- s - Variable in class uni.bielefeld.cmg.reflexiv.pipeline.ReflexivMainTest
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- screenDump() - Method in class uni.bielefeld.cmg.reflexiv.util.InfoDumper
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This method prints the structured message to the screen.
- screenDump() - Method in class uni.bielefeld.cmg.reflexiv.util.InfoLogger
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This method prints the structured message to the screen.
- setBufferReader() - Method in class uni.bielefeld.cmg.reflexiv.io.TextFileBufferInput
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This method sets the BufferedReader based on the preset InputStreamReader.
- setBufferWriter() - Method in class uni.bielefeld.cmg.reflexiv.io.TextFileBufferOutput
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set class BufferWriter object outputBufferWriter
- setFileOutputStream(boolean) - Method in class uni.bielefeld.cmg.reflexiv.io.TextFileBufferOutput
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set class FileOutputStream object outputFileStream.
- setInput(String) - Method in class uni.bielefeld.cmg.reflexiv.io.TextFileBufferInput
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This method sets up an input file stream for an input file.
- setInput(BufferedReader) - Method in interface uni.bielefeld.cmg.reflexiv.pipeline.Pipeline
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Sets input buffer reader.
- setInput(BufferedReader) - Method in class uni.bielefeld.cmg.reflexiv.pipeline.Pipelines
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This method sets input buffer reader.
- setKmerOverlap(int) - Method in class uni.bielefeld.cmg.reflexiv.util.DefaultParam
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This method initiates the overlap between k-mers.
- setKmerSize(int) - Method in class uni.bielefeld.cmg.reflexiv.util.DefaultParam
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This method initiates the K-mer size parameter.
- setMinErrorCoverage(int) - Method in class uni.bielefeld.cmg.reflexiv.util.DefaultParam
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This method initiates the minimal coverage for error correction.
- setOutput(String, boolean) - Method in class uni.bielefeld.cmg.reflexiv.io.TextFileBufferOutput
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This method sets up an output file stream for an output file.
- setOutput(BufferedWriter) - Method in interface uni.bielefeld.cmg.reflexiv.pipeline.Pipeline
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Sets output buffer writer.
- setOutput(BufferedWriter) - Method in class uni.bielefeld.cmg.reflexiv.pipeline.Pipelines
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This method sets output buffer writer.
- setOutput(String, boolean) - Method in class uni.bielefeld.cmg.reflexiv.util.InfoLogger
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This method parses the output path and sets a BufferedWriter for the output
- setOutputStreamWriter() - Method in class uni.bielefeld.cmg.reflexiv.io.TextFileBufferOutput
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set class OutputStreamWriter object outputStreamWriter.
- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.reflexiv.pipeline.ReflexivCounter
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- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.reflexiv.pipeline.ReflexivMain
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- setParam(DefaultParam) - Method in class uni.bielefeld.cmg.reflexiv.pipeline.ReflexivReAssembler
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- setParameter(DefaultParam) - Method in class uni.bielefeld.cmg.reflexiv.io.ContigReader
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This method sets all correspond parameters for reference
data structure construction.
- setParameter(DefaultParam) - Method in interface uni.bielefeld.cmg.reflexiv.pipeline.Pipeline
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Sets correspond parameter.
- setParameter(DefaultParam) - Method in class uni.bielefeld.cmg.reflexiv.pipeline.Pipelines
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This method sets correspond parameters.
- setSubKmerSize(int) - Method in class uni.bielefeld.cmg.reflexiv.util.DefaultParam
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This method initiates the sub K-mer size parameter.
- setUp() - Method in class uni.bielefeld.cmg.reflexiv.pipeline.ReflexivMainTest
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- SparkKryoRegistrator - Class in uni.bielefeld.cmg.reflexiv.serializer
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An class used to register all classes for Spark kryo serializer.
- SparkKryoRegistrator() - Constructor for class uni.bielefeld.cmg.reflexiv.serializer.SparkKryoRegistrator
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- subKmerSize - Variable in class uni.bielefeld.cmg.reflexiv.util.DefaultParam
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