BEASTObject that performs calculations based on the State.
Unordered set mapping keys to values
Class representing alignment data
Alignment based on a filter operation on another alignment
filter, data, constantSiteWeights, sequence, taxa, statecount, dataType, userDataType, strip, weights, ascertained, excludefrom, excludeto, excludeevery, includefrom, includeto, includeevery, *
| type: java.lang.String |
| specifies which of the sites in the input alignment should be selected First site is 1.Filter specs are comma separated, either a singleton, a range [from]-[to] or iteration [from]:[to]:[step]; 1-100 defines a range, 1-100 or 1:100:3 defines every third in range 1-100, 1::3,2::3 removes every third site. Default for range [1]-[last site], default for iterator [1]:[last site]:[1] |
| Required input |
| type: beast.evolution.alignment.Alignment |
| alignment to be filtered |
| Required input |
| type: beast.core.parameter.IntegerParameter |
| if specified, constant sites will be added with weights specified by the input. The dimension and order of weights must match the datatype. For example for nucleotide data, a 4 dimensional parameter with weights for A, C, G and T respectively need to be specified. |
| Optional input |
| type: beast.evolution.alignment.Sequence*** |
| sequence and meta data for particular taxon |
| Optional input |
| type: beast.evolution.alignment.TaxonSet |
| An optional taxon-set used only to sort the sequences into the same order as they appear in the taxon-set. |
| Optional input |
| type: java.lang.Integer |
| maximum number of states in all sequences |
| Optional input |
| type: java.lang.String |
| data type, one of {aminoacid=aminoacid, binary=binary, integer=integer, nucleotide=nucleotide, standard=standard, twoStateCovarion=twoStateCovarion, user defined=user defined} |
| Optional input. Default: nucleotide |
| type: beast.evolution.datatype.DataType$Base |
| non-standard, user specified data type, if specified 'dataType' is ignored |
| Optional input |
| type: java.lang.Boolean |
| sets weight to zero for sites that are invariant (e.g. all 1, all A or all unkown) |
| Optional input. Default: false |
| type: java.lang.String |
| comma separated list of weights, one for each site in the sequences. If not specified, each site has weight 1 |
| Forbidden: must not be specified |
| type: java.lang.Boolean |
| is true if the alignment allows ascertainment correction, i.e., conditioning the Felsenstein likelihood on excluding constant sites from the alignment |
| Optional input. Default: false |
| type: java.lang.Integer |
| first site to condition on, default 0 |
| Optional input. Default: 0 |
| type: java.lang.Integer |
| last site to condition on (but excluding this site), default 0 |
| Optional input. Default: 0 |
| type: java.lang.Integer |
| interval between sites to condition on (default 1) |
| Optional input. Default: 1 |
| type: java.lang.Integer |
| first site to condition on, default 0 |
| Optional input. Default: 0 |
| type: java.lang.Integer |
| last site to condition on, default 0 |
| Optional input. Default: 0 |
| type: java.lang.Integer |
| interval between sites to condition on (default 1) |
| Optional input. Default: 1 |
| type: java.lang.String |
| Input containing the map |
| Optional input |