Package 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	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	Description
AlignerHelper()

Method Summary

Modifier and Type	Method	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, 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 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 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)