org.biojava3.alignment.routines
public class AlignerHelper extends java.lang.Object
Modifier and Type | Class and Description |
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static class |
AlignerHelper.Cut
Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
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static class |
AlignerHelper.Last
Defines 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).
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Constructor and Description |
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AlignerHelper() |
Modifier and Type | Method and Description |
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static short |
addAnchors(AlignerHelper.Cut[] cuts,
short[] scores,
boolean addScore,
int[] anchors) |
static AlignerHelper.Cut[] |
getCuts(int k,
int[] subproblem,
int[] dim,
boolean anchor0) |
static int[] |
getNextSubproblem(int[] anchors)
Returns the coordinates for the next subproblem.
|
static void |
setCuts(int x,
int[] subproblem,
AlignerHelper.Last[][] pointers,
AlignerHelper.Cut[] cuts) |
static AlignerHelper.Last |
setScorePoint(int x,
int y,
short gep,
short sub,
short[][][] scores) |
static AlignerHelper.Last[] |
setScorePoint(int x,
int y,
short gop,
short gep,
short sub,
short[][][] scores) |
static AlignerHelper.Last[][] |
setScoreVector(int x,
int[] subproblem,
short gep,
short[] subs,
boolean storing,
short[][][] scores) |
static AlignerHelper.Last[][] |
setScoreVector(int x,
int[] subproblem,
short gop,
short gep,
short[] subs,
boolean storing,
short[][][] scores) |
static AlignerHelper.Last[][] |
setScoreVector(int x,
int xb,
int yb,
int ye,
short gep,
short[] subs,
boolean storing,
short[][][] scores) |
static AlignerHelper.Last[][] |
setScoreVector(int x,
int xb,
int yb,
int ye,
short gep,
short[] subs,
boolean storing,
short[][][] scores,
int[] xyMax,
int score) |
static AlignerHelper.Last[][] |
setScoreVector(int x,
int xb,
int yb,
int ye,
short gop,
short gep,
short[] subs,
boolean storing,
short[][][] scores) |
static AlignerHelper.Last[][] |
setScoreVector(int x,
int xb,
int yb,
int ye,
short gop,
short gep,
short[] subs,
boolean storing,
short[][][] scores,
int[] xyMax,
int score) |
static AlignerHelper.Last[][] |
setScoreVector(int x,
short gep,
short[] subs,
boolean storing,
short[][][] scores) |
static AlignerHelper.Last[][] |
setScoreVector(int x,
short gep,
short[] subs,
boolean storing,
short[][][] scores,
int[] xyMax,
int score) |
static AlignerHelper.Last[][] |
setScoreVector(int x,
short gop,
short gep,
short[] subs,
boolean storing,
short[][][] scores) |
static AlignerHelper.Last[][] |
setScoreVector(int x,
short gop,
short gep,
short[] subs,
boolean storing,
short[][][] scores,
int[] xyMax,
int score) |
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) |
static int[] |
setSteps(AlignerHelper.Last[][][] traceback,
int[] xyMax,
java.util.List<AlignedSequence.Step> sx,
java.util.List<AlignedSequence.Step> sy) |
static int[] |
setSteps(AlignerHelper.Last[][][] traceback,
short[][][] scores,
java.util.List<AlignedSequence.Step> sx,
java.util.List<AlignedSequence.Step> sy) |
static int[] |
setSteps(int[] anchors,
java.util.List<AlignedSequence.Step> sx,
java.util.List<AlignedSequence.Step> sy)
Sets the alignment path following the list of anchors.
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public static short addAnchors(AlignerHelper.Cut[] cuts, short[] scores, boolean addScore, int[] anchors)
public static AlignerHelper.Cut[] getCuts(int k, int[] subproblem, int[] dim, boolean anchor0)
public static int[] getNextSubproblem(int[] anchors)
null
.anchors
- current list of anchorspublic static void setCuts(int x, int[] subproblem, AlignerHelper.Last[][] pointers, AlignerHelper.Cut[] cuts)
public static AlignerHelper.Last[] setScorePoint(int x, int y, short gop, short gep, short sub, short[][][] scores)
public static AlignerHelper.Last setScorePoint(int x, int y, short gep, short sub, short[][][] scores)
public static AlignerHelper.Last[][] setScoreVector(int x, short gop, short gep, short[] subs, boolean storing, short[][][] scores)
public static AlignerHelper.Last[][] setScoreVector(int x, int[] subproblem, short gop, short gep, short[] subs, boolean storing, short[][][] scores)
public static AlignerHelper.Last[][] setScoreVector(int x, int xb, int yb, int ye, short gop, short gep, short[] subs, boolean storing, short[][][] scores)
public static AlignerHelper.Last[][] setScoreVector(int x, short gep, short[] subs, boolean storing, short[][][] scores)
public static AlignerHelper.Last[][] setScoreVector(int x, int[] subproblem, short gep, short[] subs, boolean storing, short[][][] scores)
public static AlignerHelper.Last[][] setScoreVector(int x, int xb, int yb, int ye, short gep, short[] subs, boolean storing, short[][][] scores)
public static AlignerHelper.Last[][] setScoreVector(int x, short gop, short gep, short[] subs, boolean storing, short[][][] scores, int[] xyMax, int score)
public static AlignerHelper.Last[][] setScoreVector(int x, int xb, int yb, int ye, short gop, short gep, short[] subs, boolean storing, short[][][] scores, int[] xyMax, int score)
public static AlignerHelper.Last[][] setScoreVector(int x, short gep, short[] subs, boolean storing, short[][][] scores, int[] xyMax, int score)
public static AlignerHelper.Last[][] setScoreVector(int x, int xb, int yb, int ye, short gep, short[] subs, boolean storing, short[][][] scores, int[] xyMax, int score)
public static int[] setSteps(int[] anchors, java.util.List<AlignedSequence.Step> sx, java.util.List<AlignedSequence.Step> sy)
anchors
- a complete list of anchors (input)sx
- steps for the query sequence (output)sy
- steps for the target sequence (output)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)
public static int[] setSteps(AlignerHelper.Last[][][] traceback, short[][][] scores, java.util.List<AlignedSequence.Step> sx, java.util.List<AlignedSequence.Step> sy)
public static int[] setSteps(AlignerHelper.Last[][][] traceback, int[] xyMax, java.util.List<AlignedSequence.Step> sx, java.util.List<AlignedSequence.Step> sy)