Constant Field Values
Contents
edu.msu.*
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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
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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"
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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"
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edu.msu.cme.rdp.classifier.train.LineageSequenceParser Modifier and Type Constant Field Value public static final java.lang.String
delimiter
";"
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edu.msu.cme.rdp.classifier.train.validation.CorrectAssignment Modifier and Type Constant Field Value public final int
bins
11
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edu.msu.cme.rdp.classifier.train.validation.DecisionMaker Modifier and Type Constant Field Value public static final int
NUM_OF_RUNS
100
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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
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edu.msu.cme.rdp.classifier.train.validation.Taxonomy Modifier and Type Constant Field Value public static final java.lang.String
GENUS
"GENUS"
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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"
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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
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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"
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edu.msu.cme.rdp.multicompare.taxon.MCTaxon Modifier and Type Constant Field Value public static final int
Count_Array_size
2