| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/align_to_alignment/ |
| H A D | AlignSequencesToAlignmentSupport.cpp | 68 auto msaObject = msaEditor->getMaObject(); in sl_activate() local
69 …SAFE_POINT(!msaObject->isStateLocked(), "The action must never be called for a readonly object!", … in sl_activate()
91 extractor.setAlphabet(msaObject->getAlphabet()); in sl_activate()
95 auto task = new AlignSequencesToAlignmentTask(msaObject, algorithmId, extractor); in sl_activate()
106 auto task = new LoadSequencesAndAlignToAlignmentTask(msaObject, algorithmId, urls); in sl_activate()
115 MultipleSequenceAlignmentObject *msaObject = msaEditor->getMaObject(); in AlignSequencesToAlignmentAction() local
116 connect(msaObject, SIGNAL(si_lockedStateChanged()), SLOT(sl_updateState())); in AlignSequencesToAlignmentAction()
126 auto msaObject = msaEditor->getMaObject(); in sl_updateState() local
127 if (msaObject == nullptr || msaObject->isStateLocked()) { in sl_updateState()
132 if (msaObject->getMultipleAlignment()->isEmpty() && !canBeUsedWithEmptyObject) { in sl_updateState()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/realign_to_alignment/ |
| H A D | RealignSequencesInAlignmentTask.cpp | 47 msaObject(nullptr), in RealignSequencesInAlignmentTask()
50 msaObject = msaObjectToClone->clone(msaObjectToClone->getEntityRef().dbiRef, stateInfo); in RealignSequencesInAlignmentTask()
53 for (int index = 0; index < msaObject->getNumRows(); index++) { in RealignSequencesInAlignmentTask()
55 msaObject->renameRow(index, name); in RealignSequencesInAlignmentTask()
62 qint64 id = msaObject->getRow(rowPos)->getRowId(); in RealignSequencesInAlignmentTask()
82 delete msaObject; in ~RealignSequencesInAlignmentTask()
86 msaObject->sortRowsByList(originalRowOrder); in report()
91 originalMsaObject->updateGapModel(msaObject->getMsa()->getMsaRows()); in report()
98 DbiConnection con(msaObject->getEntityRef().dbiRef, stateInfo); in report()
101 con.dbi->getObjectDbi()->removeObject(msaObject->getEntityRef().entityId, true, stateInfo); in report()
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| H A D | RealignSequencesInAlignmentTask.h | 38 …RealignSequencesInAlignmentTask(MultipleSequenceAlignmentObject *msaObject, const QSet<qint64> &se…
48 MultipleSequenceAlignmentObject *msaObject; variable
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/phy_tree/ |
| H A D | MSAEditorTreeManager.cpp | 66 : QObject(msaEditor), editor(msaEditor), msaObject(nullptr), addExistingTree(false) { in MSAEditorTreeManager()
76 CHECK(msaObject != nullptr, ); in sl_onDocumentRemovedFromProject()
77 if (doc == msaObject->getDocument()) { in sl_onDocumentRemovedFromProject()
78 msaObject = nullptr; in sl_onDocumentRemovedFromProject()
86 msaObject->removeObjectRelation(treeRelation); in sl_onDocumentRemovedFromProject()
92 msaObject = editor->getMaObject(); in loadRelatedTrees()
106 msaObject = editor->getMaObject(); in buildTreeWithDialog()
119 settings.rowsOrder = msaObject->getMultipleAlignment()->getRowNames(); in buildTreeWithDialog()
134 const MultipleSequenceAlignment msa = msaObject->getMultipleAlignment(); in createPhyTreeGeneratorTask()
173 const GUrl &msaURL = msaObject->getDocument()->getURL(); in sl_openTree()
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| H A D | MSAEditorTreeManager.h | 73 QPointer<MultipleSequenceAlignmentObject> msaObject; variable
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| /dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/utils/ |
| H A D | AlignMsaAction.cpp | 34 MultipleSequenceAlignmentObject *msaObject = msaEditor->getMaObject(); in AlignMsaAction() local
35 connect(msaObject, SIGNAL(si_lockedStateChanged()), SLOT(sl_updateState())); in AlignMsaAction()
