[med-svn] [ugene] 02/04: Update upstream source from tag 'upstream/1.28.1+dfsg'
Andreas Tille
tille at debian.org
Sun Dec 3 18:08:35 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository ugene.
commit a34b993ff554907bc87b8014d786eab116e80f81
Merge: b5b837e 07b8965
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 3 19:06:33 2017 +0100
Update upstream source from tag 'upstream/1.28.1+dfsg'
Update to upstream version '1.28.1+dfsg'
with Debian dir 21eaefd971bbe6d2ea175d20bab4ef5243d17205
.gitignore | 46 +
.gitmodules | 4 +
.travis.yml | 14 +
CMakeLists.txt | 97 +
COPYRIGHT | 33 -
LICENSE.3rd_party.txt | 28 +-
README.md | 74 +
data/cmdline/align-to-reference.uwl | 102 +
data/cmdline/extract_consensus_sequence.uwl | 2 +-
data/samples/APR/DNA.apr | 1525 ++++++
data/samples/APR/gyrA.apr | 459 ++
.../Sanger sequencing/trim-and-align.uwl | 177 +-
installer/_common_data/Associate_files_to_UGENE.sh | 0
installer/_common_data/LICENSE.3rd_party | 28 +-
installer/linux/X11/README | 27 +
installer/linux/X11/create_bundle.sh | 232 +
installer/linux/X11/create_bundle_common.sh | 71 +
installer/linux/X11/i686/dump_syms | Bin 0 -> 2723028 bytes
installer/linux/X11/x86_64/dump_syms | Bin 0 -> 3287614 bytes
installer/linux/fedora/devel/ugene.spec | 75 -
installer/linux/fedora/mkinstaller.sh | 0
installer/linux/fedora/ugene.spec | 67 +-
installer/linux/ubuntu/build.sh | 0
installer/linux/ubuntu/debian/copyright | 28 +-
installer/linux/ubuntu/debian/rules | 7 +-
installer/linux/ubuntu/pack.sh | 0
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installer/windows_x64/build.cmd | 108 +
installer/windows_x64/bundle_binary_zip.cmd | 156 +
installer/windows_x64/bundle_ugene.vbs | 30 +
installer/windows_x64/copy_executable.cmd | 4 +
installer/windows_x64/copy_lib.cmd | 4 +
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installer/windows_x64/images/header.bmp | Bin 0 -> 25818 bytes
installer/windows_x64/images/install.ico | Bin 0 -> 25214 bytes
installer/windows_x64/images/install2.ico | Bin 0 -> 11502 bytes
installer/windows_x64/images/uninstall.ico | Bin 0 -> 766 bytes
installer/windows_x64/images/welcome.bmp | Bin 0 -> 154050 bytes
installer/windows_x64/resort_symbols.py | 31 +
installer/windows_x64/ugene.nsh | 337 ++
installer/windows_x64/ugene_extensions.nsh | 158 +
src/Plugin.cmake | 34 +
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src/corelibs/U2Core/src/dbi/DbiDocumentFormat.cpp | 66 +-
src/corelibs/U2Core/src/dbi/DbiDocumentFormat.h | 8 +-
src/corelibs/U2Core/src/dbi/U2AbstractDbi.h | 2 +-
src/corelibs/U2Core/src/dbi/U2AssemblyDbi.h | 3 +-
src/corelibs/U2Core/src/dbi/U2AttributeDbi.h | 2 +-
.../U2Core/src/dbi/U2CrossDatabaseReferenceDbi.h | 2 +-
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src/corelibs/U2Core/src/dbi/U2Dbi.h | 22 +-
src/corelibs/U2Core/src/dbi/U2DbiPackUtils.cpp | 300 +-
src/corelibs/U2Core/src/dbi/U2DbiPackUtils.h | 39 +-
src/corelibs/U2Core/src/dbi/U2DbiRegistry.cpp | 8 +-
src/corelibs/U2Core/src/dbi/U2DbiRegistry.h | 8 +-
src/corelibs/U2Core/src/dbi/U2DbiUtils.cpp | 84 +-
src/corelibs/U2Core/src/dbi/U2DbiUtils.h | 9 +-
src/corelibs/U2Core/src/dbi/U2FeatureDbi.h | 2 +-
src/corelibs/U2Core/src/dbi/U2FormatCheckResult.h | 4 +-
src/corelibs/U2Core/src/dbi/U2ModDbi.h | 2 +-
src/corelibs/U2Core/src/dbi/U2MsaDbi.h | 4 +-
src/corelibs/U2Core/src/dbi/U2ObjectDbi.cpp | 2 +-
src/corelibs/U2Core/src/dbi/U2ObjectDbi.h | 10 +-
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src/corelibs/U2Core/src/dbi/U2ObjectRelationsDbi.h | 2 +-
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src/corelibs/U2Core/src/dbi/U2SQLiteTripleStore.h | 2 +-
src/corelibs/U2Core/src/dbi/U2SequenceDbi.h | 5 +-
src/corelibs/U2Core/src/dbi/U2SqlHelpers.cpp | 61 +-
src/corelibs/U2Core/src/dbi/U2SqlHelpers.h | 85 +-
src/corelibs/U2Core/src/dbi/U2VariantDbi.h | 2 +-
src/corelibs/U2Core/src/dbi/UdrDbi.cpp | 2 +-
src/corelibs/U2Core/src/dbi/UdrDbi.h | 4 +-
src/corelibs/U2Core/src/globals/AppContext.cpp | 2 +-
src/corelibs/U2Core/src/globals/AppContext.h | 112 +-
src/corelibs/U2Core/src/globals/AppFileStorage.cpp | 18 +-
src/corelibs/U2Core/src/globals/AppFileStorage.h | 6 +-
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src/corelibs/U2Core/src/globals/AppGlobalObject.h | 4 +-
src/corelibs/U2Core/src/globals/AppResources.cpp | 6 +-
src/corelibs/U2Core/src/globals/AppResources.h | 8 +-
src/corelibs/U2Core/src/globals/AppSettings.h | 2 +-
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src/corelibs/U2Core/src/globals/Counter.cpp | 2 +-
src/corelibs/U2Core/src/globals/Counter.h | 13 +-
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src/corelibs/U2Core/src/globals/CredentialsAsker.h | 2 +-
src/corelibs/U2Core/src/globals/DBXRefRegistry.cpp | 13 +-
src/corelibs/U2Core/src/globals/DBXRefRegistry.h | 12 +-
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src/corelibs/U2Core/src/globals/DataBaseRegistry.h | 10 +-
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src/corelibs/U2Core/src/globals/DataPathRegistry.h | 6 +-
.../U2Core/src/globals/ExternalToolRegistry.cpp | 14 +-
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src/corelibs/U2Core/src/globals/FormatSettings.cpp | 2 +-
src/corelibs/U2Core/src/globals/FormatSettings.h | 4 +-
src/corelibs/U2Core/src/globals/GUrl.cpp | 10 +-
src/corelibs/U2Core/src/globals/GUrl.h | 4 +-
src/corelibs/U2Core/src/globals/Identifiable.h | 2 +-
src/corelibs/U2Core/src/globals/L10n.h | 8 +-
src/corelibs/U2Core/src/globals/Log.cpp | 4 +-
src/corelibs/U2Core/src/globals/Log.h | 10 +-
src/corelibs/U2Core/src/globals/LogCache.cpp | 2 +-
src/corelibs/U2Core/src/globals/LogCache.h | 8 +-
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.../U2Core/src/globals/PasswordStorage.cpp | 2 +-
src/corelibs/U2Core/src/globals/PasswordStorage.h | 10 +-
src/corelibs/U2Core/src/globals/PluginModel.cpp | 2 +-
src/corelibs/U2Core/src/globals/PluginModel.h | 9 +-
.../src/globals/ProjectFilterTaskRegistry.cpp | 2 +-
.../U2Core/src/globals/ProjectFilterTaskRegistry.h | 2 +-
src/corelibs/U2Core/src/globals/ProjectService.cpp | 2 +-
src/corelibs/U2Core/src/globals/ProjectService.h | 8 +-
.../globals/ProjectTreeControllerModeSettings.cpp | 2 +-
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src/corelibs/U2Core/src/globals/ResourceTracker.h | 10 +-
.../U2Core/src/globals/ScriptingToolRegistry.cpp | 2 +-
.../U2Core/src/globals/ScriptingToolRegistry.h | 7 +-
src/corelibs/U2Core/src/globals/ServiceModel.cpp | 2 +-
src/corelibs/U2Core/src/globals/ServiceModel.h | 8 +-
src/corelibs/U2Core/src/globals/ServiceTypes.h | 2 +-
src/corelibs/U2Core/src/globals/Settings.h | 6 +-
src/corelibs/U2Core/src/globals/Task.cpp | 2 +-
src/corelibs/U2Core/src/globals/Task.h | 15 +-
src/corelibs/U2Core/src/globals/Timer.cpp | 2 +-
src/corelibs/U2Core/src/globals/Timer.h | 4 +-
src/corelibs/U2Core/src/globals/U2OpStatus.h | 2 +-
src/corelibs/U2Core/src/globals/U2SafePoints.h | 7 +-
.../U2Core/src/globals/UserActionsWriter.cpp | 2 +-
.../U2Core/src/globals/UserActionsWriter.h | 2 +-
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.../U2Core/src/globals/UserApplicationsSettings.h | 4 +-
src/corelibs/U2Core/src/globals/Version.cpp | 2 +-
src/corelibs/U2Core/src/globals/Version.h | 2 +-
src/corelibs/U2Core/src/globals/global.h | 31 +-
.../U2Core/src/gobjects/AnnotationTableObject.cpp | 2 +-
.../U2Core/src/gobjects/AnnotationTableObject.h | 2 +-
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src/corelibs/U2Core/src/gobjects/AssemblyObject.h | 2 +-
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.../U2Core/src/gobjects/DNAChromatogramObject.h | 6 +-
.../U2Core/src/gobjects/DNASequenceObject.cpp | 17 +-
.../U2Core/src/gobjects/DNASequenceObject.h | 8 +-
.../U2Core/src/gobjects/GObjectRelationRoles.cpp | 7 +-
.../U2Core/src/gobjects/GObjectRelationRoles.h | 5 +-
src/corelibs/U2Core/src/gobjects/GObjectTypes.cpp | 6 +-
src/corelibs/U2Core/src/gobjects/GObjectTypes.h | 7 +-
src/corelibs/U2Core/src/gobjects/GObjectUtils.cpp | 9 +-
src/corelibs/U2Core/src/gobjects/GObjectUtils.h | 2 +-
.../U2Core/src/gobjects/MAlignmentObject.cpp | 813 ---
.../U2Core/src/gobjects/MAlignmentObject.h | 224 -
.../src/gobjects/MultipleAlignmentObject.cpp | 623 +++
.../U2Core/src/gobjects/MultipleAlignmentObject.h | 171 +
.../MultipleChromatogramAlignmentObject.cpp | 313 ++
.../gobjects/MultipleChromatogramAlignmentObject.h | 90 +
.../gobjects/MultipleSequenceAlignmentObject.cpp | 261 +
.../src/gobjects/MultipleSequenceAlignmentObject.h | 80 +
.../U2Core/src/gobjects/PFMatrixObject.cpp | 2 +-
src/corelibs/U2Core/src/gobjects/PFMatrixObject.h | 2 +-
.../U2Core/src/gobjects/PWMatrixObject.cpp | 2 +-
src/corelibs/U2Core/src/gobjects/PWMatrixObject.h | 2 +-
src/corelibs/U2Core/src/gobjects/PhyTreeObject.cpp | 2 +-
src/corelibs/U2Core/src/gobjects/PhyTreeObject.h | 2 +-
src/corelibs/U2Core/src/gobjects/TextObject.cpp | 2 +-
src/corelibs/U2Core/src/gobjects/TextObject.h | 2 +-
.../U2Core/src/gobjects/UnloadedObject.cpp | 2 +-
src/corelibs/U2Core/src/gobjects/UnloadedObject.h | 2 +-
.../U2Core/src/gobjects/VariantTrackObject.cpp | 2 +-
.../U2Core/src/gobjects/VariantTrackObject.h | 2 +-
.../U2Core/src/io/DatabaseConnectionAdapter.cpp | 2 +-
.../U2Core/src/io/DatabaseConnectionAdapter.h | 2 +-
src/corelibs/U2Core/src/io/HttpFileAdapter.cpp | 21 +-
src/corelibs/U2Core/src/io/HttpFileAdapter.h | 15 +-
src/corelibs/U2Core/src/io/IOAdapter.cpp | 2 +-
src/corelibs/U2Core/src/io/IOAdapter.h | 6 +-
src/corelibs/U2Core/src/io/InputStream.h | 2 +-
src/corelibs/U2Core/src/io/LocalFileAdapter.cpp | 2 +-
src/corelibs/U2Core/src/io/LocalFileAdapter.h | 4 +-
src/corelibs/U2Core/src/io/OutputStream.h | 2 +-
src/corelibs/U2Core/src/io/StringAdapter.cpp | 2 +-
src/corelibs/U2Core/src/io/StringAdapter.h | 2 +-
src/corelibs/U2Core/src/io/VFSAdapter.cpp | 2 +-
src/corelibs/U2Core/src/io/VFSAdapter.h | 4 +-
src/corelibs/U2Core/src/io/VirtualFileSystem.cpp | 4 +-
src/corelibs/U2Core/src/io/VirtualFileSystem.h | 10 +-
src/corelibs/U2Core/src/io/ZlibAdapter.cpp | 2 +-
src/corelibs/U2Core/src/io/ZlibAdapter.h | 2 +-
src/corelibs/U2Core/src/models/BunchMimeData.cpp | 2 +-
src/corelibs/U2Core/src/models/BunchMimeData.h | 2 +-
src/corelibs/U2Core/src/models/DocumentImport.cpp | 21 +-
src/corelibs/U2Core/src/models/DocumentImport.h | 30 +-
src/corelibs/U2Core/src/models/DocumentModel.cpp | 29 +-
src/corelibs/U2Core/src/models/DocumentModel.h | 14 +-
src/corelibs/U2Core/src/models/DocumentUtils.cpp | 9 +-
src/corelibs/U2Core/src/models/DocumentUtils.h | 4 +-
src/corelibs/U2Core/src/models/Folder.cpp | 2 +-
src/corelibs/U2Core/src/models/Folder.h | 6 +-
src/corelibs/U2Core/src/models/GHints.cpp | 2 +-
src/corelibs/U2Core/src/models/GHints.h | 4 +-
src/corelibs/U2Core/src/models/GObject.cpp | 6 +-
src/corelibs/U2Core/src/models/GObject.h | 8 +-
.../U2Core/src/models/GObjectReference.cpp | 6 +-
src/corelibs/U2Core/src/models/GObjectReference.h | 10 +-
.../U2Core/src/models/MimeDataIterator.cpp | 2 +-
src/corelibs/U2Core/src/models/MimeDataIterator.h | 2 +-
src/corelibs/U2Core/src/models/ProjectModel.cpp | 4 +-
src/corelibs/U2Core/src/models/ProjectModel.h | 8 +-
.../U2Core/src/models/StateLockableDataModel.cpp | 34 +-
.../U2Core/src/models/StateLockableDataModel.h | 13 +-
.../U2Core/src/selection/AnnotationSelection.cpp | 2 +-
.../U2Core/src/selection/AnnotationSelection.h | 2 +-
.../U2Core/src/selection/DNASequenceSelection.h | 2 +-
.../U2Core/src/selection/DocumentSelection.cpp | 2 +-
.../U2Core/src/selection/DocumentSelection.h | 2 +-
.../U2Core/src/selection/FolderSelection.cpp | 2 +-
.../U2Core/src/selection/FolderSelection.h | 2 +-
.../U2Core/src/selection/GObjectSelection.cpp | 2 +-
.../U2Core/src/selection/GObjectSelection.h | 2 +-
.../U2Core/src/selection/LRegionsSelection.cpp | 5 +-
.../U2Core/src/selection/LRegionsSelection.h | 2 +-
.../U2Core/src/selection/SelectionModel.cpp | 2 +-
src/corelibs/U2Core/src/selection/SelectionModel.h | 5 +-
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src/corelibs/U2Core/src/selection/SelectionTypes.h | 2 +-
.../U2Core/src/selection/SelectionUtils.cpp | 2 +-
src/corelibs/U2Core/src/selection/SelectionUtils.h | 4 +-
src/corelibs/U2Core/src/selection/TextSelection.h | 2 +-
.../U2Core/src/tasks/AbstractProjectFilterTask.cpp | 2 +-
.../U2Core/src/tasks/AbstractProjectFilterTask.h | 2 +-
src/corelibs/U2Core/src/tasks/AddDocumentTask.cpp | 2 +-
src/corelibs/U2Core/src/tasks/AddDocumentTask.h | 4 +-
.../U2Core/src/tasks/AddObjectsToDocumentTask.cpp | 2 +-
.../U2Core/src/tasks/AddObjectsToDocumentTask.h | 2 +-
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.../U2Core/src/tasks/AddSequencesToAlignmentTask.h | 14 +-
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.../U2Core/src/tasks/CleanupFileStorageTask.cpp | 2 +-
.../U2Core/src/tasks/CleanupFileStorageTask.h | 2 +-
src/corelibs/U2Core/src/tasks/CloneObjectTask.cpp | 4 +-
src/corelibs/U2Core/src/tasks/CloneObjectTask.h | 4 +-
.../U2Core/src/tasks/CmdlineInOutTaskRunner.cpp | 2 +-
.../U2Core/src/tasks/CmdlineInOutTaskRunner.h | 2 +-
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src/corelibs/U2Core/src/tasks/CmdlineTaskRunner.h | 5 +-
.../U2Core/src/tasks/ConnectSharedDatabaseTask.cpp | 2 +-
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.../U2Core/src/tasks/ConsoleShutdownTask.cpp | 2 +-
.../U2Core/src/tasks/ConsoleShutdownTask.h | 4 +-
src/corelibs/U2Core/src/tasks/CopyDataTask.cpp | 4 +-
src/corelibs/U2Core/src/tasks/CopyDataTask.h | 2 +-
src/corelibs/U2Core/src/tasks/CopyDocumentTask.cpp | 8 +-
src/corelibs/U2Core/src/tasks/CopyDocumentTask.h | 2 +-
src/corelibs/U2Core/src/tasks/CopyFileTask.cpp | 54 +
src/corelibs/U2Core/src/tasks/CopyFileTask.h | 46 +
.../U2Core/src/tasks/CreateAnnotationTask.cpp | 2 +-
.../U2Core/src/tasks/CreateAnnotationTask.h | 2 +-
.../U2Core/src/tasks/DeleteObjectsTask.cpp | 2 +-
src/corelibs/U2Core/src/tasks/DeleteObjectsTask.h | 2 +-
.../U2Core/src/tasks/DocumentProviderTask.cpp | 4 +-
.../U2Core/src/tasks/DocumentProviderTask.h | 2 +-
.../U2Core/src/tasks/ExternalToolRunTask.cpp | 16 +-
.../U2Core/src/tasks/ExternalToolRunTask.h | 6 +-
.../src/tasks/ExtractAnnotatedRegionTask.cpp | 2 +-
.../U2Core/src/tasks/ExtractAnnotatedRegionTask.h | 2 +-
src/corelibs/U2Core/src/tasks/FailTask.h | 2 +-
src/corelibs/U2Core/src/tasks/LoadDocumentTask.cpp | 44 +-
src/corelibs/U2Core/src/tasks/LoadDocumentTask.h | 11 +-
.../U2Core/src/tasks/LoadRemoteDocumentTask.cpp | 18 +-
.../U2Core/src/tasks/LoadRemoteDocumentTask.h | 10 +-
.../U2Core/src/tasks/ModifySequenceObjectTask.cpp | 10 +-
.../U2Core/src/tasks/ModifySequenceObjectTask.h | 2 +-
