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Searched refs:U2AssemblyRead (Results 1 – 25 of 67) sorted by relevance

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/dports/biology/ugene/ugene-40.1/src/plugins/api_tests/src/core/dbi/assembly/
H A DAssemblyDbiTestUtil.h33 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);
H A DAssemblyDbiTestUtil.cpp44 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()
H A DAssemblyDbiUnitTests.cpp192 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()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/
H A DSQLiteAssemblyDbi.h54 …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> {
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H A DSQLiteAssemblyDbi.cpp153 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()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/util/
H A DMysqlMultiTableAssemblyAdapter.h59 …virtual U2DbiIterator<U2AssemblyRead> *getReads(const U2Region &region, U2OpStatus &os, bool sorte…
60 …virtual U2DbiIterator<U2AssemblyRead> *getReadsByRow(const U2Region &region, 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;
H A DMysqlAssemblyAdapter.cpp41 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()
H A DMysqlAssemblyAdapter.h44 class MysqlAssemblyNameFilter : public MysqlRSFilter<U2AssemblyRead> {
47 virtual bool filter(const U2AssemblyRead &r);
53 class MysqlSimpleAssemblyReadLoader : public MysqlRSLoader<U2AssemblyRead> {
55 U2AssemblyRead load(U2SqlQuery *q);
H A DMysqlMultiTableAssemblyAdapter.cpp167 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()
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H A DMysqlSingleTableAssemblyAdapter.cpp153 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()
H A DMysqlAssemblyUtils.h42 …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);
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/sqlite_dbi/assembly/
H A DMultiTableAssemblyAdapter.h58 …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;
H A DRTreeAssemblyAdapter.cpp95 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()
H A DSingleTableAssemblyAdapter.cpp140 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()
H A DMultiTableAssemblyAdapter.cpp180 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()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/dbi/
H A DU2AssemblyDbi.h38 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…
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/mysql_dbi/
H A DMysqlAssemblyDbi.h56 …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…
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_assembly/
H A DAssemblyCellRenderer.cpp130 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);
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H A DAssemblyReadsAreaHint.cpp94 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()
H A DAssemblyReadsAreaHint.h38 static QString getReadDataAsString(const U2AssemblyRead &r);
42 void setData(U2AssemblyRead r, QList<U2AssemblyRead> mates);
/dports/biology/ugene/ugene-40.1/src/plugins/dbi_bam/src/
H A DDbi.h144 …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 &…
H A DConvertToSQLiteTask.cpp84 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()
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H A DDbi.cpp644 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 …]
H A DSamtoolsBasedDbi.h70 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…
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Formats/src/util/
H A DAssemblyAdapter.h56 …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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