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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/datatype/
H A DU2Region.h41 U2Region() in U2Region() function
85 U2Region intersect(const U2Region &r) const;
149 static U2Region containingRegion(const U2Region &r1, const U2Region &r2);
152 static U2Region containingRegion(const QVector<U2Region> &regions);
161 static QVector<U2Region> join(QVector<U2Region> &regions);
184 static QList<U2Region> split(const U2Region &region, qint64 blockSize);
204 inline bool U2Region::intersects(const U2Region &r) const { in intersects()
209 inline U2Region U2Region::intersect(const U2Region &r) const { in intersect()
213 return U2Region(); in intersect()
218 inline U2Region U2Region::containingRegion(const U2Region &r1, const U2Region &r2) { in containingRegion()
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H A DU2Region.cpp50 QVector<U2Region> U2Region::circularContainingRegion(QVector<U2Region> &_regions, int seqLen) { in circularContainingRegion()
71 QVector<U2Region> U2Region::join(QVector<U2Region> &regions) { in join()
98 void U2Region::mirror(qint64 mirrorPos, QVector<U2Region> &regions) { in mirror()
106 void U2Region::divide(qint64 div, QVector<U2Region> &regions) { in divide()
113 void U2Region::multiply(qint64 mult, QVector<U2Region> &regions) { in multiply()
120 void U2Region::reverse(QVector<U2Region> &regions) { in reverse()
128 void U2Region::shift(qint64 offset, QVector<U2Region> &regions) { in shift()
136 QList<U2Region> U2Region::split(const U2Region &region, qint64 blockSize) { in split()
148 qint64 U2Region::sumLength(const QVector<U2Region> &regions) { in sumLength()
176 U2Region U2Region::fromXRange(const QRect &rect) { in fromXRange()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/helpers/
H A DRowHeightController.cpp84 U2Region globalYRegion = getGlobalYRegionByViewRowsRegion(U2Region(0, viewRowCount)); in getTotalAlignmentHeight()
120 return U2Region(globalYPosition, rowHeight); in getGlobalYRegionByMaRowIndex()
126 return U2Region(globalYPosition, rowHeight); in getGlobalYRegionByMaRowIndex()
139 return U2Region(-OUT_OF_RANGE_OFFSET, 0); in getGlobalYRegionByViewRowIndex()
145 U2Region startOfView = getGlobalYRegionByViewRowIndex(0); in getGlobalYRegionByViewRowIndex()
155 U2Region RowHeightController::getGlobalYRegionByViewRowsRegion(const U2Region &viewRowsRegion) cons… in getGlobalYRegionByViewRowsRegion()
158 return U2Region::containingRegion(startPosRegion, endPosRegion); in getGlobalYRegionByViewRowsRegion()
161 U2Region RowHeightController::getScreenYRegionByViewRowsRegion(const U2Region &viewRowsRegion) cons… in getScreenYRegionByViewRowsRegion()
164 return U2Region::containingRegion(startPosRegion, endPosRegion); in getScreenYRegionByViewRowsRegion()
172 U2Region rowRange = getGlobalYRegionByMaRowIndex(maRowIndex); in getScreenYRegionByMaRowIndex()
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H A DBaseWidthController.h31 class U2Region; variable
47 int getBasesWidth(const U2Region &region) const;
49 U2Region getBaseGlobalRange(int position) const;
50 U2Region getBasesGlobalRange(int startPosition, int count) const;
51 U2Region getBasesGlobalRange(const U2Region &region) const;
53 U2Region getBaseScreenRange(int position) const;
54 U2Region getBasesScreenRange(const U2Region &region) const;
56 U2Region getBaseScreenRange(int position, int screenXOrigin) const;
57 U2Region getBasesScreenRange(int startPosition, int count, int screenXOrigin) const;
58 U2Region getBasesScreenRange(const U2Region &region, int screenXOrigin) const;
H A DRowHeightController.h51 U2Region getGlobalYRegionByMaRowIndex(int maRowIndex) const;
52 U2Region getGlobalYRegionByMaRowIndex(int maRowIndex, const QList<int> &maRowIndexes) const;
53 U2Region getGlobalYRegionByViewRowIndex(int viewRowIndex) const;
55 U2Region getGlobalYRegionByViewRowsRegion(const U2Region &viewRowsRegion) const;
56 U2Region getScreenYRegionByViewRowsRegion(const U2Region &viewRowsRegion) const;
58 U2Region getScreenYRegionByMaRowIndex(int maRowIndex) const;
60 U2Region getScreenYRegionByMaRowIndex(int maRowIndex, int screenYOrigin) const;
62 U2Region getScreenYRegionByViewRowIndex(int viewRowIndex) const;
71 U2Region mapGlobalToScreen(const U2Region &globalRegion) const;
