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

Description

Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex, int targetEndIndex)

Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex, int targetEndIndex, boolean isAnchored)
Method Summary

Modifier and Type

Method

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 Details
- Subproblem
  
  public Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex, int targetEndIndex)
- Subproblem
  
  public Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex, int targetEndIndex, boolean isAnchored)
Method Details
- 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