[med-svn] [ugene] branch upstream updated (20c61aa -> a8a1cc6)
Sascha Steinbiss
satta at debian.org
Thu Jul 28 06:06:38 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch upstream
in repository ugene.
from 20c61aa Imported Upstream version 1.21.0+dfsg
new a8a1cc6 Imported Upstream version 1.23.1+dfsg
The 1 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 | 33 +-
data/DBXRefRegistry.txt | 2 +-
data/cmdline/hmm3-search.uwl | 132 +
installer/linux/fedora/ugene.spec | 170 +-
installer/linux/ubuntu/debian/control | 2 +-
installer/linux/ubuntu/debian/rules | 2 -
src/corelibs/U2Algorithm/CMakeLists.txt | 26 +
src/corelibs/U2Algorithm/U2Algorithm.pro | 37 +-
src/corelibs/U2Algorithm/src/misc/EnzymeModel.cpp | 3 +-
src/corelibs/U2Algorithm/src/misc/EnzymeModel.h | 3 +-
.../U2Algorithm/src/misc/FindAlgorithm.cpp | 4 +-
src/corelibs/U2Algorithm/src/misc/FindAlgorithm.h | 2 +
.../src/util_msaedit/MSAColorScheme.cpp | 1322 ----
.../U2Algorithm/src/util_msaedit/MSAColorScheme.h | 475 --
.../color_schemes/ColorSchemeUtils.cpp | 269 +
.../util_msaedit/color_schemes/ColorSchemeUtils.h | 54 +
.../util_msaedit/color_schemes/MsaColorScheme.cpp | 568 ++
.../util_msaedit/color_schemes/MsaColorScheme.h | 137 +
.../color_schemes/MsaColorSchemeClustalX.cpp | 264 +
.../color_schemes/MsaColorSchemeClustalX.h | 80 +
.../color_schemes/MsaColorSchemeCustom.cpp | 68 +
.../color_schemes/MsaColorSchemeCustom.h | 50 +
...saColorSchemePercentageIdententityGrayscale.cpp | 44 +
.../MsaColorSchemePercentageIdententityGrayscale.h | 44 +
.../MsaColorSchemePercentageIdentity.cpp | 94 +
.../MsaColorSchemePercentageIdentity.h | 65 +
.../color_schemes/MsaColorSchemeStatic.cpp | 48 +
.../color_schemes/MsaColorSchemeStatic.h | 56 +
.../highlighting_schemes/MsaHighlightingScheme.cpp | 164 +
.../highlighting_schemes/MsaHighlightingScheme.h | 109 +
.../MsaHighlightingSchemeAgreements.cpp | 52 +
.../MsaHighlightingSchemeAgreements.h | 47 +
.../MsaHighlightingSchemeConservation.cpp | 101 +
.../MsaHighlightingSchemeConservation.h | 60 +
.../MsaHighlightingSchemeDisagreements.cpp | 53 +
.../MsaHighlightingSchemeDisagreements.h | 46 +
.../MsaHighlightingSchemeGaps.cpp | 59 +
.../MsaHighlightingSchemeGaps.h | 48 +
.../MsaHighlightingSchemeNoColors.cpp | 48 +
.../MsaHighlightingSchemeNoColors.h | 46 +
.../MsaHighlightingSchemeTransitions.cpp | 73 +
.../MsaHighlightingSchemeTransitions.h | 46 +
.../MsaHighlightingSchemeTransversions.cpp | 73 +
.../MsaHighlightingSchemeTransversions.h | 47 +
src/corelibs/U2Algorithm/transl/english.ts | 180 +-
src/corelibs/U2Algorithm/transl/russian.ts | 180 +-
src/corelibs/U2Core/CMakeLists.txt | 33 +
src/corelibs/U2Core/U2Core.pri | 10 +-
src/corelibs/U2Core/U2Core.pro | 6 +
.../U2Core/src/cmdline/CMDLineRegistry.cpp | 2 +
src/corelibs/U2Core/src/cmdline/CMDLineRegistry.h | 3 +
src/corelibs/U2Core/src/cmdline/CMDLineUtils.cpp | 30 +
src/corelibs/U2Core/src/cmdline/CMDLineUtils.h | 2 +
src/corelibs/U2Core/src/datatype/Annotation.cpp | 14 +
src/corelibs/U2Core/src/datatype/Annotation.h | 2 +
.../U2Core/src/datatype/AnnotationModification.h | 3 +-
.../U2Core/src/datatype/DNASequenceUtils.cpp | 3 +-
.../U2Core/src/datatype/U2CoreAttributes.cpp | 8 +
.../U2Core/src/datatype/U2CoreAttributes.h | 2 +
src/corelibs/U2Core/src/datatype/U2FeatureType.cpp | 6 +-
src/corelibs/U2Core/src/datatype/U2FeatureType.h | 5 +-
src/corelibs/U2Core/src/dbi/U2AbstractDbi.h | 5 +
src/corelibs/U2Core/src/dbi/U2ObjectDbi.h | 5 +
.../U2Core/src/dbi/U2SQLiteTripleStore.cpp | 2 +-
src/corelibs/U2Core/src/dbi/U2SqlHelpers.cpp | 2 +-
src/corelibs/U2Core/src/globals/AppContext.h | 12 +-
.../U2Core/src/globals/AutoAnnotationsSupport.cpp | 35 +-
.../U2Core/src/globals/AutoAnnotationsSupport.h | 14 +-
.../U2Core/src/globals/BaseDocumentFormats.cpp | 2 +-
.../U2Core/src/globals/ClipboardController.cpp | 4 +
.../U2Core/src/globals/ClipboardController.h | 2 +-
src/corelibs/U2Core/src/globals/Log.h | 3 -
src/corelibs/U2Core/src/globals/PluginModel.h | 10 +-
src/corelibs/U2Core/src/globals/Task.h | 2 +
.../U2Core/src/globals/UserActionsWriter.cpp | 122 +-
.../U2Core/src/globals/UserActionsWriter.h | 27 +-
.../src/globals/UserApplicationsSettings.cpp | 18 +
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src/corelibs/U2Core/src/globals/global.h | 12 +-
.../U2Core/src/gobjects/AssemblyObject.cpp | 80 +-
src/corelibs/U2Core/src/gobjects/AssemblyObject.h | 3 +
src/corelibs/U2Core/src/io/ZlibAdapter.cpp | 7 +-
src/corelibs/U2Core/src/models/DocumentModel.cpp | 4 +
src/corelibs/U2Core/src/models/DocumentModel.h | 3 +
.../U2Core/src/tasks/CmdlineInOutTaskRunner.cpp | 128 +
.../U2Core/src/tasks/CmdlineInOutTaskRunner.h | 71 +
.../U2Core/src/tasks/CmdlineTaskRunner.cpp | 311 +
src/corelibs/U2Core/src/tasks/CmdlineTaskRunner.h | 83 +
.../U2Core/src/tasks/ExternalToolRunTask.cpp | 210 +-
.../U2Core/src/tasks/ExternalToolRunTask.h | 85 +-
src/corelibs/U2Core/src/tasks/LoadDocumentTask.cpp | 3 +
src/corelibs/U2Core/src/tasks/SaveDocumentTask.cpp | 2 +-
.../U2Core/src/tasks/SequenceDbiWalkerTask.cpp | 17 +-
.../U2Core/src/util/FileAndDirectoryUtils.cpp | 9 +
.../U2Core/src/util/FileAndDirectoryUtils.h | 3 +
src/corelibs/U2Core/src/util/FormatUtils.cpp | 22 +-
src/corelibs/U2Core/src/util/FormatUtils.h | 1 +
src/corelibs/U2Core/src/util/GUrlUtils.cpp | 2 +-
src/corelibs/U2Core/src/util/GenbankFeatures.cpp | 2 +-
src/corelibs/U2Core/src/util/SNPTablesUtils.cpp | 358 -
src/corelibs/U2Core/src/util/SyncHttp.cpp | 96 +
src/corelibs/U2Core/src/util/SyncHttp.h | 61 +
src/corelibs/U2Core/src/util/U2SequenceUtils.cpp | 2 +-
src/corelibs/U2Core/transl/english.ts | 524 +-
src/corelibs/U2Core/transl/russian.ts | 525 +-
src/corelibs/U2Designer/CMakeLists.txt | 27 +
src/corelibs/U2Designer/U2Designer.pro | 40 +-
src/corelibs/U2Designer/html/Dashboard.html | 1 +
src/corelibs/U2Designer/html/EstimationReport.html | 1 +
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src/corelibs/U2Designer/src/DatasetWidget.cpp | 2 +-
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src/corelibs/U2Designer/src/DbFolderItem.cpp | 4 +-
src/corelibs/U2Designer/src/DbFolderItem.h | 8 +-
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src/corelibs/U2Designer/src/DirectoryItem.h | 2 +-
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src/corelibs/U2Designer/src/GrouperEditorWidget.h | 2 +-
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src/corelibs/U2Designer/src/MarkerEditorWidget.h | 2 +-
.../U2Designer/src/{ui => }/MarkerEditorWidget.ui | 0
.../U2Designer/src/{ui => }/MsaActionDialog.ui | 0
.../U2Designer/src/NewBreakpointDialog.cpp | 12 +-
src/corelibs/U2Designer/src/NewBreakpointDialog.h | 13 +-
.../U2Designer/src/{ui => }/NewBreakpointDialog.ui | 0
.../U2Designer/src/NewGrouperSlotDialog.cpp | 10 +-
src/corelibs/U2Designer/src/NewGrouperSlotDialog.h | 10 +-
.../src/{ui => }/NewGrouperSlotDialog.ui | 0
src/corelibs/U2Designer/src/OutputFileDialog.h | 8 +-
.../U2Designer/src/{ui => }/OutputFileDialog.ui | 0
.../src/{ui => }/SequenceActionDialog.ui | 0
.../U2Designer/src/{ui => }/StringActionDialog.ui | 0
.../U2Designer/src/support/URLLineEdit.cpp | 2 +-
src/corelibs/U2Designer/transl/english.ts | 239 +-
src/corelibs/U2Designer/transl/russian.ts | 243 +-
src/corelibs/U2Formats/CMakeLists.txt | 26 +
src/corelibs/U2Formats/U2Formats.pri | 13 +-
.../U2Formats/src/AbstractVariationFormat.cpp | 2 +-
src/corelibs/U2Formats/src/BAMUtils.cpp | 13 +-
src/corelibs/U2Formats/src/BAMUtils.h | 5 +-
src/corelibs/U2Formats/src/DocumentFormatUtils.cpp | 12 +-
src/corelibs/U2Formats/src/DocumentFormatUtils.h | 6 +-
.../U2Formats/src/EMBLGenbankAbstractDocument.cpp | 143 +-
.../U2Formats/src/EMBLGenbankAbstractDocument.h | 13 +-
src/corelibs/U2Formats/src/EMBLPlainTextFormat.cpp | 3 +
src/corelibs/U2Formats/src/FastqFormat.cpp | 136 +-
src/corelibs/U2Formats/src/GFFFormat.cpp | 41 +-
src/corelibs/U2Formats/src/GFFFormat.h | 2 +-
.../U2Formats/src/GenbankLocationParser.cpp | 530 +-
src/corelibs/U2Formats/src/GenbankLocationParser.h | 12 +-
