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satta pushed a change to branch upstream
in repository ugene.

      from  a8a1cc6   Imported Upstream version 1.23.1+dfsg
       new  adee81f   New upstream version 1.24.2+dfsg

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Summary of changes:
 .../{hmm3-search.uwl => hmm3-build-and-search.uwl} |   96 +-
 data/workflow_samples/NGS/call_variants_full.uwl   |  413 +++
 data/workflow_samples/NGS/fastqc.uwl               |    2 +-
 .../NGS/raw_ngs/chipseq/chipseq_paired.uwl         |   97 +-
 .../NGS/raw_ngs/chipseq/chipseq_single.uwl         |   66 +-
 .../NGS/raw_ngs/dnaseq/dna_paired.uwl              |   91 +-
 .../NGS/raw_ngs/dnaseq/dna_single.uwl              |   60 +-
 .../NGS/raw_ngs/rnaseq/rnaseq_paired.uwl           |   79 +-
 .../NGS/raw_ngs/rnaseq/rnaseq_single.uwl           |   42 +-
 data/workflow_samples/NGS/variation_annotation.uwl |   38 +-
 data/workflow_samples/Scenarios/length_filter.uwl  |  131 +
 data/workflow_samples/users/LengthMarker.usa       |   14 +
 .../U2Algorithm/src/misc/DnaAssemblyMultiTask.cpp  |   10 +-
 .../U2Algorithm/src/misc/DnaAssemblyMultiTask.h    |    5 +-
 .../U2Algorithm/src/registry/DnaAssemblyTask.cpp   |    2 +-
 .../U2Algorithm/src/registry/DnaAssemblyTask.h     |    7 +-
 src/corelibs/U2Core/U2Core.pro                     |   16 +-
 src/corelibs/U2Core/src/datatype/Annotation.cpp    |    9 +-
 src/corelibs/U2Core/src/datatype/Annotation.h      |    4 +-
 src/corelibs/U2Core/src/datatype/U2Assembly.h      |   24 +-
 .../src/datatype/U2Qualifier.cpp}                  |   40 +-
 src/corelibs/U2Core/src/datatype/U2Qualifier.h     |   15 +-
 .../U2Core/src/datatype/U2Variant.cpp}             |   46 +-
 src/corelibs/U2Core/src/datatype/U2Variant.h       |   29 +-
 src/corelibs/U2Core/src/dbi/U2DbiUtils.cpp         |   89 +-
 src/corelibs/U2Core/src/dbi/U2DbiUtils.h           |    6 +
 .../U2Core/src/globals/ExternalToolRegistry.h      |    2 +
 src/corelibs/U2Core/src/globals/L10n.h             |    3 +
 .../U2Core/src/gobjects/VariantTrackObject.cpp     |   20 +-
 .../U2Core/src/gobjects/VariantTrackObject.h       |    1 +
 src/corelibs/U2Core/src/models/DocumentModel.cpp   |    4 +-
 src/corelibs/U2Core/src/models/DocumentModel.h     |    2 +
 .../src/tasks/AddSequencesToAlignmentTask.cpp      |    2 +-
 .../U2Core/src/tasks/RemoveDocumentTask.cpp        |    6 +-
 src/corelibs/U2Core/src/tasks/SaveDocumentTask.cpp |   18 +-
 .../U2Core/src/tasks/SequenceDbiWalkerTask.cpp     |    5 +-
 .../U2Core/src/util/AnnotationCreationPattern.cpp} |   15 +-
 .../U2Core/src/util/AnnotationCreationPattern.h}   |   22 +-
 src/corelibs/U2Core/src/util/GenbankFeatures.cpp   |    2 +-
 src/corelibs/U2Core/src/util/SnpeffDictionary.cpp  |  162 ++
 .../U2Core/src/util/SnpeffDictionary.h}            |   34 +-
 src/corelibs/U2Core/src/util/U1AnnotationUtils.cpp |   18 +
 src/corelibs/U2Core/src/util/U1AnnotationUtils.h   |    3 +
 src/corelibs/U2Core/src/util/U2AlphabetUtils.h     |    2 +-
 src/corelibs/U2Core/src/util/U2AssemblyUtils.cpp   |   91 +-
 src/corelibs/U2Core/src/util/U2AssemblyUtils.h     |   11 +
 src/corelibs/U2Core/src/util/U2AttributeUtils.cpp  |    7 +-
 src/corelibs/U2Core/src/util/U2AttributeUtils.h    |    3 +-
 src/corelibs/U2Core/src/util/U2FeatureUtils.cpp    |    2 +-
 src/corelibs/U2Core/src/util/U2VariationUtils.cpp  |    4 +-
 src/corelibs/U2Core/transl/english.ts              |    7 +-
 src/corelibs/U2Core/transl/russian.ts              |    7 +-
 .../U2Designer/src/BreakpointHitCountDialog.cpp    |    2 +-
 src/corelibs/U2Designer/src/DelegateEditors.cpp    |    4 +
 src/corelibs/U2Designer/src/DelegateEditors.h      |    2 +
 .../U2Designer/src/EditBreakpointLabelsDialog.cpp  |    2 +-
 .../U2Designer/src/EditMarkerGroupDialog.cpp       |    4 +-
 .../U2Designer/src/NewBreakpointDialog.cpp         |    2 +-
 .../U2Designer/src/NewGrouperSlotDialog.cpp        |   10 +-
 .../U2Designer/src/dashboard/StatisticsWidget.cpp  |    5 +-
 .../U2Designer/src/support/URLLineEdit.cpp         |   11 +-
 src/corelibs/U2Formats/U2Formats.pro               |   12 +-
 .../U2Formats/src/AbstractVariationFormat.cpp      |  320 ++-
 .../U2Formats/src/AbstractVariationFormat.h        |   10 +-
 src/corelibs/U2Formats/src/BAMUtils.cpp            |    8 +-
 src/corelibs/U2Formats/src/BAMUtils.h              |    2 +-
 src/corelibs/U2Formats/src/SAMFormat.cpp           |    2 +-
 src/corelibs/U2Formats/src/StockholmFormat.cpp     |    4 +-
 src/corelibs/U2Formats/src/VCF4VariationFormat.cpp |    2 +-
 .../U2Formats/src/ace/ConvertAceToSqliteTask.cpp   |    4 +-
 src/corelibs/U2Formats/src/mysql_dbi/MysqlDbi.cpp  |    2 +
 .../U2Formats/src/mysql_dbi/MysqlVariantDbi.cpp    |    4 +-
 .../src/mysql_dbi/util/MysqlAssemblyUtils.cpp      |    8 +-
 .../upgraders/MysqlUpgraderFrom_1_16_To_1_24.cpp   |  217 ++
 .../upgraders/MysqlUpgraderFrom_1_16_To_1_24.h     |   54 +
 .../U2Formats/src/sqlite_dbi/SQLiteAssemblyDbi.cpp |    8 +-
 .../U2Formats/src/sqlite_dbi/SQLiteVariantDbi.cpp  |    4 +-
 src/corelibs/U2Formats/src/tasks/ConvertFileTask.h |    1 +
 .../ConvertSnpeffVariationsToAnnotationsTask.cpp   |  233 ++
 .../ConvertSnpeffVariationsToAnnotationsTask.h     |   89 +
