- OPTION_BARCODE_IN_HEADER - Static variable in class biolockj.util.DemuxUtil
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- OPTION_BARCODE_IN_MAPPING - Static variable in class biolockj.util.DemuxUtil
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- OPTION_BARCODE_IN_SEQ - Static variable in class biolockj.util.DemuxUtil
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- OPTION_DO_NOT_DEMUX - Static variable in class biolockj.util.DemuxUtil
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- OPTION_ID_IN_HEADER - Static variable in class biolockj.util.DemuxUtil
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- ORDER - Static variable in class biolockj.Constants
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- ORDER_DELIM - Static variable in class biolockj.node.OtuNodeImpl
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Standard classifier output level delimiter for ORDER
- orderedQiimeIDs - Static variable in class biolockj.module.implicit.parser.r16s.QiimeParser
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Qiime IDs are listed in the same order in each taxonomy level report.
- OtherPipeline - Interface in biolockj.pipelines
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- OtherPipelineFactory - Class in biolockj.pipelines
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- OtherPipelineImpl - Class in biolockj.pipelines
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The defaults here should be suitable for representing pipelines made by the current version of BioLockJ.
- OtherPipelineImpl(File) - Constructor for class biolockj.pipelines.OtherPipelineImpl
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- OTU_COUNT - Static variable in class biolockj.Constants
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Included in the file name of each file output.
- OTU_SEPARATOR - Static variable in class biolockj.Constants
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A pipe is used to separate each taxa "|"
- OTU_SUMMARY_FILE - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
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- OTU_TABLE - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier
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File produced by OTU picking scripts holding read taxonomy assignments: "otu_table.biom"
- OTU_TABLE_PREFIX - Static variable in class biolockj.Constants
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QIIME OTU table prefix: "otu_table"
- OtuCountLine(String) - Constructor for class biolockj.util.OtuUtil.OtuCountLine
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Each OTU count file line has 2 parts: OTU Name and OTU Count
- OtuCountModule - Class in biolockj.module.report.otu
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OtuCount modules reads OTU count assignment tables (1 file/sample) with 2 columns.
Col1: Full OTU pathway spanning top to bottom level Col2: Count (# of reads) for the sample.
- OtuCountModule() - Constructor for class biolockj.module.report.otu.OtuCountModule
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- OtuFileException - Exception in biolockj.exception
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OtuFileException is thrown if errors occur processing OTU files.
- OtuFileException(String) - Constructor for exception biolockj.exception.OtuFileException
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Create standard error to throw for OTU file errors.
- OtuNode - Interface in biolockj.node
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Classes that implement this interface store taxonomy assignment info for one sequence, as output by a classifier.
- OtuNodeImpl - Class in biolockj.node
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The default implementation of
OtuNode is also the superclass for all WGS and 16S OtuNode
classes.
- OtuNodeImpl() - Constructor for class biolockj.node.OtuNodeImpl
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- OtuUtil - Class in biolockj.util
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This utility helps work with OTU count files as formatted by the
ParserModule.
- OtuUtil.OtuCountLine - Class in biolockj.util
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This inner class is used to hold a single line from an OTU count file.
- out(Class<?>) - Static method in class biolockj.Log
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Returns the Logger for the callingClass.
- OUTPUT_DIR - Static variable in interface biolockj.module.BioModule
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Name of the output sub-directory: "output"
- OUTPUT_FILE_SUFFIX - Static variable in class biolockj.util.ValidationUtil
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Append the String "_validation.txt" to the name of the validated module to get the output file name.
- OutsidePipelineWriter - Interface in biolockj.module
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Implementing modules get to have write permissions outside of the pipeline.