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tille pushed a change to branch upstream
in repository prottest.
from 3ae2f93 Imported Upstream version 3.4.1+dfsg
new d45fe91 Imported Upstream version 3.4.2+dfsg
The 1 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:
COPYING | 0
INSTALL | 0
README.md | 10 +-
build.xml | 109 +++-
buildconf/build-impl.xml | 707 ---------------------
buildconf/project.properties | 80 ---
manifest.mf | 2 +-
.../services/org.jdesktop.application.Application | 0
.../java/es/uvigo/darwin/prottest/ProtTest.java | 40 +-
.../uvigo/darwin/prottest/consensus/Consensus.java | 0
.../uvigo/darwin/prottest/consensus/package.html | 0
.../darwin/prottest/exe/AminoAcidRunEstimator.java | 0
.../prottest/exe/ExternalExecutionManager.java | 0
.../darwin/prottest/exe/ExternalExecutor.java | 0
.../prottest/exe/ParallelModelEstimator.java | 0
.../prottest/exe/PhyMLv3AminoAcidRunEstimator.java | 108 +++-
.../darwin/prottest/exe/PhymlStreamGobbler.java | 0
.../prottest/exe/RaxMLAminoAcidRunEstimator.java | 16 +-
.../darwin/prottest/exe/RaxMLStreamGobbler.java | 0
.../es/uvigo/darwin/prottest/exe/RunEstimator.java | 0
.../darwin/prottest/exe/RunEstimatorImpl.java | 0
.../uvigo/darwin/prottest/exe/StreamGobbler.java | 0
.../java/es/uvigo/darwin/prottest/exe/package.html | 0
.../prottest/exe/util/TemporaryFileManager.java | 0
.../es/uvigo/darwin/prottest/exe/util/package.html | 0
.../darwin/prottest/facade/ProtTestFacade.java | 0
.../darwin/prottest/facade/ProtTestFacadeImpl.java | 0
.../darwin/prottest/facade/ProtTestFacadeMPJ.java | 0
.../prottest/facade/ProtTestFacadeSequential.java | 0
.../prottest/facade/ProtTestFacadeThread.java | 0
.../uvigo/darwin/prottest/facade/TreeFacade.java | 0
.../darwin/prottest/facade/TreeFacadeImpl.java | 0
.../es/uvigo/darwin/prottest/facade/package.html | 0
.../facade/strategy/DistributionStrategy.java | 0
.../prottest/facade/strategy/Distributor.java | 0
.../strategy/DynamicDistributionStrategy.java | 0
.../strategy/HybridDistributionStrategy.java | 0
.../ImprovedDynamicDistributionStrategy.java | 0
.../facade/strategy/MultipleDistributor.java | 0
.../strategy/StaticDistributionStrategy.java | 0
.../darwin/prottest/facade/strategy/package.html | 0
.../facade/thread/ThreadPoolSynchronizer.java | 0
.../darwin/prottest/facade/thread/package.html | 0
.../prottest/facade/util/ProtTestParameterVO.java | 0
.../prottest/facade/util/SelectionChunk.java | 0
.../uvigo/darwin/prottest/facade/util/package.html | 0
.../global/AminoAcidApplicationGlobals.java | 0
.../darwin/prottest/global/ApplicationGlobals.java | 0
.../prottest/global/ProtTestConsoleParameters.java | 2 +
.../darwin/prottest/global/ProtTestConstants.java | 0
.../global/RaxmlAminoAcidApplicationGlobals.java | 0
.../global/options/ApplicationOptions.java | 39 +-
.../options/SerializableApplicationOptions.java | 0
.../darwin/prottest/global/options/package.html | 0
.../es/uvigo/darwin/prottest/global/package.html | 0
.../darwin/prottest/model/AminoAcidModel.java | 0
.../java/es/uvigo/darwin/prottest/model/Model.java | 0
.../es/uvigo/darwin/prottest/model/package.html | 0
.../prottest/model/state/ModelEmptyLkState.java | 0
.../prottest/model/state/ModelFilledLkState.java | 0
.../darwin/prottest/model/state/ModelLkState.java | 0
.../uvigo/darwin/prottest/model/state/package.html | 0
.../prottest/observer/ModelUpdaterObserver.java | 0