 .../U2Formats/src/util/SnpeffInfoParser.cpp        |  277 ++
 src/corelibs/U2Formats/src/util/SnpeffInfoParser.h |  147 +
 src/corelibs/U2Formats/transl/russian.ts           |    2 +-
 src/corelibs/U2Gui/src/ToolsMenu.cpp               |    2 +
 src/corelibs/U2Gui/src/ToolsMenu.h                 |    1 +
 .../U2Gui/src/util/AddNewDocumentDialogImpl.cpp    |    2 +-
 .../U2Gui/src/util/AuthenticationDialog.cpp        |    2 +-
 .../src/util/BreakpointConditionEditDialog.cpp     |    2 +-
 .../U2Gui/src/util/CreateAnnotationDialog.cpp      |    2 +-
 .../src/util/CreateAnnotationWidgetController.cpp  |   11 +-
 .../src/util/CreateAnnotationWidgetController.h    |    2 +
 .../CreateDocumentFromTextDialogController.cpp     |    2 +-
 .../U2Gui/src/util/DownloadRemoteFileDialog.cpp    |    4 +-
 .../U2Gui/src/util/EditQualifierDialog.cpp         |    2 +-
 .../src/util/EditSequenceDialogController.cpp      |    2 +-
 .../U2Gui/src/util/ExportAnnotationsDialog.cpp     |    2 +-
 .../src/util/ExportDocumentDialogController.cpp    |   10 +-
 src/corelibs/U2Gui/src/util/ExportImageDialog.cpp  |   17 +-
 src/corelibs/U2Gui/src/util/ExportImageDialog.ui   |    2 +-
 .../src/util/ImportDialogs/AceImportDialog.cpp     |    2 +-
 src/corelibs/U2Gui/src/util/RangeSelector.cpp      |    2 +-
 .../RemovePartFromSequenceDialogController.cpp     |    2 +-
 .../U2Gui/src/util/SaveDocumentController.cpp      |   19 +-
 src/corelibs/U2Gui/src/util/ScriptEditorDialog.cpp |    2 +-
 .../util/SearchGenbankSequenceDialogController.cpp |    2 +-
 .../util/shared_db/CommonImportOptionsDialog.cpp   |    2 +-
 .../src/util/shared_db/EditConnectionDialog.cpp    |    2 +-
 .../src/util/shared_db/ImportToDatabaseDialog.cpp  |    2 +-
 .../src/util/shared_db/ItemToImportEditDialog.cpp  |    2 +-
 .../src/util/shared_db/SharedConnectionsDialog.cpp |    4 +-
 src/corelibs/U2Gui/transl/english.ts               |   16 +-
 src/corelibs/U2Gui/transl/russian.ts               |   18 +-
 .../U2Lang/src/library/BaseOneOneWorker.cpp        |    2 +
 .../U2Lang/src/model/ConfigurationEditor.cpp       |    2 +
 .../U2Lang/src/model/ConfigurationEditor.h         |    3 +
 .../U2Private/src/DocumentFormatRegistryImpl.cpp   |    2 +-
 src/corelibs/U2Private/transl/english.ts           |   35 +-
 src/corelibs/U2Private/transl/russian.ts           |   35 +-
 .../U2View/src/ov_assembly/AssemblyBrowser.cpp     |    6 +-
 .../U2View/src/ov_assembly/AssemblyInfoWidget.cpp  |    2 +-
 .../U2View/src/ov_assembly/AssemblyModel.cpp       |   24 +-
 .../src/ov_assembly/AssemblyNavigationWidget.cpp   |    2 +-
 .../U2View/src/ov_assembly/AssemblyReadsArea.cpp   |    4 +
 .../src/ov_assembly/AssemblySettingsWidget.cpp     |    2 +-
 .../ov_assembly/CalculateCoveragePerBaseTask.cpp   |   79 +-
 .../src/ov_assembly/CalculateCoveragePerBaseTask.h |   13 +-
 .../U2View/src/ov_assembly/CoverageInfo.cpp        |   48 +-
 src/corelibs/U2View/src/ov_assembly/CoverageInfo.h |    5 +-
 .../src/ov_assembly/ExportConsensusDialog.cpp      |    2 +-
 .../ExportConsensusVariationsDialog.cpp            |    2 +-
 .../src/ov_assembly/ExportCoverageDialog.cpp       |    2 +-
 .../U2View/src/ov_assembly/ExportCoverageTask.h    |    1 +
 .../U2View/src/ov_assembly/ExportReadsDialog.cpp   |    2 +-
 .../ov_assembly/ExtractAssemblyRegionDialog.cpp    |    2 +-
 .../src/ov_msa/ColorSchemaDialogController.cpp     |    4 +-
 .../src/ov_msa/ColorSchemaSettingsController.cpp   |    2 +-
 .../ov_msa/CreateSubalignmentDialogController.cpp  |    2 +-
 .../U2View/src/ov_msa/DeleteGapsDialog.cpp         |    2 +-
 .../MSAExportConsensusTabFactory.cpp               |    2 +-
 .../ov_msa/ExportHighlightedDialogController.cpp   |    2 +-
 .../src/ov_msa/General/MSAGeneralTabFactory.cpp    |    2 +-
 .../Highlighting/MSAHighlightingTabFactory.cpp     |    2 +-
 .../U2View/src/ov_msa/MSAEditorSequenceArea.cpp    |    4 +-
 .../src/ov_msa/MSASelectSubalignmentDialog.cpp     |    2 +-
 .../src/ov_msa/Overview/MSAGraphOverview.cpp       |    2 +
 .../U2View/src/ov_msa/Overview/MSAGraphOverview.h  |    4 +-
 .../src/ov_msa/Overview/MSAOverviewContextMenu.cpp |    1 +
 .../ov_msa/Overview/MSAOverviewImageExportTask.cpp |    8 +-
 .../src/ov_msa/PairAlign/PairAlignFactory.cpp      |    2 +-
 ...SaveSelectedSequenceFromMSADialogController.cpp |    2 +-
 .../SeqStatistics/SeqStatisticsWidgetFactory.cpp   |    2 +-
 .../TreeOptions/TreeOptionsWidgetFactory.cpp       |    6 +-
 .../ov_sequence/CreateRulerDialogController.cpp    |    2 +-
 .../src/ov_sequence/GraphLabelsSelectDialog.cpp    |    2 +-
 .../U2View/src/ov_sequence/GraphSettingsDialog.cpp |    2 +-
 .../U2View/src/ov_sequence/PanViewRows.cpp         |   27 +-
 .../SaveGraphCutoffsDialogController.cpp           |    2 +-
 .../src/ov_sequence/SearchQualifierDialog.cpp      |    3 +-
 .../AnnotHighlightWidgetFactory.cpp                |    2 +-
 .../ov_sequence/find_pattern/FindPatternWidget.cpp |  147 +-
 .../find_pattern/FindPatternWidgetFactory.cpp      |    2 +-
 .../sequence_info/SequenceInfoFactory.cpp          |    2 +-
 .../U2View/src/phyltree/BranchSettingsDialog.cpp   |    4 +-
 .../src/phyltree/CreatePhyTreeDialogController.cpp |    6 +-
 .../U2View/src/phyltree/TextSettingsDialog.cpp     |    2 +-