.../U2Formats/src/GenbankPlainTextFormat.cpp | 3 +
src/corelibs/U2Formats/src/PDBFormat.cpp | 2 +-
.../U2Formats/src/SwissProtPlainTextFormat.cpp | 3 +
.../U2Formats/src/VectorNtiSequenceFormat.cpp | 6 +-
.../U2Formats/src/mysql_dbi/MysqlObjectDbi.cpp | 13 +
.../U2Formats/src/mysql_dbi/MysqlObjectDbi.h | 5 +
.../src/sqlite_dbi/SQLiteBlobInputStream.cpp | 2 +-
.../src/sqlite_dbi/SQLiteBlobOutputStream.cpp | 2 +-
.../U2Formats/src/sqlite_dbi/SQLiteDbi.cpp | 2 +-
.../U2Formats/src/sqlite_dbi/SQLiteObjectDbi.cpp | 13 +
.../U2Formats/src/sqlite_dbi/SQLiteObjectDbi.h | 5 +
src/corelibs/U2Formats/src/tasks/MergeBamTask.cpp | 45 +-
src/corelibs/U2Formats/src/tasks/MergeBamTask.h | 3 +-
src/corelibs/U2Formats/transl/english.ts | 659 +-
src/corelibs/U2Formats/transl/russian.ts | 281 +-
src/corelibs/U2Gui/CMakeLists.txt | 28 +
src/corelibs/U2Gui/U2Gui.pro | 77 +-
src/corelibs/U2Gui/U2Gui.qrc | 2 +
src/corelibs/U2Gui/images/codon_table.png | Bin 0 -> 21278 bytes
.../U2Gui/images/extract_assembly_region.png | Bin 0 -> 23943 bytes
src/corelibs/U2Gui/src/MainWindow.h | 3 +-
src/corelibs/U2Gui/src/OpenViewTask.cpp | 53 +-
src/corelibs/U2Gui/src/OpenViewTask.h | 14 +-
src/corelibs/U2Gui/src/ToolsMenu.cpp | 2 -
src/corelibs/U2Gui/src/ToolsMenu.h | 1 -
src/corelibs/U2Gui/src/UnloadDocumentTask.cpp | 4 +-
.../U2Gui/src/options_panel/GroupOptionsWidget.h | 2 +-
.../U2Gui/src/util/AddNewDocumentDialog.ui | 121 +
.../U2Gui/src/util/AddNewDocumentDialogImpl.cpp | 146 +-
.../U2Gui/src/util/AddNewDocumentDialogImpl.h | 18 +-
.../U2Gui/src/util/AuthenticationDialog.cpp | 4 +-
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src/corelibs/U2Gui/src/util/AuthenticationWidget.h | 2 +-
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src/corelibs/U2Script/src/UgeneContextWrapper.h | 1 -
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src/corelibs/U2Script/transl/english.ts | 11 +-
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.../U2View/src/ov_assembly/AssemblyBrowser.cpp | 33 +-
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.../src/ov_assembly/ExportConsensusDialog.cpp | 55 +-
.../U2View/src/ov_assembly/ExportConsensusDialog.h | 10 +-
.../ov_assembly/{ui => }/ExportConsensusDialog.ui | 0
.../ExportConsensusVariationsDialog.cpp | 53 +-
.../ov_assembly/ExportConsensusVariationsDialog.h | 25 +-
.../src/ov_assembly/ExportCoverageDialog.cpp | 129 +-
.../U2View/src/ov_assembly/ExportCoverageDialog.h | 9 +-
.../U2View/src/ov_assembly/ExportCoverageDialog.ui | 188 +
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.../src/ov_assembly/{ui => }/ExportReadsDialog.ui | 0
.../ov_assembly/ExtractAssemblyRegionDialog.cpp | 118 +
.../src/ov_assembly/ExtractAssemblyRegionDialog.h | 63 +
.../src/ov_assembly/ExtractAssemblyRegionDialog.ui | 126 +
.../src/ov_assembly/ExtractAssemblyRegionTask.cpp | 98 +
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.../src/ov_assembly/ui/ExportCoverageDialog.ui | 194 -
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.../src/ov_msa/ColorSchemaDialogController.cpp | 34 +-
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.../src/ov_msa/ColorSchemaSettingsController.h | 4 +-
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.../ov_msa/{ui => }/CreateSubalignmentDialog.ui | 0
.../ov_msa/CreateSubalignmentDialogController.cpp | 99 +-
.../ov_msa/CreateSubalignmentDialogController.h | 20 +-
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src/corelibs/U2View/src/ov_msa/DeleteGapsDialog.h | 7 +-
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.../src/ov_msa/{ui => Export}/MSAExportSettings.ui | 0
.../ExportConsensus/ExportConsensusWidget.ui | 139 +
.../ExportConsensus/MSAExportConsensusTab.cpp | 111 +-
.../ov_msa/ExportConsensus/MSAExportConsensusTab.h | 11 +-
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.../src/ov_msa/{ui => }/ExportHighlightedDialog.ui | 0
.../ov_msa/ExportHighlightedDialogController.cpp | 104 +-
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.../src/ov_msa/General/MSAGeneralTabFactory.cpp | 2 +-
.../src/ov_msa/Highlighting/MSAHighlightingTab.cpp | 97 +-
.../src/ov_msa/Highlighting/MSAHighlightingTab.h | 3 +-
.../Highlighting/MSAHighlightingTabFactory.cpp | 2 +-
src/corelibs/U2View/src/ov_msa/MSAEditor.cpp | 29 +-
src/corelibs/U2View/src/ov_msa/MSAEditorFactory.h | 2 +-
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.../src/ov_msa/MSASelectSubalignmentDialog.cpp | 2 +-
.../src/ov_msa/MSASelectSubalignmentDialog.h | 2 +-
.../src/ov_msa/MsaEditorSimilarityColumn.cpp | 2 +
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.../src/ov_msa/Overview/MSAGraphCalculationTask.h | 12 +-
.../src/ov_msa/Overview/MSAGraphOverview.cpp | 7 +-
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.../src/ov_msa/PhyTrees/MSAEditorTreeViewer.cpp | 2 +-
.../ov_msa/PhyTrees/MSAEditorTreeViewerTasks.cpp | 244 -
.../src/ov_msa/PhyTrees/MSAEditorTreeViewerTasks.h | 100 -
.../{ui => }/SaveSelectedSequenceFromMSADialog.ui | 0
...SaveSelectedSequenceFromMSADialogController.cpp | 72 +-
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.../src/ov_msa/SeqStatistics/SeqStatisticsWidget.h | 2 +-
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.../src/ov_msa/{ui => }/SequenceSelectorWidget.ui | 0
.../src/ov_msa/SequenceSelectorWidgetController.h | 2 +-
.../src/ov_msa/TreeOptions/AddTreeWidget.cpp | 172 -
.../U2View/src/ov_msa/TreeOptions/AddTreeWidget.h | 55 -
.../src/ov_msa/TreeOptions/TreeOptionsWidget.h | 2 +-
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.../TreeOptions/TreeOptionsWidgetFactory.cpp | 6 +-
.../U2View/src/ov_msa/ui/ExportConsensusWidget.ui | 139 -
.../src/ov_sequence/ADVSequenceObjectContext.cpp | 51 +-
.../src/ov_sequence/ADVSequenceObjectContext.h | 3 +-
.../src/ov_sequence/ADVSingleSequenceWidget.cpp | 18 +-
.../src/ov_sequence/ADVSingleSequenceWidget.h | 1 +
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.../U2View/src/ov_sequence/AnnotatedDNAView.cpp | 57 +-
.../U2View/src/ov_sequence/AnnotatedDNAView.h | 6 +-
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.../U2View/src/ov_sequence/AnnotationsTreeView.h | 10 +-
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src/corelibs/U2View/src/ov_sequence/DetView.cpp | 13 +-
src/corelibs/U2View/src/ov_sequence/DetView.h | 3 +
.../ov_sequence/EditAnnotationDialogController.cpp | 144 -
.../ov_sequence/EditAnnotationDialogController.h | 56 -
.../src/ov_sequence/GSequenceLineViewAnnotated.cpp | 4 +-
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.../annot_highlight/AnnotHighlightTree.cpp | 2 +-
.../AnnotHighlightWidgetFactory.cpp | 2 +-
.../src/ov_sequence/codon_table/CodonTable.cpp | 11 -
.../src/ov_sequence/codon_table/CodonTable.h | 8 -
.../find_pattern/{ui => }/FindPatternForm.ui | 0
.../ov_sequence/find_pattern/FindPatternWidget.h | 2 +-
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.../src/ov_sequence/ui/EditAnnotationDialog.ui | 119 -
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.../src/phyltree/{ui => }/CreatePhyTreeDialog.ui | 0
.../src/phyltree/CreatePhyTreeDialogController.cpp | 57 +-
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.../src/util_dna_assembly/AssemblyToSamDialog.ui | 102 +
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.../src/util_dna_assembly/DnaAssemblyDialog.h | 22 +-
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.../src/util_dna_assembly/GenomeAssemblyDialog.h | 2 +-
.../{ui => }/GenomeAssemblyDialog.ui | 0
.../util_dna_assembly/ui/AssemblyToSamDialog.ui | 69 -
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src/corelibs/U2View/transl/english.ts | 2230 +++---
src/corelibs/U2View/transl/russian.ts | 2234 +++---
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src/include/U2Algorithm/ColorSchemeUtils.h | 1 +
src/include/U2Algorithm/MSAColorScheme.h | 1 -
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src/libs_3rdparty/gtest/src/gtest/gtest.h | 2155 ------
