[med-svn] [ugene] branch master updated (7e7a104 -> 6dd6ede)
Andreas Tille
tille at debian.org
Fri Jan 8 18:38:41 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository ugene.
from 7e7a104 Upload to unstable
new 5a6ce9d Imported Upstream version 1.20.0
new 4f8522f Merge tag 'upstream/1.20.0'
new 1610790 New upstream version
new 2b7a0f5 Build-Depends: libprocps-dev (instead of libprocps4-dev)
new 30a2ee1 Adapt quilt patches
new 73149d3 add repacksuffix to d/watch
new 8b9d86f Imported Upstream version 1.20.0+dfsg
new 6dd6ede Merge tag 'upstream/1.20.0+dfsg'
The 8 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
build.txt | 12 +
data/cmdline/das_annotation.uwl | 112 -
data/workflow_samples/NGS/cistrome/chip_seq.uwl | 12 +-
.../NGS/cistrome/chip_seq_with_control.uwl | 30 +-
debian/changelog | 9 +
debian/control | 2 +-
debian/patches/hardening.patch | 36 +-
debian/patches/use_debian_sqlite.patch | 144 +-
debian/watch | 2 +-
installer/_common_data/ugene | 6 +-
installer/_common_data/ugened | 6 +-
installer/linux/fedora/ugene.spec | 33 +-
installer/linux/ubuntu/debian/control | 6 +-
installer/linux/ubuntu/debian/rules | 6 +-
.../U2Algorithm/src/misc/BinaryFindOpenCL.cpp | 101 +-
.../src/msa_alignment/SimpleAddingToAlignment.cpp | 3 +-
.../U2Algorithm/src/registry/OpenCLGpuRegistry.cpp | 3 +
.../U2Algorithm/src/registry/OpenCLGpuRegistry.h | 7 +-
.../U2Algorithm/src/util_orf/ORFFinder.cpp | 2 +-
src/corelibs/U2Algorithm/transl/english.ts | 57 +-
src/corelibs/U2Algorithm/transl/russian.ts | 59 +-
src/corelibs/U2Core/U2Core.pro | 10 +-
src/corelibs/U2Core/src/datatype/BaseAlphabets.cpp | 6 +-
src/corelibs/U2Core/src/datatype/BioStruct3D.cpp | 20 +-
src/corelibs/U2Core/src/datatype/BioStruct3D.h | 8 +-
src/corelibs/U2Core/src/datatype/DASSource.cpp | 236 --
src/corelibs/U2Core/src/datatype/DASSource.h | 102 -
.../U2Core/src/datatype/DNASequenceUtils.cpp | 28 +-
.../U2Core/src/datatype/DNASequenceUtils.h | 6 +
src/corelibs/U2Core/src/dbi/U2MsaDbi.h | 6 +
src/corelibs/U2Core/src/globals/AppContext.h | 4 -
src/corelibs/U2Core/src/globals/AppResources.cpp | 13 +
src/corelibs/U2Core/src/globals/AppResources.h | 11 +-
.../U2Core/src/globals/ExternalToolRegistry.h | 1 +
src/corelibs/U2Core/src/globals/L10n.h | 6 +-
.../U2Core/src/globals/UserActionsWriter.cpp | 386 ++--
.../U2Core/src/globals/UserActionsWriter.h | 38 +-
.../U2Core/src/gobjects/MAlignmentObject.cpp | 65 +-
.../U2Core/src/gobjects/MAlignmentObject.h | 19 +-
src/corelibs/U2Core/src/io/HttpFileAdapter.cpp | 2 +-
src/corelibs/U2Core/src/io/LocalFileAdapter.cpp | 14 +-
src/corelibs/U2Core/src/io/LocalFileAdapter.h | 1 +
src/corelibs/U2Core/src/models/DocumentModel.cpp | 2 +
src/corelibs/U2Core/src/models/DocumentModel.h | 2 +
.../src/tasks/AddSequencesToAlignmentTask.cpp | 76 +-
.../U2Core/src/tasks/AddSequencesToAlignmentTask.h | 25 +-
.../U2Core/src/tasks/ExternalToolRunTask.cpp | 5 +
.../U2Core/src/tasks/LoadDASDocumentTask.cpp | 840 -------
.../U2Core/src/tasks/LoadDASDocumentTask.h | 216 --
src/corelibs/U2Core/src/tasks/PicrApiTask.cpp | 619 -----
src/corelibs/U2Core/src/tasks/PicrApiTask.h | 237 --
src/corelibs/U2Core/src/tasks/SaveDocumentTask.cpp | 9 +-
src/corelibs/U2Core/src/tasks/UniprotBlastTask.cpp | 749 ------
src/corelibs/U2Core/src/tasks/UniprotBlastTask.h | 293 ---
.../U2Core/src/util/DatatypeSerializeUtils.cpp | 11 +-
src/corelibs/U2Core/src/util/IOAdapterUtils.cpp | 10 +-
src/corelibs/U2Core/src/util/IOAdapterUtils.h | 2 +-
.../U2Core/src/util/MAlignmentImporter.cpp | 1 +
src/corelibs/U2Core/src/util/MsaDbiUtils.cpp | 146 +-
src/corelibs/U2Core/src/util/MsaDbiUtils.h | 28 +
src/corelibs/U2Core/src/util/TaskWatchdog.cpp | 57 +
src/corelibs/U2Core/src/util/TaskWatchdog.h | 62 +
src/corelibs/U2Core/src/util/U2AlphabetUtils.cpp | 26 +-
src/corelibs/U2Core/transl/english.ts | 214 +-
src/corelibs/U2Core/transl/russian.ts | 214 +-
.../U2Designer/src/BreakpointHitCountDialog.cpp | 2 +-
src/corelibs/U2Designer/src/DatasetsListWidget.cpp | 4 +
.../U2Designer/src/EditBreakpointLabelsDialog.cpp | 2 +-
.../U2Designer/src/EditMarkerGroupDialog.cpp | 4 +-
.../U2Designer/src/NewBreakpointDialog.cpp | 2 +-
.../U2Designer/src/NewGrouperSlotDialog.cpp | 10 +-
.../src/support/OutputDirectoryWidget.cpp | 1 +
.../U2Designer/src/wizard/WizardController.cpp | 31 +-
.../U2Designer/src/wizard/WizardController.h | 3 +-
src/corelibs/U2Designer/transl/english.ts | 51 +-
src/corelibs/U2Designer/transl/russian.ts | 51 +-
src/corelibs/U2Formats/src/ABIFormat.cpp | 3 +-
src/corelibs/U2Formats/src/ASNFormat.cpp | 7 +-
.../U2Formats/src/AbstractVariationFormat.cpp | 8 +-
src/corelibs/U2Formats/src/BAMUtils.cpp | 2 +-
src/corelibs/U2Formats/src/ClustalWAlnFormat.cpp | 1 -
src/corelibs/U2Formats/src/DifferentialFormat.cpp | 4 +-
src/corelibs/U2Formats/src/DocumentFormatUtils.cpp | 1 -
src/corelibs/U2Formats/src/DocumentFormatUtils.h | 2 +-
.../U2Formats/src/EMBLGenbankAbstractDocument.cpp | 18 +-
.../U2Formats/src/EMBLGenbankAbstractDocument.h | 2 +-
src/corelibs/U2Formats/src/FastaFormat.cpp | 9 +-
src/corelibs/U2Formats/src/FastqFormat.cpp | 14 +-
src/corelibs/U2Formats/src/FpkmTrackingFormat.cpp | 5 +-
src/corelibs/U2Formats/src/GFFFormat.cpp | 16 +-
src/corelibs/U2Formats/src/GFFFormat.h | 2 +
src/corelibs/U2Formats/src/GTFFormat.cpp | 5 +-
.../U2Formats/src/GenbankPlainTextFormat.cpp | 2 +-
src/corelibs/U2Formats/src/MSFFormat.cpp | 11 +-
src/corelibs/U2Formats/src/MegaFormat.cpp | 1 -
src/corelibs/U2Formats/src/PDBFormat.cpp | 82 +-
src/corelibs/U2Formats/src/PDBFormat.h | 4 +
src/corelibs/U2Formats/src/PDWFormat.cpp | 2 -
src/corelibs/U2Formats/src/PhylipFormat.cpp | 1 -
.../U2Formats/src/RawDNASequenceFormat.cpp | 5 +-
src/corelibs/U2Formats/src/SAMFormat.h | 1 -
src/corelibs/U2Formats/src/SCFFormat.cpp | 9 +-
.../U2Formats/src/SwissProtPlainTextFormat.cpp | 3 +-
.../U2Formats/src/VectorNtiSequenceFormat.cpp | 8 +-
src/corelibs/U2Formats/src/ace/AceFormat.cpp | 13 +-
src/corelibs/U2Formats/src/ace/AceImportUtils.cpp | 15 +-
src/corelibs/U2Formats/src/ace/AceImportUtils.h | 1 -
.../U2Formats/src/mysql_dbi/MysqlMsaDbi.cpp | 14 +
src/corelibs/U2Formats/src/mysql_dbi/MysqlMsaDbi.h | 9 +-
.../U2Formats/src/sqlite_dbi/SQLiteFeatureDbi.cpp | 2 +-
.../U2Formats/src/sqlite_dbi/SQLiteMsaDbi.cpp | 15 +
.../U2Formats/src/sqlite_dbi/SQLiteMsaDbi.h | 10 +-
src/corelibs/U2Formats/transl/english.ts | 321 +--
src/corelibs/U2Formats/transl/russian.ts | 323 +--
src/corelibs/U2Gui/U2Gui.qrc | 1 +
src/corelibs/U2Gui/images/notch.png | Bin 227 -> 296 bytes