36 connect(msaObject, SIGNAL(si_alignmentBecomesEmpty(bool)), SLOT(sl_updateState())); in AlignMsaAction()
44 auto *msaObject = msaEditor->getMaObject(); in sl_updateState() local
45 setEnabled(!msaObject->isStateLocked() && !msaEditor->isAlignmentEmpty()); in sl_updateState()
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| /dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/blast_plus/align_worker_subtasks/ |
| H A D | BlastReadsSubTask.cpp | 167 int rowCount = msaObject->getNumRows(); in onSubTaskFinished()
170 referenceGaps = msaObject->getMsaRow(0)->getGapModel(); in onSubTaskFinished()
171 readGaps = msaObject->getMsaRow(1)->getGapModel(); in onSubTaskFinished()
178 msaObject->crop(msaObject->getRow(1)->getCoreRegion()); in onSubTaskFinished()
183 MSADistanceAlgorithm *algo = factory->createAlgorithm(msaObject->getMsa()); in onSubTaskFinished()
389 U2DataId referenceId = msaObject->getMsaRow(0)->getRowDbInfo().sequenceId; in createSettings()
390 U2DataId readId = msaObject->getMsaRow(1)->getRowDbInfo().sequenceId; in createSettings()
393 settings->alphabet = msaObject->getAlphabet()->getId(); in createSettings()
395 settings->msaRef = msaObject->getEntityRef(); in createSettings()
396 settings->firstSequenceRef = U2EntityRef(msaObject->getEntityRef().dbiRef, referenceId); in createSettings()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/ |
| H A D | CreateSubalignmentDialogController.cpp | 52 …: QDialog(p), msaObject(obj), selectedRowIds(preSelectedRowIdList), selectedColumnRegion(preSelect… in CreateSubalignmentDialogController()
58 startLineEdit->setValidator(new QIntValidator(1, msaObject->getLength(), startLineEdit)); in CreateSubalignmentDialogController()
59 endLineEdit->setValidator(new QIntValidator(1, msaObject->getLength(), endLineEdit)); in CreateSubalignmentDialogController()
68 int rowCount = (int)msaObject->getNumRows(); in CreateSubalignmentDialogController()
69 int msaLength = (int)msaObject->getLength(); in CreateSubalignmentDialogController()
87 const MultipleSequenceAlignment msa = msaObject->getMsa(); in CreateSubalignmentDialogController()
147 if (end <= start || end > msaObject->getLength()) { in sl_regionChanged()
156 …efaultFileName = GUrlUtils::getNewLocalUrlByFormat(msaObject->getDocument()->getURLString(), msaOb… in initSaveController()
198 int seqLen = msaObject->getLength(); in accept()
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| H A D | MSAEditorSequenceArea.cpp | 424 MultipleSequenceAlignmentObject *msaObject = getEditor()->getMaObject(); in sl_createSubalignment() local
426 const MultipleAlignment &alignment = msaObject->getMultipleAlignment(); in sl_createSubalignment()
559 MultipleAlignmentObject *msaObject = editor->getMaObject(); in runPasteTask() local
560 if (msaObject->isStateLocked()) { in runPasteTask()
575 MultipleSequenceAlignmentObject *msaObject = getEditor()->getMaObject(); in sl_pasteTaskFinished() local
576 CHECK(!msaObject->isStateLocked(), ); in sl_pasteTaskFinished()
611 MultipleSequenceAlignmentObject *msaObject = getEditor()->getMaObject(); in sl_addSeqFromFile() local
612 if (msaObject->isStateLocked()) { in sl_addSeqFromFile()
640 MultipleSequenceAlignmentObject *msaObject = getEditor()->getMaObject(); in sl_addSeqFromProject() local
641 if (msaObject->isStateLocked()) { in sl_addSeqFromProject()
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| H A D | MSAEditor.cpp | 738 MultipleSequenceAlignmentObject *msaObject = getMaObject(); in sortSequences() local
739 CHECK(!msaObject->isStateLocked(), ); in sortSequences()
753 msaObject->updateRowsOrder(os, msa->getRowsIds()); in sortSequences()
