[med-svn] [ugene] branch master updated (34b5cd0 -> 3b58136)
Sascha Steinbiss
satta at debian.org
Thu Jul 28 06:06:32 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch master
in repository ugene.
from 34b5cd0 Upload to unstable
new a8a1cc6 Imported Upstream version 1.23.1+dfsg
new 06e0bd5 Merge tag 'upstream/1.23.1+dfsg'
new 68b21f4 Debian version bump
new bbafce9 add changelog entry for rebuild
new 05342d0 rename fixperms target
new ea26930 refresh patches
new a6fc8be dch -r
new 36f05d0 bump Standards-Version
new ed54e4e use secure Vcs-Git
new 3b58136 enable full hardening
The 10 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 +
debian/changelog | 14 +
debian/control | 4 +-
debian/patches/hardening.patch | 4 +-
debian/patches/use_debian_sqlite.patch | 79 +-
debian/rules | 4 +-
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 +
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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 +-
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src/corelibs/U2Core/src/globals/global.h | 12 +-
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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 +
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src/corelibs/U2Core/src/tasks/CmdlineTaskRunner.h | 83 +
.../U2Core/src/tasks/ExternalToolRunTask.cpp | 210 +-
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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 +
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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/DbFolderItem.cpp | 4 +-
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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 +-
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.../U2Designer/src/NewGrouperSlotDialog.cpp | 10 +-
src/corelibs/U2Designer/src/NewGrouperSlotDialog.h | 10 +-
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src/corelibs/U2Designer/src/OutputFileDialog.h | 8 +-
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.../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 +
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src/corelibs/U2Remote/src/TaskDistributor.h | 87 -
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src/corelibs/U2Remote/transl/russian.ts | 516 --
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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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.../ov_assembly/ExportConsensusVariationsDialog.h | 25 +-
.../src/ov_assembly/ExportCoverageDialog.cpp | 129 +-
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.../ov_assembly/ExtractAssemblyRegionDialog.cpp | 118 +
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.../src/ov_assembly/ExtractAssemblyRegionTask.cpp | 98 +
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.../src/ov_assembly/ui/ExportCoverageDialog.ui | 194 -
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.../src/ov_msa/Highlighting/MSAHighlightingTab.cpp | 97 +-
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src/corelibs/U2View/src/ov_msa/MSAEditor.cpp | 29 +-
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.../src/ov_msa/MsaEditorSimilarityColumn.cpp | 2 +
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.../ov_msa/PhyTrees/MSAEditorTreeViewerTasks.cpp | 244 -
.../src/ov_msa/PhyTrees/MSAEditorTreeViewerTasks.h | 100 -
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.../src/ov_msa/SequenceSelectorWidgetController.h | 2 +-
.../src/ov_msa/TreeOptions/AddTreeWidget.cpp | 172 -
.../U2View/src/ov_msa/TreeOptions/AddTreeWidget.h | 55 -
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.../U2View/src/ov_msa/ui/ExportConsensusWidget.ui | 139 -
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.../src/ov_sequence/ADVSingleSequenceWidget.h | 1 +
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.../U2View/src/ov_sequence/AnnotatedDNAView.cpp | 57 +-
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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 +-
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.../src/ov_sequence/codon_table/CodonTable.cpp | 11 -
.../src/ov_sequence/codon_table/CodonTable.h | 8 -
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.../ov_sequence/find_pattern/FindPatternWidget.h | 2 +-
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.../src/phyltree/CreatePhyTreeDialogController.cpp | 57 +-
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.../src/util_dna_assembly/DnaAssemblyDialog.h | 22 +-
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.../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/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/{ui => bwa}/BwaSettings.ui | 0
.../src/bwa/BwaSettingsWidget.cpp | 46 +-
.../src/bwa/BwaSettingsWidget.h | 8 +-
.../src/{ui => bwa}/BwaSwSettings.ui | 0
.../external_tool_support/src/bwa/BwaTask.cpp | 329 +-
.../external_tool_support/src/bwa/BwaTask.h | 17 +-
.../src/cap3/CAP3SupportDialog.cpp | 61 +-
.../src/cap3/CAP3SupportDialog.h | 19 +-
.../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 +-
1614 files changed, 39170 insertions(+), 106126 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%)
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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
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rename src/corelibs/U2Gui/src/util/{ui => }/AuthenticationWidget.ui (100%)
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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
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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
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create mode 100644 src/corelibs/U2Gui/src/util/shared_db/EditConnectionDialog.ui
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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
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delete mode 100644 src/corelibs/U2Remote/src/RemoteMachineMonitor.cpp
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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
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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
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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
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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
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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%)
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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 => 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
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delete mode 100644 src/corelibs/U2View/src/ov_sequence/EditAnnotationDialogController.cpp
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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
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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
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rename src/plugins/test_runner/src/{ui => }/TestView.ui (100%)
create mode 100644 src/plugins/weight_matrix/CMakeLists.txt
rename src/plugins/weight_matrix/src/{ui => }/MatrixAndLogoWidget.ui (100%)
rename src/plugins/weight_matrix/src/{ui => }/PWMBuildDialog.ui (100%)
rename src/plugins/weight_matrix/src/{ui => }/PWMSearchDialog.ui (100%)
rename src/plugins/weight_matrix/src/{ui => }/SearchJASPARDatabase.ui (100%)
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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