src/corelibs/U2Core/src/tasks/MultiTask.cpp | 2 +-
src/corelibs/U2Core/src/tasks/MultiTask.h | 2 +-
.../U2Core/src/tasks/RemoveAnnotationsTask.cpp | 2 +-
.../U2Core/src/tasks/RemoveAnnotationsTask.h | 2 +-
.../U2Core/src/tasks/RemoveDocumentTask.cpp | 2 +-
src/corelibs/U2Core/src/tasks/RemoveDocumentTask.h | 4 +-
.../U2Core/src/tasks/ReverseSequenceTask.cpp | 2 +-
.../U2Core/src/tasks/ReverseSequenceTask.h | 2 +-
.../U2Core/src/tasks/SaveDocumentStreamingTask.cpp | 2 +-
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src/corelibs/U2Core/src/tasks/SaveDocumentTask.cpp | 2 +-
src/corelibs/U2Core/src/tasks/SaveDocumentTask.h | 23 +-
src/corelibs/U2Core/src/tasks/ScriptTask.cpp | 4 +-
src/corelibs/U2Core/src/tasks/ScriptTask.h | 6 +-
.../U2Core/src/tasks/SequenceDbiWalkerTask.cpp | 2 +-
.../U2Core/src/tasks/SequenceDbiWalkerTask.h | 4 +-
.../U2Core/src/tasks/SequenceWalkerTask.cpp | 2 +-
src/corelibs/U2Core/src/tasks/SequenceWalkerTask.h | 2 +-
src/corelibs/U2Core/src/tasks/TLSTask.cpp | 2 +-
src/corelibs/U2Core/src/tasks/TLSTask.h | 4 +-
src/corelibs/U2Core/src/tasks/TaskSignalMapper.cpp | 2 +-
src/corelibs/U2Core/src/tasks/TaskSignalMapper.h | 4 +-
src/corelibs/U2Core/src/tasks/TaskStarter.cpp | 2 +-
src/corelibs/U2Core/src/tasks/TaskStarter.h | 2 +-
src/corelibs/U2Core/src/tasks/TmpDirChecker.cpp | 8 +-
src/corelibs/U2Core/src/tasks/TmpDirChecker.h | 4 +-
.../tasks/shared_db/ImportDirToDatabaseTask.cpp | 14 +-
.../src/tasks/shared_db/ImportDirToDatabaseTask.h | 5 +-
.../shared_db/ImportDocumentToDatabaseTask.cpp | 2 +-
.../tasks/shared_db/ImportDocumentToDatabaseTask.h | 4 +-
.../tasks/shared_db/ImportFileToDatabaseTask.cpp | 4 +-
.../src/tasks/shared_db/ImportFileToDatabaseTask.h | 2 +-
.../tasks/shared_db/ImportObjectToDatabaseTask.cpp | 4 +-
.../tasks/shared_db/ImportObjectToDatabaseTask.h | 4 +-
.../src/tasks/shared_db/ImportToDatabaseTask.cpp | 4 +-
.../src/tasks/shared_db/ImportToDatabaseTask.h | 2 +-
.../U2Core/src/util/AnnotationCreationPattern.cpp | 2 +-
.../U2Core/src/util/AnnotationCreationPattern.h | 2 +-
src/corelibs/U2Core/src/util/AssemblyImporter.cpp | 2 +-
src/corelibs/U2Core/src/util/AssemblyImporter.h | 2 +-
src/corelibs/U2Core/src/util/ChromatogramUtils.cpp | 343 ++
src/corelibs/U2Core/src/util/ChromatogramUtils.h | 60 +
.../U2Core/src/util/DatatypeSerializeUtils.cpp | 10 +-
.../U2Core/src/util/DatatypeSerializeUtils.h | 2 +-
.../U2Core/src/util/DnaChromatogramUtils.cpp | 57 +
.../U2Core/src/util/DnaChromatogramUtils.h | 39 +
.../U2Core/src/util/FileAndDirectoryUtils.cpp | 6 +-
.../U2Core/src/util/FileAndDirectoryUtils.h | 2 +-
src/corelibs/U2Core/src/util/FileStorageUtils.cpp | 2 +-
src/corelibs/U2Core/src/util/FileStorageUtils.h | 2 +-
src/corelibs/U2Core/src/util/FilesIterator.cpp | 2 +-
src/corelibs/U2Core/src/util/FilesIterator.h | 4 +-
src/corelibs/U2Core/src/util/FormatUtils.cpp | 2 +-
src/corelibs/U2Core/src/util/FormatUtils.h | 4 +-
src/corelibs/U2Core/src/util/GAutoDeleteList.cpp | 2 +-
src/corelibs/U2Core/src/util/GAutoDeleteList.h | 4 +-
src/corelibs/U2Core/src/util/GUrlUtils.cpp | 75 +-
src/corelibs/U2Core/src/util/GUrlUtils.h | 27 +-
src/corelibs/U2Core/src/util/GenbankFeatures.cpp | 8 +-
src/corelibs/U2Core/src/util/GenbankFeatures.h | 10 +-
src/corelibs/U2Core/src/util/IOAdapterUtils.cpp | 2 +-
src/corelibs/U2Core/src/util/IOAdapterUtils.h | 2 +-
.../U2Core/src/util/ImportToDatabaseOptions.cpp | 4 +-
.../U2Core/src/util/ImportToDatabaseOptions.h | 2 +-
.../U2Core/src/util/MAlignmentExporter.cpp | 187 -
src/corelibs/U2Core/src/util/MAlignmentExporter.h | 64 -
.../U2Core/src/util/MAlignmentImporter.cpp | 245 -
src/corelibs/U2Core/src/util/MAlignmentImporter.h | 58 -
src/corelibs/U2Core/src/util/MAlignmentWalker.cpp | 151 -
src/corelibs/U2Core/src/util/MAlignmentWalker.h | 48 -
src/corelibs/U2Core/src/util/MSAUtils.cpp | 207 +-
src/corelibs/U2Core/src/util/MSAUtils.h | 44 +-
src/corelibs/U2Core/src/util/MaIterator.cpp | 154 +
src/corelibs/U2Core/src/util/MaIterator.h | 74 +
.../U2Core/src/util/MaModificationInfo.cpp | 48 +
src/corelibs/U2Core/src/util/MaModificationInfo.h | 56 +
src/corelibs/U2Core/src/util/McaDbiUtils.cpp | 375 ++
src/corelibs/U2Core/src/util/McaDbiUtils.h | 52 +
src/corelibs/U2Core/src/util/McaRowInnerData.cpp | 38 +
src/corelibs/U2Core/src/util/McaRowInnerData.h | 56 +
src/corelibs/U2Core/src/util/MsaDbiUtils.cpp | 796 +--
src/corelibs/U2Core/src/util/MsaDbiUtils.h | 122 +-
src/corelibs/U2Core/src/util/MsaRowUtils.cpp | 550 +-
src/corelibs/U2Core/src/util/MsaRowUtils.h | 45 +-
.../util/MultipleChromatogramAlignmentExporter.cpp | 196 +
.../util/MultipleChromatogramAlignmentExporter.h | 51 +
.../util/MultipleChromatogramAlignmentImporter.cpp | 237 +
.../util/MultipleChromatogramAlignmentImporter.h | 51 +
.../src/util/MultipleSequenceAlignmentExporter.cpp | 187 +
.../src/util/MultipleSequenceAlignmentExporter.h | 64 +
.../src/util/MultipleSequenceAlignmentImporter.cpp | 245 +
.../src/util/MultipleSequenceAlignmentImporter.h | 58 +
.../src/util/MultipleSequenceAlignmentWalker.cpp | 153 +
.../src/util/MultipleSequenceAlignmentWalker.h | 48 +
.../U2Core/src/util/PMatrixSerializeUtils.h | 3 +-
.../U2Core/src/util/QObjectScopedPointer.h | 2 +-
src/corelibs/U2Core/src/util/QVariantUtils.cpp | 2 +-
src/corelibs/U2Core/src/util/QVariantUtils.h | 2 +-
src/corelibs/U2Core/src/util/SequenceUtils.cpp | 6 +-
src/corelibs/U2Core/src/util/SequenceUtils.h | 4 +-
src/corelibs/U2Core/src/util/SignalBlocker.cpp | 37 +
src/corelibs/U2Core/src/util/SignalBlocker.h | 41 +
src/corelibs/U2Core/src/util/SnpeffDictionary.cpp | 2 +-
src/corelibs/U2Core/src/util/SnpeffDictionary.h | 4 +-
src/corelibs/U2Core/src/util/StrPackUtils.cpp | 105 +
src/corelibs/U2Core/src/util/StrPackUtils.h | 75 +
src/corelibs/U2Core/src/util/SyncHttp.cpp | 6 +-
src/corelibs/U2Core/src/util/SyncHttp.h | 12 +-
src/corelibs/U2Core/src/util/TaskWatchdog.cpp | 2 +-
src/corelibs/U2Core/src/util/TaskWatchdog.h | 4 +-
src/corelibs/U2Core/src/util/TextUtils.cpp | 2 +-
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.../U2View/src/ov_msa/MSACollapsibleModel.h | 63 +-
src/corelibs/U2View/src/ov_msa/MSAEditor.cpp | 920 +---
src/corelibs/U2View/src/ov_msa/MSAEditor.h | 341 +-
.../U2View/src/ov_msa/MSAEditorConsensusArea.cpp | 688 +--
.../U2View/src/ov_msa/MSAEditorConsensusArea.h | 129 +-
.../U2View/src/ov_msa/MSAEditorConsensusCache.cpp | 61 +-
.../U2View/src/ov_msa/MSAEditorConsensusCache.h | 43 +-
.../U2View/src/ov_msa/MSAEditorFactory.cpp | 138 -
src/corelibs/U2View/src/ov_msa/MSAEditorFactory.h | 54 -
.../U2View/src/ov_msa/MSAEditorNameList.cpp | 928 ----
src/corelibs/U2View/src/ov_msa/MSAEditorNameList.h | 156 -
.../U2View/src/ov_msa/MSAEditorOffsetsView.cpp | 179 +-
.../U2View/src/ov_msa/MSAEditorOffsetsView.h | 38 +-
.../U2View/src/ov_msa/MSAEditorOverviewArea.cpp | 80 +-
.../U2View/src/ov_msa/MSAEditorOverviewArea.h | 43 +-
.../U2View/src/ov_msa/MSAEditorSequenceArea.cpp | 2419 +--------
.../U2View/src/ov_msa/MSAEditorSequenceArea.h | 396 +-
src/corelibs/U2View/src/ov_msa/MSAEditorState.cpp | 104 -
src/corelibs/U2View/src/ov_msa/MSAEditorState.h | 66 -
.../U2View/src/ov_msa/MSAEditorStatusBar.cpp | 248 -
.../U2View/src/ov_msa/MSAEditorStatusBar.h | 87 -
src/corelibs/U2View/src/ov_msa/MSAEditorTasks.cpp | 311 --
src/corelibs/U2View/src/ov_msa/MSAEditorTasks.h | 108 -
.../U2View/src/ov_msa/MSAEditorUndoFramework.cpp | 135 -
.../U2View/src/ov_msa/MSAEditorUndoFramework.h | 91 -
.../src/ov_msa/MSASelectSubalignmentDialog.cpp | 52 +-
.../src/ov_msa/MSASelectSubalignmentDialog.h | 16 +-
.../src/ov_msa/MaConsensusMismatchController.cpp | 147 +
.../src/ov_msa/MaConsensusMismatchController.h | 71 +
src/corelibs/U2View/src/ov_msa/MaEditor.cpp | 470 ++
src/corelibs/U2View/src/ov_msa/MaEditor.h | 202 +
.../src/ov_msa/MaEditorConsensusAreaSettings.cpp | 51 +
.../src/ov_msa/MaEditorConsensusAreaSettings.h | 60 +
src/corelibs/U2View/src/ov_msa/MaEditorFactory.cpp | 195 +
src/corelibs/U2View/src/ov_msa/MaEditorFactory.h | 102 +
.../U2View/src/ov_msa/MaEditorNameList.cpp | 910 ++++
src/corelibs/U2View/src/ov_msa/MaEditorNameList.h | 171 +
src/corelibs/U2View/src/ov_msa/MaEditorState.cpp | 126 +
src/corelibs/U2View/src/ov_msa/MaEditorState.h | 64 +
.../U2View/src/ov_msa/MaEditorStatusBar.cpp | 173 +
src/corelibs/U2View/src/ov_msa/MaEditorStatusBar.h | 97 +
src/corelibs/U2View/src/ov_msa/MaEditorTasks.cpp | 374 ++
src/corelibs/U2View/src/ov_msa/MaEditorTasks.h | 146 +
src/corelibs/U2View/src/ov_msa/McaEditor.cpp | 315 ++
src/corelibs/U2View/src/ov_msa/McaEditor.h | 106 +
.../U2View/src/ov_msa/McaEditorConsensusArea.cpp | 73 +
.../U2View/src/ov_msa/McaEditorConsensusArea.h | 58 +
.../U2View/src/ov_msa/McaEditorNameList.cpp | 152 +
src/corelibs/U2View/src/ov_msa/McaEditorNameList.h | 82 +
.../U2View/src/ov_msa/McaEditorOverviewArea.cpp | 40 +
.../U2View/src/ov_msa/McaEditorOverviewArea.h | 45 +
.../U2View/src/ov_msa/McaEditorReferenceArea.cpp | 369 ++
.../U2View/src/ov_msa/McaEditorReferenceArea.h | 96 +
.../U2View/src/ov_msa/McaEditorSequenceArea.cpp | 468 ++
.../U2View/src/ov_msa/McaEditorSequenceArea.h | 134 +
.../U2View/src/ov_msa/McaEditorStatusBar.cpp | 94 +
.../U2View/src/ov_msa/McaEditorStatusBar.h | 51 +
src/corelibs/U2View/src/ov_msa/McaEditorWgt.cpp | 178 +
src/corelibs/U2View/src/ov_msa/McaEditorWgt.h | 73 +
.../src/ov_msa/McaReferenceCharController.cpp | 161 +
.../U2View/src/ov_msa/McaReferenceCharController.h | 77 +
.../U2View/src/ov_msa/MsaEditorNameList.cpp | 65 +
src/corelibs/U2View/src/ov_msa/MsaEditorNameList.h | 46 +
.../src/ov_msa/MsaEditorSimilarityColumn.cpp | 83 +-
.../U2View/src/ov_msa/MsaEditorSimilarityColumn.h | 30 +-
.../U2View/src/ov_msa/MsaEditorStatusBar.cpp | 237 +
.../U2View/src/ov_msa/MsaEditorStatusBar.h | 73 +
.../src/ov_msa/MsaEditorUserModStepController.cpp | 2 +-
.../src/ov_msa/MsaEditorUserModStepController.h | 2 +-
src/corelibs/U2View/src/ov_msa/MsaEditorWgt.cpp | 159 +
src/corelibs/U2View/src/ov_msa/MsaEditorWgt.h | 90 +
src/corelibs/U2View/src/ov_msa/MsaOpSavableTab.cpp | 2 +-
src/corelibs/U2View/src/ov_msa/MsaOpSavableTab.h | 2 +-
.../U2View/src/ov_msa/MsaUpdatedWidgetInterface.h | 12 +-
.../ov_msa/Overview/MSAGraphCalculationTask.cpp | 277 -
.../src/ov_msa/Overview/MSAGraphCalculationTask.h | 125 -
.../src/ov_msa/Overview/MSAGraphOverview.cpp | 369 --
.../U2View/src/ov_msa/Overview/MSAGraphOverview.h | 132 -
.../U2View/src/ov_msa/Overview/MSAOverview.cpp | 97 -
.../U2View/src/ov_msa/Overview/MSAOverview.h | 89 -
.../src/ov_msa/Overview/MSAOverviewContextMenu.cpp | 245 -
.../src/ov_msa/Overview/MSAOverviewContextMenu.h | 103 -
.../ov_msa/Overview/MSAOverviewImageExportTask.cpp | 137 -
.../ov_msa/Overview/MSAOverviewImageExportTask.h | 83 -
.../src/ov_msa/Overview/MSASimpleOverview.cpp | 267 -
.../U2View/src/ov_msa/Overview/MSASimpleOverview.h | 77 -
.../src/ov_msa/Overview/MaEditorOverviewArea.cpp | 62 +
.../src/ov_msa/Overview/MaEditorOverviewArea.h | 58 +
.../src/ov_msa/Overview/MaGraphCalculationTask.cpp | 277 +
.../src/ov_msa/Overview/MaGraphCalculationTask.h | 125 +
.../U2View/src/ov_msa/Overview/MaGraphOverview.cpp | 357 ++
.../U2View/src/ov_msa/Overview/MaGraphOverview.h | 130 +
.../U2View/src/ov_msa/Overview/MaOverview.cpp | 120 +
.../U2View/src/ov_msa/Overview/MaOverview.h | 88 +
.../src/ov_msa/Overview/MaOverviewContextMenu.cpp | 250 +
.../src/ov_msa/Overview/MaOverviewContextMenu.h | 99 +
.../ov_msa/Overview/MaOverviewImageExportTask.cpp | 132 +
.../ov_msa/Overview/MaOverviewImageExportTask.h | 83 +
.../src/ov_msa/Overview/MaSangerOverview.cpp | 311 ++
.../U2View/src/ov_msa/Overview/MaSangerOverview.h | 87 +
.../src/ov_msa/Overview/MaSimpleOverview.cpp | 245 +
.../U2View/src/ov_msa/Overview/MaSimpleOverview.h | 75 +
.../U2View/src/ov_msa/PairAlign/PairAlign.cpp | 113 +-
.../U2View/src/ov_msa/PairAlign/PairAlign.h | 10 +-
.../src/ov_msa/PairAlign/PairAlignFactory.cpp | 7 +-
.../U2View/src/ov_msa/PairAlign/PairAlignFactory.h | 3 +-
.../PairwiseAlignmentOptionsPanelWidget.ui | 2 +-
.../ov_msa/PhyTrees/MSAEditorMultiTreeViewer.cpp | 8 +-
.../src/ov_msa/PhyTrees/MSAEditorMultiTreeViewer.h | 17 +-
.../src/ov_msa/PhyTrees/MSAEditorTreeManager.cpp | 22 +-
.../src/ov_msa/PhyTrees/MSAEditorTreeManager.h | 10 +-
.../src/ov_msa/PhyTrees/MSAEditorTreeViewer.cpp | 56 +-
.../src/ov_msa/PhyTrees/MSAEditorTreeViewer.h | 15 +-
.../src/ov_msa/PhyTrees/MsaEditorTreeTabArea.cpp | 5 +-
.../src/ov_msa/PhyTrees/MsaEditorTreeTabArea.h | 2 +-
...SaveSelectedSequenceFromMSADialogController.cpp | 10 +-
.../SaveSelectedSequenceFromMSADialogController.h | 6 +-
.../U2View/src/ov_msa/SelectSubalignmentDialog.ui | 4 +-
.../MSADistancesColumnSettingsWidget.ui | 28 +-
.../ov_msa/SeqStatistics/SeqStatisticsWidget.cpp | 8 +-
.../src/ov_msa/SeqStatistics/SeqStatisticsWidget.h | 6 +-
.../SeqStatistics/SeqStatisticsWidgetFactory.cpp | 7 +-
.../SeqStatistics/SeqStatisticsWidgetFactory.h | 3 +-
.../ov_msa/SequenceSelectorWidgetController.cpp | 48 +-
.../src/ov_msa/SequenceSelectorWidgetController.h | 4 +-
.../src/ov_msa/TreeOptions/TreeOptionsWidget.cpp | 32 +-
.../src/ov_msa/TreeOptions/TreeOptionsWidget.h | 6 +-
.../TreeOptions/TreeOptionsWidgetFactory.cpp | 17 +-
.../ov_msa/TreeOptions/TreeOptionsWidgetFactory.h | 5 +-
.../src/ov_msa/helpers/BaseWidthController.cpp | 120 +
.../src/ov_msa/helpers/BaseWidthController.h | 73 +
.../U2View/src/ov_msa/helpers/DrawHelper.cpp | 91 +
.../U2View/src/ov_msa/helpers/DrawHelper.h | 56 +
.../helpers/MaAmbiguousCharactersController.cpp | 156 +
.../helpers/MaAmbiguousCharactersController.h | 69 +
.../src/ov_msa/helpers/McaRowHeightController.cpp | 45 +
.../src/ov_msa/helpers/McaRowHeightController.h | 40 +
.../src/ov_msa/helpers/MsaRowHeightController.cpp | 40 +
.../src/ov_msa/helpers/MsaRowHeightController.h | 40 +
.../src/ov_msa/helpers/RowHeightController.cpp | 184 +
.../src/ov_msa/helpers/RowHeightController.h | 80 +
.../U2View/src/ov_msa/helpers/ScrollController.cpp | 457 ++
.../U2View/src/ov_msa/helpers/ScrollController.h | 130 +
.../view_rendering/MaConsensusAreaRenderer.cpp | 366 ++
.../view_rendering/MaConsensusAreaRenderer.h | 126 +
.../view_rendering/MaEditorConsensusArea.cpp | 442 ++
.../ov_msa/view_rendering/MaEditorConsensusArea.h | 151 +
.../ov_msa/view_rendering/MaEditorSelection.cpp | 110 +
.../src/ov_msa/view_rendering/MaEditorSelection.h | 72 +
.../ov_msa/view_rendering/MaEditorSequenceArea.cpp | 1596 ++++++
.../ov_msa/view_rendering/MaEditorSequenceArea.h | 337 ++
.../src/ov_msa/view_rendering/MaEditorUtils.cpp | 180 +
.../src/ov_msa/view_rendering/MaEditorUtils.h | 106 +
.../src/ov_msa/view_rendering/MaEditorWgt.cpp | 289 +
.../U2View/src/ov_msa/view_rendering/MaEditorWgt.h | 149 +
