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 |