com.milaboratory.core.alignment

Class AlignmentIteratorForward<S extends Sequence<S>>

java.lang.Object

com.milaboratory.core.alignment.AlignmentIteratorForward<S>

Type Parameters:

S - sequence type

All Implemented Interfaces:

AlignmentIterator<S>

public final class AlignmentIteratorForward<S extends Sequence<S>>
extends Object
implements AlignmentIterator<S>

Iterates over all positions in alignment

Constructor Summary

Constructors

Constructor and Description
AlignmentIteratorForward(Mutations<S> mutations, Range seq1Range) Create alignment iterator
AlignmentIteratorForward(Mutations<S> mutations, Range seq1Range, int seq2Position) Create alignment iterator

Method Summary

Methods

Modifier and Type	Method and Description
boolean	advance() Advance to the next alignment 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

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentIteratorForward

public AlignmentIteratorForward(Mutations<S> mutations,
                        Range seq1Range)

Create alignment iterator

Parameters:

mutations - mutations (alignment)

seq1Range - aligned range

AlignmentIteratorForward

public AlignmentIteratorForward(Mutations<S> mutations,
                        Range seq1Range,
                        int seq2Position)

Create alignment iterator

Parameters:

mutations - mutations (alignment)

seq1Range - aligned range

seq2Position - seq2 start position

Method Detail

advance

public boolean advance()

Advance to the next alignment position

Specified by:

advance in interface AlignmentIterator<S extends Sequence<S>>

Returns:

true if iteration successful; false if iteration ended

getSeq1Position

public int getSeq1Position()

Description copied from interface: AlignmentIterator

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

Specified by:

getSeq1Position in interface AlignmentIterator<S extends Sequence<S>>

getSeq2Position

public int getSeq2Position()

Description copied from interface: AlignmentIterator

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

Specified by:

getSeq2Position in interface AlignmentIterator<S extends Sequence<S>>

getMutationsPointer

public int getMutationsPointer()

Description copied from interface: AlignmentIterator

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

Specified by:

getMutationsPointer in interface AlignmentIterator<S extends Sequence<S>>

getCurrentMutation

public int getCurrentMutation()

Description copied from interface: AlignmentIterator

Current mutation or Mutation.NON_MUTATION if on match

Specified by:

getCurrentMutation in interface AlignmentIterator<S extends Sequence<S>>