src/{ugeneui => corelibs/U2Gui}/images/paste.png | Bin
src/corelibs/U2Gui/images/ruler_coverage.png | Bin 333 -> 376 bytes
src/corelibs/U2Gui/images/set_reference.png | Bin 5141 -> 16147 bytes
src/corelibs/U2Gui/images/tooltip.png | Bin 377 -> 409 bytes
src/corelibs/U2Gui/src/MainWindow.h | 1 +
src/corelibs/U2Gui/src/OpenViewTask.cpp | 89 -
src/corelibs/U2Gui/src/OpenViewTask.h | 22 -
src/corelibs/U2Gui/src/ToolsMenu.cpp | 3 +
src/corelibs/U2Gui/src/ToolsMenu.h | 3 +-
.../U2Gui/src/options_panel/GroupOptionsWidget.cpp | 7 +-
.../U2Gui/src/util/AddNewDocumentDialogImpl.cpp | 2 +-
.../U2Gui/src/util/AuthenticationDialog.cpp | 2 +-
.../src/util/BreakpointConditionEditDialog.cpp | 2 +-
.../U2Gui/src/util/CreateAnnotationDialog.cpp | 2 +-
.../CreateDocumentFromTextDialogController.cpp | 2 +-
.../U2Gui/src/util/DownloadRemoteFileDialog.cpp | 99 +-
.../U2Gui/src/util/DownloadRemoteFileDialog.h | 1 -
.../U2Gui/src/util/EditQualifierDialog.cpp | 2 +-
.../src/util/EditSequenceDialogController.cpp | 2 +-
.../U2Gui/src/util/ExportAnnotationsDialog.cpp | 2 +-
.../src/util/ExportDocumentDialogController.cpp | 4 +-
src/corelibs/U2Gui/src/util/ExportImageDialog.cpp | 16 +-
src/corelibs/U2Gui/src/util/GUIUtils.cpp | 10 -
src/corelibs/U2Gui/src/util/GUIUtils.h | 1 -
.../src/util/ImportDialogs/AceImportDialog.cpp | 2 +-
.../U2Gui/src/util/ObjectViewTreeController.cpp | 8 +-
src/corelibs/U2Gui/src/util/RangeSelector.cpp | 2 +-
.../RemovePartFromSequenceDialogController.cpp | 2 +-
src/corelibs/U2Gui/src/util/ScriptEditorDialog.cpp | 2 +-
.../util/SearchGenbankSequenceDialogController.cpp | 2 +-
.../src/util/project/ProjectTreeController.cpp | 16 +-
.../U2Gui/src/util/project/ProjectTreeController.h | 1 +
.../U2Gui/src/util/project/ProjectUtils.cpp | 25 +
src/corelibs/U2Gui/src/util/project/ProjectUtils.h | 6 +
.../src/util/project/ProjectViewFilterModel.cpp | 2 +-
.../util/shared_db/CommonImportOptionsDialog.cpp | 2 +-
.../src/util/shared_db/EditConnectionDialog.cpp | 2 +-
.../src/util/shared_db/ImportToDatabaseDialog.cpp | 2 +-
.../src/util/shared_db/ItemToImportEditDialog.cpp | 2 +-
.../src/util/shared_db/SharedConnectionsDialog.cpp | 4 +-
.../U2Gui/src/util/ui/DownloadRemoteFileDialog.ui | 53 +-
.../U2Gui/src/util/ui/ExportImageDialog.ui | 7 +-
src/corelibs/U2Gui/transl/english.ts | 106 +-
src/corelibs/U2Gui/transl/russian.ts | 106 +-
.../U2Lang/src/library/BaseActorCategories.cpp | 4 +-
.../U2Lang/src/support/WorkflowRunTask.cpp | 3 +-
src/corelibs/U2Lang/src/support/WorkflowUtils.cpp | 6 +-
.../U2Lang/src/support/serialize/Utils.cpp | 2 +-
src/corelibs/U2Lang/transl/english.ts | 16 +-
src/corelibs/U2Lang/transl/russian.ts | 32 +-
src/corelibs/U2Private/src/AppContextImpl.h | 5 -
.../src/crash_handler/CrashHandlerPrivateWin.h | 1 +
src/corelibs/U2Private/transl/english.ts | 38 +-
src/corelibs/U2Private/transl/russian.ts | 38 +-
.../U2Remote/src/RemoteMachineMonitorDialogImpl.h | 2 +-
src/corelibs/U2Script/src/UgeneContextWrapper.cpp | 7 -
src/corelibs/U2Script/src/UgeneContextWrapper.h | 2 -
src/corelibs/U2Script/transl/english.ts | 2 +-
src/corelibs/U2Script/transl/russian.ts | 2 +-
src/corelibs/U2Test/U2Test.pri | 9 +-
src/corelibs/U2Test/U2Test.pro | 23 +-
src/corelibs/U2Test/src/gui_tests/GUITestBase.cpp | 31 +-
src/corelibs/U2Test/src/gui_tests/GUITestBase.h | 43 +-
.../U2Test/src/gui_tests/GUITestLauncher.cpp | 41 +-
.../U2Test/src/gui_tests/GUITestLauncher.h | 5 +-
.../U2Test/src/gui_tests/GUITestService.cpp | 168 +-
src/corelibs/U2Test/src/gui_tests/GUITestService.h | 64 +-
.../U2Test/src/gui_tests/GUITestThread.cpp | 221 ++
.../U2Test/src/gui_tests/GUITestThread.h} | 40 +-
.../U2Test/src/gui_tests/GUITestWindow.cpp | 14 +-
src/corelibs/U2Test/transl/english.ts | 40 +-
src/corelibs/U2Test/transl/russian.ts | 40 +-
src/corelibs/U2View/U2View.pro | 31 +-
src/corelibs/U2View/src/UndoRedoFramework.cpp | 8 +-
.../U2View/src/ov_assembly/AssemblyBrowser.cpp | 57 +-
.../U2View/src/ov_assembly/AssemblyBrowser.h | 1 +
.../src/ov_assembly/AssemblyBrowserTasks.cpp | 19 +-
.../U2View/src/ov_assembly/AssemblyInfoWidget.cpp | 2 +-
.../src/ov_assembly/AssemblyNavigationWidget.cpp | 2 +-
.../src/ov_assembly/AssemblySettingsWidget.cpp | 2 +-
.../src/ov_assembly/ExportConsensusDialog.cpp | 2 +-
.../ExportConsensusVariationsDialog.cpp | 2 +-
.../src/ov_assembly/ExportCoverageDialog.cpp | 2 +-
.../U2View/src/ov_assembly/ExportReadsDialog.cpp | 2 +-
.../AlignSequencesToAlignmentTask.cpp | 651 +++---
.../AlignSequencesToAlignmentTask.h | 4 +
.../Clipboard/SubalignmentToClipboardTask.cpp | 2 +-
.../src/ov_msa/ColorSchemaDialogController.cpp | 4 +-
.../src/ov_msa/ColorSchemaSettingsController.cpp | 2 +-
.../ov_msa/CreateSubalignmentDialogController.cpp | 2 +-
.../U2View/src/ov_msa/DeleteGapsDialog.cpp | 2 +-
.../src/ov_msa/Export/MSAImageExportTask.cpp | 20 +-
.../MSAExportConsensusTabFactory.cpp | 2 +-
.../ov_msa/ExportHighlightedDialogController.cpp | 2 +-
.../src/ov_msa/General/MSAGeneralTabFactory.cpp | 2 +-
.../src/ov_msa/Highlighting/MSAHighlightingTab.cpp | 9 +-
.../Highlighting/MSAHighlightingTabFactory.cpp | 2 +-
src/corelibs/U2View/src/ov_msa/MSAEditor.cpp | 8 +-
src/corelibs/U2View/src/ov_msa/MSAEditor.h | 15 +-
.../U2View/src/ov_msa/MSAEditorDataList.cpp | 514 -----
src/corelibs/U2View/src/ov_msa/MSAEditorDataList.h | 277 ---
.../U2View/src/ov_msa/MSAEditorNameList.cpp | 7 +-
.../U2View/src/ov_msa/MSAEditorSequenceArea.cpp | 205 +-
.../U2View/src/ov_msa/MSAEditorSequenceArea.h | 32 +-
src/corelibs/U2View/src/ov_msa/MSAEditorTasks.cpp | 2 +-
.../src/ov_msa/MSASelectSubalignmentDialog.cpp | 2 +-
.../src/ov_msa/MsaEditorSimilarityColumn.cpp | 281 +++
.../U2View/src/ov_msa/MsaEditorSimilarityColumn.h | 149 ++
.../U2View/src/ov_msa/MsaUpdatedWidgetInterface.h | 60 +
.../src/ov_msa/Overview/MSAGraphOverview.cpp | 39 +-
.../U2View/src/ov_msa/Overview/MSAGraphOverview.h | 1 +
.../src/ov_msa/Overview/MSASimpleOverview.cpp | 40 +-
.../U2View/src/ov_msa/Overview/MSASimpleOverview.h | 4 +
.../src/ov_msa/PairAlign/PairAlignFactory.cpp | 2 +-
.../ov_msa/PhyTrees/MSAEditorMultiTreeViewer.cpp | 12 +-
.../src/ov_msa/PhyTrees/MSAEditorMultiTreeViewer.h | 8 +-
.../src/ov_msa/PhyTrees/MSAEditorTreeManager.cpp | 2 +-
.../src/ov_msa/PhyTrees/MSAEditorTreeViewer.cpp | 108 +-
.../src/ov_msa/PhyTrees/MSAEditorTreeViewer.h | 6 +-
.../src/ov_msa/PhyTrees/MsaEditorTreeTabArea.cpp | 161 ++
.../src/ov_msa/PhyTrees/MsaEditorTreeTabArea.h | 94 +
...SaveSelectedSequenceFromMSADialogController.cpp | 2 +-
.../ov_msa/SeqStatistics/SeqStatisticsWidget.cpp | 4 +-
