MaximalSegmentPair
, NeedlemanWunsch
, NeedlemanWunschAffine
, NeedlemanWunschLinearSpace
, NeedlemanWunschLinearSpaceAffine
, NonOverlapMultipleLocalAffine
, OldNeedlemanWunschAffine
, OverlapAlign
, SmithWaterman
, SmithWatermanLinearSpace
, SmithWatermanLinearSpaceAffine
public abstract class Align
extends java.lang.Object
Modifier and Type | Method | Description |
---|---|---|
abstract void |
doAlignment(java.lang.String sq1,
java.lang.String sq2) |
Performs the alignment, abstract.
|
void |
doMatch(Output out,
java.lang.String msg) |
Print the score and the alignment
|
void |
doMatch(Output out,
java.lang.String msg,
boolean outputFMatrix) |
Print the score, the F matrix, and the alignment
|
java.lang.String |
formatScore(float val) |
|
java.lang.String[] |
getMatch() |
|
abstract float |
getScore() |
|
Traceback |
next(Traceback tb) |
Get the next state in the traceback
|
abstract void |
prepareAlignment(java.lang.String seq1,
java.lang.String seq2) |
Initialises the matrices for the alignment.
|
abstract void |
printf(Output out) |
Print the matrix (matrices) used to compute the alignment
|
void |
setGapOpen(float d) |
|
void |
setScores(Scores sub) |
|
void |
traceback(TracebackPlotter plotter) |
public Align(Scores sub, float d)
public abstract void doAlignment(java.lang.String sq1, java.lang.String sq2)
sq1
- sq2
- public abstract void prepareAlignment(java.lang.String seq1, java.lang.String seq2)
seq1
- seq2
- public void setGapOpen(float d)
public void setScores(Scores sub)
public java.lang.String[] getMatch()
public java.lang.String formatScore(float val)
val
- public void doMatch(Output out, java.lang.String msg, boolean outputFMatrix)
out
- output to print tomsg
- message printed at startoutputFMatrix
- print the score matrixpublic void traceback(TracebackPlotter plotter)
public void doMatch(Output out, java.lang.String msg)
out
- output to print tomsg
- msg printed at the startpublic Traceback next(Traceback tb)
tb
- current Tracebackpublic abstract float getScore()
public abstract void printf(Output out)
out
- output to print tohttp://code.google.com/p/jebl2/