 .../U2View/src/phyltree/TreeSettingsDialog.cpp     |    2 +-
 .../src/util_dna_assembly/BuildIndexDialog.cpp     |   12 +-
 .../ConvertAssemblyToSamDialog.cpp                 |    2 +-
 .../src/util_dna_assembly/DnaAssemblyDialog.cpp    |   12 +-
 .../src/util_dna_assembly/DnaAssemblyUtils.cpp     |    9 +-
 .../src/util_dna_assembly/DnaAssemblyUtils.h       |    5 +-
 .../src/util_dna_assembly/GenomeAssemblyDialog.cpp |    2 +-
 .../util_sec_struct_predict/SecStructDialog.cpp    |    8 +-
 .../util_smith_waterman/SmithWatermanDialog.cpp    |    2 +-
 src/corelibs/U2View/transl/english.ts              |   64 +-
 src/corelibs/U2View/transl/russian.ts              |   92 +-
 src/include/U2Core/AnnotationCreationPattern.h     |    1 +
 src/include/U2Core/SnpeffDictionary.h              |    1 +
 .../ConvertSnpeffVariationsToAnnotationsTask.h     |    1 +
 src/include/U2Formats/SnpeffInfoParser.h           |    1 +
 .../GUITestBase/src/GTUtilsWorkflowDesigner.cpp    |   10 +-
 .../GUITestBase/src/GTUtilsWorkflowDesigner.h      |    3 +-
 src/plugins/GUITestBase/src/GUITestBasePlugin.cpp  |   14 +-
 .../GTTestsRegressionScenarios_2001_3000.cpp       |   21 +
 .../GTTestsRegressionScenarios_2001_3000.h         |    1 +
 .../GTTestsRegressionScenarios_4001_5000.cpp       |   66 +-
 .../GTTestsRegressionScenarios_4001_5000.h         |    2 +
 .../GTTestsRegressionScenarios_5001_6000.cpp       |  272 +-
 .../GTTestsRegressionScenarios_5001_6000.h         |   11 +-
 .../annotator/src/CollocationsDialogController.cpp |    2 +-
 .../annotator/src/CustomAutoAnnotationDialog.cpp   |    2 +-
 .../datatype/annotations/AnnotationUnitTests.cpp   |    2 +-
 .../src/core/dbi/assembly/AssemblyDbiUnitTests.cpp |    4 +-
 .../biostruct3d_view/src/SelectModelsDialog.cpp    |    2 +-
 .../biostruct3d_view/src/SettingsDialog.cpp        |    2 +-
 .../src/StructuralAlignmentDialog.cpp              |    2 +-
 .../src/deprecated/SelectModelsDialog.cpp          |    2 +-
 .../src/deprecated/SettingsDialog.cpp              |    2 +-
 .../src/deprecated/StructuralAlignmentDialog.cpp   |    2 +-
 src/plugins/biostruct3d_view/transl/english.ts     |   80 +-
 src/plugins/biostruct3d_view/transl/russian.ts     |   80 +-
 .../src/CircularViewSettingsWidgetFactory.cpp      |    2 +-
 src/plugins/dbi_bam/src/BAMFormat.cpp              |    2 +-
 src/plugins/dbi_bam/src/ConvertToSQLiteDialog.cpp  |    2 +-
 src/plugins/dbi_bam/src/ConvertToSQLiteDialog.ui   |   65 +-
 src/plugins/dbi_bam/src/ConvertToSQLiteTask.cpp    |    7 +-
 .../src/CSVColumnConfigurationDialog.cpp           |    2 +-
 .../dna_export/src/DNASequenceGeneratorDialog.cpp  |    4 +-
 .../dna_export/src/ExportBlastResultDialog.cpp     |    2 +-
 .../dna_export/src/ExportChromatogramDialog.cpp    |    2 +-
 src/plugins/dna_export/src/ExportMSA2MSADialog.cpp |    2 +-
 .../dna_export/src/ExportMSA2SequencesDialog.cpp   |    2 +-
 .../dna_export/src/ExportSequences2MSADialog.cpp   |    2 +-
 .../dna_export/src/ExportSequencesDialog.cpp       |    2 +-
 .../dna_export/src/GetSequenceByIdDialog.cpp       |    2 +-
 .../src/ImportAnnotationsFromCSVDialog.cpp         |    2 +-
 src/plugins/dna_export/transl/russian.ts           |    2 +-
 src/plugins/dna_flexibility/src/DNAFlexDialog.cpp  |    2 +-
 .../dna_stat/src/DNAStatMSAProfileDialog.cpp       |    2 +-
 .../src/DistanceMatrixMSAProfileDialog.cpp         |    2 +-
 src/plugins/dotplot/src/DotPlotDialog.cpp          |    2 +-
 src/plugins/dotplot/src/DotPlotDialog.ui           |    5 +-
 src/plugins/dotplot/src/DotPlotFilesDialog.cpp     |    2 +-
 src/plugins/dotplot/src/DotPlotFilterDialog.cpp    |    2 +-
 .../enzymes/src/ConstructMoleculeDialog.cpp        |    4 +-
 src/plugins/enzymes/src/CreateFragmentDialog.cpp   |    4 +-
 src/plugins/enzymes/src/DNAFragment.cpp            |   11 +-
 src/plugins/enzymes/src/DNAFragment.h              |    2 +-
 src/plugins/enzymes/src/DigestSequenceDialog.cpp   |    2 +-
 src/plugins/enzymes/src/EditFragmentDialog.cpp     |    2 +-
 src/plugins/enzymes/src/EnzymesQuery.cpp           |    2 +-
 src/plugins/enzymes/src/FindEnzymesDialog.cpp      |    2 +-
 src/plugins/enzymes/src/FindEnzymesTask.cpp        |   30 +-
 src/plugins/enzymes/transl/english.ts              |   24 +-
 src/plugins/enzymes/transl/russian.ts              |   24 +-
 .../external_tool_support.pro                      |   38 +
 .../external_tool_support.qrc                      |    1 +
 .../external_tool_support/images/hmmer.png}        |  Bin
 .../src/ExternalToolSupportPlugin.cpp              |  224 +-
 .../src/ExternalToolSupportPlugin.h                |    3 +
 .../src/ExternalToolSupportSettingsController.cpp  |    2 +-
 .../src/bigWigTools/BedGraphToBigWigTask.cpp       |    3 +-
 .../src/bigWigTools/BedGraphToBigWigTask.h         |    2 +-
 .../src/bigWigTools/BedGraphToBigWigWorker.cpp     |    3 +-
 .../src/blast/FormatDBSupport.h                    |    1 +
 .../src/blast/FormatDBSupportRunDialog.cpp         |    2 +-
 .../src/blast/FormatDBSupportTask.cpp              |  143 +-
 .../src/blast/FormatDBSupportTask.h                |    8 +
 .../src/blast_plus/BlastDBCmdDialog.cpp            |    2 +-
 .../src/bowtie/BowtieTask.cpp                      |    8 +-
