[med-svn] [ray] 03/08: Merge tag 'upstream/2.3.1'
Andreas Tille
tille at debian.org
Thu Sep 25 15:09:23 UTC 2014
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tille pushed a commit to branch master
in repository ray.
commit 359fae562c02be800237126135fdd1166202281c
Merge: c3a06a2 01b721d
Author: Andreas Tille <tille at debian.org>
Date: Thu Sep 25 16:53:19 2014 +0200
Merge tag 'upstream/2.3.1'
Upstream version 2.3.1
Documentation/RELEASE_PROCEDURE.txt | 7 +-
Documentation/Releases.txt | 1 +
MANUAL_PAGE.txt | 21 +-
Makefile | 6 +-
README.md | 3 +
RayPlatform/Makefile | 4 +-
RayPlatform/README.md | 3 +
RayPlatform/RayPlatform/actors/Actor.cpp | 1 +
RayPlatform/RayPlatform/actors/Playground.cpp | 26 ++
RayPlatform/RayPlatform/actors/Playground.h | 7 +
.../RayPlatform/communication/BufferedData.cpp | 14 +-
RayPlatform/RayPlatform/communication/Message.cpp | 333 ++++++++++++--
RayPlatform/RayPlatform/communication/Message.h | 105 +++--
.../RayPlatform/communication/MessageQueue.cpp | 12 +-
.../RayPlatform/communication/MessageRouter.cpp | 107 +++--
.../RayPlatform/communication/MessagesHandler.cpp | 207 ++++++---
.../RayPlatform/communication/MessagesHandler.h | 6 +-
.../communication/VirtualCommunicator.cpp | 50 +--
RayPlatform/RayPlatform/core/ComputeCore.cpp | 485 ++++++++++++++++-----
RayPlatform/RayPlatform/core/ComputeCore.h | 13 +-
RayPlatform/RayPlatform/core/OperatingSystem.cpp | 4 +-
RayPlatform/RayPlatform/core/RankProcess.h | 10 +-
RayPlatform/RayPlatform/cryptography/crypto.cpp | 4 +-
RayPlatform/RayPlatform/files/FileReader.cpp | 4 +
RayPlatform/RayPlatform/files/FileReader.h | 1 +
.../RayPlatform/handlers/MasterModeExecutor.cpp | 4 +-
.../RayPlatform/handlers/MessageTagExecutor.cpp | 4 +-
.../RayPlatform/handlers/SlaveModeExecutor.cpp | 4 +-
.../memory/ChunkAllocatorWithDefragmentation.cpp | 6 +-
.../RayPlatform/memory/DefragmentationGroup.cpp | 36 +-
.../RayPlatform/memory/DefragmentationLane.cpp | 8 +-
RayPlatform/RayPlatform/memory/DirtyBuffer.h | 3 +
RayPlatform/RayPlatform/memory/MyAllocator.cpp | 12 +-
.../RayPlatform/memory/ReusableMemoryStore.cpp | 14 +-
RayPlatform/RayPlatform/memory/RingAllocator.cpp | 60 ++-
RayPlatform/RayPlatform/memory/RingAllocator.h | 1 +
RayPlatform/RayPlatform/memory/allocator.cpp | 2 +-
RayPlatform/RayPlatform/profiling/TickLogger.cpp | 12 +-
.../routing/GraphImplementationDeBruijn.cpp | 2 +-
.../routing/GraphImplementationExperimental.cpp | 2 +-
.../routing/GraphImplementationGroup.cpp | 2 +-
.../routing/GraphImplementationKautz.cpp | 2 +-
.../routing/GraphImplementationRandom.cpp | 2 +-
RayPlatform/RayPlatform/routing/Polytope.cpp | 18 +-
RayPlatform/RayPlatform/routing/Torus.cpp | 24 +-
RayPlatform/RayPlatform/scheduling/SwitchMan.cpp | 24 +-
RayPlatform/RayPlatform/scheduling/TaskCreator.cpp | 4 +-
.../RayPlatform/scheduling/VirtualProcessor.cpp | 14 +-
RayPlatform/RayPlatform/structures/MyHashTable.h | 52 +--
.../RayPlatform/structures/MyHashTableGroup.h | 28 +-
.../RayPlatform/structures/MyHashTableIterator.h | 4 +-
RayPlatform/RayPlatform/structures/MyStack.h | 2 +-
.../RayPlatform/structures/SplayTreeIterator.h | 2 +-
.../RayPlatform/structures/StaticVector.cpp | 4 +-
code/CoverageGatherer/CoverageDistribution.cpp | 2 +-
