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Searched refs:DnaAssemblyToRefTaskSettings (Results 1 – 25 of 35) sorted by relevance

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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/registry/
H A DDnaAssemblyTask.cpp33 const QString DnaAssemblyToRefTaskSettings::INDEX = "Index";
34 const QString DnaAssemblyToRefTaskSettings::SEQUENCE = "Sequence";
36 DnaAssemblyToReferenceTask::DnaAssemblyToReferenceTask(const DnaAssemblyToRefTaskSettings &settings… in DnaAssemblyToReferenceTask()
93 QVariant DnaAssemblyToRefTaskSettings::getCustomValue(const QString &optionName, const QVariant &de… in getCustomValue()
101 bool DnaAssemblyToRefTaskSettings::hasCustomValue(const QString &name) const { in hasCustomValue()
105 void DnaAssemblyToRefTaskSettings::setCustomValue(const QString &optionName, const QVariant &val) { in setCustomValue()
109 QList<GUrl> DnaAssemblyToRefTaskSettings::getShortReadUrls() const { in getShortReadUrls()
118 DnaAssemblyToRefTaskSettings::DnaAssemblyToRefTaskSettings() in DnaAssemblyToRefTaskSettings() function in U2::DnaAssemblyToRefTaskSettings
128 void DnaAssemblyToRefTaskSettings::setCustomSettings(const QMap<QString, QVariant> &settings) { in setCustomSettings()
H A DDnaAssemblyTask.h57 class U2ALGORITHM_EXPORT DnaAssemblyToRefTaskSettings {
59 DnaAssemblyToRefTaskSettings();
94 …DnaAssemblyToReferenceTask(const DnaAssemblyToRefTaskSettings &settings, TaskFlags flags = TaskFla…
99 const DnaAssemblyToRefTaskSettings &getSettings() const { in getSettings()
110 DnaAssemblyToRefTaskSettings settings;
117 …virtual DnaAssemblyToReferenceTask *createTaskInstance(const DnaAssemblyToRefTaskSettings &setting…
129 …DnaAssemblyToReferenceTask *createTaskInstance(const DnaAssemblyToRefTaskSettings &s, bool justBui…
/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/util_dna_assembly/
H A DDnaAssemblyUtils.h31 class DnaAssemblyToRefTaskSettings; variable
38 …static QMap<QString, QString> toConvert(const DnaAssemblyToRefTaskSettings &settings, QList<GUrl> …
52 FilterUnpairedReadsTask(const DnaAssemblyToRefTaskSettings &settings);
62 DnaAssemblyToRefTaskSettings settings;
70 …DnaAssemblyTaskWithConversions(const DnaAssemblyToRefTaskSettings &settings, bool viewResult = fal…
74 const DnaAssemblyToRefTaskSettings &getSettings() const;
78 DnaAssemblyToRefTaskSettings settings;
H A DDnaAssemblyUtils.cpp97 DnaAssemblyToRefTaskSettings s; in sl_showDnaAssemblyDialog()
147 DnaAssemblyToRefTaskSettings s; in sl_showBuildIndexDialog()
225 QMap<QString, QString> DnaAssemblySupport::toConvert(const DnaAssemblyToRefTaskSettings &settings, … in toConvert()
260 FilterUnpairedReadsTask::FilterUnpairedReadsTask(const DnaAssemblyToRefTaskSettings &settings) in FilterUnpairedReadsTask()
319 DnaAssemblyTaskWithConversions::DnaAssemblyTaskWithConversions(const DnaAssemblyToRefTaskSettings &… in DnaAssemblyTaskWithConversions()
324 const DnaAssemblyToRefTaskSettings &DnaAssemblyTaskWithConversions::getSettings() const { in getSettings()
H A DDnaAssemblyDialog.cpp208 DnaAssemblyToRefTaskSettings settings = DnaAssemblyGUIUtils::getSettings(this); in accept()
425 DnaAssemblyToRefTaskSettings DnaAssemblyGUIUtils::getSettings(DnaAssemblyDialog *dialog) { in getSettings()
426 DnaAssemblyToRefTaskSettings s; in getSettings()
445 DnaAssemblyToRefTaskSettings s = getSettings(dlg.data()); in runAssembly2ReferenceDialog()
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bwa/