H A DBaseWidthController.cpp65 int BaseWidthController::getBasesWidth(const U2Region &region) const { in getBasesWidth()
69 U2Region BaseWidthController::getBaseGlobalRange(int position) const { in getBaseGlobalRange()
73 U2Region BaseWidthController::getBasesGlobalRange(int startPosition, int count) const { in getBasesGlobalRange()
74 return U2Region(getBaseGlobalOffset(startPosition), getBasesWidth(count)); in getBasesGlobalRange()
77 U2Region BaseWidthController::getBasesGlobalRange(const U2Region &region) const { in getBasesGlobalRange()
81 U2Region BaseWidthController::getBaseScreenRange(int position) const { in getBaseScreenRange()
85 U2Region BaseWidthController::getBasesScreenRange(const U2Region &region) const { in getBasesScreenRange()
89 U2Region BaseWidthController::getBaseScreenRange(int position, int screenXOrigin) const { in getBaseScreenRange()
94 const U2Region globalRange = getBasesGlobalRange(startPosition, count); in getBasesScreenRange()
95 return U2Region(globalRange.startPos - screenXOrigin, globalRange.length); in getBasesScreenRange()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/selection/
H A DLRegionsSelection.cpp28 …(this, SIGNAL(si_selectionChanged(LRegionsSelection *, QVector<U2Region>, QVector<U2Region>)), SLO… in LRegionsSelection()
32 for (const U2Region &region : qAsConst(regions)) { in contains()
44 QVector<U2Region> removedRegions = regions; in clear()
45 QVector<U2Region> addedRegions; in clear()
52 QVector<U2Region> LRegionsSelection::cropSelection(qint64 sequenceLength, const QVector<U2Region> &… in cropSelection()
53 QVector<U2Region> result; in cropSelection()
69 QVector<U2Region> addedRegions = {r}; in addRegion()
70 QVector<U2Region> removedRegions; in addRegion()
80 QVector<U2Region> addedRegions; in removeRegion()
81 QVector<U2Region> removedRegions = {r}; in removeRegion()
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H A DLRegionsSelection.h37 const QVector<U2Region> &getSelectedRegions() const;
43 void setSelectedRegions(const QVector<U2Region> &newSelection);
46 void addRegion(const U2Region &r);
49 void removeRegion(const U2Region &r);
52 void setRegion(const U2Region &r);
63 static QVector<U2Region> cropSelection(qint64 sequenceLength, const QVector<U2Region> &regions);
67 …selectionChanged(LRegionsSelection *thiz, const QVector<U2Region> &added, const QVector<U2Region> …
70 QVector<U2Region> regions;
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_sequence/view_rendering/
H A DDetViewSingleLineRenderer.h36 const U2Region &visibleRange,
44 U2Region seqBlockRegion;
63 …U2Region> getAnnotationYRegions(Annotation *annotation, int locationRegionIndex, const AnnotationS…
67 U2Region getCutSiteYRange(const U2Strand &mStrand, int availableHeight) const override;
79 QSize getBaseCanvasSize(const U2Region &visibleRange) const override;
91 void drawDirect(QPainter &p, int availableHeight, const U2Region &visibleRange);
92 void drawComplement(QPainter &p, int availableHeight, const U2Region &visibleRange);
101 const U2Region &visibleRange,
108 const U2Region &visibleRange,
114 void drawRuler(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange);
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H A DDetViewMultiLineRenderer.cpp49 U2Region firstLineVisibleRange(visibleRange.startPos, symbolsPerLine); in coordToPos()
77 QList<U2Region> yRegionList; in getAnnotationYRegions()
78 const U2Region &locationRegion = annotation->getRegions()[locationRegionIndex]; in getAnnotationYRegions()
79 U2Region visibleLocationRegion = visibleRange.intersect(locationRegion); in getAnnotationYRegions()
91 U2Region DetViewMultiLineRenderer::getCutSiteYRange(const U2Strand &, int) const { in getCutSiteYRange()
92 FAIL("The method must never be called", U2Region()); in getCutSiteYRange()
97 U2Region range(visibleRange.startPos, qMin(symbolsPerLine, visibleRange.length)); in isOnTranslationsLine()
142 QSize DetViewMultiLineRenderer::getBaseCanvasSize(const U2Region &visibleRange) const { in getBaseCanvasSize()
154 U2Region oneLineRegion(visibleRange.startPos, symbolsPerLine); in drawAll()
189 U2Region oneLineRegion(visibleRange.startPos, symbolsPerLine); in drawSelection()
