Uses of Class
org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem

Packages that use AlignerHelper.Subproblem

Package	Description
org.biojava.nbio.alignment.routines
org.biojava.nbio.alignment.template

Uses of AlignerHelper.Subproblem in org.biojava.nbio.alignment.routines

Methods in org.biojava.nbio.alignment.routines that return types with arguments of type AlignerHelper.Subproblem

Modifier and Type	Method	Description
static List<AlignerHelper.Subproblem>	AlignerHelper.Subproblem.getSubproblems(List<AlignerHelper.Anchor> anchors, int querySequenceLength, int targetSequenceLength)	Convert a list of anchors into a subproblem list.

Methods in org.biojava.nbio.alignment.routines with parameters of type AlignerHelper.Subproblem

Modifier and Type	Method	Description
static AlignerHelper.Cut[]	AlignerHelper.getCuts(int k, AlignerHelper.Subproblem subproblem, int[] dim, boolean anchor0)
static void	AlignerHelper.setCuts(int x, AlignerHelper.Subproblem subproblem, AlignerHelper.Last[][] pointers, AlignerHelper.Cut[] cuts)
static AlignerHelper.Last[][]	AlignerHelper.setScoreVector(int x, AlignerHelper.Subproblem subproblem, int gep, int[] subs, boolean storing, int[][][] scores)	Score global alignment for a given position in the query sequence for a linear gap penalty
static AlignerHelper.Last[][]	AlignerHelper.setScoreVector(int x, AlignerHelper.Subproblem subproblem, int gop, int gep, int[] subs, boolean storing, int[][][] scores)	Score global alignment for a given position in the query sequence
void	AlignerHelper.Cut.update(int x, AlignerHelper.Subproblem subproblem, AlignerHelper.Last[][] pointers)

Uses of AlignerHelper.Subproblem in org.biojava.nbio.alignment.template

Methods in org.biojava.nbio.alignment.template with parameters of type AlignerHelper.Subproblem

Modifier and Type	Method	Description
protected int[]	AbstractMatrixAligner.getSubstitutionScoreVector(int queryColumn, AlignerHelper.Subproblem subproblem)	Returns score for the alignment of the query column to all target columns