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 |
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" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
delimiter |
";" |
Modifier and Type | Constant Field | Value |
---|---|---|
public final int |
bins |
11 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
NUM_OF_RUNS |
100 |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
MIN_BOOTSTRSP_WORDS |
5 |
public static final long |
seed |
1L |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final java.lang.String |
GENUS |
"GENUS" |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
step |
25 |
public static final int |
window_size |
200 |
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" |
Modifier and Type | Constant Field | Value |
---|---|---|
public static final int |
Count_Array_size |
2 |