.../view_rendering/McaConsensusAreaRenderer.cpp | 58 +
.../view_rendering/McaConsensusAreaRenderer.h | 43 +
.../view_rendering/McaReferenceAreaRenderer.cpp | 96 +
.../view_rendering/McaReferenceAreaRenderer.h | 48 +
.../ov_msa/view_rendering/SequenceAreaRenderer.cpp | 155 +
.../ov_msa/view_rendering/SequenceAreaRenderer.h | 56 +
.../SequenceWithChromatogramAreaRenderer.cpp | 497 ++
.../SequenceWithChromatogramAreaRenderer.h | 86 +
.../U2View/src/ov_phyltree/CreateBranchesTask.h | 2 +-
.../src/ov_phyltree/CreateCircularBranchesTask.cpp | 4 +-
.../src/ov_phyltree/CreateCircularBranchesTask.h | 2 +-
.../ov_phyltree/CreateRectangularBranchesTask.cpp | 2 +-
.../ov_phyltree/CreateRectangularBranchesTask.h | 2 +-
.../src/ov_phyltree/CreateUnrootedBranchesTask.cpp | 4 +-
.../src/ov_phyltree/CreateUnrootedBranchesTask.h | 2 +-
.../U2View/src/ov_phyltree/GraphicsBranchItem.cpp | 6 +-
.../U2View/src/ov_phyltree/GraphicsBranchItem.h | 2 +-
.../U2View/src/ov_phyltree/GraphicsButtonItem.cpp | 4 +-
.../U2View/src/ov_phyltree/GraphicsButtonItem.h | 2 +-
.../src/ov_phyltree/GraphicsCircularBranchItem.cpp | 28 +-
.../src/ov_phyltree/GraphicsCircularBranchItem.h | 2 +-
.../ov_phyltree/GraphicsRectangularBranchItem.cpp | 22 +-
.../ov_phyltree/GraphicsRectangularBranchItem.h | 2 +-
.../src/ov_phyltree/GraphicsUnrootedBranchItem.cpp | 30 +-
.../src/ov_phyltree/GraphicsUnrootedBranchItem.h | 2 +-
src/corelibs/U2View/src/ov_phyltree/TreeSettings.h | 6 +-
src/corelibs/U2View/src/ov_phyltree/TreeViewer.cpp | 14 +-
src/corelibs/U2View/src/ov_phyltree/TreeViewer.h | 12 +-
.../U2View/src/ov_phyltree/TreeViewerFactory.cpp | 2 +-
.../U2View/src/ov_phyltree/TreeViewerFactory.h | 2 +-
.../U2View/src/ov_phyltree/TreeViewerState.cpp | 2 +-
.../U2View/src/ov_phyltree/TreeViewerState.h | 4 +-
.../U2View/src/ov_phyltree/TreeViewerTasks.cpp | 4 +-
.../U2View/src/ov_phyltree/TreeViewerTasks.h | 2 +-
.../U2View/src/ov_phyltree/TreeViewerUtils.cpp | 9 +-
.../U2View/src/ov_phyltree/TreeViewerUtils.h | 4 +-
.../src/ov_sequence/ADVAnnotationCreation.cpp | 2 +-
.../U2View/src/ov_sequence/ADVAnnotationCreation.h | 2 +-
.../U2View/src/ov_sequence/ADVClipboard.cpp | 2 +-
src/corelibs/U2View/src/ov_sequence/ADVClipboard.h | 2 +-
.../U2View/src/ov_sequence/ADVGraphModel.cpp | 2 +-
.../U2View/src/ov_sequence/ADVGraphModel.h | 6 +-
.../src/ov_sequence/ADVSequenceObjectContext.cpp | 344 +-
.../src/ov_sequence/ADVSequenceObjectContext.h | 88 +-
.../U2View/src/ov_sequence/ADVSequenceWidget.cpp | 2 +-
.../U2View/src/ov_sequence/ADVSequenceWidget.h | 12 +-
.../src/ov_sequence/ADVSingleSequenceWidget.cpp | 12 +-
.../src/ov_sequence/ADVSingleSequenceWidget.h | 4 +-
.../U2View/src/ov_sequence/ADVSplitWidget.h | 2 +-
.../U2View/src/ov_sequence/ADVSyncViewManager.cpp | 11 +-
.../U2View/src/ov_sequence/ADVSyncViewManager.h | 2 +-
src/corelibs/U2View/src/ov_sequence/ADVUtils.cpp | 2 +-
src/corelibs/U2View/src/ov_sequence/ADVUtils.h | 4 +-
.../U2View/src/ov_sequence/AnnotatedDNAView.cpp | 39 +-
.../U2View/src/ov_sequence/AnnotatedDNAView.h | 4 +-
.../src/ov_sequence/AnnotatedDNAViewFactory.cpp | 2 +-
.../src/ov_sequence/AnnotatedDNAViewFactory.h | 2 +-
.../src/ov_sequence/AnnotatedDNAViewState.cpp | 2 +-
.../U2View/src/ov_sequence/AnnotatedDNAViewState.h | 4 +-
.../src/ov_sequence/AnnotatedDNAViewTasks.cpp | 14 +-
.../U2View/src/ov_sequence/AnnotatedDNAViewTasks.h | 2 +-
.../U2View/src/ov_sequence/AnnotationsTreeView.cpp | 6 +-
.../U2View/src/ov_sequence/AnnotationsTreeView.h | 2 +-
.../U2View/src/ov_sequence/AutoAnnotationUtils.cpp | 4 +-
.../U2View/src/ov_sequence/AutoAnnotationUtils.h | 2 +-
.../ov_sequence/CreateRulerDialogController.cpp | 32 +-
.../src/ov_sequence/CreateRulerDialogController.h | 18 +-
src/corelibs/U2View/src/ov_sequence/DetView.cpp | 4 +-
src/corelibs/U2View/src/ov_sequence/DetView.h | 4 +-
.../U2View/src/ov_sequence/GSequenceGraphView.cpp | 14 +-
.../U2View/src/ov_sequence/GSequenceGraphView.h | 10 +-
.../ov_sequence/GSequenceGraphViewWithFactory.cpp | 2 +-
.../ov_sequence/GSequenceGraphViewWithFactory.h | 2 +-
.../U2View/src/ov_sequence/GSequenceLineView.cpp | 16 +-
.../U2View/src/ov_sequence/GSequenceLineView.h | 29 +-
.../src/ov_sequence/GSequenceLineViewAnnotated.cpp | 4 +-
.../src/ov_sequence/GSequenceLineViewAnnotated.h | 4 +-
.../U2View/src/ov_sequence/GraphLabelModel.cpp | 2 +-
.../U2View/src/ov_sequence/GraphLabelModel.h | 2 +-
.../src/ov_sequence/GraphLabelsSelectDialog.cpp | 28 +-
.../src/ov_sequence/GraphLabelsSelectDialog.h | 9 +-
src/corelibs/U2View/src/ov_sequence/GraphMenu.cpp | 25 +-
src/corelibs/U2View/src/ov_sequence/GraphMenu.h | 9 +-
.../U2View/src/ov_sequence/GraphSettingsDialog.cpp | 54 +-
.../U2View/src/ov_sequence/GraphSettingsDialog.h | 10 +-
src/corelibs/U2View/src/ov_sequence/Overview.cpp | 4 +-
src/corelibs/U2View/src/ov_sequence/Overview.h | 9 +-
src/corelibs/U2View/src/ov_sequence/PanView.cpp | 43 +-
src/corelibs/U2View/src/ov_sequence/PanView.h | 16 +-
.../U2View/src/ov_sequence/PanViewRows.cpp | 4 +-
src/corelibs/U2View/src/ov_sequence/PanViewRows.h | 2 +-
.../src/ov_sequence/SaveGraphCutoffsDialog.ui | 6 +
.../SaveGraphCutoffsDialogController.cpp | 23 +-
.../ov_sequence/SaveGraphCutoffsDialogController.h | 14 +-
.../src/ov_sequence/SaveGraphCutoffsTask.cpp | 2 +-
.../U2View/src/ov_sequence/SaveGraphCutoffsTask.h | 2 +-
.../src/ov_sequence/SearchQualifierDialog.cpp | 4 +-
.../U2View/src/ov_sequence/SearchQualifierDialog.h | 2 +-
.../src/ov_sequence/SequenceObjectContext.cpp | 384 ++
.../U2View/src/ov_sequence/SequenceObjectContext.h | 122 +
.../src/ov_sequence/WindowStepSelectorWidget.cpp | 74 +-
.../src/ov_sequence/WindowStepSelectorWidget.h | 25 +-
.../annot_highlight/AnnotHighlightSettings.cpp | 2 +-
.../annot_highlight/AnnotHighlightSettings.h | 5 +-
.../annot_highlight/AnnotHighlightTree.cpp | 17 +-
.../annot_highlight/AnnotHighlightTree.h | 13 +-
.../annot_highlight/AnnotHighlightTreeItem.cpp | 2 +-
.../annot_highlight/AnnotHighlightTreeItem.h | 2 +-
.../annot_highlight/AnnotHighlightWidget.cpp | 15 +-
.../annot_highlight/AnnotHighlightWidget.h | 7 +-
.../AnnotHighlightWidgetFactory.cpp | 7 +-
.../annot_highlight/AnnotHighlightWidgetFactory.h | 3 +-
.../src/ov_sequence/codon_table/CodonTable.cpp | 40 +-
.../src/ov_sequence/codon_table/CodonTable.h | 12 +-
.../ov_sequence/find_pattern/FindPatternTask.cpp | 2 +-
.../src/ov_sequence/find_pattern/FindPatternTask.h | 4 +-
.../ov_sequence/find_pattern/FindPatternWidget.cpp | 51 +-
.../ov_sequence/find_pattern/FindPatternWidget.h | 9 +-
.../find_pattern/FindPatternWidgetFactory.cpp | 7 +-
.../find_pattern/FindPatternWidgetFactory.h | 3 +-
.../find_pattern/FindPatternWidgetSavableTab.cpp | 2 +-
.../find_pattern/FindPatternWidgetSavableTab.h | 4 +-
.../ov_sequence/image_export/ExportImagePainter.h | 2 +-
.../image_export/SequenceExportSettingsWidget.cpp | 2 +-
.../image_export/SequenceExportSettingsWidget.h | 2 +-
.../ov_sequence/image_export/SequencePainter.cpp | 4 +-
.../src/ov_sequence/image_export/SequencePainter.h | 2 +-
.../SingleSequenceImageExportController.cpp | 2 +-
.../SingleSequenceImageExportController.h | 2 +-
.../image_export/SingleSequenceImageExportTask.cpp | 4 +-
.../image_export/SingleSequenceImageExportTask.h | 2 +-
.../ov_sequence/sequence_info/CharOccurTask.cpp | 2 +-
.../src/ov_sequence/sequence_info/CharOccurTask.h | 2 +-
.../sequence_info/DNAStatisticsTask.cpp | 2 +-
.../ov_sequence/sequence_info/DNAStatisticsTask.h | 6 +-
.../ov_sequence/sequence_info/DinuclOccurTask.cpp | 2 +-
.../ov_sequence/sequence_info/DinuclOccurTask.h | 2 +-
.../src/ov_sequence/sequence_info/SequenceInfo.cpp | 2 +-
.../src/ov_sequence/sequence_info/SequenceInfo.h | 2 +-
.../sequence_info/SequenceInfoFactory.cpp | 7 +-
.../sequence_info/SequenceInfoFactory.h | 3 +-
.../view_rendering/DetViewMultiLineRenderer.cpp | 4 +-
.../view_rendering/DetViewMultiLineRenderer.h | 4 +-
.../ov_sequence/view_rendering/DetViewRenderer.cpp | 6 +-
.../ov_sequence/view_rendering/DetViewRenderer.h | 6 +-
.../view_rendering/DetViewSingleLineRenderer.cpp | 4 +-
.../view_rendering/DetViewSingleLineRenderer.h | 4 +-
.../ov_sequence/view_rendering/PanViewRenderer.cpp | 74 +-
.../ov_sequence/view_rendering/PanViewRenderer.h | 43 +-
.../SequenceViewAnnotatedRenderer.cpp | 4 +-
.../view_rendering/SequenceViewAnnotatedRenderer.h | 4 +-
.../view_rendering/SequenceViewRenderer.cpp | 4 +-
.../view_rendering/SequenceViewRenderer.h | 8 +-
.../U2View/src/ov_text/SimpleTextObjectView.cpp | 11 +-
.../U2View/src/ov_text/SimpleTextObjectView.h | 8 +-
.../src/ov_text/SimpleTextObjectViewTasks.cpp | 2 +-
.../U2View/src/ov_text/SimpleTextObjectViewTasks.h | 2 +-
.../U2View/src/phyltree/BaseSettingsDialog.cpp | 2 +-
.../U2View/src/phyltree/BaseSettingsDialog.h | 2 +-
.../U2View/src/phyltree/BranchSettingsDialog.cpp | 12 +-
.../U2View/src/phyltree/BranchSettingsDialog.h | 2 +-
.../U2View/src/phyltree/CreatePhyTreeDialog.ui | 8 +-
.../src/phyltree/CreatePhyTreeDialogController.cpp | 35 +-
.../src/phyltree/CreatePhyTreeDialogController.h | 13 +-
.../U2View/src/phyltree/CreatePhyTreeWidget.cpp | 4 +-
.../U2View/src/phyltree/CreatePhyTreeWidget.h | 7 +-
.../src/phyltree/PhyTreeDisplayOptionsWidget.cpp | 2 +-
.../src/phyltree/PhyTreeDisplayOptionsWidget.h | 2 +-
.../U2View/src/phyltree/TextSettingsDialog.cpp | 12 +-
.../U2View/src/phyltree/TextSettingsDialog.h | 2 +-
.../U2View/src/phyltree/TreeSettingsDialog.cpp | 4 +-
.../U2View/src/phyltree/TreeSettingsDialog.h | 2 +-
.../src/util_dna_assembly/AssemblyToRefDialog.ui | 18 +-
.../src/util_dna_assembly/BuildIndexDialog.cpp | 27 +-
.../src/util_dna_assembly/BuildIndexDialog.h | 4 +-
.../util_dna_assembly/BuildIndexFromRefDialog.ui | 4 +-
.../ConvertAssemblyToSamDialog.cpp | 4 +-
.../util_dna_assembly/ConvertAssemblyToSamDialog.h | 2 +-
.../src/util_dna_assembly/DnaAssemblyDialog.cpp | 14 +-
.../src/util_dna_assembly/DnaAssemblyDialog.h | 2 +-
.../util_dna_assembly/DnaAssemblyGUIExtension.cpp | 2 +-
.../util_dna_assembly/DnaAssemblyGUIExtension.h | 9 +-
.../src/util_dna_assembly/DnaAssemblyUtils.cpp | 28 +-
.../src/util_dna_assembly/DnaAssemblyUtils.h | 2 +-
.../src/util_dna_assembly/GenomeAssemblyDialog.cpp | 21 +-
.../src/util_dna_assembly/GenomeAssemblyDialog.h | 12 +-
.../AlignmentAlgorithmGUIExtension.cpp | 2 +-
.../AlignmentAlgorithmGUIExtension.h | 22 +-
.../util_sec_struct_predict/SecStructDialog.cpp | 6 +-
.../src/util_sec_struct_predict/SecStructDialog.h | 2 +-
.../SecStructPredictUtils.cpp | 2 +-
.../SecStructPredictUtils.h | 2 +-
.../util_smith_waterman/SmithWatermanDialog.cpp | 9 +-
.../src/util_smith_waterman/SmithWatermanDialog.h | 2 +-
.../util_smith_waterman/SmithWatermanDialogBase.ui | 13 +-
.../util_smith_waterman/SmithWatermanDialogImpl.h | 2 +-
.../src/util_smith_waterman/SubstMatrixDialog.cpp | 23 +-
.../src/util_smith_waterman/SubstMatrixDialog.h | 8 +-
src/corelibs/U2View/transl/english.ts | 3251 ++++++-----
src/corelibs/U2View/transl/russian.ts | 3253 ++++++-----
src/include/U2Algorithm/MAlignmentUtilTasks.h | 1 -
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.../SpadesGenomeAssemblyDialogFiller.h | 2 +-
.../plugins/external_tools/TCoffeeDailogFiller.cpp | 11 +-
.../plugins/external_tools/TCoffeeDailogFiller.h | 2 +-
.../ugene/plugins/orf_marker/OrfDialogFiller.cpp | 2 +-
.../ugene/plugins/orf_marker/OrfDialogFiller.h | 2 +-
.../ugene/plugins/pcr/AddPrimerDialogFiller.cpp | 2 +-
.../ugene/plugins/pcr/AddPrimerDialogFiller.h | 2 +-
.../plugins/pcr/ExportPrimersDialogFiller.cpp | 2 +-
.../ugene/plugins/pcr/ExportPrimersDialogFiller.h | 2 +-
.../plugins/pcr/ImportPrimersDialogFiller.cpp | 2 +-
.../ugene/plugins/pcr/ImportPrimersDialogFiller.h | 2 +-
.../plugins/pcr/PrimerLibrarySelectorFiller.cpp | 2 +-
.../plugins/pcr/PrimerLibrarySelectorFiller.h | 2 +-
.../plugins/pcr/PrimersDetailsDialogFiller.cpp | 2 +-
.../ugene/plugins/pcr/PrimersDetailsDialogFiller.h | 2 +-
.../plugins/weight_matrix/PwmBuildDialogFiller.cpp | 2 +-
.../plugins/weight_matrix/PwmBuildDialogFiller.h | 2 +-
.../weight_matrix/PwmSearchDialogFiller.cpp | 2 +-
.../plugins/weight_matrix/PwmSearchDialogFiller.h | 2 +-
.../workflow_designer/AliasesDialogFiller.cpp | 14 +-
.../workflow_designer/AliasesDialogFiller.h | 2 +-
.../ConfigurationWizardFiller.cpp | 2 +-
.../workflow_designer/ConfigurationWizardFiller.h | 2 +-
.../CreateElementWithCommandLineFiller.cpp | 2 +-
.../CreateElementWithCommandLineToolFiller.h | 2 +-
.../CreateElementWithScriptDialogFiller.cpp | 2 +-
.../CreateElementWithScriptDialogFiller.h | 2 +-
.../DashboardsManagerDialogFiller.cpp | 2 +-
.../DashboardsManagerDialogFiller.h | 2 +-
.../DatasetNameEditDialogFiller.cpp | 2 +-
.../DatasetNameEditDialogFiller.h | 2 +-
.../workflow_designer/DefaultWizardFiller.cpp | 2 +-
.../workflow_designer/DefaultWizardFiller.h | 2 +-
.../workflow_designer/RPackageDialorFiller.cpp | 2 +-
.../workflow_designer/RPackageDialorFiller.h | 2 +-
.../workflow_designer/StartupDialogFiller.cpp | 2 +-
.../workflow_designer/StartupDialogFiller.h | 2 +-
.../plugins/workflow_designer/WizardFiller.cpp | 26 +-
.../ugene/plugins/workflow_designer/WizardFiller.h | 11 +-
.../workflow_designer/WorkflowMetadialogFiller.cpp | 14 +-
.../workflow_designer/WorkflowMetadialogFiller.h | 2 +-
.../MAFFT/MAFFTSupportRunDialogFiller.cpp | 48 +-
.../MAFFT/MAFFTSupportRunDialogFiller.h | 32 +-
.../clustalw/ClustalWDialogFiller.cpp | 14 +-
.../clustalw/ClustalWDialogFiller.h | 2 +-
.../hmm3/HmmerSearchDialogFiller.cpp | 53 +
.../hmm3/HmmerSearchDialogFiller.h | 41 +
.../hmm3/UHMM3PhmmerDialogFiller.cpp | 2 +-
.../hmm3/UHMM3PhmmerDialogFiller.h | 4 +-
.../hmm3/UHMM3SearchDialogFiller.cpp | 48 -
.../hmm3/UHMM3SearchDialogFiller.h | 41 -
.../plugins_3rdparty/kalign/KalignDialogFiller.cpp | 14 +-
.../plugins_3rdparty/kalign/KalignDialogFiller.h | 2 +-
.../primer3/Primer3DialogFiller.cpp | 2 +-
.../plugins_3rdparty/primer3/Primer3DialogFiller.h | 2 +-
.../umuscle/MuscleDialogFiller.cpp | 20 +-
.../plugins_3rdparty/umuscle/MuscleDialogFiller.h | 2 +-
.../ugeneui/ConvertAceToSqliteDialogFiller.cpp | 13 +-
.../ugene/ugeneui/ConvertAceToSqliteDialogFiller.h | 2 +-
.../ugene/ugeneui/CreateNewProjectWidgetFiller.cpp | 17 +-
.../ugene/ugeneui/CreateNewProjectWidgetFiller.h | 2 +-
.../ugeneui/DocumentFormatSelectorDialogFiller.cpp | 12 +-
.../ugeneui/DocumentFormatSelectorDialogFiller.h | 2 +-
.../DocumentProviderSelectorDialogFiller.cpp | 2 +-
.../ugeneui/DocumentProviderSelectorDialogFiller.h | 2 +-
.../ugene/ugeneui/ExportProjectDialogFiller.cpp | 17 +-
.../ugene/ugeneui/ExportProjectDialogFiller.h | 2 +-
.../ugene/ugeneui/NCBISearchDialogFiller.cpp | 4 +-
.../ugene/ugeneui/NCBISearchDialogFiller.h | 6 +-