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src/libs_3rdparty/gtest/src/gtest_main.cc | 40 -
src/libs_3rdparty/gtest/src/gtest_prod_test.cc | 57 -
src/libs_3rdparty/gtest/src/gtest_unittest.cc | 7337 --------------------
.../gtest/src/src/gtest-death-test.cc | 1234 ----
src/libs_3rdparty/gtest/src/src/gtest-filepath.cc | 380 -
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src/libs_3rdparty/gtest/src/src/gtest-port.cc | 746 --
src/libs_3rdparty/gtest/src/src/gtest-printers.cc | 356 -
src/libs_3rdparty/gtest/src/src/gtest-test-part.cc | 110 -
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src/libs_3rdparty/gtest/src/src/gtest.cc | 4898 -------------
src/libs_3rdparty/gtest/src/test/production.cc | 36 -
src/libs_3rdparty/gtest/src/test/production.h | 55 -
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.../src/cap3/CAP3SupportDialog.ui | 509 ++
.../src/clustalo/ClustalOSupport.cpp | 2 +-
.../src/clustalo/ClustalOSupportRunDialog.cpp | 94 +-
.../src/clustalo/ClustalOSupportRunDialog.h | 18 +-
.../src/clustalo/ClustalOSupportRunDialog.ui | 400 ++
.../src/clustalw/ClustalWSupport.cpp | 2 +-
.../src/clustalw/ClustalWSupportRunDialog.cpp | 97 +-
.../src/clustalw/ClustalWSupportRunDialog.h | 20 +-
.../src/clustalw/ClustalWSupportRunDialog.ui | 639 ++
.../src/cufflinks/CuffdiffSupportTask.cpp | 3 +
.../src/cufflinks/CufflinksSupportTask.cpp | 2 +
.../external_tool_support/src/macs/MACSWorker.cpp | 11 +-
.../src/mafft/MAFFTSupportRunDialog.cpp | 92 +-
.../src/mafft/MAFFTSupportRunDialog.h | 27 +-
.../src/mafft/MAFFTSupportRunDialog.ui | 314 +
.../src/{ui => mrbayes}/MrBayesDialog.ui | 0
.../src/mrbayes/MrBayesDialogWidget.h | 2 +-
.../external_tool_support/src/phyml/PhyMLDialog.ui | 587 ++
.../src/phyml/PhyMLDialogWidget.h | 2 +-
.../src/snpeff/SnpEffSupport.cpp | 45 +-
.../src/snpeff/SnpEffTask.cpp | 91 +-
.../src/{ui => spades}/SpadesSettings.ui | 0
.../src/spades/SpadesSettingsWidget.h | 2 +-
.../src/tcoffee/TCoffeeSupportRunDialog.cpp | 90 +-
.../src/tcoffee/TCoffeeSupportRunDialog.h | 24 +-
.../src/tcoffee/TCoffeeSupportRunDialog.ui | 284 +
.../src/tophat/TopHatSettings.cpp | 25 +-
.../src/tophat/TopHatSupportTask.cpp | 4 +
.../src/ui/BlastDBCmdDialog.ui | 137 -
.../src/ui/BlastDBSelectorWidget.ui | 81 -
.../src/ui/BwaBuildSettings.ui | 90 -
.../src/ui/CAP3SupportDialog.ui | 512 --
.../src/ui/ClustalOSupportRunDialog.ui | 368 -
.../src/ui/ClustalWSupportRunDialog.ui | 607 --
.../src/ui/MAFFTSupportRunDialog.ui | 282 -
.../external_tool_support/src/ui/PhyMLDialog.ui | 587 --
.../src/ui/TCoffeeSupportRunDialog.ui | 252 -
.../src/utils/BaseShortReadsAlignerWorker.cpp | 86 +-
.../src/utils/BaseShortReadsAlignerWorker.h | 11 +-
.../src/{ui => utils}/BlastAllSupportDialog.ui | 0
.../src/utils/BlastDBSelectorWidget.ui | 81 +
.../src/utils/BlastDBSelectorWidgetController.h | 2 +-
.../src/utils/BlastRunCommonDialog.cpp | 2 +-
.../src/utils/BlastRunCommonDialog.h | 2 +-
.../src/utils/ExternalToolValidateTask.cpp | 6 +-
.../src/utils/ExternalToolValidateTask.h | 2 +
.../external_tool_support/transl/english.ts | 1236 ++--
.../external_tool_support/transl/russian.ts | 1258 ++--
src/plugins/genome_aligner/CMakeLists.txt | 3 +
src/plugins/genome_aligner/genome_aligner.pro | 6 +-
.../genome_aligner/src/BuildSArraySettingsWidget.h | 2 +-
.../src/{ui => }/BuildSuffixArraySettings.ui | 0
.../src/{ui => }/GenomeAlignerSettings.ui | 0
.../src/GenomeAlignerSettingsController.cpp | 2 +-
.../src/GenomeAlignerSettingsController.h | 2 +-
.../src/GenomeAlignerSettingsWidget.h | 2 +-
.../src/{ui => }/GenomeAlignerSettingsWidget.ui | 0
src/plugins/genome_aligner/transl/english.ts | 82 +-
src/plugins/genome_aligner/transl/russian.ts | 82 +-
src/plugins/linkdata_support/CMakeLists.txt | 3 +
.../opencl_support/src/OpenCLSupportPlugin.cpp | 22 +-
.../opencl_support/src/OpenCLSupportPlugin.h | 6 +-
.../src/OpenCLSupportSettingsController.cpp | 2 +-
src/plugins/orf_marker/CMakeLists.txt | 3 +
src/plugins/orf_marker/orf_marker.pro | 2 +-
src/plugins/orf_marker/src/ORFDialog.cpp | 4 +-
src/plugins/orf_marker/src/ORFDialog.h | 2 +-
src/plugins/orf_marker/src/{ui => }/ORFDialogUI.ui | 0
src/plugins/orf_marker/src/ORFMarkerTask.cpp | 6 +-
src/plugins/pcr/CMakeLists.txt | 3 +
src/plugins/pcr/html/report.html | 1 +
src/plugins/pcr/pcr.pro | 16 +-
src/plugins/pcr/src/EditPrimerDialog.cpp | 5 +-
src/plugins/pcr/src/EditPrimerDialog.h | 2 +-
src/plugins/pcr/src/{ui => }/EditPrimerDialog.ui | 0
src/plugins/pcr/src/InSilicoPcrOPWidgetFactory.cpp | 2 +-
.../pcr/src/InSilicoPcrOptionPanelWidget.cpp | 10 +-
src/plugins/pcr/src/InSilicoPcrOptionPanelWidget.h | 2 +-
.../src/{ui => }/InSilicoPcrOptionPanelWidget.ui | 0
src/plugins/pcr/src/InSilicoPcrProductsTable.cpp | 7 +-
src/plugins/pcr/src/InSilicoPcrTask.cpp | 41 +-
src/plugins/pcr/src/Primer.cpp | 2 +
src/plugins/pcr/src/Primer.h | 2 +
src/plugins/pcr/src/PrimerDimersFinder.cpp | 3 +-
src/plugins/pcr/src/PrimerGroupBox.cpp | 134 +-
src/plugins/pcr/src/PrimerGroupBox.h | 23 +-
src/plugins/pcr/src/{ui => }/PrimerGroupBox.ui | 0
src/plugins/pcr/src/PrimerLibrary.cpp | 19 +-
src/plugins/pcr/src/PrimerLibrary.h | 1 +
src/plugins/pcr/src/PrimerLibrarySelector.cpp | 2 +-
src/plugins/pcr/src/PrimerLibrarySelector.h | 2 +-
.../pcr/src/{ui => }/PrimerLibrarySelector.ui | 0
src/plugins/pcr/src/PrimerLibraryTable.cpp | 4 +-
src/plugins/pcr/src/PrimerLibraryWidget.cpp | 4 +-
src/plugins/pcr/src/PrimerLibraryWidget.h | 2 +-
.../pcr/src/{ui => }/PrimerLibraryWidget.ui | 0
src/plugins/pcr/src/PrimerLineEdit.cpp | 16 +-
src/plugins/pcr/src/PrimerLineEdit.h | 2 +-
src/plugins/pcr/src/PrimerStatistics.cpp | 66 +-
src/plugins/pcr/src/PrimerStatistics.h | 9 +-
src/plugins/pcr/src/PrimersDetailsDialog.cpp | 2 +-
src/plugins/pcr/src/PrimersDetailsDialog.h | 2 +-
.../pcr/src/{ui => }/PrimersDetailsDialog.ui | 0
src/plugins/pcr/src/export/ExportPrimersDialog.cpp | 90 +-
src/plugins/pcr/src/export/ExportPrimersDialog.h | 9 +-
.../pcr/src/{ui => export}/ExportPrimersDialog.ui | 0
.../pcr/src/import/ImportPrimerFromObjectTask.cpp | 10 +-
.../pcr/src/import/ImportPrimerFromObjectTask.h | 2 +
src/plugins/pcr/src/import/ImportPrimersDialog.cpp | 4 +-
src/plugins/pcr/src/import/ImportPrimersDialog.h | 2 +-
.../pcr/src/{ui => import}/ImportPrimersDialog.ui | 0
src/plugins/pcr/transl/english.ts | 197 +-
src/plugins/pcr/transl/russian.ts | 197 +-
src/plugins/perf_monitor/CMakeLists.txt | 3 +
src/plugins/query_designer/CMakeLists.txt | 3 +
src/plugins/query_designer/query_designer.pro | 8 +-
.../src/{ui => }/AddConstraintDialog.ui | 0
.../query_designer/src/{ui => }/QDDialog.ui | 0
src/plugins/query_designer/src/QDRunDialog.cpp | 91 +-
src/plugins/query_designer/src/QDRunDialog.h | 22 +-
.../src/{ui => }/QueryEditorWidget.ui | 0
.../query_designer/src/QueryViewController.cpp | 2 +-
.../query_designer/src/{ui => }/RunQueryDialog.ui | 0
src/plugins/query_designer/transl/english.ts | 80 +-
src/plugins/query_designer/transl/russian.ts | 80 +-
src/plugins/remote_blast/CMakeLists.txt | 3 +
src/plugins/remote_blast/remote_blast.pro | 2 +-
.../remote_blast/src/{ui => }/RemoteBLASTDialog.ui | 0
.../remote_blast/src/SendSelectionDialog.cpp | 2 +-
src/plugins/remote_blast/src/SendSelectionDialog.h | 2 +-
src/plugins/remote_blast/transl/english.ts | 152 +-
src/plugins/remote_blast/transl/russian.ts | 152 +-
src/plugins/remote_service/remote_service.license | 339 -
src/plugins/remote_service/remote_service.pri | 7 -
src/plugins/remote_service/remote_service.pro | 29 -
src/plugins/remote_service/src/Base64File.cpp | 107 -
src/plugins/remote_service/src/Base64File.h | 58 -
.../remote_service/src/BufferedDataReader.cpp | 200 -
.../remote_service/src/BufferedDataReader.h | 60 -
.../remote_service/src/RemoteServiceCommon.h | 14 -
.../remote_service/src/RemoteServiceMachine.cpp | 627 --
.../remote_service/src/RemoteServiceMachine.h | 178 -
.../remote_service/src/RemoteServicePingTask.cpp | 78 -
.../remote_service/src/RemoteServicePingTask.h | 46 -
