Package jebl.evolution.align
Class NonOverlapMultipleLocalAffine
- java.lang.Object
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- jebl.evolution.align.Align
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- jebl.evolution.align.NonOverlapMultipleLocalAffine
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public class NonOverlapMultipleLocalAffine extends Align
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 Constructor Description NonOverlapMultipleLocalAffine(Scores sub, float d, float e, int T)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
doAlignment(java.lang.String sq1, java.lang.String sq2)
Performs the alignment.java.lang.String[][]
getAlignments()
The indices for these correspond to those for the getScoreMatrix() matrix.java.lang.String[]
getMatch()
java.lang.String
getMatchScores(int width)
float
getScore()
float[]
getScores()
The indices for these correspond to those for the getAlignments() matrix.Traceback
next(Traceback tb)
Get the next state in the tracebackvoid
prepareAlignment(java.lang.String sq1, java.lang.String sq2)
Initialises the matrices for the alignment.void
printf(Output out)
Print matrix used to calculate this alignment.void
recurseAlignment(java.lang.String sq1, int leftIndex)
void
setGapExtend(float e)
void
setThreshold(int T)
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Methods inherited from class jebl.evolution.align.Align
doMatch, doMatch, formatScore, setGapOpen, setScores, traceback
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Constructor Detail
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NonOverlapMultipleLocalAffine
public NonOverlapMultipleLocalAffine(Scores sub, float d, float e, int T)
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Method Detail
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doAlignment
public void doAlignment(java.lang.String sq1, java.lang.String sq2)
Performs the alignment. Abstract.- Parameters:
sq1
-sq2
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recurseAlignment
public void recurseAlignment(java.lang.String sq1, int leftIndex)
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getMatch
public java.lang.String[] getMatch()
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getMatchScores
public java.lang.String getMatchScores(int width)
- 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
public java.lang.String[][] 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
public void printf(Output out)
Print matrix used to calculate this alignment.- Parameters:
out
- Output to print to.
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prepareAlignment
public void prepareAlignment(java.lang.String sq1, java.lang.String sq2)
Description copied from class:Align
Initialises the matrices for the alignment.
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setGapExtend
public void setGapExtend(float e)
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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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setThreshold
public void setThreshold(int T)
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