.../ugene/ugeneui/SaveProjectDialogFiller.cpp | 11 +-
.../ugene/ugeneui/SaveProjectDialogFiller.h | 8 +-
.../ugeneui/SelectDocumentFormatDialogFiller.cpp | 14 +-
.../ugeneui/SelectDocumentFormatDialogFiller.h | 2 +-
.../SequenceReadingModeSelectorDialogFiller.cpp | 14 +-
.../SequenceReadingModeSelectorDialogFiller.h | 2 +-
.../GUITestBase/src/test_runner/GUITestRunner.cpp | 4 +-
.../GUITestBase/src/test_runner/GUITestRunner.h | 2 +-
.../GUITestBase/src/tests/GUIInitialChecks.cpp | 234 -
.../GUITestBase/src/tests/GUIInitialChecks.h | 57 -
.../GUITestBase/src/tests/PosteriorActions.cpp | 147 +
.../GUITestBase/src/tests/PosteriorActions.h | 47 +
.../GUITestBase/src/tests/PosteriorChecks.cpp | 52 +
.../GUITestBase/src/tests/PosteriorChecks.h | 44 +
.../GUITestBase/src/tests/PreliminaryActions.cpp | 125 +
.../GUITestBase/src/tests/PreliminaryActions.h | 49 +
.../Assembly_browser/GTTestsAssemblyBrowser.cpp | 13 +-
.../Assembly_browser/GTTestsAssemblyBrowser.h | 2 +-
.../Assembling/bowtie2/GTTestsBowtie2.cpp | 2 +-
.../Assembling/bowtie2/GTTestsBowtie2.h | 2 +-
.../Assembling/dna_assembly/GTTestsDnaAssembly.cpp | 2 +-
.../Assembling/dna_assembly/GTTestsDnaAssembly.h | 2 +-
.../Assembling/dna_assembly/GTTestsIndexReuse.cpp | 18 +-
.../Assembling/dna_assembly/GTTestsIndexReuse.h | 2 +-
.../conversions/GTTestsDnaAssemblyConversions.cpp | 2 +-
.../conversions/GTTestsDnaAssemblyConversions.h | 2 +-
.../common_scenarios/Assembling/sam/GTTestsSAM.cpp | 2 +-
.../common_scenarios/Assembling/sam/GTTestsSAM.h | 2 +-
.../NIAID_pipelines/GTTestsNiaidPipelines.cpp | 19 +-
.../NIAID_pipelines/GTTestsNiaidPipelines.h | 2 +-
.../Query_Designer/GTTestsQuerryDesigner.cpp | 8 +-
.../Query_Designer/GTTestsQuerryDesigner.h | 2 +-
.../annotations/GTTestsAnnotations.cpp | 15 +-
.../annotations/GTTestsAnnotations.h | 2 +-
.../annotations/GTTestsCreateAnnotationWidget.cpp | 230 +-
.../annotations/GTTestsCreateAnnotationWidget.h | 4 +-
.../annotations/edit/GTTestsAnnotationsEdit.cpp | 6 +-
.../annotations/edit/GTTestsAnnotationsEdit.h | 2 +-
.../qualifiers/GTTestsAnnotationsQualifiers.cpp | 2 +-
.../qualifiers/GTTestsAnnotationsQualifiers.h | 2 +-
.../GTTestsAnnotationsImport.cpp | 139 +-
.../annotations_import/GTTestsAnnotationsImport.h | 2 +-
.../circular_view/GTTestsCvGeneral.cpp | 2 +-
.../circular_view/GTTestsCvGeneral.h | 2 +-
.../common_scenarios/cloning/GTTestsCloning.cpp | 2 +-
.../common_scenarios/cloning/GTTestsCloning.h | 2 +-
.../document_from_text/GTTestsDocumentFromText.cpp | 2 +-
.../document_from_text/GTTestsDocumentFromText.h | 2 +-
.../common_scenarios/dp_view/GTTestsDpView.cpp | 2 +-
.../tests/common_scenarios/dp_view/GTTestsDpView.h | 2 +-
.../mca_editor/GTTestsMcaEditor.cpp | 5647 ++++++++++++++++++++
.../common_scenarios/mca_editor/GTTestsMcaEditor.h | 95 +
.../msa_editor/GTTestsMsaEditor.cpp | 1016 ++--
.../common_scenarios/msa_editor/GTTestsMsaEditor.h | 7 +-
.../msa_editor/align/GTTestsAlignSequenceToMsa.cpp | 259 +-
.../msa_editor/align/GTTestsAlignSequenceToMsa.h | 7 +-
.../msa_editor/colors/GTTestsMSAEditorColors.cpp | 223 +-
.../msa_editor/colors/GTTestsMSAEditorColors.h | 4 +-
.../consensus/GTTestsMSAEditorConsensus.cpp | 2 +-
.../consensus/GTTestsMSAEditorConsensus.h | 2 +-
.../msa_editor/edit/GTTestsMSAEditorEdit.cpp | 234 +-
.../msa_editor/edit/GTTestsMSAEditorEdit.h | 2 +-
.../overview/GTTestsMSAEditorOverview.cpp | 332 +-
.../msa_editor/overview/GTTestsMSAEditorOverview.h | 2 +-
.../GTTestsMSAEditorReplaceCharacter.cpp | 4 +-
.../GTTestsMSAEditorReplaceCharacter.h | 2 +-
.../options_panel/GTTestsOptionPanel.cpp | 2 +-
.../options_panel/GTTestsOptionPanel.h | 2 +-
.../options_panel/msa/GTTestsOptionPanelMSA.cpp | 238 +-
.../options_panel/msa/GTTestsOptionPanelMSA.h | 2 +-
.../GTTestsOptionPanelSequenceView.cpp | 11 +-
.../sequence_view/GTTestsOptionPanelSequenceView.h | 2 +-
.../common_scenarios/pcr/GTTestsInSilicoPcr.cpp | 28 +-
.../common_scenarios/pcr/GTTestsInSilicoPcr.h | 3 +-
.../common_scenarios/pcr/GTTestsPrimerLibrary.cpp | 22 +-
.../common_scenarios/pcr/GTTestsPrimerLibrary.h | 2 +-
.../phyml/GTTestsCommonScenariosPhyml.cpp | 353 ++
.../phyml/GTTestsCommonScenariosPhyml.h | 45 +
.../common_scenarios/project/GTTestsProject.cpp | 88 +-
.../common_scenarios/project/GTTestsProject.h | 2 +-
.../GTTestsProjectAnonymousProject.cpp | 4 +-
.../GTTestsProjectAnonymousProject.h | 2 +-
.../project/bookmarks/GTTestsBookmarks.cpp | 4 +-
.../project/bookmarks/GTTestsBookmarks.h | 2 +-
.../GTTestsProjectDocumentModifying.cpp | 2 +-
.../GTTestsProjectDocumentModifying.h | 2 +-
.../multiple_docs/GTTestsProjectMultipleDocs.cpp | 2 +-
.../multiple_docs/GTTestsProjectMultipleDocs.h | 2 +-
.../project_filtering/GTTestsProjectFiltering.cpp | 2 +-
.../project_filtering/GTTestsProjectFiltering.h | 2 +-
.../project/relations/GTTestsProjectRelations.cpp | 22 +-
.../project/relations/GTTestsProjectRelations.h | 2 +-
.../remote_request/GTTestsProjectRemoteRequest.cpp | 134 +-
.../remote_request/GTTestsProjectRemoteRequest.h | 4 +-
.../GTTestsProjectSequenceExporting.cpp | 112 +-
.../GTTestsProjectSequenceExporting.h | 2 +-
.../from_project_view/GTTestsFromProjectView.cpp | 163 +-
.../from_project_view/GTTestsFromProjectView.h | 2 +-
.../user_locking/GTTestsProjectUserLocking.cpp | 20 +-
.../user_locking/GTTestsProjectUserLocking.h | 2 +-
.../repeat_finder/GTTestsRepeatFinder.cpp | 11 +-
.../repeat_finder/GTTestsRepeatFinder.h | 2 +-
.../common_scenarios/sanger/GTTestsSanger.cpp | 480 ++
.../tests/common_scenarios/sanger/GTTestsSanger.h | 49 +
.../sequence_edit/GTTestsSequenceEdit.cpp | 4 +-
.../sequence_edit/GTTestsSequenceEdit.h | 2 +-
.../sequence_view/GTTestsSequenceView.cpp | 5 +-
.../sequence_view/GTTestsSequenceView.h | 2 +-
.../shared_database/GTTestsSharedDatabase.cpp | 8 +-
.../shared_database/GTTestsSharedDatabase.h | 2 +-
.../smith_waterman_dialog/GTTestsSWDialog.cpp | 13 +-
.../smith_waterman_dialog/GTTestsSWDialog.h | 2 +-
.../start_page/GTTestsStartPage.cpp | 10 +-
.../common_scenarios/start_page/GTTestsStartPage.h | 2 +-
.../toggle_view/GTTestsToggleView.cpp | 4 +-
.../toggle_view/GTTestsToggleView.h | 2 +-
.../GTTestsCommonScenariousTreeviewer.cpp | 47 +-
.../GTTestsCommonScenariousTreeviewer.h | 2 +-
.../common_scenarios/undo_redo/GTTestsUndoRedo.cpp | 508 +-
.../common_scenarios/undo_redo/GTTestsUndoRedo.h | 2 +-
.../workflow_designer/GTTestsWorkflowDesigner.cpp | 213 +-
.../workflow_designer/GTTestsWorkflowDesigner.h | 4 +-
.../estimating/GTTestsWorkflowEstimating.cpp | 6 +-
.../estimating/GTTestsWorkflowEstimating.h | 2 +-
.../name_filter/GTTestsWorkflowNameFilter.cpp | 8 +-
.../name_filter/GTTestsWorkflowNameFilter.h | 2 +-
.../GTTestsWorkflowParameterValidation.cpp | 320 ++
.../GTTestsWorkflowParameterValidation.h | 45 +
.../GTTestsWorkflowParemeterValidation.cpp | 319 --
.../GTTestsWorkflowParemeterValidation.h | 45 -
.../scripting/GTTestsWorkflowScripting.cpp | 13 +-
.../scripting/GTTestsWorkflowScripting.h | 2 +-
.../shared_db/GTTestsSharedDbWd.cpp | 70 +-
.../shared_db/GTTestsSharedDbWd.h | 2 +-
.../src/tests/crazy_user/GTAbstractGUIAction.cpp | 2 +-
.../src/tests/crazy_user/GTAbstractGUIAction.h | 2 +-
.../tests/crazy_user/GTRandomGUIActionFactory.cpp | 10 +-
.../tests/crazy_user/GTRandomGUIActionFactory.h | 2 +-
.../src/tests/crazy_user/GUICrazyUserTest.cpp | 8 +-
.../src/tests/crazy_user/GUICrazyUserTest.h | 2 +-
.../GTTestsRegressionScenarios_1001_2000.cpp | 569 +-
.../GTTestsRegressionScenarios_1001_2000.h | 2 +-
.../GTTestsRegressionScenarios_1_1000.cpp | 139 +-
.../GTTestsRegressionScenarios_1_1000.h | 2 +-
.../GTTestsRegressionScenarios_2001_3000.cpp | 327 +-
.../GTTestsRegressionScenarios_2001_3000.h | 2 +-
.../GTTestsRegressionScenarios_3001_4000.cpp | 163 +-
.../GTTestsRegressionScenarios_3001_4000.h | 3 +-
.../GTTestsRegressionScenarios_4001_5000.cpp | 411 +-
.../GTTestsRegressionScenarios_4001_5000.h | 8 +-
.../GTTestsRegressionScenarios_5001_6000.cpp | 2830 +++++++++-
.../GTTestsRegressionScenarios_5001_6000.h | 63 +-
src/plugins/annotator/src/AnnotatorPlugin.cpp | 2 +-
src/plugins/annotator/src/AnnotatorPlugin.h | 11 +-
src/plugins/annotator/src/AnnotatorTests.cpp | 14 +-
src/plugins/annotator/src/AnnotatorTests.h | 4 +-
src/plugins/annotator/src/CollocationWorker.cpp | 7 +-
src/plugins/annotator/src/CollocationWorker.h | 4 +-
.../annotator/src/CollocationsDialogController.cpp | 4 +-
.../annotator/src/CollocationsDialogController.h | 16 +-
.../annotator/src/CollocationsSearchAlgorithm.cpp | 2 +-
.../annotator/src/CollocationsSearchAlgorithm.h | 2 +-
.../annotator/src/CustomAutoAnnotationDialog.cpp | 11 +-
.../annotator/src/CustomAutoAnnotationDialog.h | 2 +-
.../annotator/src/CustomPatternAnnotationTask.cpp | 4 +-
.../annotator/src/CustomPatternAnnotationTask.h | 4 +-
src/plugins/annotator/src/GeneByGeneReportTask.cpp | 6 +-
src/plugins/annotator/src/GeneByGeneReportTask.h | 2 +-
.../annotator/src/GeneByGeneReportWorker.cpp | 4 +-
src/plugins/annotator/src/GeneByGeneReportWorker.h | 6 +-
src/plugins/annotator/transl/english.ts | 48 +-
src/plugins/annotator/transl/russian.ts | 48 +-
src/plugins/api_tests/api_tests.pri | 9 +-
src/plugins/api_tests/api_tests.pro | 37 +-
src/plugins/api_tests/src/ApiTestsPlugin.cpp | 2 +-
src/plugins/api_tests/src/ApiTestsPlugin.h | 2 +-
src/plugins/api_tests/src/UnitTestSuite.cpp | 13 +-
src/plugins/api_tests/src/UnitTestSuite.h | 2 +-
.../annotations/AnnotationGroupUnitTests.cpp | 4 +-
.../annotations/AnnotationGroupUnitTests.h | 2 +-
.../datatype/annotations/AnnotationUnitTests.cpp | 4 +-
.../datatype/annotations/AnnotationUnitTests.h | 2 +-
.../core/datatype/msa/MAlignmentRowUnitTests.cpp | 1605 ------
.../src/core/datatype/msa/MAlignmentRowUnitTests.h | 462 --
.../src/core/datatype/msa/MAlignmentUnitTests.cpp | 1003 ----
.../src/core/datatype/msa/MAlignmentUnitTests.h | 347 --
.../src/core/datatype/msa/MsaRowUnitTests.cpp | 1537 ++++++
.../src/core/datatype/msa/MsaRowUnitTests.h | 462 ++
.../src/core/datatype/msa/MsaUnitTests.cpp | 919 ++++
.../api_tests/src/core/datatype/msa/MsaUnitTests.h | 347 ++
.../datatype/udr/RawDataUdrSchemaUnitTests.cpp | 2 +-
.../core/datatype/udr/RawDataUdrSchemaUnitTests.h | 2 +-
.../src/core/datatype/udr/UdrSchemaUnitTests.cpp | 2 +-
.../src/core/datatype/udr/UdrSchemaUnitTests.h | 2 +-
src/plugins/api_tests/src/core/dbi/DbiTest.cpp | 4 +-
.../src/core/dbi/assembly/AssemblyDbiUnitTests.cpp | 0
.../src/core/dbi/assembly/AssemblyDbiUnitTests.h | 0
.../core/dbi/attribute/AttributeDbiUnitTests.cpp | 0
.../src/core/dbi/attribute/AttributeDbiUnitTests.h | 0
.../src/core/dbi/features/FeatureDbiUnitTests.cpp | 2 +-
.../src/core/dbi/features/FeatureDbiUnitTests.h | 2 +-
.../api_tests/src/core/dbi/msa/MsaDbiUnitTests.cpp | 2 +-
.../api_tests/src/core/dbi/msa/MsaDbiUnitTests.h | 2 +-
.../src/core/dbi/sequence/SequenceDbiUnitTests.cpp | 4 +-
.../src/core/dbi/sequence/SequenceDbiUnitTests.h | 0
.../api_tests/src/core/dbi/udr/UdrDbiUnitTests.cpp | 2 +-
.../api_tests/src/core/dbi/udr/UdrDbiUnitTests.h | 2 +-
.../CInterfaceManualTests.cpp | 48 +-
.../base_scheme_interface/CInterfaceManualTests.h | 2 +-
.../base_scheme_interface/CInterfaceSasTests.cpp | 7 +-
.../base_scheme_interface/CInterfaceSasTests.h | 58 +-
.../SchemeSimilarityUtils.cpp | 4 +-
.../base_scheme_interface/SchemeSimilarityUtils.h | 4 +-
.../src/core/format/fastq/FastqUnitTests.cpp | 4 +-
.../src/core/format/fastq/FastqUnitTests.h | 0
.../format/genbank/LocationParserUnitTests.cpp | 2 +-
.../core/format/genbank/LocationParserUnitTests.h | 0
.../ModDbiSQLiteSpecificUnitTests.cpp | 40 +-
.../sqlite_mod_dbi/ModDbiSQLiteSpecificUnitTests.h | 2 +-
.../MsaDbiSQLiteSpecificUnitTests.cpp | 40 +-
.../sqlite_msa_dbi/MsaDbiSQLiteSpecificUnitTests.h | 2 +-
.../sqlite_object_dbi/SQLiteObjectDbiUnitTests.cpp | 38 +-
.../sqlite_object_dbi/SQLiteObjectDbiUnitTests.h | 2 +-
.../SequenceDbiSQLiteSpecificUnitTests.cpp | 4 +-
.../SequenceDbiSQLiteSpecificUnitTests.h | 2 +-
.../core/gobjects/BioStruct3DObjectUnitTests.cpp | 2 +-
.../src/core/gobjects/BioStruct3DObjectUnitTests.h | 2 +-
.../gobjects/DNAChromatogramObjectUnitTests.cpp | 2 +-
.../core/gobjects/DNAChromatogramObjectUnitTests.h | 2 +-
.../core/gobjects/FeaturesTableObjectUnitTest.cpp | 8 +-
.../core/gobjects/FeaturesTableObjectUnitTest.h | 2 +-
.../core/gobjects/MAlignmentObjectUnitTests.cpp | 214 -
.../src/core/gobjects/MAlignmentObjectUnitTests.h | 68 -
.../src/core/gobjects/MsaObjectUnitTests.cpp | 214 +
.../src/core/gobjects/MsaObjectUnitTests.h | 68 +
.../src/core/gobjects/PhyTreeObjectUnitTests.cpp | 2 +-
.../src/core/gobjects/PhyTreeObjectUnitTests.h | 2 +-
.../src/core/gobjects/TextObjectUnitTests.cpp | 2 +-
.../src/core/gobjects/TextObjectUnitTests.h | 2 +-
.../core/util/DatatypeSerializeUtilsUnitTest.cpp | 2 +-
.../src/core/util/DatatypeSerializeUtilsUnitTest.h | 2 +-
.../util/MAlignmentImporterExporterUnitTests.cpp | 93 -
.../util/MAlignmentImporterExporterUnitTests.h | 52 -
.../src/core/util/MsaDbiUtilsUnitTests.cpp | 599 +--
.../api_tests/src/core/util/MsaDbiUtilsUnitTests.h | 26 +-
.../src/core/util/MsaImporterExporterUnitTests.cpp | 90 +
.../src/core/util/MsaImporterExporterUnitTests.h | 52 +
.../api_tests/src/core/util/MsaUtilsUnitTests.cpp | 94 +-
.../api_tests/src/core/util/MsaUtilsUnitTests.h | 2 +-
src/plugins/api_tests/src/unittest.h | 0
src/plugins/biostruct3d_view/biostruct3d_view.pri | 4 +
.../biostruct3d_view/src/AnaglyphRenderer.cpp | 2 +-
.../biostruct3d_view/src/AnaglyphRenderer.h | 2 +-
.../src/BallAndStickGLRenderer.cpp | 2 +-
.../biostruct3d_view/src/BallAndStickGLRenderer.h | 2 +-
.../src/BioStruct3DColorScheme.cpp | 5 +-
.../biostruct3d_view/src/BioStruct3DColorScheme.h | 12 +-
.../src/BioStruct3DGLImageExportTask.cpp | 2 +-
.../src/BioStruct3DGLImageExportTask.h | 2 +-
.../biostruct3d_view/src/BioStruct3DGLRender.cpp | 2 +-
.../biostruct3d_view/src/BioStruct3DGLRender.h | 6 +-
.../biostruct3d_view/src/BioStruct3DGLWidget.cpp | 11 +-
.../biostruct3d_view/src/BioStruct3DGLWidget.h | 2 +-
.../biostruct3d_view/src/BioStruct3DSplitter.cpp | 16 +-
.../biostruct3d_view/src/BioStruct3DSplitter.h | 2 +-
.../src/BioStruct3DSubsetEditor.cpp | 2 +-
.../biostruct3d_view/src/BioStruct3DSubsetEditor.h | 2 +-
.../biostruct3d_view/src/BioStruct3DViewPlugin.cpp | 11 +-
.../biostruct3d_view/src/BioStruct3DViewPlugin.h | 10 +-
.../biostruct3d_view/src/GLFrameManager.cpp | 2 +-
src/plugins/biostruct3d_view/src/GLFrameManager.h | 4 +-
src/plugins/biostruct3d_view/src/GraphicUtils.cpp | 2 +-
src/plugins/biostruct3d_view/src/GraphicUtils.h | 2 +-
.../src/MolecularSurfaceRenderer.cpp | 2 +-
.../src/MolecularSurfaceRenderer.h | 6 +-
