com.milaboratory.core.alignment

Interface AlignmentIterator<S extends Sequence<S>>

Type Parameters:

S - sequence type

All Known Implementing Classes:

AlignmentIteratorForward, AlignmentIteratorReverse

public interface AlignmentIterator<S extends Sequence<S>>

Iterates over all positions in alignment

Method Summary

Methods

Modifier and Type	Method and Description
boolean	advance() Advance iterator to the next position
int	getCurrentMutation() Current mutation or Mutation.NON_MUTATION if on match
int	getMutationsPointer() Points to current mutation or if currentMutation == Mutation.NON_MUTATION points to the next mutation.
int	getSeq1Position() Points to current position in sequence1; if on insertion points to the next position after insertion point
int	getSeq2Position() Points to current position in sequence2; if deletion points to the next position after deletion

Method Detail

getSeq1Position

int getSeq1Position()

Points to current position in sequence1; if on insertion points to the next position after insertion point

getSeq2Position

int getSeq2Position()

Points to current position in sequence2; if deletion points to the next position after deletion

getMutationsPointer

int getMutationsPointer()

Points to current mutation or if currentMutation == Mutation.NON_MUTATION points to the next mutation.

getCurrentMutation

int getCurrentMutation()

Current mutation or Mutation.NON_MUTATION if on match

advance

boolean advance()

Advance iterator to the next position

Returns:

true if success, false if iteration is finished