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H A DDetViewMultiLineRenderer.h39 …qint64 coordToPos(const QPoint &p, const QSize &canvasSize, const U2Region &visibleRange) const ov…
40 … int posToXCoord(qint64 pos, const QSize &canvasSize, const U2Region &visibleRange) const override;
43 …U2Region> getAnnotationYRegions(Annotation *annotation, int locationRegionIndex, const AnnotationS…
45 U2Region getCutSiteYRange(const U2Strand &mStrand, int availableHeight) const override;
55 QSize getBaseCanvasSize(const U2Region &visibleRange) const override;
57 …bool isOnTranslationsLine(const QPoint &p, const QSize &canvasSize, const U2Region &visibleRange) …
58 …nt region, const AnnotationSettings *as, const QSize &canvasSize, const U2Region &visibleRange) co…
60 void drawAll(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange) override;
61 void drawSelection(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange) override;
62 void drawCursor(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange) override;
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H A DPanViewRenderer.h47 …qint64 coordToPos(const QPoint &p, const QSize &canvasSize, const U2Region &visibleRange) const ov…
51 …U2Region getAnnotationYRange(Annotation *a, int r, const AnnotationSettings *as, int availableHeig…
53 U2Region getCutSiteYRange(const U2Strand &mStrand, int availableHeight) const override;
59 QSize getBaseCanvasSize(const U2Region &visibleRange) const override;
61 void drawAll(QPainter &p, const U2Region &visibleRange);
63 void drawAll(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange) override;
65 void drawSelection(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange) override;
67 …void drawAnnotations(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange, const Ann…
77 virtual void drawSequence(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange);
78 void drawSequenceSelection(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange);
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H A DDetViewSingleLineRenderer.cpp109 return U2Region(y, commonMetrics.lineHeight); in getAnnotationYRange()
115 return U2Region(y, commonMetrics.lineHeight); in getCutSiteYRange()
279 foreach (U2Region reg, regions) { in translateSelection()
352 QVector<U2Region> revesedRegions; in translateComplSelection()
353 foreach (const U2Region &reg, regions) { in translateComplSelection()
359 U2Region::reverse(revesedRegions); in translateComplSelection()
471 QVector<U2Region> regions; in drawComplementTranslations()
472 …QList<QVector<U2Region>> sortedRegions = QList<QVector<U2Region>>() << QVector<U2Region>() << QVec… in drawComplementTranslations()
479 foreach (const U2Region &reg, regions) { in drawComplementTranslations()
733 const U2Region tripletRange = strand.isCompementary() ? U2Region(pos - 2, 2) : U2Region(pos, 2); in deriveTranslationCharColor()
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H A DSequenceViewAnnotatedRenderer.h82 …virtual qint64 coordToPos(const QPoint &p, const QSize &canvasSize, const U2Region &visibleRange) …
87 virtual U2Region getCutSiteYRange(const U2Strand &mStrand, int availableHeight) const = 0;
91 virtual void drawAll(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange) = 0;
92 …virtual void drawSelection(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange) = 0;
94 …virtual void drawAnnotations(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange, c…
95 …virtual void drawAnnotationSelection(QPainter &p, const QSize &canvasSize, const U2Region &visible…
98 …virtual void drawAnnotation(QPainter &p, const QSize &canvasSize, const U2Region &visibleRange, An…
110 …virtual U2Region getAnnotationYRange(Annotation *annotation, int locationRegionIndex, const Annota…
114 …st AnnotationDisplaySettings &drawSettings, const QSize &canvasSize, const U2Region &visibleRange);
116 …tationData &aData, const U2Region &r, const QRect &annotationRect, const QColor &color, const QSiz…
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/util/
H A DU1AnnotationUtils.cpp61 QList<QVector<U2Region>> res; in fixLocationsForReplacedRegion()
69 res << QVector<U2Region>(); in fixLocationsForReplacedRegion()
70 QVector<U2Region> &updated = res[0]; in fixLocationsForReplacedRegion()
72 foreach (U2Region r, original) { in fixLocationsForReplacedRegion()