780 auto msaObject = getMaObject(); in sl_convertBetweenDnaAndRnaAlphabets() local
783 U2UseCommonUserModStep userModStep(msaObject->getEntityRef(), os); in sl_convertBetweenDnaAndRnaAlphabets()
787 msaObject->replaceAllCharacters(fromChar, toChar, resultAlphabet); in sl_convertBetweenDnaAndRnaAlphabets()
796 auto msaObject = getMaObject(); in sl_convertRawToDnaAlphabet() local
803 msaObject->morphAlphabet(resultAlphabet, replacementMap); in sl_convertRawToDnaAlphabet()
812 auto msaObject = getMaObject(); in sl_convertRawToAminoAlphabet() local
817 msaObject->morphAlphabet(resultAlphabet); in sl_convertRawToAminoAlphabet()
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| H A D | MaEditorTasks.cpp | 122 MultipleAlignmentObject *msaObject = msaEd->getMaObject(); in updateTitle() local
123 … QString newViewName = GObjectViewUtils::genUniqueViewName(msaObject->getDocument(), msaObject); in updateTitle()
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| H A D | CreateSubalignmentDialogController.h | 67 MultipleSequenceAlignmentObject *msaObject; variable
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/sort/ |
| H A D | MsaEditorSortSequencesWidget.cpp | 68 MultipleSequenceAlignmentObject *msaObject = msaEditor->getMaObject(); in MsaEditorSortSequencesWidget() local
69 sortButton->setEnabled(!msaObject->isStateLocked()); in MsaEditorSortSequencesWidget()
70 connect(msaObject, SIGNAL(si_lockedStateChanged()), SLOT(sl_msaObjectStateChanged())); in MsaEditorSortSequencesWidget()
80 MultipleSequenceAlignmentObject *msaObject = msaEditor->getMaObject(); in sl_msaObjectStateChanged() local
81 sortButton->setEnabled(!msaObject->isStateLocked()); in sl_msaObjectStateChanged()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/phyltree/ |
| H A D | CreatePhyTreeDialogController.cpp | 54 …ialogController(QWidget *parent, const MultipleSequenceAlignmentObject *msaObject, CreatePhyTreeSe… in CreatePhyTreeDialogController() argument
56 msa(msaObject->getMsaCopy()), in CreatePhyTreeDialogController()
75 initSaveController(msaObject); in CreatePhyTreeDialogController()
172 …eatePhyTreeDialogController::initSaveController(const MultipleSequenceAlignmentObject *msaObject) { in initSaveController() argument
174 …ultFileName = GUrlUtils::getNewLocalUrlByExtension(msaObject->getDocument()->getURLString(), msaOb… in initSaveController()
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| H A D | CreatePhyTreeDialogController.h | 43 …CreatePhyTreeDialogController(QWidget *parent, const MultipleSequenceAlignmentObject *msaObject, C…
56 void initSaveController(const MultipleSequenceAlignmentObject *msaObject);
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| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/phylip/src/ |
| H A D | PhylipTask.cpp | 38 MultipleSequenceAlignmentObject *msaObject = new MultipleSequenceAlignmentObject("msa", msaRef); in prepare() local
39 msaObject->setParent(this); in prepare()
41 treeTask = new NeighborJoinCalculateTreeTask(msaObject->getMultipleAlignment(), settings); in prepare()
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| H A D | PhylipCmdlineTask.cpp | 52 …: PhyTreeGeneratorTask(msa, settings), cmdlineTask(nullptr), msaObject(nullptr), treeObject(nullpt… in PhylipCmdlineTask()
88 …msaObject = MultipleSequenceAlignmentImporter::createAlignment(dbiRef, const_cast<MultipleSequence… in createCmdlineTask()
90 msaObject->setParent(this); in createCmdlineTask()
91 config.inputObjects << msaObject; in createCmdlineTask()
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| H A D | PhylipCmdlineTask.h | 60 MultipleSequenceAlignmentObject *msaObject; variable
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| /dports/biology/ugene/ugene-40.1/src/plugins/external_tool_support/src/clustalo/ |
