[med-svn] [ugene] branch master updated (3b58136 -> e929c7a)
Sascha Steinbiss
satta at debian.org
Sat Sep 17 16:53:34 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch master
in repository ugene.
from 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 -
.../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 -
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 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
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_keyhash.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_keyhash.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_minimizer.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_minimizer.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_msa.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_msa.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_msacluster.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_msacluster.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_msaweight.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_msaweight.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_random.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_random.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_randomseq.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_randomseq.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_ratematrix.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_ratematrix.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_rootfinder.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_rootfinder.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_scorematrix.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_scorematrix.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_sq.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_sq.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_sse.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_sse.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_stack.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_stack.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_stats.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_stats.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_tree.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_tree.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_vectorops.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_vectorops.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/easel/esl_wuss.cpp
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delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/emit.cpp
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delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/eweight.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/hmmer.cpp
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delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/hmmer3_funcs.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/decoding.cpp
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delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/msvfilter.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/impl_sse/null2.cpp
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delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/logsum.cpp
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delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/p7_alidisplay.cpp
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delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/p7_hmm.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/p7_pipeline.cpp
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delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/p7_profile.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/p7_spensemble.cpp
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delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/seqmodel.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/hmmer3/tracealign.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/phmmer/uHMM3PhmmerDialogImpl.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/phmmer/uhmm3PhmmerTask.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/phmmer/uhmm3PhmmerTask.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/phmmer/uhmm3phmmer.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/phmmer/uhmm3phmmer.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/search/Hmmer3SearchWorkflowTask.cpp
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delete mode 100644 src/plugins_3rdparty/hmm3/src/search/uHMM3SearchDialogImpl.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/search/uHMM3SearchTask.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/search/uHMM3SearchTask.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/search/uhmm3QDActor.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/search/uhmm3QDActor.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/search/uhmm3SearchResult.cpp
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delete mode 100644 src/plugins_3rdparty/hmm3/src/task_local_storage/uHMMSearchTaskLocalData.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/task_local_storage/uHMMSearchTaskLocalStorage.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/tests/uhmmer3BuildTests.cpp
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delete mode 100644 src/plugins_3rdparty/hmm3/src/tests/uhmmer3PhmmerTests.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/tests/uhmmer3PhmmerTests.h
delete mode 100644 src/plugins_3rdparty/hmm3/src/tests/uhmmer3SearchTests.cpp
delete mode 100644 src/plugins_3rdparty/hmm3/src/tests/uhmmer3SearchTests.h
delete mode 100644 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
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