.../remote_service/src/RemoteServicePlugin.cpp | 117 -
.../remote_service/src/RemoteServicePlugin.h | 53 -
.../remote_service/src/RemoteServiceSettingsUI.cpp | 118 -
.../remote_service/src/RemoteServiceSettingsUI.h | 49 -
.../remote_service/src/RemoteServiceUtilTasks.cpp | 123 -
.../remote_service/src/RemoteServiceUtilTasks.h | 75 -
.../remote_service/src/RemoteTasksDialog.cpp | 232 -
src/plugins/remote_service/src/RemoteTasksDialog.h | 72 -
.../remote_service/src/UctpRequestBuilders.cpp | 172 -
.../remote_service/src/UctpRequestBuilders.h | 110 -
.../remote_service/src/WebTransportProtocol.cpp | 230 -
.../remote_service/src/WebTransportProtocol.h | 200 -
src/plugins/remote_service/src/base64/cdecode.c | 109 -
src/plugins/remote_service/src/base64/cdecode.h | 28 -
src/plugins/remote_service/src/base64/cencode.c | 130 -
src/plugins/remote_service/src/base64/cencode.h | 31 -
.../src/ui/RemoteServiceSupportUI.ui | 262 -
.../remote_service/src/ui/TaskStatisticsDialog.ui | 157 -
src/plugins/remote_service/transl/english.ts | 316 -
src/plugins/remote_service/transl/russian.ts | 316 -
src/plugins/repeat_finder/CMakeLists.txt | 3 +
src/plugins/repeat_finder/repeat_finder.pri | 13 -
src/plugins/repeat_finder/repeat_finder.pro | 4 +-
.../repeat_finder/src/FindRepeatsDialog.cpp | 2 +-
src/plugins/repeat_finder/src/FindRepeatsDialog.h | 2 +-
.../src/{ui => }/FindRepeatsDialog.ui | 0
.../repeat_finder/src/FindTandemsDialog.cpp | 2 +-
src/plugins/repeat_finder/src/FindTandemsDialog.h | 2 +-
.../src/{ui => }/FindTandemsDialog.ui | 0
src/plugins/repeat_finder/src/RepeatTest.cpp | 29 -
src/plugins/repeat_finder/src/RepeatTest.h | 25 -
src/plugins/repeat_finder/transl/english.ts | 92 +-
src/plugins/repeat_finder/transl/russian.ts | 92 +-
src/plugins/smith_waterman/CMakeLists.txt | 5 +
src/plugins/smith_waterman/smith_waterman.pro | 2 +-
.../PairwiseAlignmentSmithWatermanGUIExtension.h | 2 +-
...AlignmentSmithWatermanOptionsPanelMainWidget.ui | 0
src/plugins/smith_waterman/src/SWAlgorithmTask.cpp | 25 +-
.../smith_waterman/src/SmithWatermanTests.cpp | 6 -
src/plugins/smith_waterman/transl/english.ts | 34 +-
src/plugins/smith_waterman/transl/russian.ts | 34 +-
src/plugins/test_runner/CMakeLists.txt | 5 +
.../test_runner/src/ExcludeReasonDialog.cpp | 2 +-
src/plugins/test_runner/src/ExcludeReasonDialog.h | 9 +-
.../src/{ui => }/ExcludeReasonDialog.ui | 0
.../src/{ui => }/ExcludeResaonDialog.ui | 0
src/plugins/test_runner/src/{ui => }/Reporter.ui | 0
src/plugins/test_runner/src/{ui => }/TestView.ui | 0
src/plugins/test_runner/src/TestViewController.h | 4 +-
src/plugins/test_runner/src/TestViewReporter.h | 4 +-
src/plugins/test_runner/test_runner.pro | 6 +-
src/plugins/test_runner/transl/english.ts | 18 +-
src/plugins/test_runner/transl/russian.ts | 18 +-
src/plugins/weight_matrix/CMakeLists.txt | 3 +
.../src/{ui => }/MatrixAndLogoWidget.ui | 0
.../weight_matrix/src/{ui => }/PWMBuildDialog.ui | 0
.../weight_matrix/src/PWMBuildDialogController.cpp | 111 +-
.../weight_matrix/src/PWMBuildDialogController.h | 28 +-
.../src/PWMJASPARDialogController.cpp | 2 +-
.../weight_matrix/src/PWMJASPARDialogController.h | 2 +-
.../weight_matrix/src/{ui => }/PWMSearchDialog.ui | 0
.../src/PWMSearchDialogController.cpp | 2 +-
.../weight_matrix/src/PWMSearchDialogController.h | 2 +-
.../src/{ui => }/SearchJASPARDatabase.ui | 0
.../src/{ui => }/SetDefaultParametersDialog.ui | 0
.../src/SetParametersDialogController.cpp | 2 +-
.../src/SetParametersDialogController.h | 2 +-
.../weight_matrix/src/{ui => }/ViewMatrixDialog.ui | 0
.../src/ViewMatrixDialogController.cpp | 2 +-
.../weight_matrix/src/ViewMatrixDialogController.h | 4 +-
src/plugins/weight_matrix/transl/english.ts | 208 +-
src/plugins/weight_matrix/transl/russian.ts | 208 +-
src/plugins/weight_matrix/weight_matrix.pro | 12 +-
src/plugins/workflow_designer/CMakeLists.txt | 3 +
.../workflow_designer/src/ChooseItemDialog.h | 2 +-
.../src/{ui => }/ChooseItemDialog.ui | 0
.../src/{ui => }/CreateScriptBlockDialog.ui | 0
.../workflow_designer/src/CreateScriptWorker.cpp | 2 +-
.../workflow_designer/src/CreateScriptWorker.h | 2 +-
.../src/DashboardsManagerDialog.cpp | 2 +-
.../src/DashboardsManagerDialog.h | 2 +-
.../src/{ui => }/DashboardsManagerDialog.ui | 0
.../{ui => }/GalaxyConfigConfigurationDialog.ui | 0
.../src/GalaxyConfigConfigurationDialogImpl.h | 2 +-
.../workflow_designer/src/ImportSchemaDialog.cpp | 2 +-
.../workflow_designer/src/ImportSchemaDialog.h | 2 +-
.../src/{ui => }/ImportSchemaDialog.ui | 0
.../src/{ui => }/PaletteWidget.ui | 0
.../src/PortAliasesConfigurationDialog.cpp | 2 +-
.../src/PortAliasesConfigurationDialog.h | 2 +-
.../src/{ui => }/PortAliasesConfigurationDialog.ui | 0
.../{ui => }/SchemaAliasesConfigurationDialog.ui | 0
.../src/SchemaAliasesConfigurationDialogImpl.cpp | 2 +-
.../src/SchemaAliasesConfigurationDialogImpl.h | 2 +-
.../workflow_designer/src/StartupDialog.cpp | 2 +-
src/plugins/workflow_designer/src/StartupDialog.h | 4 +-
.../src/{ui => }/StartupDialog.ui | 0
.../src/WorkflowDesignerPlugin.cpp | 7 +-
.../workflow_designer/src/WorkflowDesignerPlugin.h | 2 -
src/plugins/workflow_designer/src/WorkflowEditor.h | 2 +-
.../src/{ui => }/WorkflowEditorWidget.ui | 0
.../workflow_designer/src/WorkflowMetaDialog.cpp | 43 +-
.../workflow_designer/src/WorkflowMetaDialog.h | 12 +-
.../src/{ui => }/WorkflowMetaDialog.ui | 0
.../workflow_designer/src/WorkflowPalette.cpp | 4 +-
.../workflow_designer/src/WorkflowPalette.h | 2 +-
.../src/WorkflowSettingsController.cpp | 2 +-
.../src/WorkflowSettingsController.h | 2 +-
.../src/{ui => }/WorkflowSettingsWidget.ui | 0
.../src/WorkflowViewController.cpp | 26 +-
.../workflow_designer/src/WorkflowViewController.h | 1 -
.../src/cmdline/WorkflowCMDLineTasks.cpp | 31 -
.../src/cmdline/WorkflowCMDLineTasks.h | 13 -
.../src/library/CreateExternalProcessDialog.cpp | 202 +-
.../src/library/CreateExternalProcessDialog.h | 4 +-
.../{ui => library}/ExternalProcessWorkerDialog.ui | 0
.../src/library/ExtractAssemblyCoverageWorker.cpp | 12 +-
.../src/tasks/ReadAssemblyTask.cpp | 2 +-
src/plugins/workflow_designer/transl/english.ts | 564 +-
src/plugins/workflow_designer/transl/russian.ts | 854 +--
.../workflow_designer/workflow_designer.pro | 26 +-
src/plugins_3rdparty/ball/CMakeLists.txt | 6 +
.../ball/src/source/COMMON/exception.cpp | 6 +-
src/plugins_3rdparty/gor4/CMakeLists.txt | 3 +
src/plugins_3rdparty/hmm2/CMakeLists.txt | 3 +
src/plugins_3rdparty/hmm2/hmm2.pro | 6 +-
.../hmm2/src/u_build/{ui => }/HMMBuildDialog.ui | 0
.../hmm2/src/u_build/HMMBuildDialogController.cpp | 48 +-
.../hmm2/src/u_build/HMMBuildDialogController.h | 18 +-
.../src/u_calibrate/{ui => }/HMMCalibrateDialog.ui | 0
.../u_calibrate/HMMCalibrateDialogController.cpp | 48 +-
.../src/u_calibrate/HMMCalibrateDialogController.h | 18 +-
.../hmm2/src/u_search/{ui => }/HMMSearchDialog.ui | 0
.../src/u_search/HMMSearchDialogController.cpp | 2 +-
.../hmm2/src/u_search/HMMSearchDialogController.h | 2 +-
src/plugins_3rdparty/hmm2/transl/english.ts | 234 +-
src/plugins_3rdparty/hmm2/transl/russian.ts | 234 +-
src/plugins_3rdparty/hmm3/CMakeLists.txt | 5 +
src/plugins_3rdparty/hmm3/hmm3.pro | 8 +-
.../hmm3/src/build/UHMM3BuildDialog.ui | 898 +++
.../hmm3/src/build/uHMM3BuildDialogImpl.cpp | 45 +-
.../hmm3/src/build/uHMM3BuildDialogImpl.h | 14 +-
.../hmm3/src/build/ui/UHMM3BuildDialog.ui | 895 ---
.../hmm3/src/hmmer3/easel/easel.cpp | 8 +-
.../hmm3/src/hmmer3/easel/esl_dirichlet.cpp | 6 +-
.../hmm3/src/hmmer3/hmmer3_funcs.cpp | 2 +-
.../hmm3/src/hmmer3/hmmer3_funcs.h | 1 +
.../hmm3/src/hmmer3/impl_sse/decoding.cpp | 4 +-
.../hmm3/src/hmmer3/impl_sse/fwdback.cpp | 8 +-
.../hmm3/src/phmmer/{ui => }/UHMM3PhmmerDialog.ui | 0
.../hmm3/src/phmmer/uHMM3PhmmerDialogImpl.cpp | 2 +-
.../hmm3/src/phmmer/uHMM3PhmmerDialogImpl.h | 2 +-
.../hmm3/src/search/Hmmer3SearchWorkflowTask.cpp | 134 +
.../hmm3/src/search/Hmmer3SearchWorkflowTask.h | 63 +
.../hmm3/src/search/{ui => }/UHMM3SearchDialog.ui | 0
.../hmm3/src/search/uHMM3SearchDialogImpl.cpp | 9 +-
.../hmm3/src/search/uHMM3SearchDialogImpl.h | 2 +-
.../hmm3/src/search/uHMM3SearchTask.cpp | 163 -
.../hmm3/src/search/uHMM3SearchTask.h | 36 -
.../hmm3/src/workers/HMM3SearchWorker.cpp | 127 +-
.../hmm3/src/workers/HMM3SearchWorker.h | 11 +-
src/plugins_3rdparty/hmm3/transl/english.ts | 463 +-
src/plugins_3rdparty/hmm3/transl/russian.ts | 463 +-
src/plugins_3rdparty/kalign/CMakeLists.txt | 3 +
src/plugins_3rdparty/kalign/kalign.pro | 5 +-
.../kalign/src/{ui => }/KalignDialog.ui | 0
.../kalign/src/KalignDialogController.cpp | 79 +-
.../kalign/src/KalignDialogController.h | 23 +-
...airwiseAlignmentHirschbergGUIExtensionFactory.h | 2 +-
...iseAlignmentHirschbergOptionsPanelMainWidget.ui | 0
.../kalign/src/kalign2/kalign2_hirschberg_large.c | 2508 -------
.../kalign/src/kalign2/kalign2_hirschberg_large.h | 71 -
.../kalign/src/kalign2/kalign2_simple_gaps.c | 869 ---
.../kalign/src/kalign2/kalign2_upgma.c | 283 -
src/plugins_3rdparty/kalign/transl/english.ts | 52 +-
src/plugins_3rdparty/kalign/transl/russian.ts | 52 +-
src/plugins_3rdparty/phylip/CMakeLists.txt | 3 +
src/plugins_3rdparty/phylip/phylip.pro | 6 +-
.../phylip/src/NeighborJoinAdapter.cpp | 3 +-
.../phylip/src/NeighborJoinWidget.h | 4 +-
.../phylip/src/{ui => }/NeighborJoinWidget.ui | 0
.../phylip/src/PhylipCmdlineTask.cpp | 120 +
.../phylip/src/PhylipCmdlineTask.h | 68 +
src/plugins_3rdparty/phylip/src/PhylipPlugin.cpp | 95 +-
src/plugins_3rdparty/phylip/src/PhylipPlugin.h | 3 +-
.../phylip/src/PhylipPluginTests.cpp | 4 +
src/plugins_3rdparty/phylip/src/PhylipTask.cpp | 62 +
src/plugins_3rdparty/phylip/src/PhylipTask.h | 54 +
src/plugins_3rdparty/phylip/transl/english.ts | 49 +-
src/plugins_3rdparty/phylip/transl/russian.ts | 49 +-
src/plugins_3rdparty/primer3/CMakeLists.txt | 3 +
src/plugins_3rdparty/primer3/primer3.pro | 2 +-
.../primer3/src/FindExonRegionsTask.cpp | 2 +-
src/plugins_3rdparty/primer3/src/Primer3Dialog.cpp | 2 +-
src/plugins_3rdparty/primer3/src/Primer3Dialog.h | 2 +-
.../primer3/src/{ui => }/Primer3Dialog.ui | 0
src/plugins_3rdparty/primer3/src/Primer3Task.cpp | 4 +-
src/plugins_3rdparty/primer3/src/Primer3Task.h | 2 +-
.../primer3/src/Primer3TaskSettings.cpp | 2 +-
.../primer3/src/Primer3TaskSettings.h | 2 +-
src/plugins_3rdparty/primer3/src/Primer3Tests.cpp | 2 +-
src/plugins_3rdparty/primer3/transl/english.ts | 532 +-
src/plugins_3rdparty/primer3/transl/russian.ts | 532 +-
src/plugins_3rdparty/psipred/CMakeLists.txt | 3 +
src/plugins_3rdparty/psipred/src/sspred_avpred.cpp | 12 +-
src/plugins_3rdparty/psipred/src/sspred_avpred.h | 2 +-
src/plugins_3rdparty/ptools/CMakeLists.txt | 3 +
src/plugins_3rdparty/sitecon/CMakeLists.txt | 3 +
src/plugins_3rdparty/sitecon/sitecon.pro | 2 +-
.../sitecon/src/{ui => }/SiteconBuildDialog.ui | 0
.../sitecon/src/SiteconBuildDialogController.cpp | 51 +-
.../sitecon/src/SiteconBuildDialogController.h | 14 +-
.../sitecon/src/{ui => }/SiteconSearchDialog.ui | 0
.../sitecon/src/SiteconSearchDialogController.cpp | 2 +-
.../sitecon/src/SiteconSearchDialogController.h | 2 +-
src/plugins_3rdparty/sitecon/transl/english.ts | 157 +-
src/plugins_3rdparty/sitecon/transl/russian.ts | 157 +-
src/plugins_3rdparty/umuscle/CMakeLists.txt | 6 +
.../umuscle/src/{ui => }/MuscleAlignDialog.ui | 0
.../umuscle/src/MuscleAlignDialogController.cpp | 79 +-
.../umuscle/src/MuscleAlignDialogController.h | 20 +-
.../umuscle/src/MuscleParallel.cpp | 4 +-
src/plugins_3rdparty/umuscle/src/MusclePlugin.cpp | 4 +-
src/plugins_3rdparty/umuscle/src/MuscleTask.cpp | 2 +-
.../umuscle/src/MuscleWorkPool.cpp | 6 +-
src/plugins_3rdparty/umuscle/src/MuscleWorkPool.h | 2 +-
.../umuscle/src/muscle/diffpaths.cpp | 20 +-
src/plugins_3rdparty/umuscle/src/muscle/mhack.cpp | 6 +-
.../umuscle/src/muscle/muscle_context.h | 6 +-
src/plugins_3rdparty/umuscle/transl/english.ts | 151 +-
src/plugins_3rdparty/umuscle/transl/russian.ts | 151 +-
src/plugins_3rdparty/umuscle/umuscle.pro | 2 +-
src/plugins_3rdparty/variants/CMakeLists.txt | 3 +
.../variants/src/SamtoolMpileupWorker.cpp | 92 +-
.../variants/src/SamtoolMpileupWorker.h | 10 +-
src/plugins_3rdparty/variants/transl/english.ts | 250 +-
src/plugins_3rdparty/variants/transl/russian.ts | 250 +-
src/plugins_checker/plugins_checker.pri | 6 +-
src/plugins_checker/src/Main.cpp | 9 +-
src/ugene_globals.pri | 18 +-
src/ugene_plugin_common.pri | 24 +-
src/ugene_plugin_descriptor.pri | 12 +-
src/ugene_version.pri | 6 +-
src/ugenecl/CMakeLists.txt | 25 +
src/ugenecl/src/Main.cpp | 13 +-
src/ugenecl/ugenecl.pri | 6 +-
src/ugenem/src/DetectWin10.cpp | 103 +
src/ugenem/src/DetectWin10.h | 92 +
src/ugenem/src/SendReportDialog.cpp | 132 +-
src/ugenem/src/SendReportDialog.h | 10 +-
src/ugenem/ugenem.pro | 8 +-
src/ugeneui/CMakeLists.txt | 30 +
src/ugeneui/html/version_news.html | 152 +-
src/ugeneui/html/welcome_page.css | 2 +-
src/ugeneui/html/welcome_page.html | 33 +-
src/ugeneui/src/Main.cpp | 62 +-
.../src/app_settings/{ui => }/AppSettingsDialog.ui | 0
.../app_settings/AppSettingsDialogController.cpp | 4 +
.../src/app_settings/AppSettingsDialogController.h | 2 +-
.../DirectoriesSettingsGUIController.cpp | 2 +-
.../DirectoriesSettingsGUIController.h | 2 +-
.../{ui => }/DirectoriesSettingsWidget.ui | 0
.../FormatSettingsGUIController.cpp | 2 +-
.../format_settings/FormatSettingsGUIController.h | 2 +-
.../{ui => }/FormatSettingsWidget.ui | 0
.../logview_settings/LogSettingsGUIController.cpp | 54 +-
.../logview_settings/LogSettingsGUIController.h | 22 +-
.../logview_settings/{ui => }/LogSettingsWidget.ui | 0
.../NetworkSettingsGUIController.cpp | 2 +-
.../NetworkSettingsGUIController.h | 2 +-
.../{ui => }/NetworkSettingsWidget.ui | 0
.../ResourceSettingsGUIController.cpp | 3 +-
.../ResourceSettingsGUIController.h | 2 +-
.../{ui => }/ResourceSettingsWidget.ui | 0
.../UserApplicationsSettingsGUIController.cpp | 6 +-
.../UserApplicationsSettingsGUIController.h | 8 +-
.../UserApplicationsSettingsWidget.ui | 193 +
.../ui/UserApplicationsSettingsWidget.ui | 177 -
.../src/main_window/{ui => }/AboutDialog.ui | 0
.../src/main_window/AboutDialogController.h | 2 +-
src/ugeneui/src/main_window/CheckUpdatesTask.cpp | 130 +-
src/ugeneui/src/main_window/CheckUpdatesTask.h | 32 +-
src/ugeneui/src/main_window/MainWindowImpl.cpp | 3 +-
.../src/main_window/{ui => }/TmpDirChangeDialog.ui | 0
.../src/main_window/TmpDirChangeDialogController.h | 2 +-
.../src/plugin_viewer/PluginViewerController.h | 4 +-
.../plugin_viewer/{ui => }/PluginViewerWidget.ui | 0
.../{ui => }/CreateNewProjectWidget.ui | 0
.../DocumentFormatSelectorController.cpp | 2 +-
.../DocumentFormatSelectorController.h | 2 +-
.../{ui => }/DocumentFormatSelectorDialog.ui | 0
.../DocumentProviderSelectorController.cpp | 2 +-
.../DocumentProviderSelectorController.h | 2 +-
.../{ui => }/DocumentProviderSelectorDialog.ui | 0
.../DocumentReadingModeSelectorController.cpp | 4 +-
.../{ui => }/ExportProjectDialog.ui | 0
.../ExportProjectDialogController.cpp | 2 +-
.../ExportProjectDialogController.h | 2 +-
...tipleDocumentsReadingModeSelectorController.cpp | 134 +-
...ultipleDocumentsReadingModeSelectorController.h | 44 +-
.../MultipleSequenceFilesReadingMode.ui | 265 +
.../src/project_support/ProjectLoaderImpl.cpp | 10 +-
.../src/project_support/ProjectLoaderImpl.h | 8 +-
.../src/project_support/ProjectTasksGui.cpp | 2 +-
.../project_support/{ui => }/SaveProjectDialog.ui | 0
.../{ui => }/SequenceReadingModeSelectorDialog.ui | 0
.../ui/MultipleSequenceFilesReadingMode.ui | 281 -
.../src/project_view/ProjectViewDocTree.cpp | 43 -
src/ugeneui/src/project_view/ProjectViewDocTree.h | 41 -
src/ugeneui/src/project_view/ProjectViewImpl.h | 2 +-
src/ugeneui/src/project_view/ProjectViewWidget.ui | 154 +
.../src/project_view/ui/ProjectViewWidget.ui | 137 -
src/ugeneui/src/shtirlitz/Shtirlitz.cpp | 10 +-
src/ugeneui/src/shtirlitz/StatisticalReport.ui | 96 +
.../src/shtirlitz/StatisticalReportController.cpp | 6 +
.../src/shtirlitz/StatisticalReportController.h | 2 +-