.../SeqStatistics/SeqStatisticsWidgetFactory.cpp | 2 +-
.../src/ov_msa/TreeOptions/TreeOptionsWidget.cpp | 3 +-
.../TreeOptions/TreeOptionsWidgetFactory.cpp | 6 +-
.../U2View/src/ov_sequence/ADVGraphModel.cpp | 210 +-
.../U2View/src/ov_sequence/ADVGraphModel.h | 36 +-
.../src/ov_sequence/ADVSequenceObjectContext.cpp | 7 +-
.../U2View/src/ov_sequence/AnnotatedDNAView.h | 2 +
.../src/ov_sequence/AnnotatedDNAViewFactory.cpp | 22 +-
.../ov_sequence/CreateRulerDialogController.cpp | 2 +-
.../ov_sequence/Das/DasOptionsPanelSavableTab.cpp | 145 --
.../ov_sequence/Das/DasOptionsPanelSavableTab.h | 43 -
.../src/ov_sequence/Das/DasOptionsPanelWidget.cpp | 635 ------
.../src/ov_sequence/Das/DasOptionsPanelWidget.h | 131 --
.../src/ov_sequence/Das/DasWidgetFactory.cpp | 83 -
.../ov_sequence/Das/ui/DasBlastSettingsWidget.ui | 190 --
.../ov_sequence/Das/ui/DasOptionsPanelWidget.ui | 395 ----
src/corelibs/U2View/src/ov_sequence/DetView.cpp | 1028 ++++-----
src/corelibs/U2View/src/ov_sequence/DetView.h | 101 +-
.../ov_sequence/EditAnnotationDialogController.cpp | 2 +-
.../U2View/src/ov_sequence/GSequenceLineView.cpp | 16 +-
.../U2View/src/ov_sequence/GSequenceLineView.h | 5 +-
.../src/ov_sequence/GSequenceLineViewAnnotated.cpp | 325 +--
.../src/ov_sequence/GSequenceLineViewAnnotated.h | 48 +-
.../src/ov_sequence/GraphLabelsSelectDialog.cpp | 2 +-
.../U2View/src/ov_sequence/GraphSettingsDialog.cpp | 3 +-
src/corelibs/U2View/src/ov_sequence/Overview.cpp | 25 +-
src/corelibs/U2View/src/ov_sequence/PanView.cpp | 674 +-----
src/corelibs/U2View/src/ov_sequence/PanView.h | 100 +-
.../SaveGraphCutoffsDialogController.cpp | 2 +-
.../src/ov_sequence/SearchQualifierDialog.cpp | 2 +-
.../annot_highlight/AnnotHighlightTree.cpp | 6 +-
.../AnnotHighlightWidgetFactory.cpp | 2 +-
.../find_pattern/FindPatternWidgetFactory.cpp | 2 +-
.../ov_sequence/find_pattern/ui/FindPatternForm.ui | 59 +-
.../ov_sequence/image_export/SequencePainter.cpp | 31 +-
.../src/ov_sequence/image_export/SequencePainter.h | 15 +-
.../sequence_info/SequenceInfoFactory.cpp | 2 +-
.../view_rendering/DetViewMultiLineRenderer.cpp | 199 ++
.../view_rendering/DetViewMultiLineRenderer.h | 72 +
.../view_rendering/DetViewRenderer.cpp} | 39 +-
.../ov_sequence/view_rendering/DetViewRenderer.h | 68 +
.../view_rendering/DetViewSingleLineRenderer.cpp | 636 ++++++
.../view_rendering/DetViewSingleLineRenderer.h | 135 ++
.../ov_sequence/view_rendering/PanViewRenderer.cpp | 426 ++++
.../ov_sequence/view_rendering/PanViewRenderer.h | 88 +
.../SequenceViewAnnotatedRenderer.cpp | 366 +++
.../view_rendering/SequenceViewAnnotatedRenderer.h | 132 ++
.../view_rendering/SequenceViewRenderer.cpp | 76 +
.../view_rendering/SequenceViewRenderer.h | 80 +
.../U2View/src/phyltree/BranchSettingsDialog.cpp | 2 +-
.../src/phyltree/CreatePhyTreeDialogController.cpp | 6 +-
.../U2View/src/phyltree/TextSettingsDialog.cpp | 2 +-
.../U2View/src/phyltree/TreeSettingsDialog.cpp | 2 +-
.../src/util_dna_assembly/BuildIndexDialog.cpp | 12 +-
.../ConvertAssemblyToSamDialog.cpp | 2 +-
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.../util_sec_struct_predict/SecStructDialog.cpp | 2 +-
.../util_smith_waterman/SmithWatermanDialog.cpp | 2 +-
src/corelibs/U2View/transl/english.ts | 769 ++++---
src/corelibs/U2View/transl/russian.ts | 768 ++++---
src/include/U2Core/DASSource.h | 1 -
src/include/U2Core/LoadDASDocumentTask.h | 1 -
src/include/U2Core/PicrApiTask.h | 1 -
src/include/U2Core/TaskWatchdog.h | 1 +
src/include/U2Core/UniprotBlastTask.h | 1 -
src/include/U2Test/CustomScenario.h | 1 +
src/include/U2Test/GUITestThread.h | 1 +
src/include/U2Test/MainThreadRunnable.h | 1 +
src/include/U2View/DasWidgetFactory.h | 1 -
src/include/U2View/MSAEditorDataList.h | 1 -
src/include/U2View/MSASimpleOverview.h | 1 +
src/include/U2View/MsaEditorSimilarityColumn.h | 1 +
src/libs_3rdparty/humimit/Doxyfile | 2384 ++++++++++++++++++++
src/libs_3rdparty/humimit/humimit.pri | 69 +
src/libs_3rdparty/humimit/humimit.pro | 110 +
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src/libs_3rdparty/humimit/src/core/global.h | 14 +
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.../ugeneui/SelectDocumentFormatDialogFiller.cpp | 11 +-
.../ugeneui/SelectDocumentFormatDialogFiller.h | 5 +-
.../SequenceReadingModeSelectorDialogFiller.cpp | 13 +-
.../SequenceReadingModeSelectorDialogFiller.h | 8 +-
.../GUITestBase/src/test_runner/GUITestRunner.cpp | 177 ++
.../GUITestBase/src/test_runner/GUITestRunner.h} | 36 +-
.../GUITestBase/src/test_runner/GUITestRunner.ui | 111 +
.../GUITestBase/src/tests/GUIInitialChecks.cpp | 225 +-
.../GUITestBase/src/tests/GUIInitialChecks.h | 42 +-
.../Assembly_browser/GTTestsAssemblyBrowser.cpp | 161 +-
.../Assembly_browser/GTTestsAssemblyBrowser.h | 10 +-
.../Assembling/bowtie2/GTTestsBowtie2.cpp | 26 +-
.../Assembling/bowtie2/GTTestsBowtie2.h | 6 +-
.../Assembling/dna_assembly/GTTestsDnaAssembly.cpp | 19 +-
.../Assembling/dna_assembly/GTTestsDnaAssembly.h | 6 +-
.../Assembling/dna_assembly/GTTestsIndexReuse.cpp | 89 +-
.../Assembling/dna_assembly/GTTestsIndexReuse.h | 6 +-
.../conversions/GTTestsDnaAssemblyConversions.cpp | 31 +-
.../conversions/GTTestsDnaAssemblyConversions.h | 7 +-
.../common_scenarios/Assembling/sam/GTTestsSAM.cpp | 15 +-
.../common_scenarios/Assembling/sam/GTTestsSAM.h | 6 +-
.../NIAID_pipelines/GTTestsNiaidPipelines.cpp | 37 +-
.../NIAID_pipelines/GTTestsNiaidPipelines.h | 6 +-
.../Query_Designer/GTTestsQuerryDesigner.cpp | 26 +-
.../Query_Designer/GTTestsQuerryDesigner.h | 6 +-
.../annotations/GTTestsAnnotations.cpp | 114 +-
.../annotations/GTTestsAnnotations.h | 6 +-
.../annotations/GTTestsCreateAnnotationWidget.cpp | 193 +-
.../annotations/GTTestsCreateAnnotationWidget.h | 6 +-
.../annotations/edit/GTTestsAnnotationsEdit.cpp | 40 +-
.../annotations/edit/GTTestsAnnotationsEdit.h | 6 +-
.../qualifiers/GTTestsAnnotationsQualifiers.cpp | 41 +-
.../qualifiers/GTTestsAnnotationsQualifiers.h | 6 +-
.../GTTestsAnnotationsImport.cpp | 55 +-
.../annotations_import/GTTestsAnnotationsImport.h | 6 +-
.../circular_view/GTTestsCvGeneral.h | 6 +-
.../common_scenarios/cloning/GTTestsCloning.cpp | 15 +-
.../common_scenarios/cloning/GTTestsCloning.h | 6 +-
.../document_from_text/GTTestsDocumentFromText.cpp | 133 +-
.../document_from_text/GTTestsDocumentFromText.h | 6 +-
.../common_scenarios/dp_view/GTTestsDpView.cpp | 77 +-
.../tests/common_scenarios/dp_view/GTTestsDpView.h | 8 +-
.../msa_editor/GTTestsMsaEditor.cpp | 394 +++-
