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java.lang.ObjectAlignments.Alignment
public class Alignment
Represents an "alignment", used very losely. Classes should extend this to
represent the different types of alignment, e.g. DuplicationAlignment
,
SequenceAlignment
.
Nested Class Summary | |
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class |
Alignment.UniqueSite
Used to represent a unique site in an alignment. |
Field Summary | |
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protected java.util.List<Site> |
data
The list of sites in the alignment |
protected boolean |
hasClasses
Whether the sites in this alignment contain site information |
protected java.util.Set<java.lang.String> |
taxa
The list of taxa in the alignment |
Constructor Summary | |
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protected |
Alignment()
Default constructor. |
|
Alignment(java.util.List<Site> data)
Creates an alignment |
Method Summary | |
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boolean |
check(java.util.Map<java.lang.String,?> map)
Checks whether the map contains an entry for every class in the alignment |
int |
getCount(Site s)
Gets a count of hoften a site occurs in the alignment |
int |
getLength()
Gets the length of the aligmnet |
int |
getNumber()
Gets the number of taxa in the alignment |
double |
getRawFreq(java.lang.String character)
Gets the frequency of a raw character |
Site |
getSite(int s)
Returns the site at a given position in the alignment |
java.util.Set<java.lang.String> |
getTaxa()
Gets the names of the taxa in the aligment |
java.util.List<Alignment.UniqueSite> |
getUniqueSites()
Returns a list of unique sites in the aligment. |
java.util.Iterator<Site> |
iterator()
|
Alignment |
limitToTaxa(java.util.Collection<java.lang.String> limit)
Returns a new Alignment which is the same as this one except it is limited to certain taxa |
Alignment |
recode(java.util.Map<java.lang.String,java.lang.String> recode)
Recodes the alignment and returns it |
Alignment |
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 |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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protected java.util.List<Site> data
protected java.util.Set<java.lang.String> taxa
protected boolean hasClasses
Constructor Detail |
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protected Alignment()
public Alignment(java.util.List<Site> data) throws AlignmentException
data
- A list of sites in the alignment
AlignmentException
- Thrown if the sites passed have different taxaMethod Detail |
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public int getLength()
public int getNumber()
public java.util.List<Alignment.UniqueSite> getUniqueSites()
public Site getSite(int s)
s
- The site to be returned
public java.util.Set<java.lang.String> getTaxa()
public java.util.Iterator<Site> iterator()
iterator
in interface java.lang.Iterable<Site>
public boolean check(java.util.Map<java.lang.String,?> map)
map
- The map
public Alignment 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 Alignment 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 Alignment limitToTaxa(java.util.Collection<java.lang.String> limit)
limit
- The taxa to limit the new alignment to
public double getRawFreq(java.lang.String character)
character
- The character to get the frequency for
public int getCount(Site s)
s
- The site
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