src/ugeneui/src/shtirlitz/ui/StatisticalReport.ui | 96 -
src/ugeneui/src/task_view/TaskViewController.cpp | 8 +-
src/ugeneui/src/update/UgeneUpdater.cpp | 126 +
src/ugeneui/src/update/UgeneUpdater.h | 69 +
src/ugeneui/src/utils/MultilingualHtmlView.cpp | 14 +-
src/ugeneui/src/welcome_page/WelcomePageWidget.cpp | 2 +-
src/ugeneui/transl/english.ts | 537 +-
src/ugeneui/transl/russian.ts | 537 +-
src/ugeneui/ugeneui.pri | 6 +-
src/ugeneui/ugeneui.pro | 42 +-
ugene.pro | 52 +-
1609 files changed, 39114 insertions(+), 106077 deletions(-)
create mode 100644 data/cmdline/hmm3-search.uwl
create mode 100644 src/corelibs/U2Algorithm/CMakeLists.txt
delete mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/MSAColorScheme.cpp
delete mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/MSAColorScheme.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/ColorSchemeUtils.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/ColorSchemeUtils.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorScheme.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorScheme.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorSchemeClustalX.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorSchemeClustalX.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorSchemeCustom.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorSchemeCustom.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorSchemePercentageIdententityGrayscale.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorSchemePercentageIdententityGrayscale.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorSchemePercentageIdentity.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorSchemePercentageIdentity.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorSchemeStatic.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/color_schemes/MsaColorSchemeStatic.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingScheme.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingScheme.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeAgreements.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeAgreements.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeConservation.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeConservation.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeDisagreements.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeDisagreements.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeGaps.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeGaps.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeNoColors.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeNoColors.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeTransitions.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeTransitions.h
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeTransversions.cpp
create mode 100644 src/corelibs/U2Algorithm/src/util_msaedit/highlighting_schemes/MsaHighlightingSchemeTransversions.h
create mode 100644 src/corelibs/U2Core/CMakeLists.txt
create mode 100644 src/corelibs/U2Core/src/tasks/CmdlineInOutTaskRunner.cpp
create mode 100644 src/corelibs/U2Core/src/tasks/CmdlineInOutTaskRunner.h
create mode 100644 src/corelibs/U2Core/src/tasks/CmdlineTaskRunner.cpp
create mode 100644 src/corelibs/U2Core/src/tasks/CmdlineTaskRunner.h
delete mode 100644 src/corelibs/U2Core/src/util/SNPTablesUtils.cpp
create mode 100644 src/corelibs/U2Core/src/util/SyncHttp.cpp
create mode 100644 src/corelibs/U2Core/src/util/SyncHttp.h
create mode 100644 src/corelibs/U2Designer/CMakeLists.txt
rename src/corelibs/U2Designer/src/{ui => }/AnnsActionDialog.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/BreakpointHitCountDialog.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/CreateDirectoryDialog.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/DatasetWidget.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/DbFolderOptions.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/DirectoryOptions.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/EditBreakpointLabelsDialog.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/EditFloatMarkerWidget.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/EditIntegerMarkerWidget.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/EditMarkerDialog.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/EditMarkerGroupDialog.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/EditStringMarkerWidget.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/GrouperEditorWidget.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/MarkerEditorWidget.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/MsaActionDialog.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/NewBreakpointDialog.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/NewGrouperSlotDialog.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/OutputFileDialog.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/SequenceActionDialog.ui (100%)
rename src/corelibs/U2Designer/src/{ui => }/StringActionDialog.ui (100%)
create mode 100644 src/corelibs/U2Formats/CMakeLists.txt
create mode 100644 src/corelibs/U2Gui/CMakeLists.txt
create mode 100644 src/corelibs/U2Gui/images/codon_table.png
create mode 100644 src/corelibs/U2Gui/images/extract_assembly_region.png
create mode 100644 src/corelibs/U2Gui/src/util/AddNewDocumentDialog.ui
rename src/corelibs/U2Gui/src/util/{ui => }/AuthenticationDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/{ui => }/AuthenticationWidget.ui (100%)
rename src/corelibs/U2Gui/src/util/{ui => }/BreakpointConditionEditDialog.ui (100%)
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rename src/corelibs/U2Gui/src/util/{ui => }/CreateDocumentFromTextDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/{ui => }/CreateObjectRelationDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/{ui => }/DownloadRemoteFileDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/{ui => }/EditQualifierDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/{ui => }/EditSequenceDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/{ui => }/ExportAnnotationsDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/{ui => }/ExportDocumentDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/{ui => }/ExportImageDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/ImportDialogs/{ui => }/AceImportDialog.ui (100%)
create mode 100644 src/corelibs/U2Gui/src/util/MultiClickMenu.cpp
create mode 100644 src/corelibs/U2Gui/src/util/MultiClickMenu.h
rename src/corelibs/U2Gui/src/util/{ui => }/MultipartDocFormatConfiguratorWidget.ui (100%)
create mode 100644 src/corelibs/U2Gui/src/util/ProjectTreeItemSelectorDialogBase.ui
rename src/corelibs/U2Gui/src/util/{ui => }/RangeSelectionDialog.ui (100%)
create mode 100644 src/corelibs/U2Gui/src/util/RegionSelectorController.cpp
create mode 100644 src/corelibs/U2Gui/src/util/RegionSelectorController.h
create mode 100644 src/corelibs/U2Gui/src/util/RegionSelectorWithExcludedRegion.cpp
create mode 100644 src/corelibs/U2Gui/src/util/RegionSelectorWithExcludedRegion.h
create mode 100644 src/corelibs/U2Gui/src/util/RegionSelectorWithExcludedRegion.ui
rename src/corelibs/U2Gui/src/util/{ui => }/RemovePartFromSequenceDialog.ui (100%)
create mode 100644 src/corelibs/U2Gui/src/util/SaveDocumentController.cpp
create mode 100644 src/corelibs/U2Gui/src/util/SaveDocumentController.h
delete mode 100644 src/corelibs/U2Gui/src/util/SaveDocumentGroupController.cpp
delete mode 100644 src/corelibs/U2Gui/src/util/SaveDocumentGroupController.h
rename src/corelibs/U2Gui/src/util/{ui => }/ScriptEditorDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/{ui => }/SearchGenbankSequenceDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/{ui => }/SeqPasterWidget.ui (100%)
create mode 100644 src/corelibs/U2Gui/src/util/project/EditableTreeView.cpp
create mode 100644 src/corelibs/U2Gui/src/util/project/EditableTreeView.h
create mode 100644 src/corelibs/U2Gui/src/util/project/FolderNameDialog.ui
