Class AlignerHelper.Subproblem
- java.lang.Object
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- org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
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- 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
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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)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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
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Constructor Detail
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Subproblem
public Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex, int targetEndIndex)
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Subproblem
public Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex, int targetEndIndex, boolean isAnchored)
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Method Detail
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getTargetStartIndex
public int getTargetStartIndex()
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getQueryEndIndex
public int getQueryEndIndex()
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getTargetEndIndex
public int getTargetEndIndex()
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getQueryStartIndex
public int getQueryStartIndex()
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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
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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 pairsquerySequenceLength
- length of query sequencetargetSequenceLength
- length of target sequence- Returns:
- list alignment subproblems
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