| H A D | ClustalOSupport.cpp | 186 MultipleSequenceAlignmentObject *msaObject = msaEditor->getMaObject(); in sl_addAlignmentToAlignment() local
198 …clustalOSupportTask = new ClustalOSupportTask(msaObject->getMultipleAlignment(), GObjectReference(… in sl_addAlignmentToAlignment()
199 connect(msaObject, SIGNAL(destroyed()), clustalOSupportTask, SLOT(cancel())); in sl_addAlignmentToAlignment()
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| H A D | ClustalOSupportTask.cpp | 314 auto msaObject = dynamic_cast<MultipleSequenceAlignmentObject *>(obj); in unlockMsaObject() local
315 if (msaObject != nullptr && msaObject->isStateLocked()) { in unlockMsaObject()
316 msaObject->unlockState(lock); in unlockMsaObject()
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| /dports/biology/ugene/ugene-40.1/src/plugins/GUITestBase/src/tests/common_scenarios/msa_editor/tree/ |
| H A D | GTTestsMSAEditorTree.cpp | 51 MultipleSequenceAlignmentObject *msaObject = msaEditor->getMaObject(); in GUI_TEST_CLASS_DEFINITION() local
52 QStringList nameList = msaObject->getMultipleAlignment()->getRowNames(); in GUI_TEST_CLASS_DEFINITION()
61 nameList = msaObject->getMultipleAlignment()->getRowNames(); in GUI_TEST_CLASS_DEFINITION()
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| /dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/umuscle/src/ |
| H A D | MusclePlugin.cpp | 223 MultipleSequenceAlignmentObject *msaObject = msaEditor->getMaObject(); in sl_alignSequencesToProfile() local
234 …auto alignTask = new MuscleAddSequencesToProfileTask(msaObject, lod.url, MuscleAddSequencesToProfi… in sl_alignSequencesToProfile()
235 connect(msaObject, SIGNAL(destroyed()), alignTask, SLOT(cancel())); in sl_alignSequencesToProfile()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2Lang/src/support/ |
| H A D | SimpleWorkflowTask.cpp | 150 …MultipleSequenceAlignmentObject *msaObject = MultipleSequenceAlignmentImporter::createAlignment(ms… in SimpleMSAWorkflow4GObjectTask() local
154 sioConf.objects << msaObject; in SimpleMSAWorkflow4GObjectTask()
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| /dports/biology/ugene/ugene-40.1/src/plugins/dna_export/src/ |
| H A D | ExportProjectViewItems.cpp | 502 auto msaObject = qobject_cast<MultipleSequenceAlignmentObject *>(msaObjectList.first()); in sl_exportNucleicAlignmentToAmino() local
503 SAFE_POINT(msaObject != nullptr, "Not an MSA object", ); in sl_exportNucleicAlignmentToAmino()
505 Document *doc = msaObject->getDocument(); in sl_exportNucleicAlignmentToAmino()
506 …QString defaultUrl = GUrlUtils::getNewLocalUrlByFormat(doc->getURL(), msaObject->getMsa()->getName… in sl_exportNucleicAlignmentToAmino()
512 const MultipleSequenceAlignment &msa = msaObject->getMsa(); in sl_exportNucleicAlignmentToAmino()
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| /dports/biology/ugene/ugene-40.1/src/corelibs/U2View/src/ov_msa/find_pattern/ |
| H A D | FindPatternMsaWidget.cpp | 327 MultipleSequenceAlignmentObject *msaObject = msaEditor->getMaObject(); in connectSlots() local
328 …connect(msaObject, SIGNAL(si_alignmentChanged(const MultipleAlignment &, const MaModificationInfo … in connectSlots()
329 …connect(msaObject, SIGNAL(si_alphabetChanged(const MaModificationInfo &, const DNAAlphabet *)), th… in connectSlots()
330 connect(msaObject, SIGNAL(si_lockedStateChanged()), SLOT(sl_msaStateChanged())); in connectSlots()
379 MultipleSequenceAlignmentObject *msaObject = msaEditor->getMaObject(); in updateActions() local
380 groupResultsButton->setEnabled(!msaObject->isStateLocked()); in updateActions()
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