rename src/corelibs/U2Gui/src/util/shared_db/{ui => }/CommonImportOptionsDialog.ui (100%)
create mode 100644 src/corelibs/U2Gui/src/util/shared_db/EditConnectionDialog.ui
rename src/corelibs/U2Gui/src/util/shared_db/{ui => }/ImportOptionsWidget.ui (100%)
rename src/corelibs/U2Gui/src/util/shared_db/{ui => }/ImportToDatabaseDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/shared_db/{ui => }/ItemToImportEditDialog.ui (100%)
rename src/corelibs/U2Gui/src/util/shared_db/{ui => }/SharedConnectionsDialog.ui (100%)
delete mode 100644 src/corelibs/U2Gui/src/util/shared_db/ui/EditConnectionDialog.ui
delete mode 100644 src/corelibs/U2Gui/src/util/ui/AddNewDocumentDialog.ui
delete mode 100644 src/corelibs/U2Gui/src/util/ui/FolderNameDialog.ui
delete mode 100644 src/corelibs/U2Gui/src/util/ui/ProjectTreeItemSelectorDialogBase.ui
create mode 100644 src/corelibs/U2Lang/CMakeLists.txt
create mode 100644 src/corelibs/U2Lang/src/support/DatasetFetcher.cpp
create mode 100644 src/corelibs/U2Lang/src/support/DatasetFetcher.h
create mode 100644 src/corelibs/U2Private/CMakeLists.txt
delete mode 100644 src/corelibs/U2Remote/U2Remote.pri
delete mode 100644 src/corelibs/U2Remote/U2Remote.pro
delete mode 100644 src/corelibs/U2Remote/src/DistributedComputingUtil.cpp
delete mode 100644 src/corelibs/U2Remote/src/DistributedComputingUtil.h
delete mode 100644 src/corelibs/U2Remote/src/PingTask.cpp
delete mode 100644 src/corelibs/U2Remote/src/PingTask.h
delete mode 100644 src/corelibs/U2Remote/src/ProtocolInfo.cpp
delete mode 100644 src/corelibs/U2Remote/src/ProtocolInfo.h
delete mode 100644 src/corelibs/U2Remote/src/ProtocolUI.cpp
delete mode 100644 src/corelibs/U2Remote/src/ProtocolUI.h
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachine.cpp
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachine.h
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineMonitor.cpp
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineMonitor.h
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineMonitorDialogController.cpp
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineMonitorDialogController.h
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineMonitorDialogImpl.cpp
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineMonitorDialogImpl.h
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineScanDialogImpl.cpp
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineScanDialogImpl.h
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineScanner.cpp
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineScanner.h
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineSettingsDialog.cpp
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineSettingsDialog.h
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineTasks.cpp
delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineTasks.h
delete mode 100644 src/corelibs/U2Remote/src/RemoteWorkflowRunTask.cpp
delete mode 100644 src/corelibs/U2Remote/src/RemoteWorkflowRunTask.h
delete mode 100644 src/corelibs/U2Remote/src/Serializable.cpp
delete mode 100644 src/corelibs/U2Remote/src/Serializable.h
delete mode 100644 src/corelibs/U2Remote/src/SerializeUtils.cpp
delete mode 100644 src/corelibs/U2Remote/src/SerializeUtils.h
delete mode 100644 src/corelibs/U2Remote/src/SynchHttp.cpp
delete mode 100644 src/corelibs/U2Remote/src/SynchHttp.h
delete mode 100644 src/corelibs/U2Remote/src/TaskDistributor.h
delete mode 100644 src/corelibs/U2Remote/src/ui/RemoteMachineMonitorDialog.ui
delete mode 100644 src/corelibs/U2Remote/src/ui/RemoteMachineScanDialog.ui
delete mode 100644 src/corelibs/U2Remote/src/ui/RemoteMachineSettingsDialog.ui
delete mode 100644 src/corelibs/U2Remote/transl/english.ts
delete mode 100644 src/corelibs/U2Remote/transl/russian.ts
create mode 100644 src/corelibs/U2Test/CMakeLists.txt
rename src/corelibs/U2Test/{ => src/gui_tests}/GUITestingWindow.ui (100%)
create mode 100644 src/corelibs/U2View/CMakeLists.txt
rename src/corelibs/U2View/src/{ui => }/LicenseDialog.ui (100%)
rename src/corelibs/U2View/src/ov_assembly/{ui => }/ExportConsensusDialog.ui (100%)
create mode 100644 src/corelibs/U2View/src/ov_assembly/ExportCoverageDialog.ui
rename src/corelibs/U2View/src/ov_assembly/{ui => }/ExportReadsDialog.ui (100%)
create mode 100644 src/corelibs/U2View/src/ov_assembly/ExtractAssemblyRegionDialog.cpp
create mode 100644 src/corelibs/U2View/src/ov_assembly/ExtractAssemblyRegionDialog.h
create mode 100644 src/corelibs/U2View/src/ov_assembly/ExtractAssemblyRegionDialog.ui
create mode 100644 src/corelibs/U2View/src/ov_assembly/ExtractAssemblyRegionTask.cpp
create mode 100644 src/corelibs/U2View/src/ov_assembly/ExtractAssemblyRegionTask.h
delete mode 100644 src/corelibs/U2View/src/ov_assembly/ui/ExportCoverageDialog.ui
rename src/corelibs/U2View/src/ov_msa/{ui => }/ColorSchemaDialog.ui (100%)
rename src/corelibs/U2View/src/ov_msa/{ui => }/ColorSchemaSettingsWidget.ui (100%)
rename src/corelibs/U2View/src/ov_msa/{ui => }/CreateMSAScheme.ui (100%)
rename src/corelibs/U2View/src/ov_msa/{ui => }/CreateSubalignmentDialog.ui (100%)
rename src/corelibs/U2View/src/ov_msa/{ui => }/DeleteGapsDialog.ui (100%)
rename src/corelibs/U2View/src/ov_msa/{ui => Export}/MSAExportSettings.ui (100%)
create mode 100644 src/corelibs/U2View/src/ov_msa/ExportConsensus/ExportConsensusWidget.ui
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rename src/corelibs/U2View/src/ov_msa/{ui => General}/GeneralTabOptionsPanelWidget.ui (100%)
rename src/corelibs/U2View/src/ov_msa/{ui => PairAlign}/PairwiseAlignmentOptionsPanelWidget.ui (100%)
delete mode 100644 src/corelibs/U2View/src/ov_msa/PhyTrees/MSAEditorTreeViewerTasks.cpp
delete mode 100644 src/corelibs/U2View/src/ov_msa/PhyTrees/MSAEditorTreeViewerTasks.h
rename src/corelibs/U2View/src/ov_msa/{ui => }/SaveSelectedSequenceFromMSADialog.ui (100%)
rename src/corelibs/U2View/src/ov_msa/{ui => }/SelectSubalignmentDialog.ui (100%)
rename src/corelibs/U2View/src/ov_msa/{ui => SeqStatistics}/MSADistancesColumnSettingsWidget.ui (100%)
rename src/corelibs/U2View/src/ov_msa/{ui => }/SequenceSelectorWidget.ui (100%)
delete mode 100644 src/corelibs/U2View/src/ov_msa/TreeOptions/AddTreeWidget.cpp
delete mode 100644 src/corelibs/U2View/src/ov_msa/TreeOptions/AddTreeWidget.h
rename src/corelibs/U2View/src/ov_msa/{ui => TreeOptions}/TreeOptionsWidget.ui (100%)
delete mode 100644 src/corelibs/U2View/src/ov_msa/ui/ExportConsensusWidget.ui
delete mode 100644 src/corelibs/U2View/src/ov_sequence/ADVSplitWidget.cpp
rename src/corelibs/U2View/src/ov_sequence/{ui => }/CreateRulerDialog.ui (100%)
delete mode 100644 src/corelibs/U2View/src/ov_sequence/EditAnnotationDialogController.cpp
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rename src/corelibs/U2View/src/ov_sequence/{ui => }/SaveGraphCutoffsDialog.ui (100%)
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rename src/corelibs/U2View/src/ov_sequence/annot_highlight/{ui => }/AnnotHighlightSettings.ui (100%)
rename src/corelibs/U2View/src/ov_sequence/find_pattern/{ui => }/FindPatternForm.ui (100%)
delete mode 100644 src/corelibs/U2View/src/ov_sequence/ui/EditAnnotationDialog.ui
rename src/corelibs/U2View/src/phyltree/{ui => }/BranchSettingsDialog.ui (100%)
rename src/corelibs/U2View/src/phyltree/{ui => }/CreatePhyTreeDialog.ui (100%)
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rename src/corelibs/U2View/src/phyltree/{ui => }/TreeSettingsDialog.ui (100%)
rename src/corelibs/U2View/src/util_dna_assembly/{ui => }/AssemblyToRefDialog.ui (100%)
create mode 100644 src/corelibs/U2View/src/util_dna_assembly/AssemblyToSamDialog.ui
rename src/corelibs/U2View/src/util_dna_assembly/{ui => }/BuildIndexFromRefDialog.ui (100%)
rename src/corelibs/U2View/src/util_dna_assembly/{ui => }/GenomeAssemblyDialog.ui (100%)
delete mode 100644 src/corelibs/U2View/src/util_dna_assembly/ui/AssemblyToSamDialog.ui
rename src/corelibs/U2View/src/util_sec_struct_predict/{ui => }/SecStructDialog.ui (100%)
rename src/corelibs/U2View/src/util_smith_waterman/{ui => }/SmithWatermanDialogBase.ui (100%)
