Constant Field Values
Contents
edu.msu.*
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edu.msu.cme.rdp.classifier.ClassifierModifier and TypeConstant FieldValue
public static final int
5000
public static final int
5
public static final int
42
public static final int
50
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edu.msu.cme.rdp.classifier.cli.CmdOptionsModifier and TypeConstant FieldValue
public static final String
"the input clluster biom file. The classification result will replace the taxonomy of the corresponding cluster id."
public static final String
"biomFile"
public static final String
"m"
public static final String
"conf"
public static final String
"the output file containing the number of matching assignments out of 100 bootstraps for major ranks. Default is null"
public static final String
"bootstrap_outfile"
public static final String
"b"
public static final String
"c"
public static final String
"format"
public static final String
"f"
public static final String
"gene"
public static final String
"g"
public static final String
"tab-delimited output file containing the assignment count for each taxon in the hierarchical format. Default is null."
public static final String
"hier_outfile"
public static final String
"h"
public static final String
"the tab delimited metadata file for the samples, with first row containing attribute name and first column containing the sample name"
public static final String
"metadata"
public static final String
"d"
public static final String
"minWords"
public static final String
"w"
public static final String
"minimum number of words for each bootstrap trial. Default(maximum) is 1/8 of the words of each sequence. Minimum is 5"
public static final String
"tab-delimited text output file for classification assignment."
public static final String
"outputFile"
public static final String
"o"
public static final String
"legacy option, no longer needed "
public static final String
"queryFile"
public static final String
"q"
public static final String
"rank"
public static final String
"r"
public static final String
"biomFile"
public static final String
"the output file containing the sequence names that are too short to be classified"
public static final String
"shortseq_outfile"
public static final String
"s"
public static final String
"taxon"
public static final String
"n"
public static final String
"property file containing the mapping of the training files if not using the default. Note: the training files and the property file should be in the same directory."
public static final String
"train_propfile"
public static final String
"t"
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edu.msu.cme.rdp.classifier.comparison.ComparisonCmdModifier and TypeConstant FieldValue
public static final String
"output file name for the comparsion results."
public static final String
"compare_outputFile"
public static final String
"o"
public static final String
"query file contains sequences in one of the following formats: Fasta, Genbank and EMBL."
public static final String
"queryFile1"
public static final String
"q1"
public static final String
"queryFile2"
public static final String
"q2"
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edu.msu.cme.rdp.classifier.train.LineageSequenceParser
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edu.msu.cme.rdp.classifier.train.validation.CorrectAssignment
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edu.msu.cme.rdp.classifier.train.validation.DecisionMaker
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edu.msu.cme.rdp.classifier.train.validation.NBClassifierModifier and TypeConstant FieldValue
public static final int
5
public static final long
1L
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edu.msu.cme.rdp.classifier.train.validation.Taxonomy
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edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMainModifier and TypeConstant FieldValue
public static final String
"h"
public static final String
"the default is to test the entire query sequence. if specifiy a length, a region of the query sequence with the specified length will be random choosen for testing"
public static final String
"length"
public static final String
"l"
public static final String
"stat of leave-one-out testing including correctness rate at each rank, misclassified rate for each taxon "
public static final String
"outputFile"
public static final String
"o"
public static final String
"query file contains sequences, same format as the training sequence file"
public static final String
"queryFile"
public static final String
"q"
public static final String
"training files in fasta format labelled with the lineage information. \nThe header of this fasta file starts with \'>\', followed by the sequence name, white space(s) and a list taxon names seperated by \';\' with highest rank taxon first\nex: Root;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Enterobacter"
public static final String
"trainSeqFile"
public static final String
"s"
public static final String
"contains the hierarchical taxonomy information, taxon name and rank together is unique. \nThe format looks like the following: taxid*taxon name*parent taxid*depth*rank Note taxid, the parent taxid and depth should be in integer format. depth indicates the depth from the root taxon."
public static final String
"trainTaxonFile"
public static final String
"t"
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edu.msu.cme.rdp.classifier.train.validation.movingwindow.FindWindowFrameModifier and TypeConstant FieldValue
public static final int
25
public static final int
200
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edu.msu.cme.rdp.classifier.utils.ClassifierFactory
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edu.msu.cme.rdp.multicompare.taxon.MCTaxon