public static class AlignerHelper.Subproblem
extends java.lang.Object
Constructor | Description |
---|---|
Subproblem(int queryStartIndex,
int targetStartIndex,
int queryEndIndex,
int targetEndIndex) |
|
Subproblem(int queryStartIndex,
int targetStartIndex,
int queryEndIndex,
int targetEndIndex,
boolean isAnchored) |
Modifier and Type | Method | Description |
---|---|---|
int |
getQueryEndIndex() |
|
int |
getQueryStartIndex() |
|
static java.util.List<AlignerHelper.Subproblem> |
getSubproblems(java.util.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
|
public Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex, int targetEndIndex)
public Subproblem(int queryStartIndex, int targetStartIndex, int queryEndIndex, int targetEndIndex, boolean isAnchored)
public int getTargetStartIndex()
public int getQueryEndIndex()
public int getTargetEndIndex()
public int getQueryStartIndex()
public boolean isStartAnchored()
public static java.util.List<AlignerHelper.Subproblem> getSubproblems(java.util.List<AlignerHelper.Anchor> anchors, int querySequenceLength, int targetSequenceLength)
anchors
- anchored read pairsquerySequenceLength
- length of query sequencetargetSequenceLength
- length of target sequence