator<U2AssemblyRead>(q, new MysqlSimpleAssemblyReadLoader(), new MysqlAssemblyN… in getReadsByName() 178 void MysqlSingleTableAssemblyAdapter::addReads(U2DbiIterator<U2AssemblyRead> *it, U2AssemblyReadsIm… in addReads() 190 U2AssemblyRead read = it->next(); in addReads()
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H A D | MysqlAssemblyUtils.h | 42 …static QByteArray packData(MysqlAssemblyDataMethod method, const U2AssemblyRead &read, U2OpStatus … 44 static void unpackData(const QByteArray &packed, U2AssemblyRead &read, U2OpStatus &os); 48 static void addToCoverage(U2AssemblyCoverageImportInfo &cii, const U2AssemblyRead &read);
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/assembly/ |
H A D | MultiTableAssemblyAdapter.h | 58 …virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2Region &r, U2OpStatus &os, bool sortedHint… 59 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByRow(const U2Region &r, qint64 minRow, qint64 maxR… 60 virtual U2DbiIterator<U2AssemblyRead> *getReadsByName(const QByteArray &name, U2OpStatus &os); 62 …virtual void addReads(U2DbiIterator<U2AssemblyRead> *it, U2AssemblyReadsImportInfo &ii, U2OpStatus… 106 void initTables(const QList<U2AssemblyRead> &reads, U2OpStatus &os); 180 class MTAReadsIterator : public U2DbiIterator<U2AssemblyRead> { 182 …MTAReadsIterator(QVector<U2DbiIterator<U2AssemblyRead> *> &iterators, const QVector<QByteArray> &i… 188 virtual U2AssemblyRead next(); 190 virtual U2AssemblyRead peek(); 193 QVector<U2DbiIterator<U2AssemblyRead> *> iterators;
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H A D | RTreeAssemblyAdapter.cpp | 95 U2DbiIterator<U2AssemblyRead> *RTreeAssemblyAdapter::getReads(const U2Region &r, U2OpStatus &os, bo… in getReads() 106 …return new SQLiteResultSetIterator<U2AssemblyRead>(q, new SimpleAssemblyReadLoader(), nullptr, U2A… in getReads() 109 U2DbiIterator<U2AssemblyRead> *RTreeAssemblyAdapter::getReadsByRow(const U2Region &r, qint64 minRow… in getReadsByRow() 119 …return new SQLiteResultSetIterator<U2AssemblyRead>(q, new SimpleAssemblyReadLoader(), nullptr, U2A… in getReadsByRow() 122 U2DbiIterator<U2AssemblyRead> *RTreeAssemblyAdapter::getReadsByName(const QByteArray &name, U2OpSta… in getReadsByName() 127 …w SQLiteResultSetIterator<U2AssemblyRead>(q, new SimpleAssemblyReadLoader(), new SQLiteAssemblyNam… in getReadsByName() 130 void RTreeAssemblyAdapter::addReads(U2DbiIterator<U2AssemblyRead> *it, U2AssemblyReadsImportInfo &i… in addReads() 139 U2AssemblyRead read = it->next(); in addReads()
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H A D | SingleTableAssemblyAdapter.cpp | 140 U2DbiIterator<U2AssemblyRead> *SingleTableAssemblyAdapter::getReads(const U2Region &r, U2OpStatus &… in getReads() 148 …return new SQLiteResultSetIterator<U2AssemblyRead>(q, new SimpleAssemblyReadLoader(), nullptr, U2A… in getReads() 151 U2DbiIterator<U2AssemblyRead> *SingleTableAssemblyAdapter::getReadsByRow(const U2Region &r, qint64 … in getReadsByRow() 158 …return new SQLiteResultSetIterator<U2AssemblyRead>(q, new SimpleAssemblyReadLoader(), nullptr, U2A… in getReadsByRow() 161 U2DbiIterator<U2AssemblyRead> *SingleTableAssemblyAdapter::getReadsByName(const QByteArray &name, U… in getReadsByName() 166 …w SQLiteResultSetIterator<U2AssemblyRead>(q, new SimpleAssemblyReadLoader(), new SQLiteAssemblyNam… in getReadsByName() 169 void SingleTableAssemblyAdapter::addReads(U2DbiIterator<U2AssemblyRead> *it, U2AssemblyReadsImportI… in addReads() 174 U2AssemblyRead read = it->next(); in addReads()
