pal.alignment
Interface CharacterAlignment
- All Superinterfaces:
- IdGroup, Report, java.io.Serializable, TableReport
- All Known Implementing Classes:
- SimpleCharacterAlignment
- public interface CharacterAlignment
- extends java.io.Serializable, IdGroup, Report, TableReport
This interface is designed to hold quantitative character states.
Each trait (a quantitative character) has two sets of
labels. One is the traitName, and the second is the environmentName. Obviously any
descriptor could be placed in these two labels, however for printing purposes
traitName is printed first. Double.NaN is assumed to be the missing value.
Field Summary |
static double |
MISSING
|
Method Summary |
java.lang.String |
getEnvironmentName(int trait)
Return name of the environments for this trait number |
int |
getSequenceCount()
Return number of sequences(taxa) in this alignment |
double |
getTrait(int seq,
int trait)
Return the trait value for a given sequence (taxon) and trait number |
int |
getTraitCount()
Return number of traits for each sequence in this alignment |
java.lang.String |
getTraitName(int trait)
Return name of the trait for this trait number |
MISSING
public static final double MISSING
getTraitName
public java.lang.String getTraitName(int trait)
- Return name of the trait for this trait number
getEnvironmentName
public java.lang.String getEnvironmentName(int trait)
- Return name of the environments for this trait number
getTrait
public double getTrait(int seq,
int trait)
- Return the trait value for a given sequence (taxon) and trait number
getSequenceCount
public int getSequenceCount()
- Return number of sequences(taxa) in this alignment
getTraitCount
public int getTraitCount()
- Return number of traits for each sequence in this alignment