pal.eval
Class SiteDetails.Utils
java.lang.Object
pal.eval.SiteDetails.Utils
- Enclosing interface:
- SiteDetails
public static final class SiteDetails.Utils
- extends java.lang.Object
Method Summary |
static SiteDetails |
create(double[][] categoryPatternConditionalProbabilities,
boolean isLoggedConditionals,
int numberOfPatterns,
int[] sitePatternMatchup,
int numberOfSites,
double[] siteLikelihoods)
Create a Postriors object with no related substitution model |
static SiteDetails |
create(double[][] categoryPatternConditionalProbabilities,
boolean isLoggedConditionals,
SubstitutionModel model,
int numberOfPatterns,
int[] sitePatternMatchup,
int numberOfSites,
double[] siteLikelihoods)
Create a Postriors object |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
SiteDetails.Utils
public SiteDetails.Utils()
create
public static final SiteDetails create(double[][] categoryPatternConditionalProbabilities,
boolean isLoggedConditionals,
SubstitutionModel model,
int numberOfPatterns,
int[] sitePatternMatchup,
int numberOfSites,
double[] siteLikelihoods)
- Create a Postriors object
- Parameters:
categoryPatternConditionalProbabilities
- An array arranged [category][pattern] that holds the conditional probabilities for each category at each siteisLoggedConditionals
- should be true if the conditional probabilities are stored as logged values, false if notmodel
- the related substitution modelsnumberOfPatterns
- the number of patternssitePatternMatchup
- an array that identifies what pattern is to used at which sitenumberOfSites
- the number of sitessiteLikelihoods
- the site likelihood (unlogged) at each site
- Returns:
- an appropriate Posteriors object
create
public static final SiteDetails create(double[][] categoryPatternConditionalProbabilities,
boolean isLoggedConditionals,
int numberOfPatterns,
int[] sitePatternMatchup,
int numberOfSites,
double[] siteLikelihoods)
- Create a Postriors object with no related substitution model
- Parameters:
categoryPatternConditionalProbabilities
- An array arranged [category][pattern] that holds the conditional probabilities for each category at each siteisLoggedConditionals
- should be true if the conditional probabilities are stored as logged values, false if notnumberOfPatterns
- the number of patternssitePatternMatchup
- an array that identifies what pattern is to used at which sitenumberOfSites
- the number of sitessiteLikelihoods
- the site likelihood (unlogged) at each site
- Returns:
- an appropriate Posteriors object