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H A D | MultiTableAssemblyAdapter.cpp | 180 initTables(QList<U2AssemblyRead>(), os); in flushTables() 304 QVector<U2DbiIterator<U2AssemblyRead> *> iterators; in getReads() 319 QVector<U2DbiIterator<U2AssemblyRead> *> iterators; in getReadsByRow() 341 QVector<U2DbiIterator<U2AssemblyRead> *> iterators; in getReadsByName() 413 initTables(QList<U2AssemblyRead>(), os); in addReads() 429 U2AssemblyRead read = it->next(); in addReads() 798 U2AssemblyRead MTAReadsIterator::next() { in next() 799 U2AssemblyRead res; in next() 805 U2AssemblyRead candidate = it->peek(); in next() 839 U2AssemblyRead MTAReadsIterator::peek() { in peek() [all …]
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/dbi/ |
H A D | U2AssemblyDbi.h | 38 virtual U2AssemblyRead next(U2OpStatus &os) = 0; 123 …virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2DataId &assemblyId, const U2Region &r, U2O… 131 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByRow(const U2DataId &assemblyId, const U2Region &r… 139 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByName(const U2DataId &assemblyId, const QByteArray… 163 …blyObject(U2Assembly &assembly, const QString &folder, U2DbiIterator<U2AssemblyRead> *it, U2Assemb… 202 …virtual void addReads(const U2DataId &assemblyId, U2DbiIterator<U2AssemblyRead> *it, U2OpStatus &o…
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/ |
H A D | MysqlAssemblyDbi.h | 56 …virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2DataId &assemblyId, const U2Region &r, U2O… 62 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByRow(const U2DataId &assemblyId, const U2Region &r… 68 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByName(const U2DataId &assemblyId, const QByteArray… 84 …blyObject(U2Assembly &assembly, const QString &folder, U2DbiIterator<U2AssemblyRead> *it, U2Assemb… 115 …virtual void addReads(const U2DataId &assemblyId, U2DbiIterator<U2AssemblyRead> *it, U2OpStatus &o… 127 …virtual void addReads(MysqlAssemblyAdapter *a, U2DbiIterator<U2AssemblyRead> *it, U2AssemblyReadsI…
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_assembly/ |
H A D | AssemblyCellRenderer.cpp | 130 virtual QPixmap cellImage(const U2AssemblyRead &read, char c); 131 virtual QPixmap cellImage(const U2AssemblyRead &read, char c, char ref); 188 QPixmap NucleotideColorsRenderer::cellImage(const U2AssemblyRead &, char c) { in cellImage() argument 210 virtual QPixmap cellImage(const U2AssemblyRead &read, char c); 211 virtual QPixmap cellImage(const U2AssemblyRead &read, char c, char ref); 276 QPixmap ComplementColorsRenderer::cellImage(const U2AssemblyRead &read, char c) { in cellImage() 299 virtual QPixmap cellImage(const U2AssemblyRead &read, char c); 300 virtual QPixmap cellImage(const U2AssemblyRead &read, char c, char ref); 334 virtual QPixmap cellImage(const U2AssemblyRead &read, char c); 335 virtual QPixmap cellImage(const U2AssemblyRead &read, char c, char ref); [all …]
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H A D | AssemblyReadsAreaHint.cpp | 94 QString AssemblyReadsAreaHint::getReadDataAsString(const U2AssemblyRead &r) { in getReadDataAsString() 135 static QString formatReadPosString(U2AssemblyRead r) { in formatReadPosString() 140 static QString formatReadInfo(U2AssemblyRead r) { in formatReadInfo() 160 void AssemblyReadsAreaHint::setData(U2AssemblyRead r, QList<U2AssemblyRead> mates) { in setData() 167 U2AssemblyRead pair = mates.first(); in setData() 172 foreach (U2AssemblyRead mate, mates) { in setData()
