Package jebl.evolution.align
Class NonOverlapMultipleLocalAffine
java.lang.Object
jebl.evolution.align.Align
jebl.evolution.align.NonOverlapMultipleLocalAffine
Performs recursive local alignments. each time splitting the longer of the two sequences
into two subsequences either side of the local alignment and aligning those.
Uses SmithWatermanLinearSpaceAffine. Stores all of the local alignments and their scores.
Threshold T is the minimum score that an alignment must be for inclusion.
- Version:
- $Id: NonOverlapMultipleLocalAffine.java 370 2006-06-29 18:57:56Z rambaut $
- Author:
- Richard Moir
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
doAlignment
(String sq1, String sq2) Performs the alignment.String[][]
The indices for these correspond to those for the getScoreMatrix() matrix.String[]
getMatch()
getMatchScores
(int width) float
getScore()
float[]
The indices for these correspond to those for the getAlignments() matrix.Get the next state in the tracebackvoid
prepareAlignment
(String sq1, String sq2) Initialises the matrices for the alignment.void
Print matrix used to calculate this alignment.void
recurseAlignment
(String sq1, int leftIndex) void
setGapExtend
(float e) void
setThreshold
(int T) Methods inherited from class jebl.evolution.align.Align
doMatch, doMatch, formatScore, setGapOpen, setScores, traceback
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Constructor Details
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NonOverlapMultipleLocalAffine
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Method Details
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doAlignment
Performs the alignment. Abstract.- Parameters:
sq1
-sq2
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recurseAlignment
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getMatch
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getMatchScores
- Parameters:
width
- length to trim lines to. -1 = infinite width.- Returns:
- String containing all local alignments with the score next to them.
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getScore
public float getScore()- Returns:
- the score of the best alignment
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getScores
public float[] getScores()The indices for these correspond to those for the getAlignments() matrix.- Returns:
- a matrix of scores for all the alignments.
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getAlignments
The indices for these correspond to those for the getScoreMatrix() matrix.- Returns:
- a 2d matrix of alignments. first index is the alignment number. second is the sequence number (0 or 1)
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printf
Print matrix used to calculate this alignment.- Parameters:
out
- Output to print to.
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prepareAlignment
Description copied from class:Align
Initialises the matrices for the alignment.- Parameters:
sq1
-sq2
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setGapExtend
public void setGapExtend(float e) -
next
Get the next state in the traceback- Parameters:
tb
- current Traceback- Returns:
- next Traceback
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setThreshold
public void setThreshold(int T)
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