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java.lang.ObjectAlignments.Site
public class Site
Represents a "site" in an "alignment". Both terms used generously.
Constructor Summary | |
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Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites)
Creates a site in a alignment with no ambiguous data |
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Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites,
Ambiguous ambig)
Creates a site in a alignment with ambiguous data |
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Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites,
Ambiguous ambig,
java.lang.String siteClass)
Creates a site in a alignment with ambiguous data and with the given class. |
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Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites,
java.lang.String siteClass)
Creates a site in a alignment with no ambiguous data and with the given class. |
Method Summary | |
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boolean |
equals(java.lang.Object o)
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Ambiguous |
getAmbiguous()
Gets the information about ambiguous states for this site |
java.util.Set<java.lang.String> |
getCharacter(java.lang.String taxa)
Gets the possible characters for a given taxa. |
ArrayMap<java.lang.String,Likelihood.NodeLikelihood> |
getInitialNodeLikelihoods(Tree t,
ArrayMap<java.lang.String,java.lang.Integer> map,
SiteConstraints scon)
Gdets initial node likelihoods based on the site, tree and any constraints. |
int |
getNum()
Get the number of taxa |
java.lang.String |
getRawCharacter(java.lang.String taxa)
Gets the raw charcater for a given taxa. |
java.lang.String |
getSiteClass()
Gets the class of this site |
java.util.Set<java.lang.String> |
getTaxa()
Get the set of taxa |
int |
hashCode()
|
Site |
limitToTaxa(java.util.Collection<java.lang.String> limit)
Returns a new Site which is the same as this one except it is limited to certain taxa |
Site |
recode(java.util.Map<java.lang.String,java.lang.String> recode)
Recodes the site and returns it |
Site |
recode(java.util.Map<java.lang.String,java.lang.String> recode,
Ambiguous ambig)
Recodes the alignment and returns it and also allows the definition of new ambiguous states |
java.lang.String |
toString()
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Methods inherited from class java.lang.Object |
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clone, finalize, getClass, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites)
sites
- Map from taxa name to statepublic Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, java.lang.String siteClass)
sites
- Map from taxa name to statesiteClass
- The class of this sitepublic Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, Ambiguous ambig)
sites
- Map from taxa name to stateambig
- Description of ambiguous datapublic Site(java.util.LinkedHashMap<java.lang.String,java.lang.String> sites, Ambiguous ambig, java.lang.String siteClass)
sites
- Map from taxa name to stateambig
- Description of ambiguous datasiteClass
- The class of this siteMethod Detail |
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public java.util.Set<java.lang.String> getCharacter(java.lang.String taxa)
taxa
- Taxa to return the character for
public java.lang.String getRawCharacter(java.lang.String taxa)
taxa
- Taxa to return the character for
public int getNum()
public java.util.Set<java.lang.String> getTaxa()
public java.lang.String getSiteClass()
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object
public java.lang.String toString()
toString
in class java.lang.Object
public ArrayMap<java.lang.String,Likelihood.NodeLikelihood> getInitialNodeLikelihoods(Tree t, ArrayMap<java.lang.String,java.lang.Integer> map, SiteConstraints scon)
t
- The treemap
- A map from state to position in arrayscon
- Any constraints on the site
public Site recode(java.util.Map<java.lang.String,java.lang.String> recode)
recode
- A map from original state to new state, e.g. to recode
DNA to RY it would contains A -> R, G -> R, C -> Y, T -> Y
public Site recode(java.util.Map<java.lang.String,java.lang.String> recode, Ambiguous ambig)
recode
- A map from original state to new state, e.g. to recode
DNA to RY it would contains A -> R, G -> R, C -> Y, T -> Yambig
- The new ambiiguous states
public Site limitToTaxa(java.util.Collection<java.lang.String> limit)
limit
- The taxa to limit the new site to
public Ambiguous getAmbiguous()
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