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src/aldenjava/common/SimpleLocation.java
src/aldenjava/common/SimpleLongLocation.java
src/aldenjava/common/TimeCounter.java
src/aldenjava/opticalmapping/data/data/DataNode.java
src/aldenjava/opticalmapping/data/data/BnxDataNode.java
src/aldenjava/opticalmapping/data/data/OptMapDataReader.java
src/aldenjava/opticalmapping/data/data/OptMapDataWriter.java
src/aldenjava/opticalmapping/data/data/ReferenceReader.java
src/aldenjava/opticalmapping/data/data/ReferenceWriter.java
src/aldenjava/opticalmapping/data/data/SimulationInfo.java
src/aldenjava/opticalmapping/data/mappingresult/OptMapResultNode.java
src/aldenjava/opticalmapping/data/mappingresult/OptMapResultReader.java
src/aldenjava/opticalmapping/data/mappingresult/OptMapResultWriter.java
src/aldenjava/opticalmapping/data/mappingresult/ResultFormat.java
src/aldenjava/opticalmapping/data/DataFormat.java
src/aldenjava/opticalmapping/data/Identifiable.java
src/aldenjava/opticalmapping/data/OMReader.java
src/aldenjava/opticalmapping/data/OMWriter.java
src/aldenjava/opticalmapping/mapper/clustermodule/ClusteredResult.java
src/aldenjava/opticalmapping/mapper/clustermodule/ClusterPathNode.java
src/aldenjava/opticalmapping/mapper/clustermodule/PathBuilderFilter.java
src/aldenjava/opticalmapping/mapper/clustermodule/ResultClusterModule.java
src/aldenjava/opticalmapping/mapper/clustermodule/VirtualMapProcessor.java
src/aldenjava/opticalmapping/mapper/multithread/MultiThreadMapper.java
src/aldenjava/opticalmapping/mapper/multithread/MultiThreadResultNode.java
src/aldenjava/opticalmapping/mapper/omblastmapper/OMBlastCore.java
src/aldenjava/opticalmapping/mapper/omblastmapper/OMBlastMapper.java
src/aldenjava/opticalmapping/mapper/omblastmapper/SeedExtension.java
src/aldenjava/opticalmapping/mapper/postmappingmodule/Filter.java
src/aldenjava/opticalmapping/mapper/postmappingmodule/PostJoinPathEdge.java
src/aldenjava/opticalmapping/mapper/postmappingmodule/PostJoinPathNode.java
src/aldenjava/opticalmapping/mapper/postmappingmodule/PostMapJoining.java
src/aldenjava/opticalmapping/mapper/seeding/Kmer.java
src/aldenjava/opticalmapping/mapper/seeding/Seed.java
src/aldenjava/opticalmapping/mapper/seeding/SeedDatabase.java
src/aldenjava/opticalmapping/mapper/Mapper.java
src/aldenjava/opticalmapping/mapper/ExtensionResult.java
src/aldenjava/opticalmapping/mapper/MapperConstructionException.java
src/aldenjava/opticalmapping/miscellaneous/Copyable.java
src/aldenjava/opticalmapping/miscellaneous/ExtendOptionParser.java
src/aldenjava/opticalmapping/miscellaneous/InvalidFileFormatException.java
src/aldenjava/opticalmapping/miscellaneous/SelectableMode.java
src/aldenjava/opticalmapping/Cigar.java
src/aldenjava/opticalmapping/GenomicPosNode.java
src/aldenjava/script/TWINResultRepeatRemover.java