This is an automated email from the git hooks/post-receive script. satta pushed a change to branch master in repository ugene.
from 3b58136 enable full hardening new adee81f New upstream version 1.24.2+dfsg new 86fce86 Merge tag 'upstream/1.24.2+dfsg' new e929c7a fix building with newer GCCs The 3 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: .../{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 + debian/changelog | 10 + debian/rules | 2 +- .../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 - 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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 +- 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+- .../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 - 538 files changed, 8545 insertions(+), 61695 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 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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 delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_keyhash.cpp delete mode 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src/plugins_3rdparty/hmm3/src/tests/uhmmer3Tests.cpp delete mode 100644 src/plugins_3rdparty/hmm3/src/uHMM3Plugin.cpp delete mode 100644 src/plugins_3rdparty/hmm3/src/uHMM3Plugin.h delete mode 100644 src/plugins_3rdparty/hmm3/src/util/uhmm3Utilities.cpp delete mode 100644 src/plugins_3rdparty/hmm3/src/util/uhmm3Utilities.h delete mode 100644 src/plugins_3rdparty/hmm3/src/workers/HMM3IOWorker.cpp delete mode 100644 src/plugins_3rdparty/hmm3/src/workers/HMM3IOWorker.h delete mode 100644 src/plugins_3rdparty/hmm3/src/workers/HMM3SearchWorker.cpp delete mode 100644 src/plugins_3rdparty/hmm3/transl/english.ts delete mode 100644 src/plugins_3rdparty/hmm3/transl/russian.ts -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ugene.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit