calhoun.analysis.crf.io
Class MultipleAlignmentInputSequence.MultipleAlignmentColumn

java.lang.Object
  calhoun.analysis.crf.io.MultipleAlignmentInputSequence.MultipleAlignmentColumn

Enclosing class:

MultipleAlignmentInputSequence

public class MultipleAlignmentInputSequence.MultipleAlignmentColumn
extends java.lang.Object

represents the column of the alignment at a given position on the reference sequence

Constructor Summary

MultipleAlignmentInputSequence.MultipleAlignmentColumn(int pos)
constructs the column at this position

Method Summary

MultipleAlignmentInputSequence	getMultipleAlignment() returns the multiple alignment input sequence that this column comes from.
RootedBinaryPhylogeneticTree	getTree() returns the tree for this alignment
int	getUniqueHash() returns a hash value for the characters in this column
char	nucleotide(int spec) returns the value of this position in the alignment for the given species
int	numSpecies() returns the number of species in the alignment

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

MultipleAlignmentInputSequence.MultipleAlignmentColumn

public MultipleAlignmentInputSequence.MultipleAlignmentColumn(int pos)

constructs the column at this position

Method Detail

getMultipleAlignment

public MultipleAlignmentInputSequence getMultipleAlignment()

returns the multiple alignment input sequence that this column comes from.

Returns:

the owning input sequence

numSpecies

public int numSpecies()

returns the number of species in the alignment

Returns:

the number of species in the alignment

nucleotide

public char nucleotide(int spec)

returns the value of this position in the alignment for the given species

Parameters:

spec - the species to retrieve. The value will be the index of the species in the speciesName list.

Returns:

the character for this species in this column

getUniqueHash

public int getUniqueHash()

returns a hash value for the characters in this column

Returns:

the hash value for the column

getTree

public RootedBinaryPhylogeneticTree getTree()

returns the tree for this alignment

Returns:

the species tree for the alignment