Package jebl.evolution.align
Class Align
java.lang.Object
jebl.evolution.align.Align
- Direct Known Subclasses:
MaximalSegmentPair
,NeedlemanWunsch
,NeedlemanWunschAffine
,NeedlemanWunschLinearSpace
,NeedlemanWunschLinearSpaceAffine
,NonOverlapMultipleLocalAffine
,OldNeedlemanWunschAffine
,OverlapAlign
,SmithWaterman
,SmithWatermanLinearSpace
,SmithWatermanLinearSpaceAffine
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionabstract void
doAlignment
(String sq1, String sq2) Performs the alignment, abstract.void
Print the score and the alignmentvoid
Print the score, the F matrix, and the alignmentformatScore
(float val) String[]
getMatch()
abstract float
getScore()
Get the next state in the tracebackabstract void
prepareAlignment
(String seq1, String seq2) Initialises the matrices for the alignment.abstract void
Print the matrix (matrices) used to compute the alignmentvoid
setGapOpen
(float d) void
void
traceback
(TracebackPlotter plotter)
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Constructor Details
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Align
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Method Details
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doAlignment
Performs the alignment, abstract.- Parameters:
sq1
-sq2
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prepareAlignment
Initialises the matrices for the alignment.- Parameters:
seq1
-seq2
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setGapOpen
public void setGapOpen(float d) -
setScores
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getMatch
- Returns:
- two-element array containing an alignment with maximal score
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formatScore
- Parameters:
val
-- Returns:
- float value of string val
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doMatch
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
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doMatch
Print the score and the alignment- Parameters:
out
- output to print tomsg
- msg printed at the start
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next
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
Print the matrix (matrices) used to compute the alignment- Parameters:
out
- output to print to
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