.../common_scenarios/msa_editor/GTTestsMsaEditor.h | 6 +-
.../msa_editor/align/GTTestsAlignSequenceToMsa.cpp | 51 +-
.../msa_editor/align/GTTestsAlignSequenceToMsa.h | 6 +-
.../msa_editor/colors/GTTestsMSAEditorColors.cpp | 36 +-
.../msa_editor/colors/GTTestsMSAEditorColors.h | 8 +-
.../consensus/GTTestsMSAEditorConsensus.cpp | 47 +-
.../consensus/GTTestsMSAEditorConsensus.h | 6 +-
.../msa_editor/edit/GTTestsMSAEditorEdit.cpp | 236 +-
.../msa_editor/edit/GTTestsMSAEditorEdit.h | 6 +-
.../overview/GTTestsMSAEditorOverview.cpp | 156 +-
.../msa_editor/overview/GTTestsMSAEditorOverview.h | 9 +-
.../GTTestsMSAEditorReplaceCharacter.cpp | 564 +++++
.../GTTestsMSAEditorReplaceCharacter.h} | 114 +-
.../options_panel/GTTestsOptionPanel.cpp | 188 +-
.../options_panel/GTTestsOptionPanel.h | 35 +-
.../options_panel/msa/GTTestsOptionPanelMSA.cpp | 149 +-
.../options_panel/msa/GTTestsOptionPanelMSA.h | 4 +-
.../GTTestsOptionPanelSequenceView.cpp | 108 +-
.../sequence_view/GTTestsOptionPanelSequenceView.h | 5 +-
.../common_scenarios/pcr/GTTestsInSilicoPcr.cpp | 29 +-
.../common_scenarios/pcr/GTTestsInSilicoPcr.h | 4 +-
.../common_scenarios/pcr/GTTestsPrimerLibrary.cpp | 29 +-
.../common_scenarios/pcr/GTTestsPrimerLibrary.h | 4 +-
.../common_scenarios/project/GTTestsProject.cpp | 79 +-
.../common_scenarios/project/GTTestsProject.h | 6 +-
.../GTTestsProjectAnonymousProject.cpp | 29 +-
.../GTTestsProjectAnonymousProject.h | 6 +-
.../project/bookmarks/GTTestsBookmarks.cpp | 31 +-
.../project/bookmarks/GTTestsBookmarks.h | 6 +-
.../GTTestsProjectDocumentModifying.cpp | 32 +-
.../GTTestsProjectDocumentModifying.h | 6 +-
.../multiple_docs/GTTestsProjectMultipleDocs.cpp | 17 +-
.../multiple_docs/GTTestsProjectMultipleDocs.h | 6 +-
.../project_filtering/GTTestsProjectFiltering.cpp | 46 +-
.../project_filtering/GTTestsProjectFiltering.h | 6 +-
.../project/relations/GTTestsProjectRelations.cpp | 8 +-
.../project/relations/GTTestsProjectRelations.h | 6 +-
.../remote_request/GTTestsProjectRemoteRequest.cpp | 36 +-
.../remote_request/GTTestsProjectRemoteRequest.h | 6 +-
.../GTTestsProjectSequenceExporting.cpp | 49 +-
.../GTTestsProjectSequenceExporting.h | 6 +-
.../from_project_view/GTTestsFromProjectView.cpp | 52 +-
.../from_project_view/GTTestsFromProjectView.h | 6 +-
.../user_locking/GTTestsProjectUserLocking.cpp | 33 +-
.../user_locking/GTTestsProjectUserLocking.h | 6 +-
.../repeat_finder/GTTestsRepeatFinder.cpp | 19 +-
.../repeat_finder/GTTestsRepeatFinder.h | 6 +-
.../sequence_edit/GTTestsSequenceEdit.cpp | 117 +-
.../sequence_edit/GTTestsSequenceEdit.h | 6 +-
.../sequence_view/GTTestsSequenceView.cpp | 553 ++++-
.../sequence_view/GTTestsSequenceView.h | 21 +-
.../shared_database/GTTestsSharedDatabase.cpp | 296 ++-
.../shared_database/GTTestsSharedDatabase.h | 4 +-
.../smith_waterman_dialog/GTTestsSWDialog.cpp | 23 +-
.../smith_waterman_dialog/GTTestsSWDialog.h | 6 +-
.../start_page/GTTestsStartPage.cpp | 30 +-
.../common_scenarios/start_page/GTTestsStartPage.h | 6 +-
.../toggle_view/GTTestsToggleView.cpp | 23 +-
.../toggle_view/GTTestsToggleView.h | 6 +-
.../GTTestsCommonScenariousTreeviewer.cpp | 94 +-
.../GTTestsCommonScenariousTreeviewer.h | 6 +-
.../common_scenarios/undo_redo/GTTestsUndoRedo.cpp | 62 +-
.../common_scenarios/undo_redo/GTTestsUndoRedo.h | 6 +-
.../workflow_designer/GTTestsWorkflowDesigner.cpp | 78 +-
.../workflow_designer/GTTestsWorkflowDesigner.h | 6 +-
.../estimating/GTTestsWorkflowEstimating.cpp | 13 +-
.../estimating/GTTestsWorkflowEstimating.h | 6 +-
.../name_filter/GTTestsWorkflowNameFilter.cpp | 33 +-
.../name_filter/GTTestsWorkflowNameFilter.h | 6 +-
.../GTTestsWorkflowParemeterValidation.cpp | 22 +-
.../GTTestsWorkflowParemeterValidation.h | 6 +-
.../scripting/GTTestsWorkflowScripting.cpp | 51 +-
.../scripting/GTTestsWorkflowScripting.h | 6 +-
.../shared_db/GTTestsSharedDbWd.cpp | 61 +-
.../shared_db/GTTestsSharedDbWd.h | 4 +-
.../src/tests/crazy_user/GTAbstractGUIAction.h | 5 +-
.../tests/crazy_user/GTRandomGUIActionFactory.cpp | 7 +-
.../src/tests/crazy_user/GUICrazyUserTest.cpp | 7 +-
.../src/tests/crazy_user/GUICrazyUserTest.h | 10 +-
.../GTTestsRegressionScenarios_1001_2000.cpp | 862 +++----
.../GTTestsRegressionScenarios_1001_2000.h | 11 +-
.../GTTestsRegressionScenarios_1_1000.cpp | 507 +++--
.../GTTestsRegressionScenarios_1_1000.h | 8 +-
.../GTTestsRegressionScenarios_2001_3000.cpp | 1092 ++++-----
.../GTTestsRegressionScenarios_2001_3000.h | 18 +-
.../GTTestsRegressionScenarios_3001_4000.cpp | 600 +++--
.../GTTestsRegressionScenarios_3001_4000.h | 13 +-
.../GTTestsRegressionScenarios_4001_5000.cpp | 1342 ++++++++++-
.../GTTestsRegressionScenarios_4001_5000.h | 55 +-
.../annotator/src/CollocationsDialogController.cpp | 2 +-
.../annotator/src/CustomAutoAnnotationDialog.cpp | 2 +-
.../src/BioStruct3DSubsetEditor.cpp | 9 +-
.../biostruct3d_view/src/SelectModelsDialog.cpp | 2 +-
.../biostruct3d_view/src/SettingsDialog.cpp | 2 +-
.../src/StructuralAlignmentDialog.cpp | 2 +-
src/plugins/chroma_view/transl/english.ts | 2 +-
src/plugins/chroma_view/transl/russian.ts | 2 +-
src/plugins/circular_view/src/CircularView.h | 1 -
.../src/CircularViewSettingsWidgetFactory.cpp | 2 +-
src/plugins/circular_view/transl/english.ts | 10 +-
src/plugins/circular_view/transl/russian.ts | 10 +-
src/plugins/dbi_bam/src/ConvertToSQLiteDialog.cpp | 2 +-
src/plugins/dbi_bam/src/SamReader.cpp | 8 +-
src/plugins/dbi_bam/src/SamReader.h | 2 +-
.../src/CSVColumnConfigurationDialog.cpp | 2 +-
.../dna_export/src/DNASequenceGeneratorDialog.cpp | 4 +-
.../dna_export/src/ExportBlastResultDialog.cpp | 2 +-
.../dna_export/src/ExportChromatogramDialog.cpp | 2 +-
src/plugins/dna_export/src/ExportMSA2MSADialog.cpp | 2 +-
.../dna_export/src/ExportMSA2SequencesDialog.cpp | 2 +-
.../dna_export/src/ExportSequences2MSADialog.cpp | 2 +-
.../dna_export/src/ExportSequencesDialog.cpp | 2 +-
.../dna_export/src/GetSequenceByIdDialog.cpp | 2 +-
.../src/ImportAnnotationsFromCSVDialog.cpp | 2 +-
src/plugins/dna_export/transl/russian.ts | 2 +-
src/plugins/dna_flexibility/src/DNAFlexDialog.cpp | 2 +-
.../dna_stat/src/DNAStatMSAProfileDialog.cpp | 2 +-
src/plugins/dna_stat/src/DNAStatPlugin.cpp | 54 -
src/plugins/dna_stat/src/DNAStatPlugin.h | 12 -
.../src/DistanceMatrixMSAProfileDialog.cpp | 2 +-
src/plugins/dotplot/src/DotPlotDialog.cpp | 2 +-
src/plugins/dotplot/src/DotPlotFilesDialog.cpp | 2 +-
src/plugins/dotplot/src/DotPlotFilterDialog.cpp | 2 +-
src/plugins/dotplot/transl/english.ts | 4 +-
src/plugins/dotplot/transl/russian.ts | 6 +-