.../prottest/observer/ObservableModelUpdater.java | 0
.../es/uvigo/darwin/prottest/observer/package.html | 0
.../java/es/uvigo/darwin/prottest/package.html | 0
.../es/uvigo/darwin/prottest/selection/AIC.java | 0
.../es/uvigo/darwin/prottest/selection/AICc.java | 0
.../es/uvigo/darwin/prottest/selection/BIC.java | 0
.../es/uvigo/darwin/prottest/selection/DT.java | 0
.../prottest/selection/InformationCriterion.java | 0
.../es/uvigo/darwin/prottest/selection/LNL.java | 0
.../selection/model/AICSelectionModel.java | 0
.../selection/model/AICcSelectionModel.java | 0
.../selection/model/BICSelectionModel.java | 0
.../prottest/selection/model/DTSelectionModel.java | 0
.../selection/model/LNLSelectionModel.java | 0
.../prottest/selection/model/SelectionModel.java | 0
.../darwin/prottest/selection/model/package.html | 0
.../uvigo/darwin/prottest/selection/package.html | 0
.../selection/printer/AminoAcidPrintFramework.java | 0
.../prottest/selection/printer/PrintFramework.java | 0
.../darwin/prottest/selection/printer/package.html | 0
.../java/es/uvigo/darwin/prottest/taxa/Taxon.java | 0
.../uvigo/darwin/prottest/taxa/TaxonomicLevel.java | 0
.../es/uvigo/darwin/prottest/taxa/package.html | 0
.../darwin/prottest/tree/TreeDistancesCache.java | 0
.../prottest/tree/TreeEuclideanDistancesCache.java | 0
.../es/uvigo/darwin/prottest/tree/TreeUtils.java | 0
.../uvigo/darwin/prottest/tree/WeightedTree.java | 0
.../es/uvigo/darwin/prottest/tree/package.html | 0
.../es/uvigo/darwin/prottest/util/FixedBitSet.java | 0
.../darwin/prottest/util/ProtTestAlignment.java | 0
.../uvigo/darwin/prottest/util/StatFramework.java | 0
.../es/uvigo/darwin/prottest/util/Utilities.java | 0
.../argumentparser/AminoAcidArgumentParser.java | 0
.../argumentparser/ProtTestArgumentParser.java | 18 +-
.../prottest/util/argumentparser/package.html | 0
.../prottest/util/attributable/Attributable.java | 0
.../util/attributable/AttributableHelper.java | 0
.../darwin/prottest/util/attributable/package.html | 0
.../util/checkpoint/CheckPointManager.java | 0
.../darwin/prottest/util/checkpoint/package.html | 0
.../util/checkpoint/status/ApplicationStatus.java | 0
.../util/checkpoint/status/ProtTestStatus.java | 0
.../prottest/util/checkpoint/status/package.html | 0
.../prottest/util/collection/ModelCollection.java | 0
.../util/collection/ParallelModelCollection.java | 0
.../util/collection/ParallelModelQueue.java | 0
.../util/collection/SingleModelCollection.java | 0
.../darwin/prottest/util/collection/package.html | 0
.../AminoAcidModelNaturalComparator.java | 0
.../prottest/util/comparator/LKComparator.java | 0
.../comparator/ModelDistributionHeuristic.java | 0
.../util/comparator/ModelWeightComparator.java | 0
.../darwin/prottest/util/comparator/package.html | 0
.../util/exception/AlignmentParseException.java | 0
.../prottest/util/exception/ImportException.java | 0
.../util/exception/ModelOptimizationException.java | 0
.../util/exception/ProtTestCheckedException.java | 0
.../util/exception/ProtTestInternalException.java | 0
.../util/exception/TreeFormatException.java | 0
.../prottest/util/factory/ProtTestFactory.java | 0
.../darwin/prottest/util/factory/package.html | 0
.../prottest/util/fileio/AlignmentReader.java | 2 +-
.../darwin/prottest/util/fileio/ImportHelper.java | 0
.../darwin/prottest/util/fileio/NexusExporter.java | 0