.../biostruct3d_view/src/SelectModelsDialog.cpp | 10 +-
.../biostruct3d_view/src/SelectModelsDialog.h | 2 +-
.../biostruct3d_view/src/SettingsDialog.cpp | 4 +-
src/plugins/biostruct3d_view/src/SettingsDialog.h | 8 +-
.../src/StructuralAlignmentDialog.cpp | 4 +-
.../src/StructuralAlignmentDialog.h | 2 +-
.../biostruct3d_view/src/TubeGLRenderer.cpp | 2 +-
src/plugins/biostruct3d_view/src/TubeGLRenderer.h | 6 +-
.../biostruct3d_view/src/VanDerWaalsGLRenderer.cpp | 2 +-
.../biostruct3d_view/src/VanDerWaalsGLRenderer.h | 2 +-
.../biostruct3d_view/src/WormsGLRenderer.cpp | 2 +-
src/plugins/biostruct3d_view/src/WormsGLRenderer.h | 10 +-
.../src/deprecated/AnaglyphRenderer.cpp | 2 +-
.../src/deprecated/AnaglyphRenderer.h | 2 +-
.../src/deprecated/BallAndStickGLRenderer.cpp | 2 +-
.../src/deprecated/BallAndStickGLRenderer.h | 2 +-
.../src/deprecated/BioStruct3DColorScheme.cpp | 5 +-
.../src/deprecated/BioStruct3DColorScheme.h | 12 +-
.../deprecated/BioStruct3DGLImageExportTask.cpp | 2 +-
.../src/deprecated/BioStruct3DGLImageExportTask.h | 2 +-
.../src/deprecated/BioStruct3DGLRender.cpp | 2 +-
.../src/deprecated/BioStruct3DGLRender.h | 6 +-
.../src/deprecated/BioStruct3DGLWidget.cpp | 14 +-
.../src/deprecated/BioStruct3DGLWidget.h | 25 +-
.../src/deprecated/BioStruct3DSplitter.cpp | 16 +-
.../src/deprecated/BioStruct3DSplitter.h | 2 +-
.../src/deprecated/BioStruct3DSubsetEditor.cpp | 2 +-
.../src/deprecated/BioStruct3DSubsetEditor.h | 2 +-
.../src/deprecated/BioStruct3DViewPlugin.cpp | 11 +-
.../src/deprecated/BioStruct3DViewPlugin.h | 10 +-
.../src/deprecated/GLFrameManager.cpp | 2 +-
.../src/deprecated/GLFrameManager.h | 6 +-
.../src/deprecated/GraphicUtils.cpp | 2 +-
.../biostruct3d_view/src/deprecated/GraphicUtils.h | 2 +-
.../src/deprecated/MolecularSurfaceRenderer.cpp | 2 +-
.../src/deprecated/MolecularSurfaceRenderer.h | 6 +-
.../src/deprecated/SelectModelsDialog.cpp | 10 +-
.../src/deprecated/SelectModelsDialog.h | 2 +-
.../src/deprecated/SettingsDialog.cpp | 6 +-
.../src/deprecated/SettingsDialog.h | 8 +-
.../src/deprecated/StructuralAlignmentDialog.cpp | 9 +-
.../src/deprecated/StructuralAlignmentDialog.h | 2 +-
.../src/deprecated/TubeGLRenderer.cpp | 2 +-
.../src/deprecated/TubeGLRenderer.h | 6 +-
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src/plugins/biostruct3d_view/transl/english.ts | 153 +-
src/plugins/biostruct3d_view/transl/russian.ts | 153 +-
.../browser_support/src/BrowserSupportPlugin.cpp | 16 +-
.../browser_support/src/BrowserSupportPlugin.h | 2 +-
src/plugins/chroma_view/src/ChromaViewPlugin.cpp | 15 +-
src/plugins/chroma_view/src/ChromaViewPlugin.h | 10 +-
src/plugins/chroma_view/src/ChromatogramView.cpp | 64 +-
src/plugins/chroma_view/src/ChromatogramView.h | 11 +-
src/plugins/chroma_view/transl/english.ts | 28 +-
src/plugins/chroma_view/transl/russian.ts | 30 +-
src/plugins/circular_view/src/CircularItems.cpp | 2 +-
src/plugins/circular_view/src/CircularItems.h | 10 +-
src/plugins/circular_view/src/CircularView.cpp | 26 +-
src/plugins/circular_view/src/CircularView.h | 2 +-
.../src/CircularViewImageExportTask.cpp | 24 +-
.../src/CircularViewImageExportTask.h | 2 +-
.../circular_view/src/CircularViewPlugin.cpp | 2 +-
src/plugins/circular_view/src/CircularViewPlugin.h | 12 +-
.../src/CircularViewSettingsWidget.cpp | 4 +-
.../circular_view/src/CircularViewSettingsWidget.h | 2 +-
.../src/CircularViewSettingsWidgetFactory.cpp | 7 +-
.../src/CircularViewSettingsWidgetFactory.h | 3 +-
.../circular_view/src/CircularViewSplitter.cpp | 8 +-
.../circular_view/src/CircularViewSplitter.h | 2 +-
.../circular_view/src/RestrictionMapWidget.cpp | 2 +-
.../circular_view/src/RestrictionMapWidget.h | 2 +-
.../circular_view/src/SetSequenceOriginDialog.cpp | 2 +-
.../circular_view/src/SetSequenceOriginDialog.h | 2 +-
.../circular_view/src/ShiftSequenceStartTask.cpp | 2 +-
.../circular_view/src/ShiftSequenceStartTask.h | 2 +-
src/plugins/circular_view/transl/english.ts | 52 +-
src/plugins/circular_view/transl/russian.ts | 52 +-
src/plugins/cuda_support/src/CudaSupportPlugin.cpp | 2 +-
src/plugins/cuda_support/src/CudaSupportPlugin.h | 2 +-
.../src/CudaSupportSettingsController.cpp | 2 +-
.../src/CudaSupportSettingsController.h | 13 +-
src/plugins/dbi_bam/dbi_bam.pri | 8 +-
src/plugins/dbi_bam/src/Alignment.cpp | 2 +-
src/plugins/dbi_bam/src/Alignment.h | 10 +-
src/plugins/dbi_bam/src/BAMDbiPlugin.cpp | 6 +-
src/plugins/dbi_bam/src/BAMDbiPlugin.h | 4 +-
src/plugins/dbi_bam/src/BAMFormat.cpp | 9 +-
src/plugins/dbi_bam/src/BAMFormat.h | 4 +-
src/plugins/dbi_bam/src/BaiReader.cpp | 2 +-
src/plugins/dbi_bam/src/BaiReader.h | 2 +-
src/plugins/dbi_bam/src/BaiWriter.cpp | 2 +-
src/plugins/dbi_bam/src/BaiWriter.h | 2 +-
src/plugins/dbi_bam/src/BgzfReader.cpp | 2 +-
src/plugins/dbi_bam/src/BgzfReader.h | 2 +-
src/plugins/dbi_bam/src/BgzfWriter.cpp | 2 +-
src/plugins/dbi_bam/src/BgzfWriter.h | 2 +-
src/plugins/dbi_bam/src/CancelledException.cpp | 2 +-
src/plugins/dbi_bam/src/CancelledException.h | 2 +-
src/plugins/dbi_bam/src/ConvertToSQLiteDialog.cpp | 17 +-
src/plugins/dbi_bam/src/ConvertToSQLiteDialog.h | 2 +-
src/plugins/dbi_bam/src/ConvertToSQLiteDialog.ui | 21 +-
src/plugins/dbi_bam/src/ConvertToSQLiteTask.cpp | 2 +-
src/plugins/dbi_bam/src/ConvertToSQLiteTask.h | 2 +-
src/plugins/dbi_bam/src/Dbi.cpp | 49 +-
src/plugins/dbi_bam/src/Dbi.h | 6 +-
src/plugins/dbi_bam/src/Exception.cpp | 2 +-
src/plugins/dbi_bam/src/Exception.h | 4 +-
src/plugins/dbi_bam/src/Header.cpp | 2 +-
src/plugins/dbi_bam/src/Header.h | 8 +-
src/plugins/dbi_bam/src/IOException.cpp | 2 +-
src/plugins/dbi_bam/src/IOException.h | 2 +-
src/plugins/dbi_bam/src/Index.cpp | 2 +-
src/plugins/dbi_bam/src/Index.h | 4 +-
src/plugins/dbi_bam/src/InvalidFormatException.cpp | 2 +-
src/plugins/dbi_bam/src/InvalidFormatException.h | 2 +-
src/plugins/dbi_bam/src/LoadBamInfoTask.cpp | 2 +-
src/plugins/dbi_bam/src/LoadBamInfoTask.h | 2 +-
src/plugins/dbi_bam/src/PrepareToImportTask.cpp | 4 +-
src/plugins/dbi_bam/src/PrepareToImportTask.h | 2 +-
src/plugins/dbi_bam/src/Reader.cpp | 2 +-
src/plugins/dbi_bam/src/Reader.h | 2 +-
src/plugins/dbi_bam/src/SamReader.cpp | 6 +-
src/plugins/dbi_bam/src/SamReader.h | 2 +-
src/plugins/dbi_bam/src/SamtoolsBasedDbi.cpp | 15 +-
src/plugins/dbi_bam/src/SamtoolsBasedDbi.h | 4 +-
src/plugins/dbi_bam/src/VirtualOffset.cpp | 2 +-
src/plugins/dbi_bam/src/VirtualOffset.h | 2 +-
src/plugins/dbi_bam/transl/english.ts | 8 +-
src/plugins/dbi_bam/transl/russian.ts | 8 +-
src/plugins/dna_export/dna_export.pro | 21 +-
src/plugins/dna_export/src/BaseContentDialog.ui | 277 -
.../dna_export/src/CSVColumnConfiguration.h | 4 +-
.../src/CSVColumnConfigurationDialog.cpp | 13 +-
.../dna_export/src/CSVColumnConfigurationDialog.h | 2 +-
src/plugins/dna_export/src/DNAExportPlugin.cpp | 28 +-
src/plugins/dna_export/src/DNAExportPlugin.h | 13 +-
.../dna_export/src/DNAExportPluginTests.cpp | 71 +-
src/plugins/dna_export/src/DNAExportPluginTests.h | 10 +-
.../dna_export/src/DNASequenceGenerator.cpp | 37 +-
src/plugins/dna_export/src/DNASequenceGenerator.h | 12 +-
.../dna_export/src/DNASequenceGeneratorDialog.cpp | 263 +-
.../dna_export/src/DNASequenceGeneratorDialog.h | 23 +-
.../dna_export/src/DNASequenceGeneratorDialog.ui | 253 +-
.../dna_export/src/ExportAlignmentViewItems.cpp | 30 +-
.../dna_export/src/ExportAlignmentViewItems.h | 7 +-
.../dna_export/src/ExportBlastResultDialog.cpp | 6 +-
.../dna_export/src/ExportBlastResultDialog.h | 2 +-
.../dna_export/src/ExportChromatogramDialog.cpp | 4 +-
.../dna_export/src/ExportChromatogramDialog.h | 2 +-
src/plugins/dna_export/src/ExportMSA2MSADialog.cpp | 6 +-
src/plugins/dna_export/src/ExportMSA2MSADialog.h | 2 +-
.../dna_export/src/ExportMSA2SequencesDialog.cpp | 11 +-
.../dna_export/src/ExportMSA2SequencesDialog.h | 6 +-
.../dna_export/src/ExportProjectViewItems.cpp | 79 +-
.../dna_export/src/ExportProjectViewItems.h | 4 +-
.../dna_export/src/ExportQualityScoresTask.cpp | 6 +-
.../dna_export/src/ExportQualityScoresTask.h | 4 +-
.../dna_export/src/ExportQualityScoresWorker.cpp | 2 +-
.../dna_export/src/ExportQualityScoresWorker.h | 2 +-
.../src/ExportSelectedSeqRegionsTask.cpp | 4 +-
.../dna_export/src/ExportSelectedSeqRegionsTask.h | 2 +-
src/plugins/dna_export/src/ExportSequenceTask.cpp | 12 +-
src/plugins/dna_export/src/ExportSequenceTask.h | 2 +-
.../dna_export/src/ExportSequenceViewItems.cpp | 58 +-
.../dna_export/src/ExportSequenceViewItems.h | 12 +-
.../dna_export/src/ExportSequences2MSADialog.cpp | 6 +-
.../dna_export/src/ExportSequences2MSADialog.h | 2 +-
.../dna_export/src/ExportSequencesDialog.cpp | 6 +-
src/plugins/dna_export/src/ExportSequencesDialog.h | 2 +-
.../dna_export/src/ExportSequencesDialog.ui | 80 +-
src/plugins/dna_export/src/ExportTasks.cpp | 33 +-
src/plugins/dna_export/src/ExportTasks.h | 20 +-
src/plugins/dna_export/src/ExportUtils.cpp | 34 +-
src/plugins/dna_export/src/ExportUtils.h | 7 +-
src/plugins/dna_export/src/GenerateDNAWorker.cpp | 36 +-
src/plugins/dna_export/src/GenerateDNAWorker.h | 2 +-
.../dna_export/src/GetSequenceByIdDialog.cpp | 18 +-
src/plugins/dna_export/src/GetSequenceByIdDialog.h | 2 +-
.../dna_export/src/GetSequenceByIdDialog.ui | 15 +-
.../src/ImportAnnotationsFromCSVDialog.cpp | 4 +-
.../src/ImportAnnotationsFromCSVDialog.h | 2 +-
.../src/ImportAnnotationsFromCSVTask.cpp | 8 +-
.../dna_export/src/ImportAnnotationsFromCSVTask.h | 8 +-
.../dna_export/src/ImportQualityScoresTask.cpp | 6 +-
.../dna_export/src/ImportQualityScoresTask.h | 10 +-
.../dna_export/src/ImportQualityScoresWorker.cpp | 33 +-
.../dna_export/src/ImportQualityScoresWorker.h | 2 +-
src/plugins/dna_export/src/McaEditorContext.cpp | 73 +
src/plugins/dna_export/src/McaEditorContext.h | 44 +
.../dna_export/src/dialogs/ExportMca2MsaDialog.cpp | 81 +
.../dna_export/src/dialogs/ExportMca2MsaDialog.h | 52 +
.../dna_export/src/dialogs/ExportMca2MsaDialog.ui | 134 +
.../dna_export/src/tasks/ConvertMca2MsaTask.cpp | 66 +
.../dna_export/src/tasks/ConvertMca2MsaTask.h | 54 +
.../dna_export/src/tasks/ExportMca2MsaTask.cpp | 69 +
.../dna_export/src/tasks/ExportMca2MsaTask.h | 53 +
src/plugins/dna_export/transl/english.ts | 539 +-
src/plugins/dna_export/transl/russian.ts | 564 +-
src/plugins/dna_flexibility/src/DNAFlexDialog.cpp | 17 +-
src/plugins/dna_flexibility/src/DNAFlexDialog.h | 2 +-
src/plugins/dna_flexibility/src/DNAFlexGraph.cpp | 2 +-
src/plugins/dna_flexibility/src/DNAFlexGraph.h | 2 +-
.../dna_flexibility/src/DNAFlexGraphAlgorithm.cpp | 2 +-
.../dna_flexibility/src/DNAFlexGraphAlgorithm.h | 2 +-
src/plugins/dna_flexibility/src/DNAFlexPlugin.cpp | 2 +-
src/plugins/dna_flexibility/src/DNAFlexPlugin.h | 2 +-
src/plugins/dna_flexibility/src/DNAFlexTask.cpp | 4 +-
src/plugins/dna_flexibility/src/DNAFlexTask.h | 2 +-
.../dna_flexibility/src/FindHighFlexRegions.cpp | 2 +-
.../dna_flexibility/src/FindHighFlexRegions.h | 2 +-
.../src/FindHighFlexRegionsAlgorithm.cpp | 2 +-
.../src/FindHighFlexRegionsAlgorithm.h | 2 +-
src/plugins/dna_flexibility/src/HighFlexResult.h | 2 +-
.../dna_flexibility/src/HighFlexSettings.cpp | 2 +-
src/plugins/dna_flexibility/src/HighFlexSettings.h | 2 +-
src/plugins/dna_flexibility/transl/english.ts | 10 +-
src/plugins/dna_flexibility/transl/russian.ts | 10 +-
src/plugins/dna_graphpack/src/BaseContentGraph.cpp | 2 +-
src/plugins/dna_graphpack/src/BaseContentGraph.h | 12 +-
src/plugins/dna_graphpack/src/CumulativeSkew.cpp | 2 +-
src/plugins/dna_graphpack/src/CumulativeSkew.h | 12 +-
.../dna_graphpack/src/DNAGraphPackPlugin.cpp | 2 +-
src/plugins/dna_graphpack/src/DNAGraphPackPlugin.h | 13 +-
src/plugins/dna_graphpack/src/DeviationGraph.cpp | 2 +-
src/plugins/dna_graphpack/src/DeviationGraph.h | 14 +-
src/plugins/dna_graphpack/src/EntropyAlgorithm.cpp | 2 +-
src/plugins/dna_graphpack/src/EntropyAlgorithm.h | 12 +-
src/plugins/dna_graphpack/src/GCFramePlot.cpp | 2 +-
src/plugins/dna_graphpack/src/GCFramePlot.h | 12 +-
.../src/KarlinSignatureDifferenceGraph.cpp | 2 +-
.../src/KarlinSignatureDifferenceGraph.h | 12 +-
src/plugins/dna_stat/dna_stat.pri | 2 +-
.../dna_stat/src/DNAStatMSAProfileDialog.cpp | 88 +-
src/plugins/dna_stat/src/DNAStatMSAProfileDialog.h | 12 +-
.../dna_stat/src/DNAStatMSAProfileDialog.ui | 6 +-
src/plugins/dna_stat/src/DNAStatPlugin.cpp | 20 +-
src/plugins/dna_stat/src/DNAStatPlugin.h | 2 +-
src/plugins/dna_stat/src/DNAStatProfileTask.cpp | 2 +-
src/plugins/dna_stat/src/DNAStatProfileTask.h | 4 +-
src/plugins/dna_stat/src/DNAStatsWindow.cpp | 19 +-
src/plugins/dna_stat/src/DNAStatsWindow.h | 9 +-
.../src/DistanceMatrixMSAProfileDialog.cpp | 101 +-
.../dna_stat/src/DistanceMatrixMSAProfileDialog.h | 10 +-
.../dna_stat/src/DistanceMatrixMSAProfileDialog.ui | 6 +-
src/plugins/dna_stat/transl/english.ts | 178 +-
src/plugins/dna_stat/transl/russian.ts | 178 +-
src/plugins/dotplot/src/DotPlotClasses.cpp | 12 +-
src/plugins/dotplot/src/DotPlotClasses.h | 30 +-
src/plugins/dotplot/src/DotPlotDialog.cpp | 11 +-
src/plugins/dotplot/src/DotPlotDialog.h | 9 +-
src/plugins/dotplot/src/DotPlotFilesDialog.cpp | 6 +-
src/plugins/dotplot/src/DotPlotFilesDialog.h | 2 +-
src/plugins/dotplot/src/DotPlotFilterDialog.cpp | 7 +-
src/plugins/dotplot/src/DotPlotFilterDialog.h | 6 +-
src/plugins/dotplot/src/DotPlotImageExportTask.cpp | 2 +-
src/plugins/dotplot/src/DotPlotImageExportTask.h | 2 +-
src/plugins/dotplot/src/DotPlotPlugin.cpp | 45 +-
src/plugins/dotplot/src/DotPlotPlugin.h | 5 +-
src/plugins/dotplot/src/DotPlotSplitter.cpp | 14 +-
src/plugins/dotplot/src/DotPlotSplitter.h | 4 +-
src/plugins/dotplot/src/DotPlotTasks.cpp | 12 +-
src/plugins/dotplot/src/DotPlotTasks.h | 74 +-
src/plugins/dotplot/src/DotPlotWidget.cpp | 113 +-
src/plugins/dotplot/src/DotPlotWidget.h | 25 +-
src/plugins/dotplot/transl/english.ts | 156 +-
src/plugins/dotplot/transl/russian.ts | 156 +-
src/plugins/enzymes/src/CloningUtilTasks.cpp | 4 +-
src/plugins/enzymes/src/CloningUtilTasks.h | 8 +-
.../enzymes/src/ConstructMoleculeDialog.cpp | 18 +-
src/plugins/enzymes/src/ConstructMoleculeDialog.h | 2 +-
src/plugins/enzymes/src/CreateFragmentDialog.cpp | 21 +-
src/plugins/enzymes/src/CreateFragmentDialog.h | 16 +-
src/plugins/enzymes/src/DNAFragment.cpp | 2 +-
src/plugins/enzymes/src/DNAFragment.h | 4 +-
src/plugins/enzymes/src/DigestSequenceDialog.cpp | 13 +-
src/plugins/enzymes/src/DigestSequenceDialog.h | 14 +-
src/plugins/enzymes/src/DigestSequenceDialog.ui | 26 -
src/plugins/enzymes/src/EditFragmentDialog.cpp | 15 +-
src/plugins/enzymes/src/EditFragmentDialog.h | 2 +-
src/plugins/enzymes/src/EnzymesIO.cpp | 4 +-
src/plugins/enzymes/src/EnzymesIO.h | 8 +-
src/plugins/enzymes/src/EnzymesPlugin.cpp | 2 +-
src/plugins/enzymes/src/EnzymesPlugin.h | 2 +-