 .../external_tool_support/src/bowtie/BowtieTask.h  |    4 +-
 .../src/bowtie/BowtieWorker.cpp                    |    4 -
 .../src/bowtie/BowtieWorker.h                      |    1 -
 .../src/bowtie2/Bowtie2Task.cpp                    |    8 +-
 .../src/bowtie2/Bowtie2Task.h                      |    4 +-
 .../src/bowtie2/Bowtie2Worker.cpp                  |    4 -
 .../src/bowtie2/Bowtie2Worker.h                    |    1 -
 .../external_tool_support/src/bwa/BwaMemWorker.cpp |    4 -
 .../external_tool_support/src/bwa/BwaMemWorker.h   |    1 -
 .../external_tool_support/src/bwa/BwaTask.cpp      |   26 +-
 .../external_tool_support/src/bwa/BwaTask.h        |   10 +-
 .../external_tool_support/src/bwa/BwaWorker.cpp    |    4 -
 .../external_tool_support/src/bwa/BwaWorker.h      |    1 -
 .../src/cap3/CAP3SupportDialog.cpp                 |    2 +-
 .../src/clustalo/ClustalOSupportRunDialog.cpp      |    4 +-
 .../src/clustalw/ClustalWSupportRunDialog.cpp      |    4 +-
 .../src/cutadapt/CutadaptWorker.cpp                |    5 +-
 .../src/hmmer/ConvertAlignment2StockholmTask.cpp   |  121 +
 .../src/hmmer/ConvertAlignment2StockholmTask.h}    |   36 +-
 .../src/hmmer/HmmerBuildDialog.cpp                 |  243 ++
 .../src/hmmer/HmmerBuildDialog.h}                  |   62 +-
 .../src/hmmer/HmmerBuildDialog.ui}                 |    4 +-
 .../src/hmmer/HmmerBuildFromFileTask.cpp           |  105 +
 .../src/hmmer/HmmerBuildFromFileTask.h}            |   54 +-
 .../src/hmmer/HmmerBuildFromMsaTask.cpp            |  116 +
 .../src/hmmer/HmmerBuildFromMsaTask.h}             |   37 +-
 .../src/hmmer/HmmerBuildSettings.cpp               |   71 +
 .../src/hmmer/HmmerBuildSettings.h                 |   83 +
 .../src/hmmer/HmmerBuildTask.cpp                   |  204 ++
 .../src/hmmer/HmmerBuildTask.h}                    |   37 +-
 .../src/hmmer/HmmerBuildWorker.cpp}                |  167 +-
 .../src/hmmer/HmmerBuildWorker.h}                  |   46 +-
 .../src/hmmer/HmmerParseSearchResultsTask.cpp      |  101 +
 .../src/hmmer/HmmerParseSearchResultsTask.h        |   79 +
 .../src/hmmer/HmmerSearchDialog.cpp                |  248 ++
 .../src/hmmer/HmmerSearchDialog.h}                 |   54 +-
 .../src/hmmer/HmmerSearchDialog.ui}                |    8 +-
 .../src/hmmer/HmmerSearchSettings.cpp              |   64 +
 .../src/hmmer/HmmerSearchSettings.h                |   79 +
 .../src/hmmer/HmmerSearchTask.cpp                  |  242 ++
 .../src/hmmer/HmmerSearchTask.h                    |   68 +
 .../src/hmmer/HmmerSearchWorker.cpp                |  332 +++
 .../src/hmmer/HmmerSearchWorker.h}                 |   57 +-
 .../src/hmmer/HmmerSupport.cpp                     |  380 +++
 .../external_tool_support/src/hmmer/HmmerSupport.h |  107 +
 .../src/hmmer/PhmmerSearchDialog.cpp               |  223 ++
 .../src/hmmer/PhmmerSearchDialog.h}                |   73 +-
 .../src/hmmer/PhmmerSearchDialog.ui}               |   45 +-
 .../src/hmmer/PhmmerSearchSettings.cpp             |   81 +
 .../src/hmmer/PhmmerSearchSettings.h               |   78 +
 .../src/hmmer/PhmmerSearchTask.cpp                 |  228 ++
 .../src/hmmer/PhmmerSearchTask.h                   |   67 +
 .../external_tool_support/src/java/JavaSupport.cpp |   12 +-
 .../external_tool_support/src/java/JavaSupport.h   |    9 +
 .../src/mafft/MAFFTSupportRunDialog.cpp            |    4 +-
 .../external_tool_support/src/phyml/PhyMLDialog.ui |   52 +-
 .../src/snpeff/SnpEffSupport.cpp                   |   10 +-
 .../src/snpeff/SnpEffTask.cpp                      |    7 +
 .../src/snpeff/SnpEffWorker.cpp                    |   58 +-
 .../src/tcoffee/TCoffeeSupportRunDialog.cpp        |    4 +-
 .../src/utils/BaseShortReadsAlignerWorker.cpp      |    6 +-
 .../src/utils/BaseShortReadsAlignerWorker.h        |    1 -
 .../src/utils/BlastRunCommonDialog.cpp             |    2 +-
 .../src/utils/ExportTasks.cpp                      |   88 +-
 .../external_tool_support/src/utils/ExportTasks.h  |   29 +-
 .../src/utils/ExternalToolValidateTask.cpp         |    4 +-
 .../src/utils/ExternalToolValidateTask.h           |    2 +
 .../external_tool_support/transl/english.ts        |    4 +-
 .../external_tool_support/transl/russian.ts        |    4 +-
 .../src/GenomeAlignerSettingsController.cpp        |    2 +-
 .../opencl_support/src/OpenCLSupportPlugin.cpp     |    2 +-
 .../src/OpenCLSupportSettingsController.cpp        |    2 +-
 src/plugins/opencl_support/transl/english.ts       |   23 +-
 src/plugins/opencl_support/transl/russian.ts       |   23 +-
 src/plugins/orf_marker/src/ORFDialog.cpp           |    2 +-
 src/plugins/pcr/src/EditPrimerDialog.cpp           |    2 +-
 src/plugins/pcr/src/InSilicoPcrOPWidgetFactory.cpp |    2 +-
 src/plugins/pcr/src/PrimerLibrarySelector.cpp      |    2 +-
 src/plugins/pcr/src/PrimerLibraryWidget.cpp        |    2 +-
 src/plugins/pcr/src/PrimersDetailsDialog.cpp       |    2 +-
 src/plugins/pcr/src/export/ExportPrimersDialog.cpp |    2 +-
 src/plugins/pcr/src/import/ImportPrimersDialog.cpp |    2 +-
 src/plugins/pcr/transl/russian.ts                  |    8 +-
 src/plugins/query_designer/src/QDRunDialog.cpp     |    4 +-
 .../query_designer/src/QueryViewController.cpp     |    2 +-
