Constant Field Values

Contents

edu.msu.*

  • 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.multicompare.taxon.MCTaxon 
    Modifier and Type Constant Field Value
    public static final int Count_Array_size 2