[med-svn] [ugene] 02/03: Merge tag 'upstream/1.24.2+dfsg'
Sascha Steinbiss
satta at debian.org
Sat Sep 17 16:53:37 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository ugene.
commit 86fce8657955c3aa9af8b6bd92f531779ce54668
Merge: 3b58136 adee81f
Author: Sascha Steinbiss <satta at debian.org>
Date: Sat Sep 17 16:22:14 2016 +0000
Merge tag 'upstream/1.24.2+dfsg'
Upstream version 1.24.2+dfsg
.../{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 +-
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.../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 +-
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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 +-
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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 +
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src/corelibs/U2Core/src/globals/L10n.h | 3 +
.../U2Core/src/gobjects/VariantTrackObject.cpp | 20 +-
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src/corelibs/U2Core/src/models/DocumentModel.cpp | 4 +-
src/corelibs/U2Core/src/models/DocumentModel.h | 2 +
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src/corelibs/U2Core/src/tasks/SaveDocumentTask.cpp | 18 +-
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.../U2Core/src/util/AnnotationCreationPattern.cpp} | 15 +-
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src/corelibs/U2Core/src/util/GenbankFeatures.cpp | 2 +-
src/corelibs/U2Core/src/util/SnpeffDictionary.cpp | 162 ++
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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 +
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.../U2Designer/src/support/URLLineEdit.cpp | 11 +-
src/corelibs/U2Formats/U2Formats.pro | 12 +-
.../U2Formats/src/AbstractVariationFormat.cpp | 320 ++-
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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 +
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.../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 ++
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src/corelibs/U2Formats/src/util/SnpeffInfoParser.h | 147 +
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src/corelibs/U2Gui/src/ToolsMenu.cpp | 2 +
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src/corelibs/U2Gui/src/util/ExportImageDialog.cpp | 17 +-
src/corelibs/U2Gui/src/util/ExportImageDialog.ui | 2 +-
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src/corelibs/U2Gui/src/util/RangeSelector.cpp | 2 +-
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src/corelibs/U2Gui/src/util/ScriptEditorDialog.cpp | 2 +-
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src/corelibs/U2Gui/transl/english.ts | 16 +-
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.../U2View/src/ov_assembly/AssemblyBrowser.cpp | 6 +-
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src/corelibs/U2View/src/ov_assembly/CoverageInfo.h | 5 +-
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src/plugins/GUITestBase/src/GUITestBasePlugin.cpp | 14 +-
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.../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(-)
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