src/plugins/enzymes/src/EnzymesQuery.cpp | 17 +-
src/plugins/enzymes/src/EnzymesQuery.h | 2 +-
src/plugins/enzymes/src/EnzymesTests.cpp | 14 +-
src/plugins/enzymes/src/EnzymesTests.h | 6 +-
src/plugins/enzymes/src/FindEnzymesAlgorithm.h | 6 +-
src/plugins/enzymes/src/FindEnzymesDialog.cpp | 12 +-
src/plugins/enzymes/src/FindEnzymesDialog.h | 2 +-
src/plugins/enzymes/src/FindEnzymesTask.cpp | 2 +-
src/plugins/enzymes/src/FindEnzymesTask.h | 8 +-
src/plugins/enzymes/transl/english.ts | 210 +-
src/plugins/enzymes/transl/russian.ts | 214 +-
.../external_tool_support.pro | 33 +
.../src/ETSProjectViewItemsContoller.cpp | 4 +-
.../src/ETSProjectViewItemsContoller.h | 11 +-
.../src/ExternalToolManager.cpp | 22 +-
.../src/ExternalToolManager.h | 14 +-
.../src/ExternalToolSupportL10N.h | 8 +-
.../src/ExternalToolSupportPlugin.cpp | 35 +-
.../src/ExternalToolSupportPlugin.h | 2 +-
.../src/ExternalToolSupportSettings.cpp | 38 +-
.../src/ExternalToolSupportSettings.h | 14 +-
.../src/ExternalToolSupportSettingsController.cpp | 40 +-
.../src/ExternalToolSupportSettingsController.h | 8 +-
.../external_tool_support/src/R/RSupport.cpp | 8 +-
src/plugins/external_tool_support/src/R/RSupport.h | 2 +-
.../external_tool_support/src/RnaSeqCommon.cpp | 2 +-
.../external_tool_support/src/RnaSeqCommon.h | 2 +-
.../external_tool_support/src/TaskLocalStorage.cpp | 2 +-
.../external_tool_support/src/TaskLocalStorage.h | 4 +-
.../src/bedtools/BedToolsWorkersLibrary.cpp | 31 +-
.../src/bedtools/BedToolsWorkersLibrary.h | 2 +-
.../src/bedtools/BedtoolsIntersectTask.cpp | 2 +-
.../src/bedtools/BedtoolsIntersectTask.h | 2 +-
.../src/bedtools/BedtoolsSupport.cpp | 2 +-
.../src/bedtools/BedtoolsSupport.h | 2 +-
.../src/bedtools/BedtoolsSupportTask.cpp | 4 +-
.../src/bedtools/BedtoolsSupportTask.h | 2 +-
.../src/bigWigTools/BedGraphToBigWigTask.cpp | 6 +-
.../src/bigWigTools/BedGraphToBigWigTask.h | 2 +-
.../src/bigWigTools/BedGraphToBigWigWorker.cpp | 29 +-
.../src/bigWigTools/BedGraphToBigWigWorker.h | 2 +-
.../src/bigWigTools/BigWigSupport.cpp | 2 +-
.../src/bigWigTools/BigWigSupport.h | 2 +-
.../src/blast/BlastAllSupport.cpp | 70 +-
.../src/blast/BlastAllSupport.h | 5 +-
.../src/blast/BlastAllSupportRunDialog.cpp | 39 +-
.../src/blast/BlastAllSupportRunDialog.h | 17 +-
.../src/blast/BlastAllSupportTask.cpp | 18 +-
.../src/blast/BlastAllSupportTask.h | 6 +-
.../src/blast/BlastAllWorker.cpp | 8 +-
.../src/blast/BlastAllWorker.h | 2 +-
.../src/blast/FormatDBSupport.cpp | 10 +-
.../src/blast/FormatDBSupport.h | 2 +-
.../src/blast/FormatDBSupportRunDialog.cpp | 19 +-
.../src/blast/FormatDBSupportRunDialog.h | 2 +-
.../src/blast/FormatDBSupportRunDialog.ui | 35 +-
.../src/blast/FormatDBSupportTask.cpp | 116 +-
.../src/blast/FormatDBSupportTask.h | 26 +-
.../src/blast/PrepareInputFastaFilesTask.cpp | 107 +
.../src/blast/PrepareInputFastaFilesTask.h | 54 +
.../src/blast_plus/AlignToReferenceBlastDialog.cpp | 403 ++
.../src/blast_plus/AlignToReferenceBlastDialog.h | 119 +
.../src/blast_plus/AlignToReferenceBlastDialog.ui | 235 +
.../src/blast_plus/AlignToReferenceBlastWorker.cpp | 390 ++
.../src/blast_plus/AlignToReferenceBlastWorker.h | 132 +
.../src/blast_plus/BlastDBCmdDialog.cpp | 4 +-
.../src/blast_plus/BlastDBCmdDialog.h | 2 +-
.../src/blast_plus/BlastDBCmdDialog.ui | 196 +-
.../src/blast_plus/BlastDBCmdSupport.cpp | 6 +-
.../src/blast_plus/BlastDBCmdSupport.h | 2 +-
.../src/blast_plus/BlastDBCmdSupportTask.cpp | 2 +-
.../src/blast_plus/BlastDBCmdSupportTask.h | 4 +-
.../src/blast_plus/BlastNPlusSupportTask.cpp | 6 +-
.../src/blast_plus/BlastNPlusSupportTask.h | 2 +-
.../src/blast_plus/BlastPPlusSupportTask.cpp | 6 +-
.../src/blast_plus/BlastPPlusSupportTask.h | 2 +-
.../src/blast_plus/BlastPlusSupport.cpp | 29 +-
.../src/blast_plus/BlastPlusSupport.h | 7 +-
.../src/blast_plus/BlastPlusSupportCommonTask.cpp | 56 +-
.../src/blast_plus/BlastPlusSupportCommonTask.h | 3 +-
.../src/blast_plus/BlastPlusSupportRunDialog.cpp | 23 +-
.../src/blast_plus/BlastPlusSupportRunDialog.h | 7 +-
.../src/blast_plus/BlastPlusWorker.cpp | 8 +-
.../src/blast_plus/BlastPlusWorker.h | 2 +-
.../src/blast_plus/BlastXPlusSupportTask.cpp | 6 +-
.../src/blast_plus/BlastXPlusSupportTask.h | 2 +-
.../src/blast_plus/RPSBlastSupportTask.cpp | 4 +-
.../src/blast_plus/RPSBlastSupportTask.h | 2 +-
.../src/blast_plus/TBlastNPlusSupportTask.cpp | 6 +-
.../src/blast_plus/TBlastNPlusSupportTask.h | 2 +-
.../src/blast_plus/TBlastXPlusSupportTask.cpp | 6 +-
.../src/blast_plus/TBlastXPlusSupportTask.h | 2 +-
.../align_worker_subtasks/BlastReadsSubTask.cpp | 371 ++
.../align_worker_subtasks/BlastReadsSubTask.h | 134 +
.../align_worker_subtasks/ComposeResultSubTask.cpp | 386 ++
.../align_worker_subtasks/ComposeResultSubTask.h | 83 +
.../align_worker_subtasks/FormatDBSubTask.cpp | 123 +
.../align_worker_subtasks/FormatDBSubTask.h | 56 +
.../PrepareReferenceSequenceTask.cpp | 110 +
.../PrepareReferenceSequenceTask.h | 63 +
.../RemoveGapsFromSequenceTask.cpp | 95 +
.../RemoveGapsFromSequenceTask.h | 68 +
.../src/bowtie/BowtieSettingsWidget.cpp | 9 +-
.../src/bowtie/BowtieSettingsWidget.h | 2 +-
.../src/bowtie/BowtieSupport.cpp | 2 +-
.../src/bowtie/BowtieSupport.h | 2 +-
.../src/bowtie/BowtieTask.cpp | 18 +-
.../external_tool_support/src/bowtie/BowtieTask.h | 10 +-
.../src/bowtie/BowtieWorker.cpp | 2 +-
.../src/bowtie/BowtieWorker.h | 2 +-
.../src/bowtie/bowtie_tests/bowtieTests.cpp | 10 +-
.../src/bowtie/bowtie_tests/bowtieTests.h | 13 +-
.../src/bowtie2/Bowtie2SettingsWidget.cpp | 11 +-
.../src/bowtie2/Bowtie2SettingsWidget.h | 2 +-
.../src/bowtie2/Bowtie2Support.cpp | 2 +-
.../src/bowtie2/Bowtie2Support.h | 2 +-
.../src/bowtie2/Bowtie2Task.cpp | 6 +-
.../src/bowtie2/Bowtie2Task.h | 4 +-
.../src/bowtie2/Bowtie2Worker.cpp | 2 +-
.../src/bowtie2/Bowtie2Worker.h | 2 +-
.../src/bwa/BwaMemSettings.ui | 684 ++-
.../external_tool_support/src/bwa/BwaMemWorker.cpp | 12 +-
.../external_tool_support/src/bwa/BwaMemWorker.h | 3 +-
.../src/bwa/BwaSettingsWidget.cpp | 4 +-
.../src/bwa/BwaSettingsWidget.h | 2 +-
.../external_tool_support/src/bwa/BwaSupport.cpp | 2 +-
.../external_tool_support/src/bwa/BwaSupport.h | 2 +-
.../external_tool_support/src/bwa/BwaTask.cpp | 30 +-
.../external_tool_support/src/bwa/BwaTask.h | 2 +-
.../external_tool_support/src/bwa/BwaWorker.cpp | 2 +-
.../external_tool_support/src/bwa/BwaWorker.h | 2 +-
.../src/bwa/bwa_tests/bwaTests.cpp | 10 +-
.../src/bwa/bwa_tests/bwaTests.h | 13 +-
.../external_tool_support/src/cap3/CAP3Support.cpp | 8 +-
.../external_tool_support/src/cap3/CAP3Support.h | 2 +-
.../src/cap3/CAP3SupportDialog.cpp | 4 +-
.../src/cap3/CAP3SupportDialog.h | 3 +-
.../src/cap3/CAP3SupportTask.cpp | 2 +-
.../src/cap3/CAP3SupportTask.h | 6 +-
.../external_tool_support/src/cap3/CAP3Worker.cpp | 16 +-
.../external_tool_support/src/cap3/CAP3Worker.h | 4 +-
.../src/ceas/CEASReportWorker.cpp | 2 +-
.../src/ceas/CEASReportWorker.h | 2 +-
.../src/ceas/CEASSettings.cpp | 2 +-
.../external_tool_support/src/ceas/CEASSettings.h | 2 +-
.../external_tool_support/src/ceas/CEASSupport.cpp | 2 +-
.../external_tool_support/src/ceas/CEASSupport.h | 2 +-
.../src/ceas/CEASSupportTask.cpp | 6 +-
.../src/ceas/CEASSupportTask.h | 2 +-
.../src/clustalo/ClustalOSupport.cpp | 31 +-
.../src/clustalo/ClustalOSupport.h | 2 +-
.../src/clustalo/ClustalOSupportRunDialog.cpp | 12 +-
.../src/clustalo/ClustalOSupportRunDialog.h | 6 +-
.../src/clustalo/ClustalOSupportTask.cpp | 80 +-
.../src/clustalo/ClustalOSupportTask.h | 14 +-
.../src/clustalo/ClustalOWorker.cpp | 16 +-
.../src/clustalo/ClustalOWorker.h | 2 +-
.../src/clustalw/ClustalWSupport.cpp | 43 +-
.../src/clustalw/ClustalWSupport.h | 2 +-
.../src/clustalw/ClustalWSupportRunDialog.cpp | 14 +-
.../src/clustalw/ClustalWSupportRunDialog.h | 6 +-
.../src/clustalw/ClustalWSupportRunDialog.ui | 82 +-
.../src/clustalw/ClustalWSupportTask.cpp | 80 +-
.../src/clustalw/ClustalWSupportTask.h | 14 +-
.../src/clustalw/ClustalWWorker.cpp | 53 +-
.../src/clustalw/ClustalWWorker.h | 4 +-
.../src/conduct_go/ConductGOSettings.cpp | 2 +-
.../src/conduct_go/ConductGOSettings.h | 2 +-
.../src/conduct_go/ConductGOSupport.cpp | 2 +-
.../src/conduct_go/ConductGOSupport.h | 2 +-
.../src/conduct_go/ConductGOTask.cpp | 4 +-
.../src/conduct_go/ConductGOTask.h | 2 +-
.../src/conduct_go/ConductGOWorker.cpp | 8 +-
.../src/conduct_go/ConductGOWorker.h | 2 +-
.../conservation_plot/ConservationPlotSettings.cpp | 2 +-
.../conservation_plot/ConservationPlotSettings.h | 2 +-
.../conservation_plot/ConservationPlotSupport.cpp | 2 +-
.../conservation_plot/ConservationPlotSupport.h | 2 +-
.../src/conservation_plot/ConservationPlotTask.cpp | 6 +-
.../src/conservation_plot/ConservationPlotTask.h | 2 +-
.../conservation_plot/ConservationPlotWorker.cpp | 4 +-
.../src/conservation_plot/ConservationPlotWorker.h | 2 +-
.../src/cufflinks/CuffdiffSupportTask.cpp | 2 +-
.../src/cufflinks/CuffdiffSupportTask.h | 2 +-
.../src/cufflinks/CuffdiffWorker.cpp | 16 +-
.../src/cufflinks/CuffdiffWorker.h | 2 +-
.../src/cufflinks/CufflinksSettings.cpp | 2 +-
.../src/cufflinks/CufflinksSettings.h | 2 +-
.../src/cufflinks/CufflinksSupport.cpp | 2 +-
.../src/cufflinks/CufflinksSupport.h | 2 +-
.../src/cufflinks/CufflinksSupportTask.cpp | 6 +-
.../src/cufflinks/CufflinksSupportTask.h | 2 +-
.../src/cufflinks/CufflinksWorker.cpp | 12 +-
.../src/cufflinks/CufflinksWorker.h | 2 +-
.../src/cufflinks/CuffmergeSupportTask.cpp | 4 +-
.../src/cufflinks/CuffmergeSupportTask.h | 2 +-
.../src/cufflinks/CuffmergeWorker.cpp | 10 +-
.../src/cufflinks/CuffmergeWorker.h | 2 +-
.../src/cufflinks/GffreadSupportTask.cpp | 2 +-
.../src/cufflinks/GffreadSupportTask.h | 2 +-
.../src/cufflinks/GffreadWorker.cpp | 8 +-
.../src/cufflinks/GffreadWorker.h | 2 +-
.../src/cutadapt/CutadaptSupport.cpp | 2 +-
.../src/cutadapt/CutadaptSupport.h | 2 +-
.../src/cutadapt/CutadaptWorker.cpp | 29 +-
.../src/cutadapt/CutadaptWorker.h | 2 +-
.../src/fastqc/FastqcSupport.cpp | 2 +-
.../src/fastqc/FastqcSupport.h | 2 +-
.../src/fastqc/FastqcTask.cpp | 6 +-
.../external_tool_support/src/fastqc/FastqcTask.h | 2 +-
.../src/fastqc/FastqcWorker.cpp | 32 +-
.../src/fastqc/FastqcWorker.h | 2 +-
.../src/hmmer/ConvertAlignment2StockholmTask.cpp | 12 +-
.../src/hmmer/ConvertAlignment2StockholmTask.h | 3 +-
.../src/hmmer/HmmerBuildDialog.cpp | 19 +-
.../src/hmmer/HmmerBuildDialog.h | 10 +-
.../src/hmmer/HmmerBuildFromFileTask.cpp | 2 +-
.../src/hmmer/HmmerBuildFromFileTask.h | 3 +-
.../src/hmmer/HmmerBuildFromMsaTask.cpp | 9 +-
.../src/hmmer/HmmerBuildFromMsaTask.h | 8 +-
.../src/hmmer/HmmerBuildSettings.cpp | 2 +-
.../src/hmmer/HmmerBuildSettings.h | 2 +-
.../src/hmmer/HmmerBuildTask.cpp | 2 +-
.../src/hmmer/HmmerBuildTask.h | 3 +-
.../src/hmmer/HmmerBuildTaskTest.cpp | 464 ++
.../src/hmmer/HmmerBuildTaskTest.h | 105 +
.../src/hmmer/HmmerBuildWorker.cpp | 14 +-
.../src/hmmer/HmmerBuildWorker.h | 2 +-
.../src/hmmer/HmmerParseSearchResultsTask.cpp | 2 +-
.../src/hmmer/HmmerParseSearchResultsTask.h | 3 +-
.../src/hmmer/HmmerSearchDialog.cpp | 22 +-
.../src/hmmer/HmmerSearchDialog.h | 6 +-
.../src/hmmer/HmmerSearchSettings.cpp | 3 +-
.../src/hmmer/HmmerSearchSettings.h | 3 +-
.../src/hmmer/HmmerSearchTask.cpp | 29 +-
.../src/hmmer/HmmerSearchTask.h | 3 +-
.../src/hmmer/HmmerSearchTaskTest.cpp | 549 ++
.../src/hmmer/HmmerSearchTaskTest.h | 145 +
.../src/hmmer/HmmerSearchWorker.cpp | 3 +-
.../src/hmmer/HmmerSearchWorker.h | 2 +-
.../src/hmmer/HmmerSupport.cpp | 62 +-
.../external_tool_support/src/hmmer/HmmerSupport.h | 2 +-
.../external_tool_support/src/hmmer/HmmerTests.h | 51 +
.../src/hmmer/PhmmerSearchDialog.cpp | 22 +-
.../src/hmmer/PhmmerSearchDialog.h | 7 +-
.../src/hmmer/PhmmerSearchSettings.cpp | 2 +-
.../src/hmmer/PhmmerSearchSettings.h | 2 +-
.../src/hmmer/PhmmerSearchTask.cpp | 34 +-
.../src/hmmer/PhmmerSearchTask.h | 5 +-
.../src/hmmer/PhmmerSearchTaskTest.cpp | 273 +
.../src/hmmer/PhmmerSearchTaskTest.h | 96 +
.../external_tool_support/src/java/JavaSupport.cpp | 36 +-
.../external_tool_support/src/java/JavaSupport.h | 9 +-
.../src/macs/MACSSettings.cpp | 2 +-
.../external_tool_support/src/macs/MACSSettings.h | 2 +-
.../external_tool_support/src/macs/MACSSupport.cpp | 2 +-
.../external_tool_support/src/macs/MACSSupport.h | 2 +-
.../external_tool_support/src/macs/MACSTask.cpp | 4 +-
.../external_tool_support/src/macs/MACSTask.h | 2 +-
.../external_tool_support/src/macs/MACSWorker.cpp | 16 +-
.../external_tool_support/src/macs/MACSWorker.h | 2 +-
.../src/mafft/MAFFTSupport.cpp | 28 +-
.../external_tool_support/src/mafft/MAFFTSupport.h | 2 +-
.../src/mafft/MAFFTSupportRunDialog.cpp | 8 +-
.../src/mafft/MAFFTSupportRunDialog.h | 2 +-
.../src/mafft/MAFFTSupportTask.cpp | 64 +-
.../src/mafft/MAFFTSupportTask.h | 16 +-
.../src/mafft/MAFFTWorker.cpp | 51 +-
.../external_tool_support/src/mafft/MAFFTWorker.h | 4 +-
.../src/mafft/MafftAddToAlignmentTask.cpp | 76 +-
.../src/mafft/MafftAddToAlignmentTask.h | 6 +-
.../src/mrbayes/MrBayesDialogWidget.cpp | 10 +-
.../src/mrbayes/MrBayesDialogWidget.h | 6 +-
.../src/mrbayes/MrBayesSupport.cpp | 6 +-
.../src/mrbayes/MrBayesSupport.h | 6 +-
.../src/mrbayes/MrBayesTask.cpp | 10 +-
.../src/mrbayes/MrBayesTask.h | 8 +-
.../src/mrbayes/MrBayesTests.cpp | 18 +-
.../src/mrbayes/MrBayesTests.h | 8 +-
.../src/peak2gene/Gene2PeakFormatLoader.cpp | 2 +-
.../src/peak2gene/Gene2PeakFormatLoader.h | 3 +-
.../src/peak2gene/Peak2GeneFormatLoader.cpp | 2 +-
.../src/peak2gene/Peak2GeneFormatLoader.h | 3 +-
.../src/peak2gene/Peak2GeneSettings.cpp | 2 +-
.../src/peak2gene/Peak2GeneSettings.h | 2 +-
.../src/peak2gene/Peak2GeneSupport.cpp | 2 +-
.../src/peak2gene/Peak2GeneSupport.h | 2 +-
.../src/peak2gene/Peak2GeneTask.cpp | 4 +-
.../src/peak2gene/Peak2GeneTask.h | 2 +-
.../src/peak2gene/Peak2GeneWorker.cpp | 2 +-
.../src/peak2gene/Peak2GeneWorker.h | 2 +-
.../src/peak2gene/TabulatedFormatReader.cpp | 2 +-
.../src/peak2gene/TabulatedFormatReader.h | 4 +-
.../external_tool_support/src/perl/PerlSupport.cpp | 2 +-
.../external_tool_support/src/perl/PerlSupport.h | 2 +-
.../external_tool_support/src/phyml/PhyMLDialog.ui | 613 ++-
.../src/phyml/PhyMLDialogWidget.cpp | 170 +-
.../src/phyml/PhyMLDialogWidget.h | 18 +-
.../src/phyml/PhyMLSupport.cpp | 6 +-
.../external_tool_support/src/phyml/PhyMLSupport.h | 6 +-
.../external_tool_support/src/phyml/PhyMLTask.cpp | 10 +-
.../external_tool_support/src/phyml/PhyMLTask.h | 8 +-
.../external_tool_support/src/phyml/PhyMLTests.cpp | 18 +-
.../external_tool_support/src/phyml/PhyMLTests.h | 12 +-
.../src/python/PythonSupport.cpp | 9 +-
.../src/python/PythonSupport.h | 2 +-
.../src/samtools/BcfToolsSupport.cpp | 2 +-