code/CoverageGatherer/CoverageGatherer.cpp | 14 +-
code/EdgePurger/EdgePurger.cpp | 6 +-
code/FusionData/FusionData.cpp | 24 +-
code/FusionTaskCreator/FusionWorker.cpp | 4 +-
code/GeneOntology/GeneOntology.cpp | 47 +-
code/GeneOntology/KeyEncoder.cpp | 14 +-
code/GenomeNeighbourhood/GenomeNeighbourhood.cpp | 28 +-
code/JoinerTaskCreator/JoinerWorker.cpp | 16 +-
code/KmerAcademyBuilder/BloomFilter.cpp | 22 +-
code/KmerAcademyBuilder/Kmer.h | 2 +-
code/KmerAcademyBuilder/KmerAcademyBuilder.cpp | 10 +-
code/Library/Library.cpp | 12 +-
code/Library/LibraryWorker.cpp | 10 +-
code/MachineHelper/MachineHelper.cpp | 19 +-
code/MessageProcessor/MessageProcessor.cpp | 114 ++---
code/Mock/Mock.cpp | 4 +-
code/Mock/Parameters.cpp | 56 ++-
code/Mock/common_functions.cpp | 4 +-
code/Mock/common_functions.h | 2 +-
code/NetworkTest/NetworkTest.cpp | 4 +-
code/Partitioner/Partitioner.cpp | 4 +-
code/Scaffolder/Scaffolder.cpp | 38 +-
code/Scaffolder/ScaffoldingAlgorithm.cpp | 10 +-
code/Scaffolder/ScaffoldingEdge.cpp | 4 +-
code/Searcher/ColorSet.cpp | 71 +--
code/Searcher/ColorSet.h | 5 +-
code/Searcher/DistributionWriter.cpp | 2 +-
code/Searcher/QualityCaller.cpp | 2 +-
code/Searcher/SearchDirectory.cpp | 56 +--
code/Searcher/Searcher.cpp | 152 +++----
code/Searcher/VirtualKmerColor.cpp | 10 +-
code/SeedExtender/BubbleTool.cpp | 10 +-
code/SeedExtender/DepthFirstSearchData.cpp | 14 +-
code/SeedExtender/Direction.cpp | 2 +-
code/SeedExtender/ReadFetcher.cpp | 16 +-
code/SeedExtender/SeedExtender.cpp | 74 ++--
code/SeedExtender/VertexMessenger.cpp | 6 +-
code/SeedingData/PathHandle.cpp | 21 +-
code/SeedingData/PathHandle.h | 15 +-
code/SeedingData/SeedWorker.cpp | 4 +-
code/SeedingData/SeedingData.cpp | 31 +-
code/SequencesIndexer/IndexerWorker.cpp | 12 +-
code/SequencesIndexer/SequencesIndexer.cpp | 12 +-
code/SequencesLoader/ArrayOfReads.cpp | 26 +-
code/SequencesLoader/BzReader.cpp | 2 +-
code/SequencesLoader/FastqGzLoader.cpp | 14 +-
code/SequencesLoader/Loader.cpp | 8 +-
code/SequencesLoader/Read.cpp | 2 +-
code/SequencesLoader/SequenceFileDetector.cpp | 10 +
code/SequencesLoader/SequencesLoader.cpp | 26 +-
.../SpuriousSeedAnnihilator/AnnihilationWorker.cpp | 6 +-
code/SpuriousSeedAnnihilator/AttributeFetcher.cpp | 2 +-
code/SpuriousSeedAnnihilator/GraphExplorer.cpp | 6 +-
.../SeedFilteringWorkflow.cpp | 4 +-
.../SeedMergingWorkflow.cpp | 4 +-
.../SpuriousSeedAnnihilator.cpp | 16 +-
code/Surveyor/CoalescenceManager.cpp | 33 +-
code/Surveyor/GenomeGraphReader.cpp | 51 ++-
code/Surveyor/GenomeGraphReader.h | 3 +
code/Surveyor/MatrixOwner.cpp | 47 +-
code/Surveyor/MatrixOwner.h | 4 +
code/Surveyor/Mother.cpp | 130 ++++--
code/Surveyor/Mother.h | 6 +-
code/Surveyor/StoreKeeper.cpp | 179 +++++++-
code/Surveyor/StoreKeeper.h | 2 +
code/TaxonomyViewer/TaxonomyViewer.cpp | 52 ++-
code/VerticesExtractor/GridTable.cpp | 34 +-
code/VerticesExtractor/GridTableIterator.cpp | 2 +-
code/VerticesExtractor/Vertex.cpp | 16 +-
code/VerticesExtractor/VerticesExtractor.cpp | 10 +-
code/application_core/Machine.cpp | 2 +-
code/application_core/Machine.h | 2 +-
127 files changed, 2339 insertions(+), 1131 deletions(-)
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