.../darwin/prottest/util/fileio/NexusImporter.java | 0
.../prottest/util/fileio/NexusTreeReader.java | 0
.../util/fileio/SimpleNewickTreeReader.java | 0
.../darwin/prottest/util/fileio/TreeReader.java | 0
.../util/logging/ProtTestLogFormatter.java | 0
.../prottest/util/logging/ProtTestLogger.java | 0
.../es/uvigo/darwin/prottest/util/package.html | 0
.../util/printer/ProtTestFormattedOutput.java | 0
.../prottest/util/printer/ProtTestPrinter.java | 35 +-
.../java/es/uvigo/darwin/xprottest/CreditsBox.java | 0
.../es/uvigo/darwin/xprottest/PreferencesView.java | 0
.../uvigo/darwin/xprottest/XProtTestAboutBox.java | 0
.../es/uvigo/darwin/xprottest/XProtTestApp.java | 0
.../es/uvigo/darwin/xprottest/XProtTestView.java | 77 ++-
.../darwin/xprottest/analysis/FrequenciesView.java | 0
.../uvigo/darwin/xprottest/analysis/TreeView.java | 0
.../darwin/xprottest/analysis/TreeWrapper.java | 0
.../xprottest/analysis/consensus/Consensus.java | 0
.../consensus/resources/Consensus.properties | 0
.../analysis/resources/FrequenciesView.properties | 0
.../analysis/resources/TreeView.properties | 0
.../darwin/xprottest/compute/OptionsView.java | 0
.../darwin/xprottest/compute/RunningFrame.java | 0
.../compute/resources/OptionsView.properties | 0
.../compute/resources/RunningFrame.properties | 0
.../xprottest/resources/CreditsBox.properties | 0
.../xprottest/resources/PreferencesView.properties | 0
.../resources/XProtTestAboutBox.properties | 0
.../xprottest/resources/XProtTestApp.properties | 4 +-
.../xprottest/resources/XProtTestView.properties | 0
.../es/uvigo/darwin/xprottest/resources/about.png | Bin 8187 -> 32741 bytes
.../xprottest/resources/busyicons/busy-icon0.png | Bin
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.../xprottest/resources/busyicons/busy-icon9.png | Bin
.../xprottest/resources/busyicons/idle-icon.png | Bin
.../darwin/xprottest/resources/prottestlogo.gif | Bin 11850 -> 29447 bytes
.../es/uvigo/darwin/xprottest/resources/splash.png | Bin 21747 -> 0 bytes
.../darwin/xprottest/results/Bundle.properties | 0
.../darwin/xprottest/results/ErrorLogView.java | 0
.../darwin/xprottest/results/ResultsView.java | 0
.../results/resources/ErrorLogView.properties | 0
.../results/resources/ResultsView.properties | 0
.../darwin/xprottest/util/BrowserLauncher.java | 583 -----------------
.../util/OptimizationStrategyWrapper.java | 0
.../darwin/xprottest/util/TextAreaAppender.java | 0
.../darwin/xprottest/util/TextAreaWriter.java | 0
src/main/resources/CHANGELOG | 11 +-
src/main/resources/COPYING | 0
src/main/resources/README | 35 +-
src/main/resources/THIRDPARTYLICENSES | 0
src/main/resources/bin/README | 10 +
src/main/resources/examples/COX2_PF0016/alignment | 0
src/main/resources/examples/COX2_PF0016/tree | 0
src/main/resources/examples/HIV1.2008.pol.nex | 0
.../examples/Ribosomal_L5_PF00673/alignment | 0
.../resources/examples/Ribosomal_L5_PF00673/tree | 0
src/main/resources/filecluster8.conf.template | 0
src/main/resources/icon.png | Bin 0 -> 44845 bytes
src/main/resources/machines | 0
src/main/resources/models/FLU | 0
src/main/resources/prottest.properties | 0
src/main/resources/prottest3 | 9 +
src/main/resources/runProtTestHPC.sh | 3 +-
src/main/resources/runXProtTestHPC.bat | 2 +-
src/main/resources/runXProtTestHPC.sh | 3 +-
204 files changed, 405 insertions(+), 1500 deletions(-)
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