rename src/corelibs/U2View/src/util_smith_waterman/{ui => }/SubstMatrixDialogBase.ui (100%)
create mode 100644 src/include/3rdparty/sqlite3/sqlite3.h
create mode 100644 src/include/3rdparty/zlib/zlib.h
create mode 100644 src/include/U2Algorithm/ColorSchemeUtils.h
delete mode 100644 src/include/U2Algorithm/MSAColorScheme.h
create mode 100644 src/include/U2Algorithm/MsaColorScheme.h
create mode 100644 src/include/U2Algorithm/MsaHighlightingScheme.h
create mode 100644 src/include/U2Core/CmdlineInOutTaskRunner.h
create mode 100644 src/include/U2Core/CmdlineTaskRunner.h
create mode 100644 src/include/U2Core/SyncHttp.h
create mode 100644 src/include/U2Gui/EditableTreeView.h
create mode 100644 src/include/U2Gui/MultiClickMenu.h
create mode 100644 src/include/U2Gui/RegionSelectorWithExcludedRegion.h
create mode 100644 src/include/U2Gui/SaveDocumentController.h
delete mode 100644 src/include/U2Gui/SaveDocumentGroupController.h
create mode 100644 src/include/U2Lang/DatasetFetcher.h
delete mode 100644 src/include/U2Remote/DistributedComputingUtil.h
delete mode 100644 src/include/U2Remote/PingTask.h
delete mode 100644 src/include/U2Remote/ProtocolInfo.h
delete mode 100644 src/include/U2Remote/ProtocolUI.h
delete mode 100644 src/include/U2Remote/RemoteMachine.h
delete mode 100644 src/include/U2Remote/RemoteMachineMonitor.h
delete mode 100644 src/include/U2Remote/RemoteMachineMonitorDialogController.h
delete mode 100644 src/include/U2Remote/RemoteMachineScanner.h
delete mode 100644 src/include/U2Remote/RemoteMachineTasks.h
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rename src/plugins/weight_matrix/src/{ui => }/SetDefaultParametersDialog.ui (100%)
rename src/plugins/weight_matrix/src/{ui => }/ViewMatrixDialog.ui (100%)
create mode 100644 src/plugins/workflow_designer/CMakeLists.txt
rename src/plugins/workflow_designer/src/{ui => }/ChooseItemDialog.ui (100%)
rename src/plugins/workflow_designer/src/{ui => }/CreateScriptBlockDialog.ui (100%)
rename src/plugins/workflow_designer/src/{ui => }/DashboardsManagerDialog.ui (100%)
rename src/plugins/workflow_designer/src/{ui => }/GalaxyConfigConfigurationDialog.ui (100%)
rename src/plugins/workflow_designer/src/{ui => }/ImportSchemaDialog.ui (100%)
rename src/plugins/workflow_designer/src/{ui => }/PaletteWidget.ui (100%)
rename src/plugins/workflow_designer/src/{ui => }/PortAliasesConfigurationDialog.ui (100%)
rename src/plugins/workflow_designer/src/{ui => }/SchemaAliasesConfigurationDialog.ui (100%)
rename src/plugins/workflow_designer/src/{ui => }/StartupDialog.ui (100%)
rename src/plugins/workflow_designer/src/{ui => }/WorkflowEditorWidget.ui (100%)
rename src/plugins/workflow_designer/src/{ui => }/WorkflowMetaDialog.ui (100%)
rename src/plugins/workflow_designer/src/{ui => }/WorkflowSettingsWidget.ui (100%)
rename src/plugins/workflow_designer/src/{ui => library}/ExternalProcessWorkerDialog.ui (100%)
create mode 100644 src/plugins_3rdparty/ball/CMakeLists.txt
create mode 100644 src/plugins_3rdparty/gor4/CMakeLists.txt
create mode 100644 src/plugins_3rdparty/hmm2/CMakeLists.txt
rename src/plugins_3rdparty/hmm2/src/u_build/{ui => }/HMMBuildDialog.ui (100%)
rename src/plugins_3rdparty/hmm2/src/u_calibrate/{ui => }/HMMCalibrateDialog.ui (100%)
rename src/plugins_3rdparty/hmm2/src/u_search/{ui => }/HMMSearchDialog.ui (100%)
create mode 100644 src/plugins_3rdparty/hmm3/CMakeLists.txt
create mode 100644 src/plugins_3rdparty/hmm3/src/build/UHMM3BuildDialog.ui
delete mode 100644 src/plugins_3rdparty/hmm3/src/build/ui/UHMM3BuildDialog.ui
rename src/plugins_3rdparty/hmm3/src/phmmer/{ui => }/UHMM3PhmmerDialog.ui (100%)
create mode 100644 src/plugins_3rdparty/hmm3/src/search/Hmmer3SearchWorkflowTask.cpp
create mode 100644 src/plugins_3rdparty/hmm3/src/search/Hmmer3SearchWorkflowTask.h
rename src/plugins_3rdparty/hmm3/src/search/{ui => }/UHMM3SearchDialog.ui (100%)
create mode 100644 src/plugins_3rdparty/kalign/CMakeLists.txt
rename src/plugins_3rdparty/kalign/src/{ui => }/KalignDialog.ui (100%)
rename src/plugins_3rdparty/kalign/src/{ui => }/PairwiseAlignmentHirschbergOptionsPanelMainWidget.ui (100%)
delete mode 100644 src/plugins_3rdparty/kalign/src/kalign2/kalign2_hirschberg_large.c
delete mode 100644 src/plugins_3rdparty/kalign/src/kalign2/kalign2_hirschberg_large.h
delete mode 100644 src/plugins_3rdparty/kalign/src/kalign2/kalign2_simple_gaps.c
delete mode 100644 src/plugins_3rdparty/kalign/src/kalign2/kalign2_upgma.c
create mode 100644 src/plugins_3rdparty/phylip/CMakeLists.txt
rename src/plugins_3rdparty/phylip/src/{ui => }/NeighborJoinWidget.ui (100%)
create mode 100644 src/plugins_3rdparty/phylip/src/PhylipCmdlineTask.cpp
create mode 100644 src/plugins_3rdparty/phylip/src/PhylipCmdlineTask.h
create mode 100644 src/plugins_3rdparty/phylip/src/PhylipTask.cpp
create mode 100644 src/plugins_3rdparty/phylip/src/PhylipTask.h
create mode 100644 src/plugins_3rdparty/primer3/CMakeLists.txt
rename src/plugins_3rdparty/primer3/src/{ui => }/Primer3Dialog.ui (100%)
create mode 100644 src/plugins_3rdparty/psipred/CMakeLists.txt
create mode 100644 src/plugins_3rdparty/ptools/CMakeLists.txt
create mode 100644 src/plugins_3rdparty/sitecon/CMakeLists.txt
rename src/plugins_3rdparty/sitecon/src/{ui => }/SiteconBuildDialog.ui (100%)
rename src/plugins_3rdparty/sitecon/src/{ui => }/SiteconSearchDialog.ui (100%)
create mode 100644 src/plugins_3rdparty/umuscle/CMakeLists.txt
rename src/plugins_3rdparty/umuscle/src/{ui => }/MuscleAlignDialog.ui (100%)
create mode 100644 src/plugins_3rdparty/variants/CMakeLists.txt
create mode 100644 src/ugenecl/CMakeLists.txt
create mode 100644 src/ugenem/src/DetectWin10.cpp
create mode 100644 src/ugenem/src/DetectWin10.h
create mode 100644 src/ugeneui/CMakeLists.txt
rename src/ugeneui/src/app_settings/{ui => }/AppSettingsDialog.ui (100%)
rename src/ugeneui/src/app_settings/directories_settings/{ui => }/DirectoriesSettingsWidget.ui (100%)
rename src/ugeneui/src/app_settings/format_settings/{ui => }/FormatSettingsWidget.ui (100%)
rename src/ugeneui/src/app_settings/logview_settings/{ui => }/LogSettingsWidget.ui (100%)
rename src/ugeneui/src/app_settings/network_settings/{ui => }/NetworkSettingsWidget.ui (100%)
rename src/ugeneui/src/app_settings/resource_settings/{ui => }/ResourceSettingsWidget.ui (100%)
create mode 100644 src/ugeneui/src/app_settings/user_apps_settings/UserApplicationsSettingsWidget.ui
delete mode 100644 src/ugeneui/src/app_settings/user_apps_settings/ui/UserApplicationsSettingsWidget.ui
rename src/ugeneui/src/main_window/{ui => }/AboutDialog.ui (100%)
rename src/ugeneui/src/main_window/{ui => }/TmpDirChangeDialog.ui (100%)
rename src/ugeneui/src/plugin_viewer/{ui => }/PluginViewerWidget.ui (100%)
rename src/ugeneui/src/project_support/{ui => }/CreateNewProjectWidget.ui (100%)
rename src/ugeneui/src/project_support/{ui => }/DocumentFormatSelectorDialog.ui (100%)
rename src/ugeneui/src/project_support/{ui => }/DocumentProviderSelectorDialog.ui (100%)
rename src/ugeneui/src/project_support/{ui => }/ExportProjectDialog.ui (100%)
create mode 100644 src/ugeneui/src/project_support/MultipleSequenceFilesReadingMode.ui
rename src/ugeneui/src/project_support/{ui => }/SaveProjectDialog.ui (100%)
rename src/ugeneui/src/project_support/{ui => }/SequenceReadingModeSelectorDialog.ui (100%)
delete mode 100644 src/ugeneui/src/project_support/ui/MultipleSequenceFilesReadingMode.ui
delete mode 100644 src/ugeneui/src/project_view/ProjectViewDocTree.cpp
delete mode 100644 src/ugeneui/src/project_view/ProjectViewDocTree.h
create mode 100644 src/ugeneui/src/project_view/ProjectViewWidget.ui
delete mode 100644 src/ugeneui/src/project_view/ui/ProjectViewWidget.ui
create mode 100644 src/ugeneui/src/shtirlitz/StatisticalReport.ui
delete mode 100644 src/ugeneui/src/shtirlitz/ui/StatisticalReport.ui
create mode 100644 src/ugeneui/src/update/UgeneUpdater.cpp
create mode 100644 src/ugeneui/src/update/UgeneUpdater.h
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