# Constant Field Values

## Contents

- edu.msu.*

## edu.msu.*

edu.msu.cme.rdp.classifier.Classifier
`public static final int` `MAX_SEQ_LEN` `5000`
`public static final int` `MIN_BOOTSTRSP_WORDS` `5`
`public static final int` `MIN_GOOD_WORDS` `42`
`public static final int` `MIN_SEQ_LEN` `50`

edu.msu.cme.rdp.classifier.cli.CmdOptions
`public static final java.lang.String` `BIOMFILE_DESC` `"the input clluster biom file. The classification result will replace the taxonomy of the corresponding cluster id."`
`public static final java.lang.String` `BIOMFILE_LONG_OPT` `"biomFile"`
`public static final java.lang.String` `BIOMFILE_SHORT_OPT` `"m"`
`public static final java.lang.String` `BOOTSTRAP_LONG_OPT` `"conf"`
`public static final java.lang.String` `BOOTSTRAP_OUTFILE_DESC` `"the output file containing the number of matching assignments out of 100 bootstraps for major ranks. Default is null"`
`public static final java.lang.String` `BOOTSTRAP_OUTFILE_LONG_OPT` `"bootstrap_outfile"`
`public static final java.lang.String` `BOOTSTRAP_OUTFILE_SHORT_OPT` `"b"`
`public static final java.lang.String` `BOOTSTRAP_SHORT_OPT` `"c"`
`public static final java.lang.String` `FORMAT_LONG_OPT` `"format"`
`public static final java.lang.String` `FORMAT_SHORT_OPT` `"f"`
`public static final java.lang.String` `GENE_LONG_OPT` `"gene"`
`public static final java.lang.String` `GENE_SHORT_OPT` `"g"`
`public static final java.lang.String` `HIER_OUTFILE_DESC` `"tab-delimited output file containing the assignment count for each taxon in the hierarchical format. Default is null."`
`public static final java.lang.String` `HIER_OUTFILE_LONG_OPT` `"hier_outfile"`
`public static final java.lang.String` `HIER_OUTFILE_SHORT_OPT` `"h"`
`public static final java.lang.String` `METADATA_DESC` `"the tab delimited metadata file for the samples, with first row containing attribute name and first column containing the sample name"`
`public static final java.lang.String` `METADATA_LONG_OPT` `"metadata"`
`public static final java.lang.String` `METADATA_SHORT_OPT` `"d"`
`public static final java.lang.String` `MIN_BOOTSTRAP_WORDS_LONG_OPT` `"minWords"`
`public static final java.lang.String` `MIN_BOOTSTRAP_WORDS_SHORT_OPT` `"w"`
`public static final java.lang.String` `MIN_WORDS_DESC` `"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 java.lang.String` `OUTFILE_DESC` `"tab-delimited text output file for classification assignment."`
`public static final java.lang.String` `OUTFILE_LONG_OPT` `"outputFile"`
`public static final java.lang.String` `OUTFILE_SHORT_OPT` `"o"`
`public static final java.lang.String` `QUERYFILE_DESC` `"legacy option, no longer needed "`
`public static final java.lang.String` `QUERYFILE_LONG_OPT` `"queryFile"`
`public static final java.lang.String` `QUERYFILE_SHORT_OPT` `"q"`
`public static final java.lang.String` `RANK_LONG_OPT` `"rank"`
`public static final java.lang.String` `RANK_SHORT_OPT` `"r"`
`public static final java.lang.String` `SAMPLE_LONG_OPT` `"biomFile"`
`public static final java.lang.String` `SHORTSEQ_OUTFILE_DESC` `"the output file containing the sequence names that are too short to be classified"`
`public static final java.lang.String` `SHORTSEQ_OUTFILE_LONG_OPT` `"shortseq_outfile"`
`public static final java.lang.String` `SHORTSEQ_OUTFILE_SHORT_OPT` `"s"`
`public static final java.lang.String` `TAXON_LONG_OPT` `"taxon"`
`public static final java.lang.String` `TAXON_SHORT_OPT` `"n"`
`public static final java.lang.String` `TRAINPROPFILE_DESC` `"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 java.lang.String` `TRAINPROPFILE_LONG_OPT` `"train_propfile"`
`public static final java.lang.String` `TRAINPROPFILE_SHORT_OPT` `"t"`

edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
`public static final java.lang.String` `COMPARE_OUTFILE_DESC` `"output file name for the comparsion results."`
`public static final java.lang.String` `COMPARE_OUTFILE_LONG_OPT` `"compare_outputFile"`
`public static final java.lang.String` `COMPARE_OUTFILE_SHORT_OPT` `"o"`
`public static final java.lang.String` `QUERYFILE_DESC` `"query file contains sequences in one of the following formats: Fasta, Genbank and EMBL."`
`public static final java.lang.String` `QUERYFILE1_LONG_OPT` `"queryFile1"`
`public static final java.lang.String` `QUERYFILE1_SHORT_OPT` `"q1"`
`public static final java.lang.String` `QUERYFILE2_LONG_OPT` `"queryFile2"`
`public static final java.lang.String` `QUERYFILE2_SHORT_OPT` `"q2"`

edu.msu.cme.rdp.classifier.train.LineageSequenceParser
`public static final java.lang.String` `delimiter` `";"`

edu.msu.cme.rdp.classifier.train.validation.CorrectAssignment
`public final int` `bins` `11`

edu.msu.cme.rdp.classifier.train.validation.DecisionMaker
`public static final int` `NUM_OF_RUNS` `100`

edu.msu.cme.rdp.classifier.train.validation.NBClassifier
`public static final int` `MIN_BOOTSTRSP_WORDS` `5`
`public static final long` `seed` `1L`

edu.msu.cme.rdp.classifier.train.validation.Taxonomy
`public static final java.lang.String` `GENUS` `"GENUS"`

edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
`public static final java.lang.String` `HIDETAXON_SHORT_OPT` `"h"`
`public static final java.lang.String` `LENGTH_DESC` `"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 java.lang.String` `LENGTH_LONG_OPT` `"length"`
`public static final java.lang.String` `LENGTH_SHORT_OPT` `"l"`
`public static final java.lang.String` `OUTFILE_DESC` `"stat of leave-one-out testing including correctness rate at each rank, misclassified rate for each taxon "`
`public static final java.lang.String` `OUTFILE_LONG_OPT` `"outputFile"`
`public static final java.lang.String` `OUTFILE_SHORT_OPT` `"o"`
`public static final java.lang.String` `QUERYFILE_DESC` `"query file contains sequences, same format as the training sequence file"`
`public static final java.lang.String` `QUERYFILE_LONG_OPT` `"queryFile"`
`public static final java.lang.String` `QUERYFILE_SHORT_OPT` `"q"`

`public static final java.lang.String`

`TRAIN_SEQFILE_DESC`

`"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 java.lang.String` `TRAIN_SEQFILE_LONG_OPT` `"trainSeqFile"`
`public static final java.lang.String` `TRAIN_SEQFILE_SHORT_OPT` `"s"`
`public static final java.lang.String` `TRAIN_TAXONFILE_DESC` `"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 java.lang.String` `TRAIN_TAXONFILE_LONG_OPT` `"trainTaxonFile"`
`public static final java.lang.String` `TRAIN_TAXONFILE_SHORT_OPT` `"t"`

edu.msu.cme.rdp.classifier.train.validation.movingwindow.FindWindowFrame
`public static final int` `step` `25`
`public static final int` `window_size` `200`

edu.msu.cme.rdp.classifier.utils.ClassifierFactory
`public static final java.lang.String` `FUNGALITS_unite_GENE` `"fungalits_unite"`
`public static final java.lang.String` `FUNGALITS_warcup_GENE` `"fungalits_warcup"`
`public static final java.lang.String` `FUNGALLSU_GENE` `"fungallsu"`
`public static final java.lang.String` `RRNA_16S_GENE` `"16srrna"`

edu.msu.cme.rdp.multicompare.taxon.MCTaxon
`public static final int` `Count_Array_size` `2`