# Constant Field Values

Contents

- edu.msu.*

edu.msu.*

edu.msu.cme.rdp.classifier.comparison.edu.msu.cme.rdp.classifier.comparison.AbstractNode.TaxonIterator
`private final int` `ROOT_INDENT` `0`

edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
`private static final float` `DEFAULT_CONF` `0.800000011920929f`
`private static final int` `DEFAULT_DEPTH` `0`
`private static final int` `DISPLAY_LIMIT` `25`
`private static final float` `MAX_CONF` `1.0f`
`private static final int` `MAX_DEPTH` `10`
`private static final int` `MAX_SEQUENCE` `40000`
`private static final float` `MIN_CONF` `0.0f`
`private static final int` `MIN_DEPTH` `2`

edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
`public static final java.lang.String` `CLASS_OUTFILE_DESC` `"output file name for classification assignments."`
`public static final java.lang.String` `CLASS_OUTFILE_LONG_OPT` `"class_outputFile"`
`public static final java.lang.String` `CLASS_OUTFILE_SHORT_OPT` `"r"`
`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` `CONF_DESC` `"specifies the assignment confidence cutoff used to determine the assignment count in the hierarchical format. Range [0-1], Default is 0.8."`
`public static final java.lang.String` `CONF_LONG_OPT` `"conf"`
`public static final java.lang.String` `CONF_SHORT_OPT` `"n"`
`public static final float` `DEFAULT_CON_CUTOFF` `0.800000011920929f`

`public static final java.lang.String`

`FORMAT_DESC`

`"tab delimited output format: [ allrank | fixrank | db ]. Default is allrank. \n allrank: outputs the results for all ranks applied for each sequence: seqname, orientation, taxon name, rank, conf, ...\n fixrank: only outputs the results for fixed ranks in order: no rank, domain, phylum, class, order, family, genus.\n db: outputs the seqname, trainset_no, tax_id, conf. Good for storing in a database."`

`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` `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"`
`private static final java.lang.String` `SAMPLE1` `"sample1"`
`private static final java.lang.String` `SAMPLE2` `"sample2"`
`public static final java.lang.String` `TRAINPROPFILE_DESC` `"a property file contains the mapping of the training files.\nNote: the training files and the property file should be in the same directory.\nThe default property file is set to data/classifier/rRNAClassifier.properties."`
`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.ComparisonManager
`private static final java.lang.String` `ABORTED` `"aborted"`
`private static final java.lang.String` `COMPLETED` `"completed"`
`private static final java.lang.String` `FAILED` `"failed"`
`private static final java.lang.String` `NOT_STARTED` `"not started"`
`private static final java.lang.String` `RUNNING` `"running"`
`private static final java.lang.String` `SAMPLE1` `"sample1"`
`private static final java.lang.String` `SAMPLE2` `"sample2"`

edu.msu.cme.rdp.classifier.comparison.SigCalculator
`private static final int` `FREQ_LIMIT` `5`

edu.msu.cme.rdp.classifier.comparison.Ztable
`private static final java.lang.String` `defaultDataProp` `"rRNAClassifier.properties"`
`private static final double` `DELIMITER_Z` `4.0`
`private static final double` `MAX_Z` `7.5`

edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
`private static final int` `MAX_ASCII` `128`

edu.msu.cme.rdp.classifier.readseqwrapper.Sequence
`public static final int` `MASK` `65535`
`public static final int` `RNA_BASES` `4`
`public static final int` `WORDSIZE` `8`

edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
`private static final int` `MAX_ASCII` `128`
`private static final java.lang.String` `TEXT_FORMAT` `"text"`
`static final java.lang.String` `UNKNOWN_SEQ` `"unknown"`

edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
`private final int` `MAX_NUM_OF_WORDS` `5000`
`public static final int` `MIN_GOOD_WORDS` `42`
`public static final int` `MIN_SEQ_LEN` `50`
`private final int` `NUM_OF_RUNS` `100`

edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd

`public static final java.lang.String`

`FORMAT_DESC`

`"all tab delimited output format: [allrank|fixrank|db]. Default is allrank. \n allrank: outputs the results for all ranks applied for each sequence: seqname, orientation, taxon name, rank, conf, ...\n fixrank: only outputs the results for fixed ranks in order: no rank, domain, phylum, class, order, family, genus\n db: outputs the seqname, trainset_no, tax_id, conf. This is good for storing in a database"`

`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` `OUTFILE_DESC` `"output file name 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` `"query file contains sequences in one of the following formats: Fasta, Genbank and EMBL"`
`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` `TRAINPROPFILE_DESC` `"a property file contains the mapping of the training files.\nNote: the training files and the property file should be in the same directory.\nThe default property file is set to data/classifier/rRNAClassifier.properties."`
`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.rrnaclassifier.ClassifierFactory
`private static final java.lang.String` `defaultDataProp` `"rRNAClassifier.properties"`

edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyVersion
`private static final java.lang.String` `regex` `"<trainsetNo>(.*)</trainsetNo><version>(.*)</version>"`

edu.msu.cme.rdp.classifier.train.GoodWordIterator
`static final int` `MASK` `65535`
`static final int` `MAX_ASCII` `128`
`static final int` `WORDSIZE` `8`

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

edu.msu.cme.rdp.classifier.train.TreeFactory
`private final float` `WF1` `0.5f`
`private final float` `WF2` `1.0f`