H A DBwaTask.h36 …const QString &referencePath, const QString &indexPath, const DnaAssemblyToRefTaskSettings &settin…
51 DnaAssemblyToRefTaskSettings settings;
57 …hortReadSet> &shortReadSets, const QString &resultPath, const DnaAssemblyToRefTaskSettings &settin…
80 DnaAssemblyToRefTaskSettings settings;
87 BwaSwAlignTask(const QString &indexPath, const DnaAssemblyToRefTaskSettings &settings);
92 DnaAssemblyToRefTaskSettings settings;
98 BwaMemAlignTask(const QString &indexPath, const DnaAssemblyToRefTaskSettings &settings);
110 DnaAssemblyToRefTaskSettings settings;
117 BwaTask(const DnaAssemblyToRefTaskSettings &settings, bool justBuildIndex = false);
205 …DnaAssemblyToReferenceTask *createTaskInstance(const DnaAssemblyToRefTaskSettings &settings, bool …
H A DBwaWorker.h29 class DnaAssemblyToRefTaskSettings; variable
42 void setGenomeIndex(DnaAssemblyToRefTaskSettings &settings);
H A DBwaMemWorker.h29 class DnaAssemblyToRefTaskSettings; variable
42 void setGenomeIndex(DnaAssemblyToRefTaskSettings &settings);
H A DBwaTask.cpp44 …const QString &referencePath, const QString &indexPath, const DnaAssemblyToRefTaskSettings &settin… in BwaBuildIndexTask()
90 …hortReadSet> &shortReadSets, const QString &resultPath, const DnaAssemblyToRefTaskSettings &settin… in BwaAlignTask()
305 BwaMemAlignTask::BwaMemAlignTask(const QString &indexPath, const DnaAssemblyToRefTaskSettings &sett… in BwaMemAlignTask()
469 BwaSwAlignTask::BwaSwAlignTask(const QString &indexPath, const DnaAssemblyToRefTaskSettings &settin… in BwaSwAlignTask()
595 BwaTask::BwaTask(const DnaAssemblyToRefTaskSettings &settings, bool justBuildIndex) in BwaTask()
674 DnaAssemblyToReferenceTask *BwaTaskFactory::createTaskInstance(const DnaAssemblyToRefTaskSettings &… in createTaskInstance()
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bowtie2/
H A DBowtie2Task.h47 Bowtie2AlignTask(const DnaAssemblyToRefTaskSettings &settings);
51 DnaAssemblyToRefTaskSettings settings;
58 Bowtie2Task(const DnaAssemblyToRefTaskSettings &settings, bool justBuildIndex = false);
95 …DnaAssemblyToReferenceTask *createTaskInstance(const DnaAssemblyToRefTaskSettings &settings, bool …
H A DBowtie2Worker.h29 class DnaAssemblyToRefTaskSettings; variable
43 void setGenomeIndex(DnaAssemblyToRefTaskSettings &settings);
H A DBowtie2Task.cpp63 Bowtie2AlignTask::Bowtie2AlignTask(const DnaAssemblyToRefTaskSettings &settings) in Bowtie2AlignTask()
240 Bowtie2Task::Bowtie2Task(const DnaAssemblyToRefTaskSettings &settings, bool justBuildIndex) in Bowtie2Task()
316 …ToReferenceTask *Bowtie2TaskFactory::createTaskInstance(const DnaAssemblyToRefTaskSettings &settin… in createTaskInstance()
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/misc/
H A DDnaAssemblyMultiTask.h37 …DnaAssemblyMultiTask(const DnaAssemblyToRefTaskSettings &settings, bool viewResult = false, bool j…
45 const DnaAssemblyToRefTaskSettings &getSettings() const { in getSettings()
50 DnaAssemblyToRefTaskSettings settings;
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bowtie/
H A DBowtieTask.h76 BowtieAlignTask(const DnaAssemblyToRefTaskSettings &settings);
97 DnaAssemblyToRefTaskSettings settings;
104 BowtieTask(const DnaAssemblyToRefTaskSettings &settings, bool justBuildIndex = false);
140 …DnaAssemblyToReferenceTask *createTaskInstance(const DnaAssemblyToRefTaskSettings &settings, bool …
H A DBowtieWorker.h29 class DnaAssemblyToRefTaskSettings; variable
42 void setGenomeIndex(DnaAssemblyToRefTaskSettings &settings);
