[med-svn] [ugene] 02/10: Merge tag 'upstream/1.23.1+dfsg'
Sascha Steinbiss
satta at debian.org
Thu Jul 28 06:06:36 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository ugene.
commit 06e0bd5afed3474acc41b4d7ec96d94f52d2fb5d
Merge: 34b5cd0 a8a1cc6
Author: Sascha Steinbiss <satta at debian.org>
Date: Wed Jul 27 21:43:12 2016 +0000
Merge tag 'upstream/1.23.1+dfsg'
Upstream version 1.23.1+dfsg
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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(-)
--
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