.../src/samtools/BcfToolsSupport.h | 2 +-
.../src/samtools/SamToolsExtToolSupport.cpp | 2 +-
.../src/samtools/SamToolsExtToolSupport.h | 2 +-
.../src/samtools/TabixSupport.cpp | 2 +-
.../src/samtools/TabixSupport.h | 2 +-
.../src/samtools/TabixSupportTask.cpp | 63 +-
.../src/samtools/TabixSupportTask.h | 18 +-
.../src/seqpos/SeqPosSettings.cpp | 2 +-
.../src/seqpos/SeqPosSettings.h | 2 +-
.../src/seqpos/SeqPosSupport.cpp | 2 +-
.../src/seqpos/SeqPosSupport.h | 2 +-
.../src/seqpos/SeqPosTask.cpp | 6 +-
.../external_tool_support/src/seqpos/SeqPosTask.h | 2 +-
.../src/seqpos/SeqPosWorker.cpp | 8 +-
.../src/seqpos/SeqPosWorker.h | 8 +-
.../src/snpeff/SnpEffDatabaseDelegate.cpp | 189 +
.../src/snpeff/SnpEffDatabaseDelegate.h | 96 +
.../src/snpeff/SnpEffDatabaseDialog.ui | 94 +
.../src/snpeff/SnpEffDatabaseListModel.cpp | 105 +
.../src/snpeff/SnpEffDatabaseListModel.h | 63 +
.../src/snpeff/SnpEffDatabaseListTask.cpp | 66 +
.../src/snpeff/SnpEffDatabaseListTask.h | 45 +
.../src/snpeff/SnpEffSupport.cpp | 30 +-
.../src/snpeff/SnpEffSupport.h | 10 +-
.../src/snpeff/SnpEffTask.cpp | 18 +-
.../external_tool_support/src/snpeff/SnpEffTask.h | 6 +-
.../src/snpeff/SnpEffWorker.cpp | 35 +-
.../src/snpeff/SnpEffWorker.h | 7 +-
.../src/spades/SpadesSettings.ui | 2 +-
.../src/spades/SpadesSettingsWidget.cpp | 4 +-
.../src/spades/SpadesSettingsWidget.h | 2 +-
.../src/spades/SpadesSupport.cpp | 2 +-
.../src/spades/SpadesSupport.h | 2 +-
.../src/spades/SpadesTask.cpp | 15 +-
.../external_tool_support/src/spades/SpadesTask.h | 4 +-
.../src/spades/SpadesWorker.cpp | 17 +-
.../src/spades/SpadesWorker.h | 2 +-
.../src/spidey/SpideySupport.cpp | 4 +-
.../src/spidey/SpideySupport.h | 2 +-
.../src/spidey/SpideySupportTask.cpp | 2 +-
.../src/spidey/SpideySupportTask.h | 6 +-
.../src/tcoffee/TCoffeeSupport.cpp | 28 +-
.../src/tcoffee/TCoffeeSupport.h | 2 +-
.../src/tcoffee/TCoffeeSupportRunDialog.cpp | 8 +-
.../src/tcoffee/TCoffeeSupportRunDialog.h | 2 +-
.../src/tcoffee/TCoffeeSupportTask.cpp | 74 +-
.../src/tcoffee/TCoffeeSupportTask.h | 14 +-
.../src/tcoffee/TCoffeeWorker.cpp | 50 +-
.../src/tcoffee/TCoffeeWorker.h | 2 +-
.../src/tophat/TopHatSettings.cpp | 2 +-
.../src/tophat/TopHatSettings.h | 4 +-
.../src/tophat/TopHatSupport.cpp | 2 +-
.../src/tophat/TopHatSupport.h | 2 +-
.../src/tophat/TopHatSupportTask.cpp | 4 +-
.../src/tophat/TopHatSupportTask.h | 2 +-
.../src/tophat/TopHatWorker.cpp | 22 +-
.../src/tophat/TopHatWorker.h | 2 +-
.../src/utils/AlignMsaAction.cpp | 4 +-
.../src/utils/AlignMsaAction.h | 2 +-
.../src/utils/BaseShortReadsAlignerWorker.cpp | 19 +-
.../src/utils/BaseShortReadsAlignerWorker.h | 3 +-
.../src/utils/BlastAllSupportDialog.ui | 375 +-
.../src/utils/BlastDBSelectorWidget.ui | 11 +-
.../src/utils/BlastDBSelectorWidgetController.cpp | 4 +-
.../src/utils/BlastDBSelectorWidgetController.h | 2 +-
.../src/utils/BlastRunCommonDialog.cpp | 20 +-
.../src/utils/BlastRunCommonDialog.h | 2 +-
.../src/utils/BlastTaskSettings.cpp | 2 +-
.../src/utils/BlastTaskSettings.h | 2 +-
.../src/utils/CistromeDelegate.cpp | 9 +-
.../src/utils/CistromeDelegate.h | 2 +-
.../src/utils/ExportTasks.cpp | 29 +-
.../external_tool_support/src/utils/ExportTasks.h | 14 +-
.../src/utils/ExternalToolSearchTask.cpp | 8 +-
.../src/utils/ExternalToolSearchTask.h | 2 +-
.../src/utils/ExternalToolSupportAction.cpp | 2 +-
.../src/utils/ExternalToolSupportAction.h | 2 +-
.../src/utils/ExternalToolUtils.cpp | 46 +-
.../src/utils/ExternalToolUtils.h | 9 +-
.../src/utils/ExternalToolValidateTask.cpp | 6 +-
.../src/utils/ExternalToolValidateTask.h | 4 +-
.../src/utils/OutputCollector.cpp | 41 +
.../src/utils/OutputCollector.h | 43 +
.../src/vcftools/VcfConsensusSupport.cpp | 2 +-
.../src/vcftools/VcfConsensusSupport.h | 2 +-
.../src/vcftools/VcfConsensusSupportTask.cpp | 13 +-
.../src/vcftools/VcfConsensusSupportTask.h | 2 +-
.../src/vcftools/VcfConsensusWorker.cpp | 2 +-
.../src/vcftools/VcfConsensusWorker.h | 2 +-
.../src/vcfutils/VcfutilsSupport.cpp | 2 +-
.../src/vcfutils/VcfutilsSupport.h | 2 +-
.../external_tool_support/transl/english.ts | 3084 +++++++----
.../external_tool_support/transl/russian.ts | 3089 ++++++-----
.../src/BuildSArraySettingsWidget.cpp | 2 +-
.../genome_aligner/src/BuildSArraySettingsWidget.h | 2 +-
.../genome_aligner/src/BuildSuffixArraySettings.ui | 36 +-
src/plugins/genome_aligner/src/DataBunch.cpp | 2 +-
src/plugins/genome_aligner/src/DataBunch.h | 2 +-
.../src/GenomeAlignerCMDLineTask.cpp | 10 +-
.../genome_aligner/src/GenomeAlignerCMDLineTask.h | 2 +-
.../genome_aligner/src/GenomeAlignerFindTask.cpp | 2 +-
.../genome_aligner/src/GenomeAlignerFindTask.h | 21 +-
src/plugins/genome_aligner/src/GenomeAlignerIO.cpp | 26 +-
src/plugins/genome_aligner/src/GenomeAlignerIO.h | 12 +-
.../genome_aligner/src/GenomeAlignerIndex.cpp | 4 +-
.../genome_aligner/src/GenomeAlignerIndex.h | 4 +-
.../genome_aligner/src/GenomeAlignerIndexPart.cpp | 2 +-
.../genome_aligner/src/GenomeAlignerIndexPart.h | 2 +-
.../genome_aligner/src/GenomeAlignerIndexTask.cpp | 3 +-
.../genome_aligner/src/GenomeAlignerIndexTask.h | 2 +-
.../src/GenomeAlignerIndexWorker.cpp | 2 +-
.../genome_aligner/src/GenomeAlignerIndexWorker.h | 2 +-
.../genome_aligner/src/GenomeAlignerPlugin.cpp | 5 +-
.../genome_aligner/src/GenomeAlignerPlugin.h | 2 +-
.../src/GenomeAlignerSearchQuery.cpp | 2 +-
.../genome_aligner/src/GenomeAlignerSearchQuery.h | 2 +-
.../genome_aligner/src/GenomeAlignerSettings.ui | 6 +-
.../src/GenomeAlignerSettingsController.cpp | 54 +-
.../src/GenomeAlignerSettingsController.h | 42 +-
.../src/GenomeAlignerSettingsWidget.cpp | 8 +-
.../src/GenomeAlignerSettingsWidget.h | 2 +-
.../src/GenomeAlignerSettingsWidget.ui | 30 -
.../genome_aligner/src/GenomeAlignerTask.cpp | 8 +-
src/plugins/genome_aligner/src/GenomeAlignerTask.h | 6 +-
.../genome_aligner/src/GenomeAlignerWorker.cpp | 12 +-
.../genome_aligner/src/GenomeAlignerWorker.h | 2 +-
.../genome_aligner/src/GenomeAlignerWriteTask.cpp | 2 +-
.../genome_aligner/src/GenomeAlignerWriteTask.h | 2 +-
.../genome_aligner/src/ReadShortReadsSubTask.cpp | 2 +-
.../genome_aligner/src/ReadShortReadsSubTask.h | 2 +-
.../src/WriteAlignedReadsSubTask.cpp | 2 +-
.../genome_aligner/src/WriteAlignedReadsSubTask.h | 2 +-
src/plugins/genome_aligner/transl/english.ts | 85 +-
src/plugins/genome_aligner/transl/russian.ts | 85 +-
.../linkdata_support/src/LinkDataScriptLibrary.cpp | 14 +-
.../linkdata_support/src/LinkDataScriptLibrary.h | 11 +-
.../linkdata_support/src/LinkDataSupportPlugin.cpp | 2 +-
.../linkdata_support/src/LinkDataSupportPlugin.h | 2 +-
.../opencl_support/src/OpenCLSupportPlugin.cpp | 6 +-
.../opencl_support/src/OpenCLSupportPlugin.h | 2 +-
.../src/OpenCLSupportSettingsController.cpp | 17 +-
.../src/OpenCLSupportSettingsController.h | 13 +-
src/plugins/opencl_support/transl/english.ts | 4 +-
src/plugins/opencl_support/transl/russian.ts | 4 +-
src/plugins/orf_marker/src/ORFDialog.cpp | 19 +-
src/plugins/orf_marker/src/ORFDialog.h | 17 +-
src/plugins/orf_marker/src/ORFDialogUI.ui | 2 +-
src/plugins/orf_marker/src/ORFMarkerPlugin.cpp | 2 +-
src/plugins/orf_marker/src/ORFMarkerPlugin.h | 2 +-
src/plugins/orf_marker/src/ORFMarkerTask.cpp | 2 +-
src/plugins/orf_marker/src/ORFMarkerTask.h | 4 +-
src/plugins/orf_marker/src/ORFMarkerTests.cpp | 2 +-
src/plugins/orf_marker/src/ORFMarkerTests.h | 4 +-
src/plugins/orf_marker/src/ORFQuery.cpp | 8 +-
src/plugins/orf_marker/src/ORFQuery.h | 2 +-
src/plugins/orf_marker/src/ORFWorker.cpp | 8 +-
src/plugins/orf_marker/src/ORFWorker.h | 2 +-
src/plugins/orf_marker/transl/english.ts | 8 +
src/plugins/orf_marker/transl/russian.ts | 8 +
src/plugins/pcr/pcr.pri | 2 +-
src/plugins/pcr/src/EditPrimerDialog.cpp | 4 +-
src/plugins/pcr/src/EditPrimerDialog.h | 2 +-
src/plugins/pcr/src/ExtractProductTask.cpp | 4 +-
src/plugins/pcr/src/ExtractProductTask.h | 2 +-
src/plugins/pcr/src/FindPrimerPairsWorker.cpp | 2 +-
src/plugins/pcr/src/FindPrimerPairsWorker.h | 4 +-
src/plugins/pcr/src/InSilicoPcrOPWidgetFactory.cpp | 4 +-
src/plugins/pcr/src/InSilicoPcrOPWidgetFactory.h | 2 +-
.../pcr/src/InSilicoPcrOptionPanelWidget.cpp | 3 +-
src/plugins/pcr/src/InSilicoPcrOptionPanelWidget.h | 2 +-
src/plugins/pcr/src/InSilicoPcrProductsTable.cpp | 2 +-
src/plugins/pcr/src/InSilicoPcrProductsTable.h | 2 +-
src/plugins/pcr/src/InSilicoPcrTask.cpp | 2 +-
src/plugins/pcr/src/InSilicoPcrTask.h | 2 +-
src/plugins/pcr/src/InSilicoPcrWorker.cpp | 7 +-
src/plugins/pcr/src/InSilicoPcrWorker.h | 2 +-
src/plugins/pcr/src/InSilicoPcrWorkflowTask.cpp | 2 +-
src/plugins/pcr/src/InSilicoPcrWorkflowTask.h | 2 +-
src/plugins/pcr/src/PcrOptionsPanelSavableTab.cpp | 2 +-
src/plugins/pcr/src/PcrOptionsPanelSavableTab.h | 2 +-
src/plugins/pcr/src/PcrPlugin.cpp | 2 +-
src/plugins/pcr/src/PcrPlugin.h | 2 +-
src/plugins/pcr/src/Primer.cpp | 2 +-
src/plugins/pcr/src/Primer.h | 2 +-
src/plugins/pcr/src/PrimerDimersFinder.cpp | 4 +-
src/plugins/pcr/src/PrimerDimersFinder.h | 2 +-
src/plugins/pcr/src/PrimerGroupBox.cpp | 2 +-
src/plugins/pcr/src/PrimerGroupBox.h | 2 +-
src/plugins/pcr/src/PrimerLibrary.cpp | 2 +-
src/plugins/pcr/src/PrimerLibrary.h | 2 +-
src/plugins/pcr/src/PrimerLibraryMdiWindow.cpp | 2 +-
src/plugins/pcr/src/PrimerLibraryMdiWindow.h | 2 +-
src/plugins/pcr/src/PrimerLibrarySelector.cpp | 4 +-
src/plugins/pcr/src/PrimerLibrarySelector.h | 2 +-
src/plugins/pcr/src/PrimerLibraryTable.cpp | 2 +-
src/plugins/pcr/src/PrimerLibraryTable.h | 2 +-
.../pcr/src/PrimerLibraryTableController.cpp | 2 +-
src/plugins/pcr/src/PrimerLibraryTableController.h | 2 +-
src/plugins/pcr/src/PrimerLibraryWidget.cpp | 4 +-
src/plugins/pcr/src/PrimerLibraryWidget.h | 2 +-
src/plugins/pcr/src/PrimerLineEdit.cpp | 6 +-
src/plugins/pcr/src/PrimerLineEdit.h | 2 +-
src/plugins/pcr/src/PrimerStatistics.cpp | 2 +-
src/plugins/pcr/src/PrimerStatistics.h | 2 +-
src/plugins/pcr/src/PrimersDetailsDialog.cpp | 4 +-
src/plugins/pcr/src/PrimersDetailsDialog.h | 2 +-
src/plugins/pcr/src/PrimersGrouperWorker.cpp | 2 +-
src/plugins/pcr/src/PrimersGrouperWorker.h | 4 +-
src/plugins/pcr/src/export/ExportPrimersDialog.cpp | 4 +-
src/plugins/pcr/src/export/ExportPrimersDialog.h | 2 +-
.../pcr/src/export/ExportPrimersToDatabaseTask.cpp | 4 +-
.../pcr/src/export/ExportPrimersToDatabaseTask.h | 2 +-
.../src/export/ExportPrimersToLocalFileTask.cpp | 2 +-
.../pcr/src/export/ExportPrimersToLocalFileTask.h | 2 +-
.../pcr/src/import/ImportPrimerFromObjectTask.cpp | 2 +-
.../pcr/src/import/ImportPrimerFromObjectTask.h | 2 +-
src/plugins/pcr/src/import/ImportPrimersDialog.cpp | 4 +-
src/plugins/pcr/src/import/ImportPrimersDialog.h | 2 +-
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.../src/cmdline/WorkflowCMDLineTasks.cpp | 34 +-
.../src/cmdline/WorkflowCMDLineTasks.h | 4 +-
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.../src/library/AlignToReferenceWorker.cpp | 855 ---
.../src/library/AlignToReferenceWorker.h | 204 -
.../src/library/AminoTranslationWorker.cpp | 4 +-
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.../library/RenameChromosomeInVariationWorker.cpp | 6 +-
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.../src/library/ReverseComplementWorker.cpp | 40 +-
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.../workflow_designer/src/library/ScriptWorker.cpp | 10 +-
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.../src/library/SequenceQualityTrimWorker.cpp | 170 +
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.../src/library/SortBamWorker.cpp | 26 +-
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.../src/tasks/SequenceQualityTrimTask.cpp | 141 +
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.../src/util/DatasetValidator.cpp | 6 +-
.../workflow_designer/src/util/DatasetValidator.h | 2 +-
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.../src/util/GrouperActionUtils.cpp | 61 +-
.../src/util/GrouperActionUtils.h | 8 +-
.../src/util/RequiredSlotsValidator.cpp | 2 +-
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.../src/util/SaveSchemaImageUtils.cpp | 20 +-
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.../src/util/WorkerNameValidator.cpp | 2 +-
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.../src/util/WriteSequenceValidator.cpp | 4 +-
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src/plugins/workflow_designer/transl/english.ts | 2327 ++++----
src/plugins/workflow_designer/transl/russian.ts | 2265 ++++----
.../workflow_designer/workflow_designer.pri | 3 +-
.../workflow_designer/workflow_designer.pro | 6 +-
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src/plugins/workflow_dump/src/WorkflowDumpPlugin.h | 2 +-
src/plugins_3rdparty/ball/src/BallPlugin.cpp | 2 +-
src/plugins_3rdparty/ball/src/BallPlugin.h | 2 +-
src/plugins_3rdparty/ball/src/SAS.cpp | 2 +-
src/plugins_3rdparty/ball/src/SAS.h | 2 +-
src/plugins_3rdparty/ball/src/SES.cpp | 2 +-
src/plugins_3rdparty/ball/src/SES.h | 2 +-
.../ball/src/include/BALL/CONFIG/config.h | 4 +-
.../ball/src/source/DATATYPE/string.cpp | 4 +-
src/plugins_3rdparty/gor4/src/GorIVAlgTask.cpp | 10 +-
src/plugins_3rdparty/gor4/src/GorIVAlgTask.h | 4 +-
src/plugins_3rdparty/gor4/src/GorIVPlugin.cpp | 19 +-
src/plugins_3rdparty/gor4/src/GorIVPlugin.h | 2 +-
src/plugins_3rdparty/gor4/src/gor.cpp | 45 +-
src/plugins_3rdparty/gor4/src/gor.h | 10 +-
src/plugins_3rdparty/gor4/transl/english.ts | 42 +-
src/plugins_3rdparty/gor4/transl/russian.ts | 42 +-
src/plugins_3rdparty/hmm2/src/HMMIO.cpp | 5 +-
src/plugins_3rdparty/hmm2/src/HMMIO.h | 6 +-
src/plugins_3rdparty/hmm2/src/HMMIOWorker.cpp | 2 +-
src/plugins_3rdparty/hmm2/src/HMMIOWorker.h | 2 +-
src/plugins_3rdparty/hmm2/src/TaskLocalStorage.cpp | 2 +-
src/plugins_3rdparty/hmm2/src/TaskLocalStorage.h | 8 +-
src/plugins_3rdparty/hmm2/src/uHMMPlugin.cpp | 49 +-
src/plugins_3rdparty/hmm2/src/uHMMPlugin.h | 8 +-
.../hmm2/src/u_build/HMMBuildDialogController.cpp | 62 +-
.../hmm2/src/u_build/HMMBuildDialogController.h | 16 +-
.../hmm2/src/u_build/HMMBuildWorker.cpp | 61 +-
.../hmm2/src/u_build/uhmmbuild.cpp | 6 +-
src/plugins_3rdparty/hmm2/src/u_build/uhmmbuild.h | 4 +-
.../u_calibrate/HMMCalibrateDialogController.cpp | 4 +-
.../src/u_calibrate/HMMCalibrateDialogController.h | 2 +-
.../hmm2/src/u_calibrate/HMMCalibrateTask.cpp | 2 +-
.../hmm2/src/u_calibrate/uhmmcalibrate.h | 4 +-
.../src/u_search/HMMSearchDialogController.cpp | 28 +-
.../hmm2/src/u_search/HMMSearchDialogController.h | 16 +-
.../hmm2/src/u_search/HMMSearchQDActor.cpp | 20 +-
.../hmm2/src/u_search/HMMSearchQDActor.h | 2 +-
.../hmm2/src/u_search/HMMSearchTask.cpp | 2 +-
.../hmm2/src/u_search/HMMSearchTask.h | 4 +-
.../hmm2/src/u_search/HMMSearchWorker.cpp | 69 +-
