# Constant Field Values

## Contents

- edu.msu.*

## edu.msu.*

edu.msu.cme.rdp.classifier.Classifier
Modifier and Type | Constant Field | Value
--- | --- | ---
`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
Modifier and Type | Constant Field | Value
--- | --- | ---
`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
Modifier and Type | Constant Field | Value
--- | --- | ---
`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
Modifier and Type | Constant Field | Value
--- | --- | ---
`public static final java.lang.String` | `delimiter` | `";"`

edu.msu.cme.rdp.classifier.train.validation.CorrectAssignment
Modifier and Type | Constant Field | Value
--- | --- | ---
`public final int` | `bins` | `11`

edu.msu.cme.rdp.classifier.train.validation.DecisionMaker
Modifier and Type | Constant Field | Value
--- | --- | ---
`public static final int` | `NUM_OF_RUNS` | `100`

edu.msu.cme.rdp.classifier.train.validation.NBClassifier
Modifier and Type | Constant Field | Value
--- | --- | ---
`public static final int` | `MIN_BOOTSTRSP_WORDS` | `5`
`public static final long` | `seed` | `1L`

edu.msu.cme.rdp.classifier.train.validation.Taxonomy
Modifier and Type | Constant Field | Value
--- | --- | ---
`public static final java.lang.String` | `GENUS` | `"GENUS"`

edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
Modifier and Type | Constant Field | Value
--- | --- | ---
`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
Modifier and Type | Constant Field | Value
--- | --- | ---
`public static final int` | `step` | `25`
`public static final int` | `window_size` | `200`

edu.msu.cme.rdp.classifier.utils.ClassifierFactory
Modifier and Type | Constant Field | Value
--- | --- | ---
`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
Modifier and Type | Constant Field | Value
--- | --- | ---
`public static final int` | `Count_Array_size` | `2`