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
 
Methods inherited from interface pal.misc.IdGroup
getIdCount, getIdentifier, setIdentifier, whichIdNumber
 
Methods inherited from interface pal.misc.Report
report
 
Methods inherited from interface pal.misc.TableReport
getTableColumnNames, getTableData, getTableTitle
 

Field Detail

MISSING

public static final double MISSING
Method Detail

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