H A DBowtieTask.cpp126 BowtieAlignTask::BowtieAlignTask(const DnaAssemblyToRefTaskSettings &settings) in BowtieAlignTask()
354 BowtieTask::BowtieTask(const DnaAssemblyToRefTaskSettings &settings, bool justBuildIndex) in BowtieTask()
430 …yToReferenceTask *BowtieTaskFactory::createTaskInstance(const DnaAssemblyToRefTaskSettings &settin… in createTaskInstance()
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/utils/
H A DBaseShortReadsAlignerWorker.cpp105 DnaAssemblyToRefTaskSettings BaseShortReadsAlignerWorker::getSettings(U2OpStatus &os) { in getSettings()
106 DnaAssemblyToRefTaskSettings settings; in getSettings()
149 DnaAssemblyToRefTaskSettings settings = getSettings(os); in tick()
326 …(referenceInputType, BaseTypes::STRING_TYPE(), true, QVariant(DnaAssemblyToRefTaskSettings::SEQUEN… in addCommonAttributes()
328 …nom->addRelation(new VisibilityRelation(REFERENCE_INPUT_TYPE, DnaAssemblyToRefTaskSettings::SEQUEN… in addCommonAttributes()
331 …Dir->addRelation(new VisibilityRelation(REFERENCE_INPUT_TYPE, DnaAssemblyToRefTaskSettings::INDEX)… in addCommonAttributes()
334 …ame->addRelation(new VisibilityRelation(REFERENCE_INPUT_TYPE, DnaAssemblyToRefTaskSettings::INDEX)… in addCommonAttributes()
352 rip[BaseShortReadsAlignerWorker::tr("Sequence")] = DnaAssemblyToRefTaskSettings::SEQUENCE; in addCommonAttributes()
353 rip[BaseShortReadsAlignerWorker::tr("Index")] = DnaAssemblyToRefTaskSettings::INDEX; in addCommonAttributes()
438 if (inputType == DnaAssemblyToRefTaskSettings::INDEX) { in composeRichDoc()
H A DBaseShortReadsAlignerWorker.h35 class DnaAssemblyToRefTaskSettings; variable
59 DnaAssemblyToRefTaskSettings getSettings(U2OpStatus &os);
60 virtual void setGenomeIndex(DnaAssemblyToRefTaskSettings &settings) = 0;
/dports/biology/ugene/ugene-40.1/src/plugins/genome_aligner/src/
H A DGenomeAlignerWorker.cpp106 DnaAssemblyToRefTaskSettings settings = getSettings(os); in tick()
156 DnaAssemblyToRefTaskSettings GenomeAlignerWorker::getSettings(U2OpStatus &os) { in getSettings()
157 DnaAssemblyToRefTaskSettings settings; in getSettings()
160 if (referenceInputType == DnaAssemblyToRefTaskSettings::INDEX) { in getSettings()
223 if (inputType == DnaAssemblyToRefTaskSettings::INDEX) { in composeRichDoc()
373 …(referenceInputType, BaseTypes::STRING_TYPE(), true, QVariant(DnaAssemblyToRefTaskSettings::SEQUEN… in init()
375 …nom->addRelation(new VisibilityRelation(REFERENCE_INPUT_TYPE, DnaAssemblyToRefTaskSettings::SEQUEN… in init()
378 …Dir->addRelation(new VisibilityRelation(REFERENCE_INPUT_TYPE, DnaAssemblyToRefTaskSettings::INDEX)… in init()
381 …ame->addRelation(new VisibilityRelation(REFERENCE_INPUT_TYPE, DnaAssemblyToRefTaskSettings::INDEX)… in init()
410 rip[GenomeAlignerWorker::tr("Sequence")] = DnaAssemblyToRefTaskSettings::SEQUENCE; in init()
[all …]
H A DReadShortReadsSubTask.h42 const DnaAssemblyToRefTaskSettings &settings,
51 const DnaAssemblyToRefTaskSettings &settings;
H A DGenomeAlignerCMDLineTask.h44 DnaAssemblyToRefTaskSettings settings;
H A DGenomeAlignerWorker.h56 DnaAssemblyToRefTaskSettings getSettings(U2OpStatus &os);
H A DGenomeAlignerTask.h55 GenomeAlignerTask(const DnaAssemblyToRefTaskSettings &settings, bool justBuildIndex = false);
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bowtie/bowtie_tests/
H A DbowtieTests.h53 DnaAssemblyToRefTaskSettings config;
/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bwa/bwa_tests/
H A DbwaTests.h53 DnaAssemblyToRefTaskSettings config;

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