.../enzymes/src/ConstructMoleculeDialog.cpp | 2 +-
src/plugins/enzymes/src/CreateFragmentDialog.cpp | 4 +-
src/plugins/enzymes/src/DigestSequenceDialog.cpp | 2 +-
src/plugins/enzymes/src/EditFragmentDialog.cpp | 2 +-
src/plugins/enzymes/src/EnzymesIO.cpp | 10 +-
src/plugins/enzymes/src/EnzymesQuery.cpp | 2 +-
src/plugins/enzymes/src/FindEnzymesDialog.cpp | 2 +-
src/plugins/enzymes/src/FindEnzymesTask.h | 1 -
.../src/ExpertDiscoveryAdvSetDialog.cpp | 2 +-
.../src/ExpertDiscoveryControlDialog.cpp | 2 +-
.../src/ExpertDiscoveryControlMrkDialog.cpp | 2 +-
.../src/ExpertDiscoveryPosNegDialog.cpp | 2 +-
.../src/ExpertDiscoveryPosNegMrkDialog.cpp | 2 +-
.../src/ExpertDiscoverySearchDialogController.cpp | 2 +-
.../src/ExpertDiscoverySetupRecBoundDialog.cpp | 2 +-
.../external_tool_support.pro | 6 +
.../src/ExternalToolSupportSettingsController.cpp | 2 +-
.../src/bedtools/BedToolsWorkersLibrary.cpp | 2 +-
.../src/blast/BlastAllSupport.cpp | 1 +
.../src/blast/BlastAllSupportRunDialog.cpp | 1 +
.../src/blast/BlastAllSupportTask.cpp | 9 +-
.../src/blast/FormatDBSupportRunDialog.cpp | 2 +-
.../src/blast_plus/BlastDBCmdDialog.cpp | 2 +-
.../src/blast_plus/BlastPlusSupport.cpp | 1 +
.../src/blast_plus/BlastPlusSupportCommonTask.cpp | 8 +-
.../src/blast_plus/BlastPlusSupportRunDialog.cpp | 1 +
.../src/cap3/CAP3SupportDialog.cpp | 2 +-
.../src/clustalo/ClustalOSupportRunDialog.cpp | 4 +-
.../src/clustalw/ClustalWSupportRunDialog.cpp | 4 +-
.../src/conduct_go/ConductGOSettings.cpp | 4 +-
.../src/conduct_go/ConductGOSettings.h | 7 +-
.../src/conduct_go/ConductGOTask.cpp | 83 +-
.../src/conduct_go/ConductGOTask.h | 18 +-
.../src/conduct_go/ConductGOWorker.cpp | 16 +-
.../src/conduct_go/ConductGOWorker.h | 2 +-
.../conservation_plot/ConservationPlotSettings.cpp | 6 +-
.../src/conservation_plot/ConservationPlotTask.cpp | 2 +-
.../conservation_plot/ConservationPlotWorker.cpp | 2 +-
.../external_tool_support/src/java/JavaSupport.cpp | 9 +-
.../src/macs/MACSSettings.cpp | 4 +-
.../external_tool_support/src/macs/MACSTask.cpp | 2 +-
.../src/mafft/MAFFTSupportRunDialog.cpp | 4 +-
.../src/peak2gene/Gene2PeakFormatLoader.cpp | 140 ++
.../src/peak2gene/Gene2PeakFormatLoader.h | 71 +
.../src/peak2gene/Peak2GeneFormatLoader.cpp | 151 ++
.../src/peak2gene/Peak2GeneFormatLoader.h | 73 +
.../src/peak2gene/Peak2GeneSettings.cpp | 6 +-
.../src/peak2gene/Peak2GeneSettings.h | 5 -
.../src/peak2gene/Peak2GeneTask.cpp | 105 +-
.../src/peak2gene/Peak2GeneTask.h | 22 +-
.../src/peak2gene/Peak2GeneWorker.cpp | 35 +-
.../src/peak2gene/TabulatedFormatReader.cpp | 94 +
.../src/peak2gene/TabulatedFormatReader.h} | 45 +-
.../src/seqpos/SeqPosTask.cpp | 2 +-
.../src/seqpos/SeqPosWorker.cpp | 2 +-
.../src/snpeff/SnpEffSupport.cpp | 10 +-
.../src/snpeff/SnpEffSupport.h | 3 +-
.../src/snpeff/SnpEffWorker.cpp | 2 +-
.../src/tcoffee/TCoffeeSupportRunDialog.cpp | 4 +-
.../src/utils/BlastDBSelectorWidgetController.cpp | 2 -
.../src/utils/BlastRunCommonDialog.cpp | 2 +-
.../src/utils/BlastTaskSettings.cpp | 1 +
.../src/utils/BlastTaskSettings.h | 2 +
.../src/vcftools/VcfConsensusWorker.cpp | 2 +-
.../external_tool_support/transl/english.ts | 150 +-
.../external_tool_support/transl/russian.ts | 194 +-
.../src/GenomeAlignerSearchQuery.cpp | 10 +-
.../src/GenomeAlignerSettingsController.cpp | 2 +-
src/plugins/genome_aligner/transl/russian.ts | 2 +-
.../opencl_support/src/OpenCLSupportPlugin.cpp | 11 +-
.../opencl_support/src/OpenCLSupportPlugin.h | 2 +
.../src/OpenCLSupportSettingsController.cpp | 2 +-
src/plugins/orf_marker/src/ORFDialog.cpp | 2 +-
src/plugins/pcr/html/report.html | 13 +
src/plugins/pcr/src/EditPrimerDialog.cpp | 2 +-
src/plugins/pcr/src/InSilicoPcrOPWidgetFactory.cpp | 2 +-
src/plugins/pcr/src/InSilicoPcrWorker.cpp | 6 +-
src/plugins/pcr/src/PrimerLibrarySelector.cpp | 2 +-
src/plugins/pcr/src/PrimerLibraryWidget.cpp | 2 +-
src/plugins/pcr/src/PrimersDetailsDialog.cpp | 2 +-
src/plugins/pcr/src/PrimersGrouperWorker.cpp | 10 +-
src/plugins/pcr/src/PrimersGrouperWorker.h | 2 +-
src/plugins/pcr/src/export/ExportPrimersDialog.cpp | 2 +-
src/plugins/pcr/src/import/ImportPrimersDialog.cpp | 2 +-
src/plugins/pcr/transl/english.ts | 2 +-
src/plugins/pcr/transl/russian.ts | 8 +-
src/plugins/query_designer/src/QDRunDialog.cpp | 10 +-
.../query_designer/src/QueryViewController.cpp | 2 +-
.../src/library/QDGcContentActor.cpp | 2 +-
src/plugins/query_designer/transl/english.ts | 20 +-
src/plugins/query_designer/transl/russian.ts | 22 +-
src/plugins/remote_blast/src/HttpRequestBLAST.cpp | 10 +-
src/plugins/remote_blast/src/RemoteBLASTConsts.cpp | 2 +-
.../remote_blast/src/SendSelectionDialog.cpp | 10 +-
.../remote_service/src/RemoteTasksDialog.cpp | 2 +-
.../repeat_finder/src/FindRepeatsDialog.cpp | 2 +-
.../repeat_finder/src/FindTandemsDialog.cpp | 2 +-
.../src/SmithWatermanAlgorithmOPENCL.cpp | 167 +-
.../weight_matrix/src/PWMBuildDialogController.cpp | 2 +-
.../src/PWMJASPARDialogController.cpp | 2 +-
.../src/PWMSearchDialogController.cpp | 2 +-
.../src/SetParametersDialogController.cpp | 2 +-
.../src/ViewMatrixDialogController.cpp | 2 +-
src/plugins/weight_matrix/transl/russian.ts | 12 +-
.../workflow_designer/src/CreateScriptWorker.cpp | 2 +-
.../src/DashboardsManagerDialog.cpp | 2 +-
.../workflow_designer/src/ImportSchemaDialog.cpp | 2 +-
.../src/PortAliasesConfigurationDialog.cpp | 2 +-
.../src/SchemaAliasesConfigurationDialogImpl.cpp | 2 +-
.../workflow_designer/src/StartupDialog.cpp | 21 +-
.../src/WorkflowDesignerPlugin.cpp | 2 +-
.../workflow_designer/src/WorkflowMetaDialog.cpp | 2 +-
.../src/WorkflowSettingsController.cpp | 2 +-
.../src/WorkflowViewController.cpp | 2 +-
.../workflow_designer/src/library/CoreLib.cpp | 4 -
.../src/library/DASAnnotationWorker.cpp | 372 ---
.../src/library/DASAnnotationWorker.h | 70 -
.../src/library/DASFetchWorker.cpp | 381 ----
.../workflow_designer/src/library/DASFetchWorker.h | 83 -
.../src/library/MultiplexerWorker.cpp | 2 +-
.../src/library/WriteAnnotationsWorker.cpp | 4 +-
.../src/ui/ExternalProcessWorkerDialog.ui | 12 +-
.../workflow_designer/src/ui/StartupDialog.ui | 12 +-
src/plugins/workflow_designer/transl/english.ts | 131 +-
src/plugins/workflow_designer/transl/russian.ts | 164 +-
.../workflow_designer/workflow_designer.pro | 4 -
src/plugins_3rdparty/hmm2/src/HMMIOWorker.cpp | 4 +-
.../hmm2/src/u_build/HMMBuildDialogController.cpp | 2 +-
.../hmm2/src/u_build/HMMBuildWorker.cpp | 2 +-
.../u_calibrate/HMMCalibrateDialogController.cpp | 2 +-
.../src/u_search/HMMSearchDialogController.cpp | 2 +-
