Package jebl.evolution.align

Class NonOverlapMultipleLocalAffine

java.lang.Object
jebl.evolution.align.Align
jebl.evolution.align.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 Details

    • NonOverlapMultipleLocalAffine

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

  • Method Details

    • doAlignment

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

    • recurseAlignment

      public void recurseAlignment(String sq1, int leftIndex)

    • getMatch

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

    • getMatchScores

      public 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 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(String sq1, 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)