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H A D | AssemblyReadsAreaHint.h | 38 static QString getReadDataAsString(const U2AssemblyRead &r); 42 void setData(U2AssemblyRead r, QList<U2AssemblyRead> mates);
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/dports/biology/ugene/ugene-40.1/src/plugins/dbi_bam/src/ |
H A D | Dbi.h | 144 …virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2DataId &assemblyId, const U2Region &r, U2O… 146 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByRow(const U2DataId &assemblyId, const U2Region &r… 148 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByName(const U2DataId &assemblyId, const QByteArray… 154 static U2AssemblyRead alignmentToRead(const Alignment &alignment); 156 U2AssemblyRead getReadById(const U2DataId &rowId, U2OpStatus &os); 160 U2AssemblyRead getReadById(const U2DataId &rowId, qint64 packedRow, U2OpStatus &os); 161 …QList<U2AssemblyRead> getReadsByIds(QList<U2DataId> rowIds, QList<qint64> packedRows, U2OpStatus &…
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H A D | ConvertToSQLiteTask.cpp | 84 virtual U2AssemblyRead next() { in next() 145 U2AssemblyRead read; 161 virtual U2AssemblyRead next() { in next() 207 U2AssemblyRead read; 223 virtual U2AssemblyRead next() { in next() 267 virtual U2AssemblyRead next() { in next() 323 virtual U2AssemblyRead next() = 0; 348 virtual U2AssemblyRead next() { in next() 357 virtual U2AssemblyRead peek() { in peek() 403 virtual U2AssemblyRead next() { in next() [all …]
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H A D | Dbi.cpp | 644 QList<U2AssemblyRead> result; in getReads() 652 return new BufferedDbiIterator<U2AssemblyRead>(result, U2AssemblyRead()); in getReads() 677 U2AssemblyRead result(new U2AssemblyReadData()); in getReadById() 688 return U2AssemblyRead(); in getReadById() 747 QList<U2AssemblyRead> result; in getReadsByRow() 755 return new BufferedDbiIterator<U2AssemblyRead>(result, U2AssemblyRead()); in getReadsByRow() 793 U2AssemblyRead row(new U2AssemblyReadData()); in alignmentToRead() 857 return U2AssemblyRead(); in getReadById() 863 QList<U2AssemblyRead> result; in getReadsByIds() 866 U2AssemblyRead read(new U2AssemblyReadData()); in getReadsByIds() [all …]
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H A D | SamtoolsBasedDbi.h | 70 class SamtoolsBasedReadsIterator : public U2DbiIterator<U2AssemblyRead> { 79 virtual U2AssemblyRead next(); 80 virtual U2AssemblyRead peek(); 89 QList<U2AssemblyRead> reads; 90 QList<U2AssemblyRead>::Iterator current; 108 …virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2DataId &assemblyId, const U2Region &r, U2O… 110 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByName(const U2DataId &assemblyId, const QByteArray… 117 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByRow(const U2DataId &assemblyId, const U2Region &r…
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/util/ |
H A D | AssemblyAdapter.h | 56 …virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2Region &r, U2OpStatus &os, bool sortedHint… 57 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByRow(const U2Region &r, qint64 minRow, qint64 maxR… 58 … virtual U2DbiIterator<U2AssemblyRead> *getReadsByName(const QByteArray &name, U2OpStatus &os) = 0; 60 …virtual void addReads(U2DbiIterator<U2AssemblyRead> *it, U2AssemblyReadsImportInfo &ii, U2OpStatus…
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