org.biojava.nbio.alignment.routines

Class AlignerHelper

java.lang.Object

org.biojava.nbio.alignment.routines.AlignerHelper

public class AlignerHelper
extends Object

Static utility to construct alignment routines from a common library of methods.

Author:

Mark Chapman, Daniel Cameron

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AlignerHelper.Anchor Compounds in query and target sequences that must align
static class	AlignerHelper.Cut Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
static class	AlignerHelper.Last Define a traceback pointer for the three edit operations: substitution (match/replacement of a query compound with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and insertion (addition of a target compound opening a gap in the query sequence).
static class	AlignerHelper.Subproblem Alignment subproblem.

Constructor Summary

Constructors

Constructor and Description
AlignerHelper()

Method Summary

Modifier and Type	Method and Description
static int	addAnchors(AlignerHelper.Cut[] cuts, int[] scores, boolean addScore, int[] anchors)
static AlignerHelper.Cut[]	getCuts(int k, AlignerHelper.Subproblem subproblem, int[] dim, boolean anchor0)
static void	setCuts(int x, AlignerHelper.Subproblem subproblem, AlignerHelper.Last[][] pointers, AlignerHelper.Cut[] cuts)
static AlignerHelper.Last	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[]	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[][]	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[][]	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[][]	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[][]	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[][]	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[][]	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[][]	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[][]	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 int[]	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[]	setSteps(AlignerHelper.Last[][][] traceback, int[][][] scores, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Find global alignment path through traceback matrix
static int[]	setSteps(AlignerHelper.Last[][][] traceback, int[] xyMax, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy) Find local alignment path through traceback matrix
static String	tracebackToString(AlignerHelper.Last[][][] traceback)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AlignerHelper

public AlignerHelper()

Method Detail

addAnchors

public static int addAnchors(AlignerHelper.Cut[] cuts,
                             int[] scores,
                             boolean addScore,
                             int[] anchors)

getCuts

public static AlignerHelper.Cut[] getCuts(int k,
                                          AlignerHelper.Subproblem subproblem,
                                          int[] dim,
                                          boolean anchor0)

setCuts

public static void setCuts(int x,
                           AlignerHelper.Subproblem subproblem,
                           AlignerHelper.Last[][] pointers,
                           AlignerHelper.Cut[] cuts)

setScorePoint

public static AlignerHelper.Last[] 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

Parameters:

x - position in query

y - position in target

gop - gap opening penalty

gep - gap extension penalty

sub - compound match score

scores - dynamic programming score matrix to fill at the given position

Returns:

traceback direction for substitution, deletion and insertion

setScorePoint

public static AlignerHelper.Last 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

Parameters:

x - position in query

y - position in target

gep - gap extension penalty

sub - compound match score

scores - dynamic programming score matrix to fill at the given position

Returns:

traceback directions for substitution, deletion and insertion respectively

setScoreVector

public static AlignerHelper.Last[][] 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

Parameters:

x -

subproblem -

gop -

gep -

subs -

storing -

scores -

Returns:

setScoreVector

public static AlignerHelper.Last[][] 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

Parameters:

x -

xb -

yb -

ye -

gop -

gep -

subs -

storing -

scores -

startAnchored -

Returns:

setScoreVector

public static AlignerHelper.Last[][] 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

Parameters:

x -

subproblem -

gep -

subs -

storing -

scores -

Returns:

setScoreVector

public static AlignerHelper.Last[][] 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

Parameters:

x -

xb -

yb -

ye -

gep -

subs -

storing -

scores -

startAnchored -

Returns:

setScoreVector

public static AlignerHelper.Last[][] 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

Parameters:

x -

gop -

gep -

subs -

storing -

scores -

xyMax -

score -

Returns:

setScoreVector

public static AlignerHelper.Last[][] 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

Parameters:

x -

xb -

yb -

ye -

gop -

gep -

subs -

storing -

scores -

xyMax -

score -

Returns:

setScoreVector

public static AlignerHelper.Last[][] 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

Parameters:

x -

gep -

subs -

storing -

scores -

xyMax -

score -

Returns:

setScoreVector

public static AlignerHelper.Last[][] 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

Parameters:

x -

xb -

yb -

ye -

gep -

subs -

storing -

scores -

xyMax -

score -

Returns:

setSteps

public static int[] 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

Parameters:

traceback -

local -

xyMax -

last -

sx -

sy -

Returns:

setSteps

public static int[] setSteps(AlignerHelper.Last[][][] traceback,
                             int[][][] scores,
                             List<AlignedSequence.Step> sx,
                             List<AlignedSequence.Step> sy)

Find global alignment path through traceback matrix

Parameters:

traceback -

scores -

sx -

sy -

Returns:

setSteps

public static int[] setSteps(AlignerHelper.Last[][][] traceback,
                             int[] xyMax,
                             List<AlignedSequence.Step> sx,
                             List<AlignedSequence.Step> sy)

Find local alignment path through traceback matrix

Parameters:

traceback -

xyMax -

sx -

sy -

Returns:

tracebackToString

public static String tracebackToString(AlignerHelper.Last[][][] traceback)