public class AlignerHelper
extends java.lang.Object
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 | Description |
---|---|
AlignerHelper() |
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,
java.util.List<AlignedSequence.Step> sx,
java.util.List<AlignedSequence.Step> sy) |
Find alignment path through traceback matrix
|
static int[] |
setSteps(AlignerHelper.Last[][][] traceback,
int[][][] scores,
java.util.List<AlignedSequence.Step> sx,
java.util.List<AlignedSequence.Step> sy) |
Find global alignment path through traceback matrix
|
static int[] |
setSteps(AlignerHelper.Last[][][] traceback,
int[] xyMax,
java.util.List<AlignedSequence.Step> sx,
java.util.List<AlignedSequence.Step> sy) |
Find local alignment path through traceback matrix
|
static java.lang.String |
tracebackToString(AlignerHelper.Last[][][] traceback) |
public static int addAnchors(AlignerHelper.Cut[] cuts, int[] scores, boolean addScore, int[] anchors)
public static AlignerHelper.Cut[] getCuts(int k, AlignerHelper.Subproblem subproblem, int[] dim, boolean anchor0)
public static void setCuts(int x, AlignerHelper.Subproblem subproblem, AlignerHelper.Last[][] pointers, AlignerHelper.Cut[] cuts)
public static AlignerHelper.Last[] setScorePoint(int x, int y, int gop, int gep, int sub, int[][][] scores)
x
- position in queryy
- position in targetgop
- gap opening penaltygep
- gap extension penaltysub
- compound match scorescores
- dynamic programming score matrix to fill at the given positionpublic static AlignerHelper.Last setScorePoint(int x, int y, int gep, int sub, int[][][] scores)
x
- position in queryy
- position in targetgep
- gap extension penaltysub
- compound match scorescores
- dynamic programming score matrix to fill at the given positionpublic static AlignerHelper.Last[][] setScoreVector(int x, AlignerHelper.Subproblem subproblem, int gop, int gep, int[] subs, boolean storing, int[][][] scores)
x
- subproblem
- gop
- gep
- subs
- storing
- scores
- 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)
x
- xb
- yb
- ye
- gop
- gep
- subs
- storing
- scores
- startAnchored
- public static AlignerHelper.Last[][] setScoreVector(int x, AlignerHelper.Subproblem subproblem, int gep, int[] subs, boolean storing, int[][][] scores)
x
- subproblem
- gep
- subs
- storing
- scores
- public static AlignerHelper.Last[][] setScoreVector(int x, int xb, int yb, int ye, int gep, int[] subs, boolean storing, int[][][] scores, boolean startAnchored)
x
- xb
- yb
- ye
- gep
- subs
- storing
- scores
- startAnchored
- public static AlignerHelper.Last[][] setScoreVector(int x, int gop, int gep, int[] subs, boolean storing, int[][][] scores, int[] xyMax, int score)
x
- gop
- gep
- subs
- storing
- scores
- xyMax
- score
- 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)
x
- xb
- yb
- ye
- gop
- gep
- subs
- storing
- scores
- xyMax
- score
- public static AlignerHelper.Last[][] setScoreVector(int x, int gep, int[] subs, boolean storing, int[][][] scores, int[] xyMax, int score)
x
- gep
- subs
- storing
- scores
- xyMax
- score
- 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)
x
- xb
- yb
- ye
- gep
- subs
- storing
- scores
- xyMax
- score
- public static int[] setSteps(AlignerHelper.Last[][][] traceback, boolean local, int[] xyMax, AlignerHelper.Last last, java.util.List<AlignedSequence.Step> sx, java.util.List<AlignedSequence.Step> sy)
traceback
- local
- xyMax
- last
- sx
- sy
- public static int[] setSteps(AlignerHelper.Last[][][] traceback, int[][][] scores, java.util.List<AlignedSequence.Step> sx, java.util.List<AlignedSequence.Step> sy)
traceback
- scores
- sx
- sy
- public static int[] setSteps(AlignerHelper.Last[][][] traceback, int[] xyMax, java.util.List<AlignedSequence.Step> sx, java.util.List<AlignedSequence.Step> sy)
traceback
- xyMax
- sx
- sy
- public static java.lang.String tracebackToString(AlignerHelper.Last[][][] traceback)