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# 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`

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