.../hmm2/src/u_search/uhmmsearch.cpp | 80 +-
.../hmm2/src/u_search/uhmmsearch.h | 2 +-
.../hmm2/src/u_search/uhmmsearch_opt.cpp | 2 +-
.../hmm2/src/u_search/uhmmsearch_opt.h | 2 +-
.../hmm2/src/u_tests/uhmmerTests.cpp | 41 +-
.../hmm2/src/u_tests/uhmmerTests.h | 2 +-
src/plugins_3rdparty/hmm2/transl/english.ts | 344 +-
src/plugins_3rdparty/hmm2/transl/russian.ts | 348 +-
src/plugins_3rdparty/kalign/src/KalignAdapter.cpp | 37 +-
src/plugins_3rdparty/kalign/src/KalignAdapter.h | 11 +-
src/plugins_3rdparty/kalign/src/KalignConstants.h | 2 +-
.../kalign/src/KalignDialogController.cpp | 16 +-
.../kalign/src/KalignDialogController.h | 6 +-
.../kalign/src/KalignException.cpp | 2 +-
src/plugins_3rdparty/kalign/src/KalignException.h | 2 +-
src/plugins_3rdparty/kalign/src/KalignPlugin.cpp | 27 +-
src/plugins_3rdparty/kalign/src/KalignPlugin.h | 8 +-
src/plugins_3rdparty/kalign/src/KalignTask.cpp | 66 +-
src/plugins_3rdparty/kalign/src/KalignTask.h | 29 +-
src/plugins_3rdparty/kalign/src/KalignUtils.cpp | 2 +-
src/plugins_3rdparty/kalign/src/KalignUtils.h | 2 +-
src/plugins_3rdparty/kalign/src/KalignWorker.cpp | 39 +-
src/plugins_3rdparty/kalign/src/KalignWorker.h | 4 +-
...rwiseAlignmentHirschbergGUIExtensionFactory.cpp | 17 +-
...airwiseAlignmentHirschbergGUIExtensionFactory.h | 19 +-
.../kalign/src/PairwiseAlignmentHirschbergTask.cpp | 44 +-
.../kalign/src/PairwiseAlignmentHirschbergTask.h | 10 +-
.../src/PairwiseAlignmentHirschbergTaskFactory.h | 2 +-
.../kalign/src/TaskLocalStorage.cpp | 2 +-
src/plugins_3rdparty/kalign/src/TaskLocalStorage.h | 4 +-
.../kalign/src/kalign_tests/KalignTests.cpp | 105 +-
.../kalign/src/kalign_tests/KalignTests.h | 26 +-
src/plugins_3rdparty/kalign/transl/english.ts | 64 +-
src/plugins_3rdparty/kalign/transl/russian.ts | 64 +-
src/plugins_3rdparty/phylip/phylip.license | 38 +-
src/plugins_3rdparty/phylip/src/DistanceMatrix.cpp | 26 +-
src/plugins_3rdparty/phylip/src/DistanceMatrix.h | 8 +-
.../phylip/src/NeighborJoinAdapter.cpp | 28 +-
.../phylip/src/NeighborJoinAdapter.h | 16 +-
.../phylip/src/NeighborJoinWidget.cpp | 16 +-
.../phylip/src/NeighborJoinWidget.h | 10 +-
.../phylip/src/PhylipCmdlineTask.cpp | 12 +-
.../phylip/src/PhylipCmdlineTask.h | 8 +-
src/plugins_3rdparty/phylip/src/PhylipPlugin.cpp | 4 +-
src/plugins_3rdparty/phylip/src/PhylipPlugin.h | 2 +-
.../phylip/src/PhylipPluginTests.cpp | 18 +-
.../phylip/src/PhylipPluginTests.h | 8 +-
src/plugins_3rdparty/phylip/src/PhylipTask.cpp | 8 +-
src/plugins_3rdparty/phylip/src/PhylipTask.h | 2 +-
src/plugins_3rdparty/phylip/src/SeqBootAdapter.cpp | 38 +-
src/plugins_3rdparty/phylip/src/SeqBootAdapter.h | 12 +-
src/plugins_3rdparty/phylip/src/cons.cpp | 29 +-
src/plugins_3rdparty/phylip/src/cons.h | 2 +-
src/plugins_3rdparty/phylip/src/dist.cpp | 36 +-
src/plugins_3rdparty/phylip/src/dist.h | 32 +-
src/plugins_3rdparty/phylip/src/dnadist.cpp | 43 +-
src/plugins_3rdparty/phylip/src/neighbor.cpp | 36 +-
src/plugins_3rdparty/phylip/src/phylip.cpp | 41 +-
src/plugins_3rdparty/phylip/src/phylip.h | 94 +-
src/plugins_3rdparty/phylip/src/protdist.cpp | 33 +-
src/plugins_3rdparty/phylip/src/seq.cpp | 48 +-
src/plugins_3rdparty/phylip/src/seq.h | 32 +-
src/plugins_3rdparty/phylip/src/seqboot.cpp | 45 +-
src/plugins_3rdparty/phylip/src/seqboot.h | 42 +-
src/plugins_3rdparty/phylip/transl/english.ts | 34 +-
src/plugins_3rdparty/phylip/transl/russian.ts | 34 +-
.../primer3/src/FindExonRegionsTask.cpp | 4 +-
.../primer3/src/FindExonRegionsTask.h | 2 +-
src/plugins_3rdparty/primer3/src/Primer3Dialog.cpp | 15 +-
src/plugins_3rdparty/primer3/src/Primer3Dialog.h | 9 +-
src/plugins_3rdparty/primer3/src/Primer3Dialog.ui | 36 +-
src/plugins_3rdparty/primer3/src/Primer3Plugin.cpp | 5 +-
src/plugins_3rdparty/primer3/src/Primer3Plugin.h | 8 +-
src/plugins_3rdparty/primer3/src/Primer3Query.cpp | 2 +-
src/plugins_3rdparty/primer3/src/Primer3Query.h | 2 +-
src/plugins_3rdparty/primer3/src/Primer3Task.cpp | 2 +-
src/plugins_3rdparty/primer3/src/Primer3Task.h | 4 +-
.../primer3/src/Primer3TaskSettings.cpp | 2 +-
.../primer3/src/Primer3TaskSettings.h | 14 +-
src/plugins_3rdparty/primer3/src/Primer3Tests.cpp | 2 +-
src/plugins_3rdparty/primer3/src/Primer3Tests.h | 4 +-
src/plugins_3rdparty/primer3/transl/english.ts | 321 +-
src/plugins_3rdparty/primer3/transl/russian.ts | 321 +-
.../psipred/src/PsipredAlgTask.cpp | 6 +-
src/plugins_3rdparty/psipred/src/PsipredAlgTask.h | 4 +-
src/plugins_3rdparty/psipred/src/PsipredPlugin.cpp | 19 +-
src/plugins_3rdparty/psipred/src/PsipredPlugin.h | 2 +-
src/plugins_3rdparty/psipred/src/seq2mtx.cpp | 5 +-
src/plugins_3rdparty/psipred/src/sspred_avpred.cpp | 11 +-
src/plugins_3rdparty/psipred/src/sspred_avpred.h | 6 +-
src/plugins_3rdparty/psipred/src/sspred_hmulti.cpp | 11 +-
src/plugins_3rdparty/psipred/src/sspred_hmulti.h | 4 +-
src/plugins_3rdparty/psipred/transl/english.ts | 6 +-
src/plugins_3rdparty/psipred/transl/russian.ts | 6 +-
src/plugins_3rdparty/ptools/src/PToolsAligner.cpp | 2 +-
src/plugins_3rdparty/ptools/src/PToolsAligner.h | 2 +-
src/plugins_3rdparty/ptools/src/PToolsPlugin.cpp | 2 +-
src/plugins_3rdparty/ptools/src/PToolsPlugin.h | 2 +-
src/plugins_3rdparty/ptools/src/PToolsTests.cpp | 8 +-
src/plugins_3rdparty/ptools/src/PToolsTests.h | 2 +-
src/plugins_3rdparty/ptools/src/ptools/basetypes.h | 2 +-
.../sitecon/src/DIPropertiesSitecon.cpp | 4 +-
.../sitecon/src/DIPropertiesSitecon.h | 8 +-
.../sitecon/src/DIPropertiesTests.cpp | 2 +-
.../sitecon/src/DIPropertiesTests.h | 4 +-
.../sitecon/src/SiteconAlgorithm.cpp | 64 +-
.../sitecon/src/SiteconAlgorithm.h | 18 +-
.../sitecon/src/SiteconAlgorithmTests.cpp | 82 +-
.../sitecon/src/SiteconAlgorithmTests.h | 12 +-
.../sitecon/src/SiteconBuildDialogController.cpp | 42 +-
.../sitecon/src/SiteconBuildDialogController.h | 8 +-
.../sitecon/src/SiteconBuildWorker.cpp | 40 +-
src/plugins_3rdparty/sitecon/src/SiteconIO.cpp | 27 +-
src/plugins_3rdparty/sitecon/src/SiteconIO.h | 6 +-
.../sitecon/src/SiteconIOWorkers.cpp | 2 +-
.../sitecon/src/SiteconIOWorkers.h | 2 +-
src/plugins_3rdparty/sitecon/src/SiteconPlugin.cpp | 2 +-
src/plugins_3rdparty/sitecon/src/SiteconPlugin.h | 8 +-
src/plugins_3rdparty/sitecon/src/SiteconQuery.cpp | 12 +-
src/plugins_3rdparty/sitecon/src/SiteconQuery.h | 2 +-
.../sitecon/src/SiteconSearchDialogController.cpp | 5 +-
.../sitecon/src/SiteconSearchDialogController.h | 14 +-
.../sitecon/src/SiteconSearchTask.cpp | 2 +-
.../sitecon/src/SiteconSearchTask.h | 4 +-
.../sitecon/src/SiteconSearchWorker.cpp | 39 +-
src/plugins_3rdparty/sitecon/src/SiteconWorkers.h | 2 +-
src/plugins_3rdparty/sitecon/transl/english.ts | 216 +-
src/plugins_3rdparty/sitecon/transl/russian.ts | 228 +-
src/plugins_3rdparty/umuscle/src/MuscleAdapter.cpp | 92 +-
src/plugins_3rdparty/umuscle/src/MuscleAdapter.h | 23 +-
.../umuscle/src/MuscleAlignDialogController.cpp | 20 +-
.../umuscle/src/MuscleAlignDialogController.h | 6 +-
src/plugins_3rdparty/umuscle/src/MuscleConstants.h | 2 +-
.../umuscle/src/MuscleParallel.cpp | 42 +-
src/plugins_3rdparty/umuscle/src/MuscleParallel.h | 10 +-
src/plugins_3rdparty/umuscle/src/MusclePlugin.cpp | 61 +-
src/plugins_3rdparty/umuscle/src/MusclePlugin.h | 8 +-
src/plugins_3rdparty/umuscle/src/MuscleTask.cpp | 164 +-
src/plugins_3rdparty/umuscle/src/MuscleTask.h | 40 +-
src/plugins_3rdparty/umuscle/src/MuscleUtils.cpp | 47 +-
src/plugins_3rdparty/umuscle/src/MuscleUtils.h | 12 +-
.../umuscle/src/MuscleWorkPool.cpp | 8 +-
src/plugins_3rdparty/umuscle/src/MuscleWorkPool.h | 14 +-
src/plugins_3rdparty/umuscle/src/MuscleWorker.cpp | 47 +-
src/plugins_3rdparty/umuscle/src/MuscleWorker.h | 2 +-
.../umuscle/src/ProfileToProfileWorker.cpp | 50 +-
.../umuscle/src/ProfileToProfileWorker.h | 19 +-
.../umuscle/src/TaskLocalStorage.cpp | 2 +-
.../umuscle/src/TaskLocalStorage.h | 4 +-
.../umuscle/src/muscle/globals.cpp | 2 +-
src/plugins_3rdparty/umuscle/src/refinehorizP.cpp | 2 +-
src/plugins_3rdparty/umuscle/src/refinevertP.cpp | 2 +-
.../umuscle/src/umuscle_tests/umuscleTests.cpp | 190 +-
.../umuscle/src/umuscle_tests/umuscleTests.h | 29 +-
src/plugins_3rdparty/umuscle/transl/english.ts | 140 +-
src/plugins_3rdparty/umuscle/transl/russian.ts | 140 +-
.../variants/src/AssemblySamtoolsMpileup.cpp | 24 +-
.../variants/src/AssemblySamtoolsMpileup.h | 2 +-
.../variants/src/SamtoolMpileupWorker.cpp | 42 +-
.../variants/src/SamtoolMpileupWorker.h | 2 +-
.../variants/src/SamtoolsPlugin.cpp | 2 +-
src/plugins_3rdparty/variants/src/SamtoolsPlugin.h | 2 +-
src/plugins_3rdparty/variants/transl/english.ts | 38 +-
src/plugins_3rdparty/variants/transl/russian.ts | 38 +-
src/plugins_3rdparty/variants/variants.pri | 15 +-
src/plugins_checker/src/Main.cpp | 2 +-
src/qclean.cmd | 27 +
src/qmake_msvc_proj_x32.cmd | 3 +
src/qmake_msvc_proj_x64.cmd | 3 +
src/ugene_globals.pri | 8 +-
src/ugene_version.pri | 4 +-
src/ugenecl/src/DumpHelpTask.cpp | 8 +-
src/ugenecl/src/DumpHelpTask.h | 2 +-
src/ugenecl/src/DumpLicenseTask.cpp | 4 +-
src/ugenecl/src/DumpLicenseTask.h | 2 +-
src/ugenecl/src/DumpVersionTask.cpp | 2 +-
src/ugenecl/src/DumpVersionTask.h | 2 +-
src/ugenecl/src/ForeverTask.cpp | 6 +-
src/ugenecl/src/ForeverTask.h | 2 +-
src/ugenecl/src/Main.cpp | 9 +-
src/ugenecl/src/TaskStatusBar.cpp | 6 +-
src/ugenecl/src/TaskStatusBar.h | 2 +-
src/ugenecl/src/TestStarter.cpp | 5 +-
src/ugenecl/src/TestStarter.h | 2 +-
src/ugenecl/ugenecl.pri | 2 +-
src/ugenem/src/DetectWin10.cpp | 2 +-
src/ugenem/src/DetectWin10.h | 2 +-
src/ugenem/src/SendReportDialog.cpp | 2 +-
src/ugenem/src/SendReportDialog.h | 2 +-
src/ugenem/src/Utils.cpp | 10 +-
src/ugenem/src/Utils.h | 4 +-
src/ugenem/src/main.cpp | 2 +-
src/ugeneui/html/version_news.html | 50 +-
src/ugeneui/html/welcome_page.css | 2 +-
src/ugeneui/html/welcome_page.html | 2 +-
src/ugeneui/src/Main.cpp | 25 +-
.../app_settings/AppSettingsDialogController.cpp | 2 +-
.../src/app_settings/AppSettingsDialogController.h | 10 +-
.../src/app_settings/AppSettingsDialogTree.h | 9 +-
.../src/app_settings/AppSettingsGUIImpl.cpp | 2 +-
src/ugeneui/src/app_settings/AppSettingsGUIImpl.h | 2 +-
.../DirectoriesSettingsGUIController.cpp | 80 +-
.../DirectoriesSettingsGUIController.h | 15 +-
.../DirectoriesSettingsWidget.ui | 315 +-
.../FormatSettingsGUIController.cpp | 4 +-
.../format_settings/FormatSettingsGUIController.h | 2 +-
.../logview_settings/LogSettingsGUIController.cpp | 4 +-
.../logview_settings/LogSettingsGUIController.h | 2 +-
.../NetworkSettingsGUIController.cpp | 6 +-
.../NetworkSettingsGUIController.h | 4 +-
.../ResourceSettingsGUIController.cpp | 4 +-
.../ResourceSettingsGUIController.h | 4 +-
.../UserApplicationsSettingsGUIController.cpp | 23 +-
.../UserApplicationsSettingsGUIController.h | 4 +-
.../UserApplicationsSettingsWidget.ui | 31 +-
.../src/main_window/AboutDialogController.cpp | 18 +-
.../src/main_window/AboutDialogController.h | 23 +-
src/ugeneui/src/main_window/CheckUpdatesTask.cpp | 2 +-
src/ugeneui/src/main_window/CheckUpdatesTask.h | 2 +-
src/ugeneui/src/main_window/DockManagerImpl.cpp | 129 +-
src/ugeneui/src/main_window/DockManagerImpl.h | 10 +-
src/ugeneui/src/main_window/DockWidgetPainter.cpp | 201 +
src/ugeneui/src/main_window/DockWidgetPainter.h | 75 +
src/ugeneui/src/main_window/MDIManagerImpl.cpp | 64 +-
src/ugeneui/src/main_window/MDIManagerImpl.h | 22 +-
src/ugeneui/src/main_window/MainWindowImpl.cpp | 8 +-
src/ugeneui/src/main_window/MainWindowImpl.h | 17 +-
src/ugeneui/src/main_window/MenuManager.cpp | 2 +-
src/ugeneui/src/main_window/MenuManager.h | 13 +-
src/ugeneui/src/main_window/ShutdownTask.cpp | 2 +-
src/ugeneui/src/main_window/ShutdownTask.h | 4 +-
src/ugeneui/src/main_window/SplashScreen.cpp | 25 +-
src/ugeneui/src/main_window/SplashScreen.h | 9 +-
.../main_window/TmpDirChangeDialogController.cpp | 8 +-
.../src/main_window/TmpDirChangeDialogController.h | 12 +-
src/ugeneui/src/main_window/ToolBarManager.cpp | 4 +-
src/ugeneui/src/main_window/ToolBarManager.h | 11 +-
.../src/plugin_viewer/PluginViewerController.cpp | 10 +-
.../src/plugin_viewer/PluginViewerController.h | 8 +-
src/ugeneui/src/plugin_viewer/PluginViewerImpl.cpp | 8 +-
src/ugeneui/src/plugin_viewer/PluginViewerImpl.h | 2 +-
.../DocumentFormatSelectorController.cpp | 20 +-
.../DocumentFormatSelectorController.h | 14 +-
.../DocumentProviderSelectorController.cpp | 195 +-
.../DocumentProviderSelectorController.h | 33 +-
.../DocumentReadingModeSelectorController.cpp | 4 +-
.../DocumentReadingModeSelectorController.h | 2 +-
.../ExportProjectDialogController.cpp | 17 +-
.../ExportProjectDialogController.h | 2 +-
...tipleDocumentsReadingModeSelectorController.cpp | 6 +-
...ultipleDocumentsReadingModeSelectorController.h | 2 +-
src/ugeneui/src/project_support/ProjectImpl.cpp | 2 +-
src/ugeneui/src/project_support/ProjectImpl.h | 4 +-
.../src/project_support/ProjectLoaderImpl.cpp | 44 +-
.../src/project_support/ProjectLoaderImpl.h | 8 +-
.../src/project_support/ProjectServiceImpl.cpp | 6 +-
.../src/project_support/ProjectServiceImpl.h | 8 +-
.../src/project_support/ProjectTasksGui.cpp | 9 +-
src/ugeneui/src/project_support/ProjectTasksGui.h | 15 +-
.../src/project_view/BuiltInObjectViews.cpp | 11 +-
src/ugeneui/src/project_view/ProjectViewImpl.cpp | 11 +-
src/ugeneui/src/project_view/ProjectViewImpl.h | 2 +-
.../src/project_view/ProjectViewSearchBox.cpp | 124 -
.../src/project_view/ProjectViewSearchBox.h | 63 -
src/ugeneui/src/project_view/ProjectViewWidget.ui | 12 +-
src/ugeneui/src/shtirlitz/Shtirlitz.cpp | 2 +-
src/ugeneui/src/shtirlitz/Shtirlitz.h | 4 +-
src/ugeneui/src/shtirlitz/StatisticalReport.ui | 15 +-
.../src/shtirlitz/StatisticalReportController.cpp | 7 +-
.../src/shtirlitz/StatisticalReportController.h | 4 +-
src/ugeneui/src/task_view/TaskStatusBar.cpp | 8 +-
src/ugeneui/src/task_view/TaskStatusBar.h | 20 +-
src/ugeneui/src/task_view/TaskViewController.cpp | 4 +-
src/ugeneui/src/task_view/TaskViewController.h | 21 +-
src/ugeneui/src/update/UgeneUpdater.cpp | 2 +-
src/ugeneui/src/update/UgeneUpdater.h | 2 +-
src/ugeneui/src/utils/MultilingualHtmlView.cpp | 2 +-
src/ugeneui/src/utils/MultilingualHtmlView.h | 2 +-
.../src/welcome_page/WelcomePageController.cpp | 7 +-
.../src/welcome_page/WelcomePageController.h | 4 +-
src/ugeneui/src/welcome_page/WelcomePageMdi.cpp | 2 +-
src/ugeneui/src/welcome_page/WelcomePageMdi.h | 2 +-
src/ugeneui/src/welcome_page/WelcomePageWidget.cpp | 2 +-
src/ugeneui/src/welcome_page/WelcomePageWidget.h | 2 +-
src/ugeneui/transl/english.ts | 625 ++-
src/ugeneui/transl/russian.ts | 637 ++-
src/ugeneui/ugeneui.pro | 4 +-
ugene.pro | 9 +-
4401 files changed, 101058 insertions(+), 57718 deletions(-)
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