Package jebl.evolution.align
Class Align
- java.lang.Object
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- jebl.evolution.align.Align
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- Direct Known Subclasses:
MaximalSegmentPair
,NeedlemanWunsch
,NeedlemanWunschAffine
,NeedlemanWunschLinearSpace
,NeedlemanWunschLinearSpaceAffine
,NonOverlapMultipleLocalAffine
,OldNeedlemanWunschAffine
,OverlapAlign
,SmithWaterman
,SmithWatermanLinearSpace
,SmithWatermanLinearSpaceAffine
public abstract class Align extends java.lang.Object
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods 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 alignmentvoid
doMatch(Output out, java.lang.String msg, boolean outputFMatrix)
Print the score, the F matrix, and the alignmentjava.lang.String
formatScore(float val)
java.lang.String[]
getMatch()
abstract float
getScore()
Traceback
next(Traceback tb)
Get the next state in the tracebackabstract 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 alignmentvoid
setGapOpen(float d)
void
setScores(Scores sub)
void
traceback(TracebackPlotter plotter)
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Constructor Detail
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Align
public Align(Scores sub, float d)
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Method Detail
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doAlignment
public abstract void doAlignment(java.lang.String sq1, java.lang.String sq2)
Performs the alignment, abstract.- Parameters:
sq1
-sq2
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prepareAlignment
public abstract void prepareAlignment(java.lang.String seq1, java.lang.String seq2)
Initialises the matrices for the alignment.- Parameters:
seq1
-seq2
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setGapOpen
public void setGapOpen(float d)
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setScores
public void setScores(Scores sub)
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getMatch
public java.lang.String[] getMatch()
- Returns:
- two-element array containing an alignment with maximal score
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formatScore
public java.lang.String formatScore(float val)
- Parameters:
val
-- Returns:
- float value of string val
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doMatch
public void doMatch(Output out, java.lang.String msg, boolean outputFMatrix)
Print the score, the F matrix, and the alignment- Parameters:
out
- output to print tomsg
- message printed at startoutputFMatrix
- print the score matrix
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traceback
public void traceback(TracebackPlotter plotter)
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doMatch
public void doMatch(Output out, java.lang.String msg)
Print the score and the alignment- Parameters:
out
- output to print tomsg
- msg printed at the start
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next
public Traceback next(Traceback tb)
Get the next state in the traceback- Parameters:
tb
- current Traceback- Returns:
- next Traceback
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getScore
public abstract float getScore()
- Returns:
- the score of the best alignment
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printf
public abstract void printf(Output out)
Print the matrix (matrices) used to compute the alignment- Parameters:
out
- output to print to
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