.../hmm2/src/u_search/HMMSearchWorker.cpp | 2 +-
src/plugins_3rdparty/hmm2/transl/english.ts | 24 +-
src/plugins_3rdparty/hmm2/transl/russian.ts | 22 +-
.../hmm3/src/build/uHMM3BuildDialogImpl.cpp | 2 +-
.../hmm3/src/phmmer/uHMM3PhmmerDialogImpl.cpp | 2 +-
.../hmm3/src/search/uHMM3SearchDialogImpl.cpp | 2 +-
src/plugins_3rdparty/hmm3/transl/russian.ts | 14 +-
.../kalign/src/KalignDialogController.cpp | 4 +-
src/plugins_3rdparty/primer3/src/Primer3Dialog.cpp | 2 +-
src/plugins_3rdparty/primer3/src/Primer3Task.cpp | 2 +-
src/plugins_3rdparty/primer3/src/Primer3Task.h | 2 +-
.../primer3/src/Primer3TaskSettings.cpp | 2 +-
.../primer3/src/Primer3TaskSettings.h | 2 +-
.../sitecon/src/SiteconBuildDialogController.cpp | 2 +-
.../sitecon/src/SiteconSearchDialogController.cpp | 2 +-
src/plugins_3rdparty/sitecon/transl/russian.ts | 12 +-
.../umuscle/src/MuscleAlignDialogController.cpp | 4 +-
.../umuscle/src/MuscleParallel.cpp | 28 +-
src/plugins_3rdparty/umuscle/src/MuscleTask.cpp | 23 +-
src/plugins_3rdparty/umuscle/src/MuscleUtils.cpp | 13 +-
.../umuscle/src/MuscleWorkPool.cpp | 3 +-
src/plugins_3rdparty/umuscle/src/muscle/clwwt.cpp | 3 +-
.../umuscle/src/muscle/muscle_context.cpp | 59 +-
.../umuscle/src/muscle/muscle_context.h | 9 +-
src/plugins_3rdparty/umuscle/transl/english.ts | 45 +-
src/plugins_3rdparty/umuscle/transl/russian.ts | 49 +-
.../variants/src/SamtoolMpileupWorker.cpp | 2 +-
src/plugins_3rdparty/variants/transl/english.ts | 21 +-
src/plugins_3rdparty/variants/transl/russian.ts | 23 +-
src/plugins_3rdparty/variants/variants.pro | 2 +
src/ugene_globals.pri | 31 +
src/ugene_version.pri | 4 +-
src/ugenecl/src/Main.cpp | 7 -
src/ugenecl/ugenecl.pri | 6 +-
src/ugenem/src/SendReportDialog.cpp | 1 +
src/ugeneui/html/version_news.html | 17 +-
src/ugeneui/src/Main.cpp | 35 +-
.../DirectoriesSettingsGUIController.cpp | 2 +-
.../FormatSettingsGUIController.cpp | 2 +-
.../logview_settings/LogSettingsGUIController.cpp | 2 +-
.../NetworkSettingsGUIController.cpp | 2 +-
.../ResourceSettingsGUIController.cpp | 2 +-
.../UserApplicationsSettingsGUIController.cpp | 2 +-
src/ugeneui/src/main_window/MainWindowImpl.cpp | 12 +-
.../DocumentFormatSelectorController.cpp | 2 +-
.../DocumentProviderSelectorController.cpp | 2 +-
.../DocumentReadingModeSelectorController.cpp | 2 +-
.../ExportProjectDialogController.cpp | 2 +-
...tipleDocumentsReadingModeSelectorController.cpp | 2 +-
.../src/project_support/ProjectLoaderImpl.cpp | 44 +-
.../src/project_support/ProjectLoaderImpl.h | 2 -
.../src/project_support/ProjectServiceImpl.cpp | 10 +-
.../src/project_support/ProjectServiceImpl.h | 1 +
src/ugeneui/src/project_view/ProjectViewImpl.cpp | 19 +-
.../src/shtirlitz/StatisticalReportController.cpp | 16 +-
.../src/shtirlitz/StatisticalReportController.h | 2 +
src/ugeneui/src/shtirlitz/ui/StatisticalReport.ui | 5 +-
src/ugeneui/src/task_view/TaskViewController.cpp | 5 +-
src/ugeneui/transl/english.ts | 268 +--
src/ugeneui/transl/russian.ts | 268 +--
src/ugeneui/ugeneui.pri | 8 +-
ugene.pro | 418 ++--
1092 files changed, 26727 insertions(+), 23094 deletions(-)
delete mode 100644 data/cmdline/das_annotation.uwl
delete mode 100644 src/corelibs/U2Core/src/datatype/DASSource.cpp
delete mode 100644 src/corelibs/U2Core/src/datatype/DASSource.h
delete mode 100644 src/corelibs/U2Core/src/tasks/LoadDASDocumentTask.cpp
delete mode 100644 src/corelibs/U2Core/src/tasks/LoadDASDocumentTask.h
delete mode 100644 src/corelibs/U2Core/src/tasks/PicrApiTask.cpp
delete mode 100644 src/corelibs/U2Core/src/tasks/PicrApiTask.h
delete mode 100644 src/corelibs/U2Core/src/tasks/UniprotBlastTask.cpp
delete mode 100644 src/corelibs/U2Core/src/tasks/UniprotBlastTask.h
create mode 100644 src/corelibs/U2Core/src/util/TaskWatchdog.cpp
create mode 100644 src/corelibs/U2Core/src/util/TaskWatchdog.h
copy src/{ugeneui => corelibs/U2Gui}/images/paste.png (100%)
create mode 100644 src/corelibs/U2Test/src/gui_tests/GUITestThread.cpp
copy src/{plugins/GUITestBase/src/runnables/ugene/corelibs/U2Gui/ItemToImportEditDialogFiller.h => corelibs/U2Test/src/gui_tests/GUITestThread.h} (50%)
delete mode 100644 src/corelibs/U2View/src/ov_msa/MSAEditorDataList.cpp
delete mode 100644 src/corelibs/U2View/src/ov_msa/MSAEditorDataList.h
create mode 100644 src/corelibs/U2View/src/ov_msa/MsaEditorSimilarityColumn.cpp
create mode 100644 src/corelibs/U2View/src/ov_msa/MsaEditorSimilarityColumn.h
create mode 100644 src/corelibs/U2View/src/ov_msa/MsaUpdatedWidgetInterface.h
create mode 100644 src/corelibs/U2View/src/ov_msa/PhyTrees/MsaEditorTreeTabArea.cpp
create mode 100644 src/corelibs/U2View/src/ov_msa/PhyTrees/MsaEditorTreeTabArea.h
delete mode 100644 src/corelibs/U2View/src/ov_sequence/Das/DasOptionsPanelSavableTab.cpp
delete mode 100644 src/corelibs/U2View/src/ov_sequence/Das/DasOptionsPanelSavableTab.h
delete mode 100644 src/corelibs/U2View/src/ov_sequence/Das/DasOptionsPanelWidget.cpp
delete mode 100644 src/corelibs/U2View/src/ov_sequence/Das/DasOptionsPanelWidget.h
delete mode 100644 src/corelibs/U2View/src/ov_sequence/Das/DasWidgetFactory.cpp
delete mode 100644 src/corelibs/U2View/src/ov_sequence/Das/ui/DasBlastSettingsWidget.ui
delete mode 100644 src/corelibs/U2View/src/ov_sequence/Das/ui/DasOptionsPanelWidget.ui
create mode 100644 src/corelibs/U2View/src/ov_sequence/view_rendering/DetViewMultiLineRenderer.cpp
create mode 100644 src/corelibs/U2View/src/ov_sequence/view_rendering/DetViewMultiLineRenderer.h
copy src/{plugins/GUITestBase/src/GTUtilsEscClicker.cpp => corelibs/U2View/src/ov_sequence/view_rendering/DetViewRenderer.cpp} (52%)
create mode 100644 src/corelibs/U2View/src/ov_sequence/view_rendering/DetViewRenderer.h
create mode 100644 src/corelibs/U2View/src/ov_sequence/view_rendering/DetViewSingleLineRenderer.cpp
create mode 100644 src/corelibs/U2View/src/ov_sequence/view_rendering/DetViewSingleLineRenderer.h
create mode 100644 src/corelibs/U2View/src/ov_sequence/view_rendering/PanViewRenderer.cpp
create mode 100644 src/corelibs/U2View/src/ov_sequence/view_rendering/PanViewRenderer.h
create mode 100644 src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.cpp
create mode 100644 src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewAnnotatedRenderer.h
create mode 100644 src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewRenderer.cpp
create mode 100644 src/corelibs/U2View/src/ov_sequence/view_rendering/SequenceViewRenderer.h
delete mode 100644 src/include/U2Core/DASSource.h
delete mode 100644 src/include/U2Core/LoadDASDocumentTask.h