 .../remote_blast/src/SendSelectionDialog.cpp       |    2 +-
 .../repeat_finder/src/FindRepeatsDialog.cpp        |    2 +-
 .../repeat_finder/src/FindTandemsDialog.cpp        |    2 +-
 .../weight_matrix/src/PWMBuildDialogController.cpp |    2 +-
 .../src/PWMJASPARDialogController.cpp              |    2 +-
 .../src/PWMSearchDialogController.cpp              |    2 +-
 .../src/SetParametersDialogController.cpp          |    2 +-
 .../src/ViewMatrixDialogController.cpp             |    2 +-
 .../workflow_designer/src/CreateScriptWorker.cpp   |    2 +-
 .../src/DashboardsManagerDialog.cpp                |    2 +-
 .../workflow_designer/src/ImportSchemaDialog.cpp   |    2 +-
 .../src/PortAliasesConfigurationDialog.cpp         |    2 +-
 .../src/SchemaAliasesConfigurationDialogImpl.cpp   |    2 +-
 .../workflow_designer/src/StartupDialog.cpp        |    2 +-
 .../src/WorkflowDesignerPlugin.cpp                 |    3 +
 .../workflow_designer/src/WorkflowMetaDialog.cpp   |    2 +-
 .../src/WorkflowSettingsController.cpp             |    2 +-
 .../src/WorkflowViewController.cpp                 |    1 +
 .../src/library/BaseDocWriter.cpp                  |    1 +
 .../ConvertSnpeffVariationsToAnnotationsWorker.cpp |  177 ++
 .../ConvertSnpeffVariationsToAnnotationsWorker.h}  |  143 +-
 .../workflow_designer/src/library/CoreLib.cpp      |   52 +-
 .../src/library/FASTQWorkersLibrary.cpp            |   15 +-
 .../src/library/FilterBamWorker.cpp                |    3 +-
 .../src/library/PassFilterWorker.cpp               |    2 +-
 .../src/library/WriteAnnotationsWorker.cpp         |    1 +
 src/plugins/workflow_designer/transl/english.ts    |    4 +-
 src/plugins/workflow_designer/transl/russian.ts    |    4 +-
 .../workflow_designer/workflow_designer.pro        |    5 +
 src/plugins_3rdparty/gor4/src/gor.cpp              |    2 +-
 .../hmm2/src/u_build/HMMBuildDialogController.cpp  |    2 +-
 .../u_calibrate/HMMCalibrateDialogController.cpp   |    2 +-
 .../src/u_search/HMMSearchDialogController.cpp     |    2 +-
 src/plugins_3rdparty/hmm3/CMakeLists.txt           |    5 -
 src/plugins_3rdparty/hmm3/hmm3.license             |  674 -----
 src/plugins_3rdparty/hmm3/hmm3.pri                 |   22 -
 src/plugins_3rdparty/hmm3/hmm3.pro                 |  152 --
 src/plugins_3rdparty/hmm3/hmm3.qrc                 |    5 -
 .../hmm3/src/build/uHMM3BuildDialogImpl.cpp        |  243 --
 .../hmm3/src/build/uHMM3BuildTask.cpp              |  331 ---
 .../hmm3/src/build/uHMM3BuildTask.h                |  100 -
 src/plugins_3rdparty/hmm3/src/build/uhmm3build.cpp |  120 -
 .../hmm3/src/format/uHMMFormat.cpp                 |  337 ---
 src/plugins_3rdparty/hmm3/src/format/uHMMFormat.h  |   68 -
 .../hmm3/src/format/uHMMFormatReader.cpp           |  924 -------
 .../hmm3/src/format/uHMMFormatReader.h             |   71 -
 .../hmm3/src/gobject/uHMMObject.cpp                |   65 -
 src/plugins_3rdparty/hmm3/src/gobject/uHMMObject.h |   60 -
 src/plugins_3rdparty/hmm3/src/hmmer3/COPYRIGHT     |   62 -
 src/plugins_3rdparty/hmm3/src/hmmer3/build.cpp     |  357 ---
 .../hmm3/src/hmmer3/easel/COPYRIGHT                |   27 -
 src/plugins_3rdparty/hmm3/src/hmmer3/easel/LICENSE |   32 -
 .../hmm3/src/hmmer3/easel/easel.cpp                | 1490 ----------
 src/plugins_3rdparty/hmm3/src/hmmer3/easel/easel.h |  377 ---
 .../hmm3/src/hmmer3/easel/esl_alphabet.cpp         | 1583 -----------
 .../hmm3/src/hmmer3/easel/esl_alphabet.h           |  133 -
 .../hmm3/src/hmmer3/easel/esl_cluster.cpp          |  197 --
 .../hmm3/src/hmmer3/easel/esl_cluster.h            |   12 -
 .../hmm3/src/hmmer3/easel/esl_config.h             |  142 -
 .../hmm3/src/hmmer3/easel/esl_dirichlet.cpp        | 1014 -------
 .../hmm3/src/hmmer3/easel/esl_dirichlet.h          |   75 -
 .../hmm3/src/hmmer3/easel/esl_distance.cpp         |  894 ------
 .../hmm3/src/hmmer3/easel/esl_distance.h           |   76 -
 .../hmm3/src/hmmer3/easel/esl_dmatrix.cpp          | 1271 ---------
 .../hmm3/src/hmmer3/easel/esl_dmatrix.h            |   90 -
 .../hmm3/src/hmmer3/easel/esl_exponential.cpp      |  442 ---
 .../hmm3/src/hmmer3/easel/esl_exponential.h        |   56 -
 .../hmm3/src/hmmer3/easel/esl_gumbel.cpp           |  920 -------
 .../hmm3/src/hmmer3/easel/esl_gumbel.h             |   60 -
 .../hmm3/src/hmmer3/easel/esl_histogram.cpp        | 1684 ------------
 .../hmm3/src/hmmer3/easel/esl_histogram.h          |  130 -
 .../hmm3/src/hmmer3/easel/esl_hmm.cpp              |  470 ----
 .../hmm3/src/hmmer3/easel/esl_hmm.h                |   62 -
 .../hmm3/src/hmmer3/easel/esl_keyhash.cpp          |  813 ------
 .../hmm3/src/hmmer3/easel/esl_keyhash.h            |   70 -
 .../hmm3/src/hmmer3/easel/esl_minimizer.cpp        |  661 -----
 .../hmm3/src/hmmer3/easel/esl_minimizer.h          |   35 -
 .../hmm3/src/hmmer3/easel/esl_msa.cpp              | 2886 --------------------
 .../hmm3/src/hmmer3/easel/esl_msa.h                |  213 --
 .../hmm3/src/hmmer3/easel/esl_msacluster.cpp       |  237 --
 .../hmm3/src/hmmer3/easel/esl_msacluster.h         |   22 -
 .../hmm3/src/hmmer3/easel/esl_msaweight.cpp        |  525 ----
 .../hmm3/src/hmmer3/easel/esl_msaweight.h          |   28 -
 .../hmm3/src/hmmer3/easel/esl_random.cpp           |  736 -----
