org.biojava.nbio.alignment.routines

Class AlignerHelper.Subproblem

java.lang.Object

org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem

Enclosing class:

AlignerHelper

public static class AlignerHelper.Subproblem
extends Object

Alignment subproblem. The bounds of the subproblem are the indicies representing the inclusive bounds of the dynamic programming alignment problem.

Author:

Daniel Cameron

Constructor Summary

Constructors

Constructor and Description
AlignerHelper.Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex, int targetEndIndex)
AlignerHelper.Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex, int targetEndIndex, boolean isAnchored)

Method Summary

Methods

Modifier and Type	Method and Description
int	getQueryEndIndex()
int	getQueryStartIndex()
static List<AlignerHelper.Subproblem>	getSubproblems(List<AlignerHelper.Anchor> anchors, int querySequenceLength, int targetSequenceLength) Convert a list of anchors into a subproblem list.
int	getTargetEndIndex()
int	getTargetStartIndex()
boolean	isStartAnchored() Indicates whether the start query and start target index compounds are anchored to each other

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignerHelper.Subproblem

public AlignerHelper.Subproblem(int queryStartIndex,
                        int targetStartIndex,
                        int queryEndIndex,
                        int targetEndIndex)

AlignerHelper.Subproblem

public AlignerHelper.Subproblem(int queryStartIndex,
                        int targetStartIndex,
                        int queryEndIndex,
                        int targetEndIndex,
                        boolean isAnchored)

Method Detail

getTargetStartIndex

public int getTargetStartIndex()

getQueryEndIndex

public int getQueryEndIndex()

getTargetEndIndex

public int getTargetEndIndex()

getQueryStartIndex

public int getQueryStartIndex()

isStartAnchored

public boolean isStartAnchored()

Indicates whether the start query and start target index compounds are anchored to each other

Returns:

true if the compounds are anchored in the alignment, false otherwise

getSubproblems

public static List<AlignerHelper.Subproblem> getSubproblems(List<AlignerHelper.Anchor> anchors,
                                            int querySequenceLength,
                                            int targetSequenceLength)

Convert a list of anchors into a subproblem list.

Parameters:

anchors - anchored read pairs

querySequenceLength - length of query sequence

targetSequenceLength - length of target sequence

Returns:

list alignment subproblems