Package jebl.evolution.align

Class NonOverlapMultipleLocalAffine

  • 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

    • Constructor Detail

      • NonOverlapMultipleLocalAffine

        public NonOverlapMultipleLocalAffine​(Scores sub,
                                     float d,
                                     float e,
                                     int T)

    • Method Detail

      • doAlignment

        public void doAlignment​(java.lang.String sq1,
                        java.lang.String sq2)
        Performs the alignment. Abstract.
        Parameters:
        sq1 -
        sq2 -

      • recurseAlignment

        public void recurseAlignment​(java.lang.String sq1,
                             int leftIndex)

      • getMatch

        public java.lang.String[] getMatch()
        Overrides:
        getMatch in class Align
        Returns:
        two-element array containing all of the local alignments separated by " - ";

      • 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.

      • getScore

        public float getScore()
        Returns:
        the score of the best alignment

      • getScores

        public float[] getScores()
        The indices for these correspond to those for the getAlignments() matrix.
        Returns:
        a matrix of scores for all the alignments.

      • 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)

      • printf

        public void printf​(Output out)
        Print matrix used to calculate this alignment.
        Parameters:
        out - Output to print to.

      • prepareAlignment

        public void prepareAlignment​(java.lang.String sq1,
                             java.lang.String sq2)
        Description copied from class: Align
        Initialises the matrices for the alignment.

      • setGapExtend

        public void setGapExtend​(float e)

      • next

        public Traceback next​(Traceback tb)
        Get the next state in the traceback
        Parameters:
        tb - current Traceback
        Returns:
        next Traceback

      • setThreshold

        public void setThreshold​(int T)