[med-svn] [prottest] branch master updated (0a2ddd5 -> 51cdeac)
Andreas Tille
tille at debian.org
Tue May 10 09:52:55 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository prottest.
from 0a2ddd5 Add missing dependency
new 70a3c5b Use repack and compress option in watch file
new f167396 New upstream version
new d45fe91 Imported Upstream version 3.4.2+dfsg
new d690e36 Merge tag 'upstream/3.4.2+dfsg'
new 59d3047 libnb-absolutelayout-java
new e7ce61c Use debian packaged phyml
new cdf9671 Deal with UTF8 strings in source code
new 51cdeac Try to provide Debian packaged JARs to Build system but failed
The 8 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 ---
debian/changelog | 8 +
debian/control | 1 -
debian/patches/build.patch | 44 +-
debian/patches/series | 1 +
debian/patches/use_debian_packaged_phyml.patch | 15 +
debian/rules | 5 +-
debian/watch | 2 +-
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 +-
211 files changed, 445 insertions(+), 1536 deletions(-)
mode change 100755 => 100644 COPYING
mode change 100755 => 100644 INSTALL
delete mode 100755 buildconf/build-impl.xml
delete mode 100755 buildconf/project.properties
create mode 100644 debian/patches/use_debian_packaged_phyml.patch
mode change 100755 => 100644 src/main/java/META-INF/services/org.jdesktop.application.Application
mode change 100755 => 100644 src/main/java/es/uvigo/darwin/prottest/ProtTest.java
mode change 100755 => 100644 src/main/java/es/uvigo/darwin/prottest/consensus/Consensus.java
mode change 100755 => 100644 src/main/java/es/uvigo/darwin/prottest/consensus/package.html
mode change 100755 => 100644 src/main/java/es/uvigo/darwin/prottest/exe/AminoAcidRunEstimator.java
mode change 100755 => 100644 src/main/java/es/uvigo/darwin/prottest/exe/ExternalExecutionManager.java
mode change 100755 => 100644 src/main/java/es/uvigo/darwin/prottest/exe/ExternalExecutor.java
mode change 100755 => 100644 src/main/java/es/uvigo/darwin/prottest/exe/ParallelModelEstimator.java
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