 .../hmm3/src/hmmer3/easel/esl_random.h             |   59 -
 .../hmm3/src/hmmer3/easel/esl_randomseq.cpp        | 1154 --------
 .../hmm3/src/hmmer3/easel/esl_randomseq.h          |   51 -
 .../hmm3/src/hmmer3/easel/esl_ratematrix.cpp       |  552 ----
 .../hmm3/src/hmmer3/easel/esl_ratematrix.h         |   36 -
 .../hmm3/src/hmmer3/easel/esl_rootfinder.cpp       |  348 ---
 .../hmm3/src/hmmer3/easel/esl_rootfinder.h         |   60 -
 .../hmm3/src/hmmer3/easel/esl_scorematrix.cpp      |  974 -------
 .../hmm3/src/hmmer3/easel/esl_scorematrix.h        |   79 -
 .../hmm3/src/hmmer3/easel/esl_sq.cpp               | 1848 -------------
 .../hmm3/src/hmmer3/easel/esl_sq.h                 |  198 --
 .../hmm3/src/hmmer3/easel/esl_sse.cpp              |  276 --
 .../hmm3/src/hmmer3/easel/esl_sse.h                |  224 --
 .../hmm3/src/hmmer3/easel/esl_stack.cpp            |  396 ---
 .../hmm3/src/hmmer3/easel/esl_stack.h              |   61 -
 .../hmm3/src/hmmer3/easel/esl_stats.cpp            |  556 ----
 .../hmm3/src/hmmer3/easel/esl_stats.h              |   30 -
 .../hmm3/src/hmmer3/easel/esl_tree.cpp             | 1218 ---------
 .../hmm3/src/hmmer3/easel/esl_tree.h               |  130 -
 .../hmm3/src/hmmer3/easel/esl_vectorops.cpp        | 1144 --------
 .../hmm3/src/hmmer3/easel/esl_vectorops.h          |  121 -
 .../hmm3/src/hmmer3/easel/esl_wuss.cpp             |  429 ---
 .../hmm3/src/hmmer3/easel/esl_wuss.h               |   28 -
 src/plugins_3rdparty/hmm3/src/hmmer3/emit.cpp      |  383 ---
 src/plugins_3rdparty/hmm3/src/hmmer3/errors.cpp    |   59 -
 src/plugins_3rdparty/hmm3/src/hmmer3/evalues.cpp   |  500 ----
 src/plugins_3rdparty/hmm3/src/hmmer3/eweight.cpp   |   98 -
 src/plugins_3rdparty/hmm3/src/hmmer3/hmmer.cpp     |  177 --
 src/plugins_3rdparty/hmm3/src/hmmer3/hmmer.h       | 1149 --------
 .../hmm3/src/hmmer3/hmmer3_funcs.cpp               |   47 -
 .../hmm3/src/hmmer3/hmmer3_funcs.h                 |   31 -
 .../hmm3/src/hmmer3/impl_sse/decoding.cpp          |  204 --
 .../hmm3/src/hmmer3/impl_sse/fwdback.cpp           |  762 ------
 .../hmm3/src/hmmer3/impl_sse/impl_sse.h            |  410 ---
 .../hmm3/src/hmmer3/impl_sse/msvfilter.cpp         |  221 --
 .../hmm3/src/hmmer3/impl_sse/null2.cpp             |  230 --
 .../hmm3/src/hmmer3/impl_sse/optacc.cpp            |  431 ---
 .../hmm3/src/hmmer3/impl_sse/p7_omx.cpp            |  632 -----
 .../hmm3/src/hmmer3/impl_sse/p7_oprofile.cpp       | 1453 ----------
 .../hmm3/src/hmmer3/impl_sse/stotrace.cpp          |  301 --
 .../hmm3/src/hmmer3/impl_sse/vitfilter.cpp         |  265 --
 src/plugins_3rdparty/hmm3/src/hmmer3/logsum.cpp    |  116 -
 .../hmm3/src/hmmer3/modelconfig.cpp                |  567 ----
 .../hmm3/src/hmmer3/modelstats.cpp                 |  233 --
 .../hmm3/src/hmmer3/p7_alidisplay.cpp              |  385 ---
 src/plugins_3rdparty/hmm3/src/hmmer3/p7_bg.cpp     |  302 --
 .../hmm3/src/hmmer3/p7_builder.cpp                 |  668 -----
 src/plugins_3rdparty/hmm3/src/hmmer3/p7_config.h   |  150 -
 .../hmm3/src/hmmer3/p7_domaindef.cpp               |  783 ------
 src/plugins_3rdparty/hmm3/src/hmmer3/p7_gmx.cpp    |  305 ---
 src/plugins_3rdparty/hmm3/src/hmmer3/p7_hmm.cpp    | 1222 ---------
 .../hmm3/src/hmmer3/p7_pipeline.cpp                |  794 ------
 src/plugins_3rdparty/hmm3/src/hmmer3/p7_prior.cpp  |  443 ---
 .../hmm3/src/hmmer3/p7_profile.cpp                 |  608 -----
 .../hmm3/src/hmmer3/p7_spensemble.cpp              |  459 ----
 .../hmm3/src/hmmer3/p7_tophits.cpp                 |  787 ------
 src/plugins_3rdparty/hmm3/src/hmmer3/p7_trace.cpp  | 1538 -----------
 src/plugins_3rdparty/hmm3/src/hmmer3/seqmodel.cpp  |  111 -
 .../hmm3/src/hmmer3/tracealign.cpp                 |  816 ------
 .../hmm3/src/phmmer/uHMM3PhmmerDialogImpl.cpp      |  227 --
 .../hmm3/src/phmmer/uhmm3PhmmerTask.cpp            |  474 ----
 .../hmm3/src/phmmer/uhmm3PhmmerTask.h              |  153 --
 .../hmm3/src/phmmer/uhmm3phmmer.cpp                |  262 --
 src/plugins_3rdparty/hmm3/src/phmmer/uhmm3phmmer.h |   95 -
 .../hmm3/src/search/Hmmer3SearchWorkflowTask.cpp   |  134 -
 .../hmm3/src/search/Hmmer3SearchWorkflowTask.h     |   63 -
 .../hmm3/src/search/uHMM3SearchDialogImpl.cpp      |  246 --
 .../hmm3/src/search/uHMM3SearchTask.cpp            |  550 ----
 .../hmm3/src/search/uHMM3SearchTask.h              |  171 --
 .../hmm3/src/search/uhmm3QDActor.cpp               |  294 --
 .../hmm3/src/search/uhmm3QDActor.h                 |   60 -
 .../hmm3/src/search/uhmm3SearchResult.cpp          |  106 -
 .../hmm3/src/search/uhmm3SearchResult.h            |   79 -
 .../hmm3/src/search/uhmm3search.cpp                |  157 --
 .../task_local_storage/uHMMSearchTaskLocalData.h   |   37 -
 .../uHMMSearchTaskLocalStorage.cpp                 |   73 -
 .../hmm3/src/tests/uhmmer3BuildTests.cpp           |  429 ---
 .../hmm3/src/tests/uhmmer3BuildTests.h             |  104 -
 .../hmm3/src/tests/uhmmer3PhmmerTests.cpp          |  260 --
 .../hmm3/src/tests/uhmmer3PhmmerTests.h            |  104 -
 .../hmm3/src/tests/uhmmer3SearchTests.cpp          |  752 -----
 .../hmm3/src/tests/uhmmer3SearchTests.h            |  146 -
 .../hmm3/src/tests/uhmmer3Tests.cpp                |   41 -
