- gapArray - Variable in class uni.bielefeld.cmg.sparkhit.matrix.ScoreMatrix
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- getBinarySeq() - Method in class uni.bielefeld.cmg.sparkhit.reference.RefStructBuilder
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This method transforms a nucletotide sequence from a string type to a binary type.
- getBufferedFastqUnit() - Method in class uni.bielefeld.cmg.sparkhit.io.ReadFastq
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Use this method to get the buffer for accessing fastq unit.
- getBufferReader() - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferInput
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Returns the preset BufferedReader.
- getEValue(int, double, double, int, long) - Static method in class uni.bielefeld.cmg.sparkhit.algorithm.Arithmetic
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This method calculates the E-value for each alignment.
- getFastaBufferedReader() - Method in class uni.bielefeld.cmg.sparkhit.io.ReadFasta
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This method sets the BufferedReader.
- getFileOutputStream() - Method in class uni.bielefeld.cmg.sparkhit.io.ObjectFileOutput
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This method sets FileOutputStream.
- getInputFileStream() - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferInput
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Returns the preset FileInputStream.
- getInputObjectStream() - Method in class uni.bielefeld.cmg.sparkhit.io.ObjectFileInput
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This method sets ObjectInputStream.
- getInputStream() - Method in class uni.bielefeld.cmg.sparkhit.io.ObjectFileInput
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This method sets FileInputStream.
- getInputStreamReader() - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferInput
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Returns the preset InputStreamReade.
- getObjectOutputStream() - Method in class uni.bielefeld.cmg.sparkhit.io.ObjectFileOutput
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This method sets ObjectOutputStream.
- getOutputBufferWriter() - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferOutput
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Returns the preset BufferedWriter.
- getOutputFileStream() - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferOutput
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Returns the preset FileOutputStream.
- getOutputStreamWriter() - Method in class uni.bielefeld.cmg.sparkhit.io.TextFileBufferOutput
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Returns the preset OutputStreamWriter.
- getStruct() - Method in class uni.bielefeld.cmg.sparkhit.reference.RefStructSerializer
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This method passes the reference of the reference index to this class.
- globalOrLocal - Variable in class uni.bielefeld.cmg.sparkhit.util.DefaultParam
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