├── .gitignore ├── LICENSE.md ├── README.md ├── bin └── mgfsm ├── pom.xml └── src └── main └── java └── de └── mpii └── fsm ├── bfs ├── BfsMiner.java └── PostingList.java ├── driver ├── DistributedMode.java ├── FsmConfig.java ├── FsmDriver.java └── SequentialMode.java ├── input ├── InputFileConverter.java ├── SequenceInputFormat.java ├── TimedSequenceInputFormat.java └── TimedSequenceRecordReader.java ├── mgfsm ├── FsmCombiner.java ├── FsmJob.java ├── FsmMapper.java ├── FsmPartitioner.java ├── FsmRawComparator.java ├── FsmReducer.java ├── FsmWriter.java ├── FsmWriterForReducer.java ├── FsmWriterSequential.java ├── encoders │ ├── BaseGapEncoder.java │ ├── SimpleGapEncoder.java │ └── SplitGapEncoder.java └── maximal │ ├── ByteSequence.java │ ├── MaxFsmCombiner.java │ ├── MaxFsmJob.java │ ├── MaxFsmMapper.java │ ├── MaxFsmReducer.java │ └── MaxUtils.java ├── output └── SequenceTranslator.java ├── stats └── StatsCollector.java ├── tools ├── ConvertSequences.java └── ConvertTextSentences.java └── util ├── Constants.java ├── DfsUtils.java ├── Dictionary.java ├── IntArrayComparator.java ├── IntArrayStrategy.java ├── IntArrayWritable.java ├── MetaDataWritable.java ├── PostingWritable.java ├── PostingWritableArray.java ├── PrimitiveUtils.java └── WordCount.java /.gitignore: -------------------------------------------------------------------------------- 1 | target/ 2 | .classpath 3 | .project 4 | .settings/ 5 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/LICENSE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/README.md -------------------------------------------------------------------------------- /bin/mgfsm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/bin/mgfsm -------------------------------------------------------------------------------- /pom.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/pom.xml -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/bfs/BfsMiner.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/bfs/BfsMiner.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/bfs/PostingList.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/bfs/PostingList.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/driver/DistributedMode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/driver/DistributedMode.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/driver/FsmConfig.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/driver/FsmConfig.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/driver/FsmDriver.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/driver/FsmDriver.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/driver/SequentialMode.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/driver/SequentialMode.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/input/InputFileConverter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/input/InputFileConverter.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/input/SequenceInputFormat.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/input/SequenceInputFormat.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/input/TimedSequenceInputFormat.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/input/TimedSequenceInputFormat.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/input/TimedSequenceRecordReader.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/input/TimedSequenceRecordReader.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/FsmCombiner.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/FsmCombiner.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/FsmJob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/FsmJob.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/FsmMapper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/FsmMapper.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/FsmPartitioner.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/FsmPartitioner.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/FsmRawComparator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/FsmRawComparator.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/FsmReducer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/FsmReducer.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/FsmWriter.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/FsmWriter.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/FsmWriterForReducer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/FsmWriterForReducer.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/FsmWriterSequential.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/FsmWriterSequential.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/encoders/BaseGapEncoder.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/encoders/BaseGapEncoder.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/encoders/SimpleGapEncoder.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/encoders/SimpleGapEncoder.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/encoders/SplitGapEncoder.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/encoders/SplitGapEncoder.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/maximal/ByteSequence.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/maximal/ByteSequence.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/maximal/MaxFsmCombiner.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/maximal/MaxFsmCombiner.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/maximal/MaxFsmJob.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/maximal/MaxFsmJob.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/maximal/MaxFsmMapper.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/maximal/MaxFsmMapper.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/maximal/MaxFsmReducer.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/maximal/MaxFsmReducer.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/mgfsm/maximal/MaxUtils.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/mgfsm/maximal/MaxUtils.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/output/SequenceTranslator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/output/SequenceTranslator.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/stats/StatsCollector.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/stats/StatsCollector.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/tools/ConvertSequences.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/tools/ConvertSequences.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/tools/ConvertTextSentences.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/tools/ConvertTextSentences.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/util/Constants.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/util/Constants.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/util/DfsUtils.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/util/DfsUtils.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/util/Dictionary.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/util/Dictionary.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/util/IntArrayComparator.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/util/IntArrayComparator.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/util/IntArrayStrategy.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/util/IntArrayStrategy.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/util/IntArrayWritable.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/util/IntArrayWritable.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/util/MetaDataWritable.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/util/MetaDataWritable.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/util/PostingWritable.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/util/PostingWritable.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/util/PostingWritableArray.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/util/PostingWritableArray.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/util/PrimitiveUtils.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/util/PrimitiveUtils.java -------------------------------------------------------------------------------- /src/main/java/de/mpii/fsm/util/WordCount.java: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/uma-pi1/mgfsm/HEAD/src/main/java/de/mpii/fsm/util/WordCount.java --------------------------------------------------------------------------------