 src/plugins_3rdparty/hmm3/src/uHMM3Plugin.cpp      |  293 --
 src/plugins_3rdparty/hmm3/src/uHMM3Plugin.h        |   88 -
 .../hmm3/src/util/uhmm3Utilities.cpp               |  246 --
 .../hmm3/src/util/uhmm3Utilities.h                 |   59 -
 .../hmm3/src/workers/HMM3IOWorker.cpp              |  322 ---
 .../hmm3/src/workers/HMM3IOWorker.h                |  137 -
 .../hmm3/src/workers/HMM3SearchWorker.cpp          |  355 ---
 src/plugins_3rdparty/hmm3/transl/english.ts        | 2209 ---------------
 src/plugins_3rdparty/hmm3/transl/russian.ts        | 2206 ---------------
 .../kalign/src/KalignDialogController.cpp          |    4 +-
 src/plugins_3rdparty/primer3/src/Primer3Dialog.cpp |    2 +-
 .../sitecon/src/SiteconBuildDialogController.cpp   |    2 +-
 .../sitecon/src/SiteconSearchDialogController.cpp  |    2 +-
 .../umuscle/src/MuscleAlignDialogController.cpp    |    4 +-
 src/ugene_version.pri                              |    8 +-
 src/ugenem/src/SendReportDialog.cpp                |    1 -
 src/ugeneui/html/version_news.html                 |   25 +-
 .../DirectoriesSettingsGUIController.cpp           |    2 +-
 .../FormatSettingsGUIController.cpp                |    2 +-
 .../logview_settings/LogSettingsGUIController.cpp  |    2 +-
 .../NetworkSettingsGUIController.cpp               |    2 +-
 .../ResourceSettingsGUIController.cpp              |    2 +-
 .../UserApplicationsSettingsGUIController.cpp      |    2 +-
 src/ugeneui/src/main_window/ShutdownTask.cpp       |  131 +-
 src/ugeneui/src/main_window/ShutdownTask.h         |   24 +-
 .../DocumentFormatSelectorController.cpp           |    2 +-
 .../DocumentProviderSelectorController.cpp         |    2 +-
 .../DocumentReadingModeSelectorController.cpp      |    2 +-
 .../ExportProjectDialogController.cpp              |    2 +-
 ...tipleDocumentsReadingModeSelectorController.cpp |    2 +-
 .../src/project_support/ProjectLoaderImpl.cpp      |    2 +-
 .../src/project_support/ProjectTasksGui.cpp        |   10 +-
 src/ugeneui/src/project_support/ProjectTasksGui.h  |    1 -
 ugene.pro                                          |    4 -
 536 files changed, 8534 insertions(+), 61694 deletions(-)
 rename data/cmdline/{hmm3-search.uwl => hmm3-build-and-search.uwl} (57%)
 create mode 100644 data/workflow_samples/NGS/call_variants_full.uwl
 create mode 100644 data/workflow_samples/Scenarios/length_filter.uwl
 create mode 100644 data/workflow_samples/users/LengthMarker.usa
 copy src/corelibs/{U2Gui/src/util/shared_db/CommonImportOptionsDialog.cpp => 
U2Core/src/datatype/U2Qualifier.cpp} (50%)
 copy src/{ugeneui/src/main_window/ShutdownTask.h => 
corelibs/U2Core/src/datatype/U2Variant.cpp} (55%)
 rename 
src/{plugins_3rdparty/hmm3/src/task_local_storage/uHMMSearchTaskLocalData.cpp 
=> corelibs/U2Core/src/util/AnnotationCreationPattern.cpp} (77%)
 rename src/{plugins_3rdparty/hmm3/src/tests/uhmmer3Tests.h => 
corelibs/U2Core/src/util/AnnotationCreationPattern.h} (70%)
 create mode 100644 src/corelibs/U2Core/src/util/SnpeffDictionary.cpp
 rename src/{plugins_3rdparty/hmm3/src/search/uhmm3search.h => 
corelibs/U2Core/src/util/SnpeffDictionary.h} (61%)
 create mode 100644 
src/corelibs/U2Formats/src/mysql_dbi/util/upgraders/MysqlUpgraderFrom_1_16_To_1_24.cpp
 create mode 100644 
src/corelibs/U2Formats/src/mysql_dbi/util/upgraders/MysqlUpgraderFrom_1_16_To_1_24.h
 create mode 100644 
src/corelibs/U2Formats/src/tasks/ConvertSnpeffVariationsToAnnotationsTask.cpp
 create mode 100644 
src/corelibs/U2Formats/src/tasks/ConvertSnpeffVariationsToAnnotationsTask.h
 create mode 100644 src/corelibs/U2Formats/src/util/SnpeffInfoParser.cpp
 create mode 100644 src/corelibs/U2Formats/src/util/SnpeffInfoParser.h
 create mode 100644 src/include/U2Core/AnnotationCreationPattern.h
 create mode 100644 src/include/U2Core/SnpeffDictionary.h
 create mode 100644 
src/include/U2Formats/ConvertSnpeffVariationsToAnnotationsTask.h
 create mode 100644 src/include/U2Formats/SnpeffInfoParser.h
 rename src/{plugins_3rdparty/hmm3/images/hmmer_16.png => 
plugins/external_tool_support/images/hmmer.png} (100%)
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/ConvertAlignment2StockholmTask.cpp
 copy src/{ugeneui/src/main_window/ShutdownTask.h => 
plugins/external_tool_support/src/hmmer/ConvertAlignment2StockholmTask.h} (59%)
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerBuildDialog.cpp
 rename src/{plugins_3rdparty/hmm3/src/build/uHMM3BuildDialogImpl.h => 
plugins/external_tool_support/src/hmmer/HmmerBuildDialog.h} (64%)
 rename src/{plugins_3rdparty/hmm3/src/build/UHMM3BuildDialog.ui => 
plugins/external_tool_support/src/hmmer/HmmerBuildDialog.ui} (99%)
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerBuildFromFileTask.cpp
 rename 
src/{plugins_3rdparty/hmm3/src/task_local_storage/uHMMSearchTaskLocalStorage.h 
=> plugins/external_tool_support/src/hmmer/HmmerBuildFromFileTask.h} (51%)
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerBuildFromMsaTask.cpp
 rename src/{plugins_3rdparty/hmm3/src/build/uhmm3build.h => 
plugins/external_tool_support/src/hmmer/HmmerBuildFromMsaTask.h} (57%)
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerBuildSettings.cpp
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerBuildSettings.h
