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

Packages that use AlignerHelper.Last

Package	Description
org.biojava.nbio.alignment.routines

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

Methods in org.biojava.nbio.alignment.routines that return AlignerHelper.Last

Modifier and Type	Method and Description
static AlignerHelper.Last	AlignerHelper.setScorePoint(int x, int y, int gep, int sub, int[][][] scores) Calculates the optimal alignment score for the given sequence positions and a linear gap penalty
static AlignerHelper.Last[]	AlignerHelper.setScorePoint(int x, int y, int gop, int gep, int sub, int[][][] scores) Calculate the optimal alignment score for the given sequence positions with an affine or constant gap penalty
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
static AlignerHelper.Last[][]	AlignerHelper.setScoreVector(int x, int gep, int[] subs, boolean storing, int[][][] scores, int[] xyMax, int score) Score local alignment for a given position in the query sequence for a linear gap penalty
static AlignerHelper.Last[][]	AlignerHelper.setScoreVector(int x, int gop, int gep, int[] subs, boolean storing, int[][][] scores, int[] xyMax, int score) Score local alignment for a given position in the query sequence
static AlignerHelper.Last[][]	AlignerHelper.setScoreVector(int x, int xb, int yb, int ye, int gep, int[] subs, boolean storing, int[][][] scores, boolean startAnchored) Score global alignment for a given position in the query sequence for a linear gap penalty
static AlignerHelper.Last[][]	AlignerHelper.setScoreVector(int x, int xb, int yb, int ye, int gep, int[] subs, boolean storing, int[][][] scores, int[] xyMax, int score) Score local alignment for a given position in the query sequence for a linear gap penalty
static AlignerHelper.Last[][]	AlignerHelper.setScoreVector(int x, int xb, int yb, int ye, int gop, int gep, int[] subs, boolean storing, int[][][] scores, boolean startAnchored) Score global alignment for a given position in the query sequence
static AlignerHelper.Last[][]	AlignerHelper.setScoreVector(int x, int xb, int yb, int ye, int gop, int gep, int[] subs, boolean storing, int[][][] scores, int[] xyMax, int score) Score local alignment for a given position in the query sequence
static AlignerHelper.Last	AlignerHelper.Last.valueOf(String name) Returns the enum constant of this type with the specified name.
static AlignerHelper.Last[]	AlignerHelper.Last.values() Returns an array containing the constants of this enum type, in the order they are declared.

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

Modifier and Type	Method and Description
static void	AlignerHelper.setCuts(int x, AlignerHelper.Subproblem subproblem, AlignerHelper.Last[][] pointers, AlignerHelper.Cut[] cuts)
static int[]	AlignerHelper.setSteps(AlignerHelper.Last[][][] traceback, boolean local, int[] xyMax, AlignerHelper.Last last, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Find alignment path through traceback matrix
static int[]	AlignerHelper.setSteps(AlignerHelper.Last[][][] traceback, boolean local, int[] xyMax, AlignerHelper.Last last, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Find alignment path through traceback matrix
static int[]	AlignerHelper.setSteps(AlignerHelper.Last[][][] traceback, int[][][] scores, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Find global alignment path through traceback matrix
static int[]	AlignerHelper.setSteps(AlignerHelper.Last[][][] traceback, int[] xyMax, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Find local alignment path through traceback matrix
static String	AlignerHelper.tracebackToString(AlignerHelper.Last[][][] traceback)
void	AlignerHelper.Cut.update(int x, AlignerHelper.Subproblem subproblem, AlignerHelper.Last[][] pointers)