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Constant Field Values

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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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