121 …const U2Region leftR = r.startPos < interR.startPos ? U2Region(r.startPos, interR.startPos - r.sta… in fixLocationsForReplacedRegion()
122 …const U2Region rightR = (r.endPos() > interR.endPos()) ? U2Region(interR.endPos() + dLen, r.endPos… in fixLocationsForReplacedRegion()
230 U2Region reg; in getCaseAnnotations()
302 QList<U2Region> lowerCaseRegs; in getRelatedLowerCaseRegions()
303 QList<U2Region> upperCaseRegs; in getRelatedLowerCaseRegions()
358 const U2Region reg = regions[i]; in mergeAnnotatiedRegionsAroundJunctionPoint()
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H A DU1AnnotationUtils.h31 using RegionsPair = QPair<U2::U2Region, U2::U2Region>;
71 … QList<QVector<U2Region>> fixLocationsForReplacedRegion(const U2Region &region2Remove, qint64 regi…
75 …nt sequenceLen, const U2Strand &strand, bool order, int region, const QVector<U2Region> &location);
80 static bool isSplitted(const U2Location &location, const U2Region &seqRange);
88 …static QList<SharedAnnotationData> finalizeUnfinishedRegion(bool isUnfinishedRegion, U2Region &unf…
94 …static QList<U2Region> getRelatedLowerCaseRegions(const U2SequenceObject *so, const QList<GObject …
103 …static QList<RegionsPair> mergeAnnotatiedRegionsAroundJunctionPoint(const QVector<U2Region> &regio…
105 …CaseRegions(char *seq, qint64 first, qint64 len, qint64 globalOffset, const QList<U2Region> &regs);
125 static QString buildLocationString(const QVector<U2Region> &regions);
144 bool isRegionValid(const U2Region &region) const;
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H A DVariationPropertiesUtils.h44 U2Region getRegion() { in getRegion()
47 QByteArray getSequenceData(const U2Region &region, U2OpStatus &os);
53 U2Region seqRegion;
93 static inline bool isInDonorSpliceSite(const U2Region &exon, qint64 varPos, int spliceSiteLen) { in isInDonorSpliceSite()
95 res = U2Region(exon.endPos() - spliceSiteLen, 2 * spliceSiteLen).contains(varPos); in isInDonorSpliceSite()
98 …static inline bool isInAcceptorSpliceSite(const U2Region &exon, qint64 varPos, int spliceSiteLen) { in isInAcceptorSpliceSite()
100 res = U2Region(exon.startPos - spliceSiteLen, 2 * spliceSiteLen).contains(varPos); in isInAcceptorSpliceSite()
109 …static U2Region getIntron(const U2Region &geneRegion, const QVector<U2Region> &exons, qint64 varPo…
111 …static bool isInSpliceSite(const QVector<U2Region> &exons, qint64 varPos, int spliceSiteLen, bool …
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/primer3/src/
H A DPrimer3TaskSettings.h56 QList<U2Region> regionList;
82 QList<U2Region> getTarget() const;
83 QList<U2Region> getProductSizeRange() const;
90 QList<U2Region> getExcludedRegion() const;
91 U2Region getIncludedRegion() const;
100 void setTarget(const QList<U2Region> &value);
107 void setExcludedRegion(const QList<U2Region> &value);
108 void setIncludedRegion(const U2Region &value);
131 const QList<U2Region> &getExonRegions() const { in getExonRegions()
135 void setExonRegions(const QList<U2Region> &regions) { in setExonRegions()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/view_rendering/
H A DMaConsensusAreaRenderer.h44 U2Region xRangeToDrawIn;
45 QMap<MaEditorConsElement, U2Region> yRangeToDrawIn;
58 U2Region firstNotchedBaseXRange;
59 U2Region lastNotchedBaseXRange;
66 U2Region region;
67 U2Region selectedRegion;
79 U2Region xRange;
80 U2Region yRange;
98 …ConsensusRenderData getConsensusRenderData(const QList<int> &seqIdx, const U2Region &region) const;
103 …U2Region getYRange(const MaEditorConsElements &visibleElements, MaEditorConsElement element) const;
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/dports/biology/ugene/ugene-40.1/src/plugins/annotator/src/
H A DCollocationsSearchAlgorithm.cpp35 foreach (const U2Region &r, item.regions) { in findN()
44 U2Region prevResult; in findN()
46 U2Region res; in findN()
47 U2Region currentRegion(i, qMin(i + distance, searchRegion.endPos()) - i); in findN()
53 foreach (const U2Region &r, item.regions) { in findN()
82 void averagingRes(U2Region &res, const U2Region &min, const U2Region &max, qint64 distance, const U… in averagingRes()
112 foreach (const U2Region &r, item.regions) { in findP()
122 U2Region prevMax; in findP()
124 U2Region res; in findP()
126 U2Region min, max; in findP()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Gui/src/util/
