jebl.evolution.alignments
Interface Patterns

All Known Subinterfaces:
Alignment
All Known Implementing Classes:
BasicAlignment, BootrappedAlignment, JackknifedAlignment, ResampledAlignment

public interface Patterns

An interface representing a set of site patterns.

Author:
Andrew Rambaut, Alexei Drummond

Method Summary
 int getPatternCount()
           
 int getPatternLength()
           
 List<Pattern> getPatterns()
          Get a list of all the patterns
 SequenceType getSequenceType()
           
 List<Taxon> getTaxa()
           
 

Method Detail

getPatternCount

int getPatternCount()

getPatternLength

int getPatternLength()

getPatterns

List<Pattern> getPatterns()
Get a list of all the patterns

Returns:
the list

getTaxa

List<Taxon> getTaxa()
Returns:
the list of taxa that the state values correspond to.

getSequenceType

SequenceType getSequenceType()
Returns:
the data type of the states in these site patterns.