| 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.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" |