H A DRegionSelectorController.cpp49 U2Region region = getOneRegionFromSelection(); in RegionSelectorSettings()
57 …U2Region region = selection->getSelectedRegions().isEmpty() ? U2Region(0, maxLen) : selection->get… in getOneRegionFromSelection()
93 return U2Region(); in getRegion()
102 return U2Region(); in getRegion()
109 return U2Region(); in getRegion()
117 return U2Region(v1, v2 - v1); in getRegion()
210 const U2Region region = gui.presetsComboBox->itemData(index).value<U2Region>(); in sl_onPresetChanged()
240 U2Region r; in sl_onRegionChanged()
242 r = U2Region(v1 - 1, v2 - (v1 - 1)); in sl_onRegionChanged()
278 const U2Region region = getRegion(); in sl_onValueEdited()
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/dports/biology/ugene/ugene-40.1/src/plugins/enzymes/src/
H A DFindEnzymesTask.cpp53 U2Region searchRegion = cfg.searchRegion; in prepare()
56 searchRegion = U2Region(0, sequenceObject.getSequenceLength()); in prepare()
132 for (const U2Region &r : qAsConst(excludedRegions)) { in onResult()
133 if (U2Region(pos, enzyme->seq.length()).intersects(r)) { in onResult()
298 U2Region chunkRegion = t->getGlobalRegion(); in onRegion()
300 if (U2Region(0, sequenceLen).contains(chunkRegion)) { in onRegion()
303 U2Region partOne = U2Region(0, sequenceLen).intersect(chunkRegion); in onRegion()
306 U2Region partTwo = U2Region(0, chunkRegion.endPos() % sequenceLen); in onRegion()
374 U2Region wholeSequenceRegion(0, sequenceLength); in createAutoAnnotationsUpdateTask()
409 objectHints->set(hintName, QVariant::fromValue<U2Region>(region)); in setRegionToHints()
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H A DFindEnzymesTask.h62 U2Region searchRegion;
65 QVector<U2Region> excludedRegions;
105 …U2Region &region, const QList<SEnzymeData> &enzymes, int maxResults = 0x7FFFFFFF, bool _circular =…
117 QVector<U2Region> excludedRegions;
132 …FindSingleEnzymeTask(const U2EntityRef &sequenceObjectRef, const U2Region &region, const SEnzymeDa…
149 U2Region region;
168 static U2Region getLastSearchRegionForObject(const U2SequenceObject *sequenceObject);
175 …static void setLastSearchRegionForObject(U2SequenceObject *sequenceObject, const U2Region &region);
178 static U2Region getLastExcludeRegionForObject(const U2SequenceObject *sequenceObject);
185 …static void setLastExcludeRegionForObject(U2SequenceObject *sequenceObject, const U2Region &region…
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_sequence/
H A DGSequenceLineView.cpp63 …NAL(si_selectionChanged(LRegionsSelection *, const QVector<U2Region> &, const QVector<U2Region> &)… in GSequenceLineView()
64 …l_onDNASelectionChanged(LRegionsSelection *, const QVector<U2Region> &, const QVector<U2Region> &)… in GSequenceLineView()
194 U2Region rgn(pos, 1); in mouseReleaseEvent()
204 resizableRegion = U2Region(); in mouseReleaseEvent()
286 return U2Region(0, height()); in getCapturingRenderAreaYRegionForPos()
373 …nDNASelectionChanged(LRegionsSelection *, const QVector<U2Region> &added, const QVector<U2Region> … in sl_onDNASelectionChanged()
555 U2Region newSelection(selStart, selLen); in resizeSelection()
558 foreach (const U2Region &reg, regions) { in resizeSelection()
560 newSelection = U2Region::join(QVector<U2Region>() << newSelection << reg).first(); in resizeSelection()
581 foreach (const U2Region &reg, regions) { in resizeSelection()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/tasks/
H A DSequenceDbiWalkerTask.cpp50 config.range = U2Region(0, sequenceObject.getSequenceLength()); in prepareSubtasks()
52 U2Region wholeSeqReg(0, sequenceObject.getSequenceLength()); in prepareSubtasks()
89 U2Region strandRange(config.range.startPos, config.range.length - i); in prepareSubtasks()
102 const U2Region &chunk = chunks[i]; in createSubs()
111 QVector<U2Region> SequenceDbiWalkerTask::splitRange(const U2Region &range, int chunkSize, int overl… in splitRange()
115 QVector<U2Region> res; in splitRange()
122 res.append(U2Region(pos, chunkLen)); in splitRange()
126 QVector<U2Region> revertedRegions; in splitRange()
127 foreach (const U2Region &r, res) { in splitRange()
128 U2Region rr(range.startPos + (range.endPos() - r.endPos()), r.length); in splitRange()
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