Uses of Class
org.biojava.nbio.alignment.routines.AlignerHelper.Subproblem
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Packages that use AlignerHelper.Subproblem Package Description org.biojava.nbio.alignment.routines org.biojava.nbio.alignment.template -
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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 penaltystatic 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 sequencevoid
AlignerHelper.Cut. update(int x, AlignerHelper.Subproblem subproblem, AlignerHelper.Last[][] pointers)
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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
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