/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/registry/ |
H A D | DnaAssemblyTask.cpp | 33 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()
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H A D | DnaAssemblyTask.h | 57 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…
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/util_dna_assembly/ |
H A D | DnaAssemblyUtils.h | 31 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;
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H A D | DnaAssemblyUtils.cpp | 97 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()
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H A D | DnaAssemblyDialog.cpp | 208 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()
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/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bwa/ |
H A D | BwaTask.h | 36 …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 …
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H A D | BwaWorker.h | 29 class DnaAssemblyToRefTaskSettings; variable 42 void setGenomeIndex(DnaAssemblyToRefTaskSettings &settings);
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H A D | BwaMemWorker.h | 29 class DnaAssemblyToRefTaskSettings; variable 42 void setGenomeIndex(DnaAssemblyToRefTaskSettings &settings);
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H A D | BwaTask.cpp | 44 …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()
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/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bowtie2/ |
H A D | Bowtie2Task.h | 47 Bowtie2AlignTask(const DnaAssemblyToRefTaskSettings &settings); 51 DnaAssemblyToRefTaskSettings settings; 58 Bowtie2Task(const DnaAssemblyToRefTaskSettings &settings, bool justBuildIndex = false); 95 …DnaAssemblyToReferenceTask *createTaskInstance(const DnaAssemblyToRefTaskSettings &settings, bool …
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H A D | Bowtie2Worker.h | 29 class DnaAssemblyToRefTaskSettings; variable 43 void setGenomeIndex(DnaAssemblyToRefTaskSettings &settings);
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H A D | Bowtie2Task.cpp | 63 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()
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Algorithm/src/misc/ |
H A D | DnaAssemblyMultiTask.h | 37 …DnaAssemblyMultiTask(const DnaAssemblyToRefTaskSettings &settings, bool viewResult = false, bool j… 45 const DnaAssemblyToRefTaskSettings &getSettings() const { in getSettings() 50 DnaAssemblyToRefTaskSettings settings;
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/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bowtie/ |
H A D | BowtieTask.h | 76 BowtieAlignTask(const DnaAssemblyToRefTaskSettings &settings); 97 DnaAssemblyToRefTaskSettings settings; 104 BowtieTask(const DnaAssemblyToRefTaskSettings &settings, bool justBuildIndex = false); 140 …DnaAssemblyToReferenceTask *createTaskInstance(const DnaAssemblyToRefTaskSettings &settings, bool …
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H A D | BowtieWorker.h | 29 class DnaAssemblyToRefTaskSettings; variable 42 void setGenomeIndex(DnaAssemblyToRefTaskSettings &settings);
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H A D | BowtieTask.cpp | 126 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()
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/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/utils/ |
H A D | BaseShortReadsAlignerWorker.cpp | 105 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()
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H A D | BaseShortReadsAlignerWorker.h | 35 class DnaAssemblyToRefTaskSettings; variable 59 DnaAssemblyToRefTaskSettings getSettings(U2OpStatus &os); 60 virtual void setGenomeIndex(DnaAssemblyToRefTaskSettings &settings) = 0;
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/dports/biology/ugene/ugene-40.1/src/plugins/genome_aligner/src/ |
H A D | GenomeAlignerWorker.cpp | 106 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 …]
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H A D | ReadShortReadsSubTask.h | 42 const DnaAssemblyToRefTaskSettings &settings, 51 const DnaAssemblyToRefTaskSettings &settings;
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H A D | GenomeAlignerCMDLineTask.h | 44 DnaAssemblyToRefTaskSettings settings;
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H A D | GenomeAlignerWorker.h | 56 DnaAssemblyToRefTaskSettings getSettings(U2OpStatus &os);
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H A D | GenomeAlignerTask.h | 55 GenomeAlignerTask(const DnaAssemblyToRefTaskSettings &settings, bool justBuildIndex = false);
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/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bowtie/bowtie_tests/ |
H A D | bowtieTests.h | 53 DnaAssemblyToRefTaskSettings config;
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/dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/bwa/bwa_tests/ |
H A D | bwaTests.h | 53 DnaAssemblyToRefTaskSettings config;
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