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerBuildTask.cpp
 copy src/{ugeneui/src/main_window/ShutdownTask.h => 
plugins/external_tool_support/src/hmmer/HmmerBuildTask.h} (56%)
 rename src/{plugins_3rdparty/hmm3/src/workers/HMM3BuildWorker.cpp => 
plugins/external_tool_support/src/hmmer/HmmerBuildWorker.cpp} (50%)
 copy src/{plugins_3rdparty/hmm3/src/workers/HMM3BuildWorker.h => 
plugins/external_tool_support/src/hmmer/HmmerBuildWorker.h} (58%)
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerParseSearchResultsTask.cpp
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerParseSearchResultsTask.h
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerSearchDialog.cpp
 rename src/{plugins_3rdparty/hmm3/src/search/uHMM3SearchDialogImpl.h => 
plugins/external_tool_support/src/hmmer/HmmerSearchDialog.h} (68%)
 rename src/{plugins_3rdparty/hmm3/src/search/UHMM3SearchDialog.ui => 
plugins/external_tool_support/src/hmmer/HmmerSearchDialog.ui} (99%)
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerSearchSettings.cpp
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerSearchSettings.h
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerSearchTask.cpp
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerSearchTask.h
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/HmmerSearchWorker.cpp
 rename src/{plugins_3rdparty/hmm3/src/workers/HMM3SearchWorker.h => 
plugins/external_tool_support/src/hmmer/HmmerSearchWorker.h} (50%)
 create mode 100644 src/plugins/external_tool_support/src/hmmer/HmmerSupport.cpp
 create mode 100644 src/plugins/external_tool_support/src/hmmer/HmmerSupport.h
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/PhmmerSearchDialog.cpp
 rename src/{plugins_3rdparty/hmm3/src/phmmer/uHMM3PhmmerDialogImpl.h => 
plugins/external_tool_support/src/hmmer/PhmmerSearchDialog.h} (56%)
 rename src/{plugins_3rdparty/hmm3/src/phmmer/UHMM3PhmmerDialog.ui => 
plugins/external_tool_support/src/hmmer/PhmmerSearchDialog.ui} (96%)
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/PhmmerSearchSettings.cpp
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/PhmmerSearchSettings.h
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/PhmmerSearchTask.cpp
 create mode 100644 
src/plugins/external_tool_support/src/hmmer/PhmmerSearchTask.h
 create mode 100644 
src/plugins/workflow_designer/src/library/ConvertSnpeffVariationsToAnnotationsWorker.cpp
 rename src/{plugins_3rdparty/hmm3/src/workers/HMM3BuildWorker.h => 
plugins/workflow_designer/src/library/ConvertSnpeffVariationsToAnnotationsWorker.h}
 (53%)
 delete mode 100644 src/plugins_3rdparty/hmm3/CMakeLists.txt
 delete mode 100644 src/plugins_3rdparty/hmm3/hmm3.license
 delete mode 100644 src/plugins_3rdparty/hmm3/hmm3.pri
 delete mode 100644 src/plugins_3rdparty/hmm3/hmm3.pro
 delete mode 100644 src/plugins_3rdparty/hmm3/hmm3.qrc
 delete mode 100644 src/plugins_3rdparty/hmm3/src/build/uHMM3BuildDialogImpl.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/build/uHMM3BuildTask.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/build/uHMM3BuildTask.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/build/uhmm3build.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/format/uHMMFormat.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/format/uHMMFormat.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/format/uHMMFormatReader.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/format/uHMMFormatReader.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/gobject/uHMMObject.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/gobject/uHMMObject.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/COPYRIGHT
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/build.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/COPYRIGHT
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/LICENSE
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/easel.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/easel.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_alphabet.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_alphabet.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_cluster.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_cluster.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_config.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_dirichlet.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_dirichlet.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_distance.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_distance.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_dmatrix.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_dmatrix.h
 delete mode 100644 
src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_exponential.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_exponential.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_gumbel.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_gumbel.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_histogram.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_histogram.h
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_hmm.cpp
 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_hmm.h
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