delete mode 100644 src/include/U2Core/PicrApiTask.h
create mode 100644 src/include/U2Core/TaskWatchdog.h
delete mode 100644 src/include/U2Core/UniprotBlastTask.h
create mode 100644 src/include/U2Test/CustomScenario.h
create mode 100644 src/include/U2Test/GUITestThread.h
create mode 100644 src/include/U2Test/MainThreadRunnable.h
delete mode 100644 src/include/U2View/DasWidgetFactory.h
delete mode 100644 src/include/U2View/MSAEditorDataList.h
create mode 100644 src/include/U2View/MSASimpleOverview.h
create mode 100644 src/include/U2View/MsaEditorSimilarityColumn.h
create mode 100644 src/libs_3rdparty/humimit/Doxyfile
create mode 100644 src/libs_3rdparty/humimit/humimit.pri
create mode 100644 src/libs_3rdparty/humimit/humimit.pro
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src}/GTGlobals.cpp (88%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src}/GTGlobals.h (65%)
rename src/{plugins/GUITestBase/src/runnables/qt => libs_3rdparty/humimit/src/base_dialogs}/ColorDialogFiller.cpp (69%)
rename src/{plugins/GUITestBase/src/runnables/qt => libs_3rdparty/humimit/src/base_dialogs}/ColorDialogFiller.h (83%)
rename src/{plugins/GUITestBase/src/runnables/qt => libs_3rdparty/humimit/src/base_dialogs}/DefaultDialogFiller.cpp (86%)
rename src/{plugins/GUITestBase/src/runnables/qt => libs_3rdparty/humimit/src/base_dialogs}/DefaultDialogFiller.h (76%)
rename src/{plugins/GUITestBase/src/runnables/qt => libs_3rdparty/humimit/src/base_dialogs}/FontDialogFiller.cpp (82%)
rename src/{plugins/GUITestBase/src/runnables/qt => libs_3rdparty/humimit/src/base_dialogs}/FontDialogFiller.h (72%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/base_dialogs}/GTFileDialog.cpp (74%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/base_dialogs}/GTFileDialog.h (51%)
rename src/{plugins/GUITestBase/src/runnables/qt => libs_3rdparty/humimit/src/base_dialogs}/MessageBoxFiller.cpp (74%)
create mode 100644 src/libs_3rdparty/humimit/src/base_dialogs/MessageBoxFiller.h
rename src/{plugins/GUITestBase/src/api/GTSystem.cpp => libs_3rdparty/humimit/src/core/CustomScenario.cpp} (89%)
copy src/{plugins/GUITestBase/src/GTUtilsToolTip.h => libs_3rdparty/humimit/src/core/CustomScenario.h} (74%)
rename src/{corelibs/U2Test/src/gui_tests => libs_3rdparty/humimit/src/core}/GUITest.cpp (63%)
rename src/{corelibs/U2Test/src/gui_tests => libs_3rdparty/humimit/src/core}/GUITest.h (78%)
rename src/{corelibs/U2Test/src/gui_tests => libs_3rdparty/humimit/src/core}/GUITestOpStatus.h (63%)
create mode 100644 src/libs_3rdparty/humimit/src/core/MainThreadRunnable.cpp
copy src/{plugins/GUITestBase/src/GTUtilsNotifications.h => libs_3rdparty/humimit/src/core/MainThreadRunnable.h} (54%)
copy src/{plugins/GUITestBase/src/runnables/ugene/plugins/orf_marker/OrfDialogFiller.cpp => libs_3rdparty/humimit/src/core/MainThreadTimer.cpp} (62%)
copy src/{plugins/GUITestBase/src/api/GTGroupBox.h => libs_3rdparty/humimit/src/core/MainThreadTimer.h} (70%)
create mode 100644 src/libs_3rdparty/humimit/src/core/global.h
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/drivers}/GTKeyboardDriver.cpp (87%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/drivers}/GTKeyboardDriver.h (52%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/drivers}/GTKeyboardDriverLinux.cpp (94%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/drivers}/GTKeyboardDriverMac.cpp (81%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/drivers}/GTKeyboardDriverWindows.cpp (72%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/drivers}/GTMouseDriver.cpp (58%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/drivers}/GTMouseDriver.h (54%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/drivers}/GTMouseDriverLinux.cpp (93%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/drivers}/GTMouseDriverMac.cpp (79%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/drivers}/GTMouseDriverWindows.cpp (93%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTAction.cpp (58%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTAction.h (59%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTCheckBox.cpp (67%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTCheckBox.h (62%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTComboBox.cpp (85%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTComboBox.h (56%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTDoubleSpinBox.cpp (65%)
create mode 100644 src/libs_3rdparty/humimit/src/primitives/GTDoubleSpinBox.h
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTGroupBox.cpp (67%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTGroupBox.h (65%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTLineEdit.cpp (77%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTLineEdit.h (55%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTListWidget.cpp (80%)
copy src/{plugins/GUITestBase/src/api/GTGraphicsItem.h => libs_3rdparty/humimit/src/primitives/GTListWidget.h} (52%)
copy src/{plugins/GUITestBase/src/runnables/ugene/corelibs/U2Gui/GraphLabelsSelectDialogFiller.cpp => libs_3rdparty/humimit/src/primitives/GTMainWindow.cpp} (50%)
copy src/{plugins/GUITestBase/src/GTUtilsToolTip.h => libs_3rdparty/humimit/src/primitives/GTMainWindow.h} (74%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTMenu.cpp (57%)
create mode 100644 src/libs_3rdparty/humimit/src/primitives/GTMenu.h
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTMenuBar.cpp (81%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTMenuBar.h (81%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTPlainTextEdit.cpp (79%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTPlainTextEdit.h (66%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTRadioButton.cpp (70%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTRadioButton.h (63%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTScrollBar.cpp (86%)
create mode 100644 src/libs_3rdparty/humimit/src/primitives/GTScrollBar.h
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTSlider.cpp (91%)
copy src/{plugins/GUITestBase/src/runnables/ugene/plugins/weight_matrix/PwmSearchDialogFiller.cpp => libs_3rdparty/humimit/src/primitives/GTSlider.h} (77%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTSpinBox.cpp (66%)
create mode 100644 src/libs_3rdparty/humimit/src/primitives/GTSpinBox.h
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTTabBar.cpp (82%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTTabBar.h (76%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTTabWidget.cpp (56%)
