org.biojava3.alignment.routines
Class AlignerHelper
java.lang.Object
org.biojava3.alignment.routines.AlignerHelper
public class AlignerHelper
- extends Object
Static utility to construct alignment routines from a common library of methods.
- Author:
- Mark Chapman
Nested Class Summary |
static class |
AlignerHelper.Cut
Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found. |
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). |
Method Summary |
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,
List<AlignedSequence.Step> sx,
List<AlignedSequence.Step> sy)
|
static int[] |
setSteps(AlignerHelper.Last[][][] traceback,
int[] xyMax,
List<AlignedSequence.Step> sx,
List<AlignedSequence.Step> sy)
|
static int[] |
setSteps(AlignerHelper.Last[][][] traceback,
short[][][] scores,
List<AlignedSequence.Step> sx,
List<AlignedSequence.Step> sy)
|
static int[] |
setSteps(int[] anchors,
List<AlignedSequence.Step> sx,
List<AlignedSequence.Step> sy)
Sets the alignment path following the list of anchors. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
AlignerHelper
public AlignerHelper()
addAnchors
public static short addAnchors(AlignerHelper.Cut[] cuts,
short[] scores,
boolean addScore,
int[] anchors)
getCuts
public static AlignerHelper.Cut[] getCuts(int k,
int[] subproblem,
int[] dim,
boolean anchor0)
getNextSubproblem
public static int[] getNextSubproblem(int[] anchors)
- Returns the coordinates for the next subproblem. The first element is the starting index in the query sequence.
The second element is the starting index in the target sequence. Similarly, the third and fourth elements are
the ending indices of the query and target sequences, respectively. When the alignment is finished, there is no
next subproblem and this method returns
null
.
- Parameters:
anchors
- current list of anchors
- Returns:
- the coordinates for the next subproblem
setCuts
public static void setCuts(int x,
int[] subproblem,
AlignerHelper.Last[][] pointers,
AlignerHelper.Cut[] cuts)
setScorePoint
public static AlignerHelper.Last[] setScorePoint(int x,
int y,
short gop,
short gep,
short sub,
short[][][] scores)
setScorePoint
public static AlignerHelper.Last setScorePoint(int x,
int y,
short gep,
short sub,
short[][][] scores)
setScoreVector
public static AlignerHelper.Last[][] setScoreVector(int x,
short gop,
short gep,
short[] subs,
boolean storing,
short[][][] scores)
setScoreVector
public static AlignerHelper.Last[][] setScoreVector(int x,
int[] subproblem,
short gop,
short gep,
short[] subs,
boolean storing,
short[][][] scores)
setScoreVector
public static AlignerHelper.Last[][] setScoreVector(int x,
int xb,
int yb,
int ye,
short gop,
short gep,
short[] subs,
boolean storing,
short[][][] scores)
setScoreVector
public static AlignerHelper.Last[][] setScoreVector(int x,
short gep,
short[] subs,
boolean storing,
short[][][] scores)
setScoreVector
public static AlignerHelper.Last[][] setScoreVector(int x,
int[] subproblem,
short gep,
short[] subs,
boolean storing,
short[][][] scores)
setScoreVector
public static AlignerHelper.Last[][] setScoreVector(int x,
int xb,
int yb,
int ye,
short gep,
short[] subs,
boolean storing,
short[][][] scores)
setScoreVector
public static AlignerHelper.Last[][] setScoreVector(int x,
short gop,
short gep,
short[] subs,
boolean storing,
short[][][] scores,
int[] xyMax,
int score)
setScoreVector
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)
setScoreVector
public static AlignerHelper.Last[][] setScoreVector(int x,
short gep,
short[] subs,
boolean storing,
short[][][] scores,
int[] xyMax,
int score)
setScoreVector
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)
setSteps
public static int[] setSteps(int[] anchors,
List<AlignedSequence.Step> sx,
List<AlignedSequence.Step> sy)
- Sets the alignment path following the list of anchors.
- Parameters:
anchors
- a complete list of anchors (input)sx
- steps for the query sequence (output)sy
- steps for the target sequence (output)
setSteps
public static int[] setSteps(AlignerHelper.Last[][][] traceback,
boolean local,
int[] xyMax,
AlignerHelper.Last last,
List<AlignedSequence.Step> sx,
List<AlignedSequence.Step> sy)
setSteps
public static int[] setSteps(AlignerHelper.Last[][][] traceback,
short[][][] scores,
List<AlignedSequence.Step> sx,
List<AlignedSequence.Step> sy)
setSteps
public static int[] setSteps(AlignerHelper.Last[][][] traceback,
int[] xyMax,
List<AlignedSequence.Step> sx,
List<AlignedSequence.Step> sy)