create mode 100644 src/libs_3rdparty/humimit/src/primitives/GTTabWidget.h
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTTableView.cpp (83%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTTableView.h (64%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTTextEdit.cpp (80%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTTextEdit.h (63%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTToolbar.cpp (73%)
copy src/{plugins/GUITestBase/src/api/GTSequenceReadingModeDialogUtils.h => libs_3rdparty/humimit/src/primitives/GTToolbar.h} (52%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTTreeView.cpp (81%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTTreeView.h (70%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTTreeWidget.cpp (83%)
create mode 100644 src/libs_3rdparty/humimit/src/primitives/GTTreeWidget.h
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/GTWebView.cpp (52%)
create mode 100644 src/libs_3rdparty/humimit/src/primitives/GTWebView.h
create mode 100644 src/libs_3rdparty/humimit/src/primitives/GTWidget.cpp
create mode 100644 src/libs_3rdparty/humimit/src/primitives/GTWidget.h
rename src/{plugins/GUITestBase/src/runnables/qt => libs_3rdparty/humimit/src/primitives}/PopupChooser.cpp (80%)
rename src/{plugins/GUITestBase/src/runnables/qt => libs_3rdparty/humimit/src/primitives}/PopupChooser.h (68%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/private/GTMenuPrivate.cpp (51%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/private/GTMenuPrivate.h (60%)
copy src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/primitives}/private/GTMenuPrivateMac.h (60%)
create mode 100644 src/libs_3rdparty/humimit/src/primitives/private/GTMenuPrivateMac.mm
create mode 100644 src/libs_3rdparty/humimit/src/system/GTClipboard.cpp
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/system}/GTClipboard.h (73%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/system}/GTFile.cpp (86%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/system}/GTFile.h (63%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/utils}/GTKeyboardUtils.cpp (85%)
rename src/{plugins/GUITestBase/src/api => libs_3rdparty/humimit/src/utils}/GTKeyboardUtils.h (64%)
rename src/{plugins/GUITestBase/src/api/GTMouse.cpp => libs_3rdparty/humimit/src/utils/GTMouseUtils.cpp} (83%)
rename src/{plugins/GUITestBase/src/api/GTMouse.h => libs_3rdparty/humimit/src/utils/GTMouseUtils.h} (77%)
create mode 100644 src/libs_3rdparty/humimit/src/utils/GTThread.cpp
copy src/{plugins/GUITestBase/src/api/private/GTMenuPrivateMac.h => libs_3rdparty/humimit/src/utils/GTThread.h} (61%)
rename src/{plugins/GUITestBase/src => libs_3rdparty/humimit/src/utils}/GTUtilsApp.cpp (55%)
rename src/{plugins/GUITestBase/src => libs_3rdparty/humimit/src/utils}/GTUtilsApp.h (75%)
rename src/{plugins/GUITestBase/src => libs_3rdparty/humimit/src/utils}/GTUtilsDialog.cpp (75%)
rename src/{plugins/GUITestBase/src => libs_3rdparty/humimit/src/utils}/GTUtilsDialog.h (62%)
rename src/{plugins/GUITestBase/src => libs_3rdparty/humimit/src/utils}/GTUtilsToolTip.cpp (85%)
rename src/{plugins/GUITestBase/src => libs_3rdparty/humimit/src/utils}/GTUtilsToolTip.h (79%)
delete mode 100644 src/plugins/CoreTests/src/LoadDASDocumentTests.cpp
delete mode 100644 src/plugins/CoreTests/src/LoadDASDocumentTests.h
create mode 100644 src/plugins/GUITestBase/GUITestBase.qrc
create mode 100644 src/plugins/GUITestBase/images/open_gui_test_runner.png
delete mode 100644 src/plugins/GUITestBase/src/api/GTClipboard.cpp
delete mode 100644 src/plugins/GUITestBase/src/api/GTDoubleSpinBox.h
delete mode 100644 src/plugins/GUITestBase/src/api/GTListWidget.h
delete mode 100644 src/plugins/GUITestBase/src/api/GTMenu.h
delete mode 100644 src/plugins/GUITestBase/src/api/GTScrollBar.h
delete mode 100644 src/plugins/GUITestBase/src/api/GTSlider.h
delete mode 100644 src/plugins/GUITestBase/src/api/GTSpinBox.h
delete mode 100644 src/plugins/GUITestBase/src/api/GTSystem.h
delete mode 100644 src/plugins/GUITestBase/src/api/GTTabWidget.h
delete mode 100644 src/plugins/GUITestBase/src/api/GTToolbar.h
delete mode 100644 src/plugins/GUITestBase/src/api/GTTreeWidget.h
delete mode 100644 src/plugins/GUITestBase/src/api/GTWebView.h
delete mode 100644 src/plugins/GUITestBase/src/api/GTWidget.cpp
delete mode 100644 src/plugins/GUITestBase/src/api/GTWidget.h
delete mode 100644 src/plugins/GUITestBase/src/api/private/GTMenuPrivateMac.mm
delete mode 100644 src/plugins/GUITestBase/src/runnables/qt/MessageBoxFiller.h
copy src/plugins/GUITestBase/src/runnables/ugene/{plugins/workflow_designer/ConfigurationWizardFiller.cpp => corelibs/U2View/ov_msa/LicenseAgreementDialogFiller.cpp} (66%)
copy src/plugins/GUITestBase/src/runnables/{qt/EscapeClicker.h => ugene/corelibs/U2View/ov_msa/LicenseAgreementDialogFiller.h} (74%)
delete mode 100644 src/plugins/GUITestBase/src/runnables/ugene/corelibs/U2View/ov_msa/LicenseAgreemntDialogFiller.h
create mode 100644 src/plugins/GUITestBase/src/test_runner/GUITestRunner.cpp
rename src/{corelibs/U2View/src/ov_sequence/Das/DasWidgetFactory.h => plugins/GUITestBase/src/test_runner/GUITestRunner.h} (59%)
create mode 100644 src/plugins/GUITestBase/src/test_runner/GUITestRunner.ui
create mode 100644 src/plugins/GUITestBase/src/tests/common_scenarios/msa_editor/replace_character/GTTestsMSAEditorReplaceCharacter.cpp
copy src/plugins/GUITestBase/src/tests/common_scenarios/msa_editor/{overview/GTTestsMSAEditorOverview.h => replace_character/GTTestsMSAEditorReplaceCharacter.h} (74%)
create mode 100644 src/plugins/external_tool_support/src/peak2gene/Gene2PeakFormatLoader.cpp
create mode 100644 src/plugins/external_tool_support/src/peak2gene/Gene2PeakFormatLoader.h
create mode 100644 src/plugins/external_tool_support/src/peak2gene/Peak2GeneFormatLoader.cpp
create mode 100644 src/plugins/external_tool_support/src/peak2gene/Peak2GeneFormatLoader.h
create mode 100644 src/plugins/external_tool_support/src/peak2gene/TabulatedFormatReader.cpp
rename src/plugins/{GUITestBase/src/api/private/GTMenuPrivateMac.h => external_tool_support/src/peak2gene/TabulatedFormatReader.h} (55%)
delete mode 100644 src/plugins/workflow_designer/src/library/DASAnnotationWorker.cpp
delete mode 100644 src/plugins/workflow_designer/src/library/DASAnnotationWorker.h
delete mode 100644 src/plugins/workflow_designer/src/library/DASFetchWorker.cpp
delete mode 100644 src/plugins/workflow_designer/src/library/DASFetchWorker.h
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