Class AlignerHelper


  • public class AlignerHelper
    extends java.lang.Object
    Static utility to construct alignment routines from a common library of methods.
    Author:
    Mark Chapman, Daniel Cameron
    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description
      static class  AlignerHelper.Anchor
      Compounds in query and target sequences that must align
      static class  AlignerHelper.Cut
      Defines a 'cut' row for divide-and-conquer alignment in which a new anchor is found.
      static class  AlignerHelper.Last
      Define a traceback pointer for the three edit operations: substitution (match/replacement of a query compound with a target compound), deletion (removal of a query compound leaving a gap in the target sequence), and insertion (addition of a target compound opening a gap in the query sequence).
      static class  AlignerHelper.Subproblem
      Alignment subproblem.
    • Constructor Summary

      Constructors 
      Constructor Description
      AlignerHelper()  
    • Constructor Detail

      • AlignerHelper

        public AlignerHelper()
    • Method Detail

      • addAnchors

        public static int addAnchors​(AlignerHelper.Cut[] cuts,
                                     int[] scores,
                                     boolean addScore,
                                     int[] anchors)
      • setScorePoint

        public static AlignerHelper.Last[] setScorePoint​(int x,
                                                         int y,
                                                         int gop,
                                                         int gep,
                                                         int sub,
                                                         int[][][] scores)
        Calculate the optimal alignment score for the given sequence positions with an affine or constant gap penalty
        Parameters:
        x - position in query
        y - position in target
        gop - gap opening penalty
        gep - gap extension penalty
        sub - compound match score
        scores - dynamic programming score matrix to fill at the given position
        Returns:
        traceback direction for substitution, deletion and insertion
      • setScorePoint

        public static AlignerHelper.Last setScorePoint​(int x,
                                                       int y,
                                                       int gep,
                                                       int sub,
                                                       int[][][] scores)
        Calculates the optimal alignment score for the given sequence positions and a linear gap penalty
        Parameters:
        x - position in query
        y - position in target
        gep - gap extension penalty
        sub - compound match score
        scores - dynamic programming score matrix to fill at the given position
        Returns:
        traceback directions for substitution, deletion and insertion respectively
      • setScoreVector

        public static AlignerHelper.Last[][] setScoreVector​(int x,
                                                            AlignerHelper.Subproblem subproblem,
                                                            int gop,
                                                            int gep,
                                                            int[] subs,
                                                            boolean storing,
                                                            int[][][] scores)
        Score global alignment for a given position in the query sequence
        Parameters:
        x -
        subproblem -
        gop -
        gep -
        subs -
        storing -
        scores -
        Returns:
      • setScoreVector

        public static AlignerHelper.Last[][] setScoreVector​(int x,
                                                            int xb,
                                                            int yb,
                                                            int ye,
                                                            int gop,
                                                            int gep,
                                                            int[] subs,
                                                            boolean storing,
                                                            int[][][] scores,
                                                            boolean startAnchored)
        Score global alignment for a given position in the query sequence
        Parameters:
        x -
        xb -
        yb -
        ye -
        gop -
        gep -
        subs -
        storing -
        scores -
        startAnchored -
        Returns:
      • setScoreVector

        public static AlignerHelper.Last[][] setScoreVector​(int x,
                                                            AlignerHelper.Subproblem subproblem,
                                                            int gep,
                                                            int[] subs,
                                                            boolean storing,
                                                            int[][][] scores)
        Score global alignment for a given position in the query sequence for a linear gap penalty
        Parameters:
        x -
        subproblem -
        gep -
        subs -
        storing -
        scores -
        Returns:
      • setScoreVector

        public static AlignerHelper.Last[][] setScoreVector​(int x,
                                                            int xb,
                                                            int yb,
                                                            int ye,
                                                            int gep,
                                                            int[] subs,
                                                            boolean storing,
                                                            int[][][] scores,
                                                            boolean startAnchored)
        Score global alignment for a given position in the query sequence for a linear gap penalty
        Parameters:
        x -
        xb -
        yb -
        ye -
        gep -
        subs -
        storing -
        scores -
        startAnchored -
        Returns:
      • setScoreVector

        public static AlignerHelper.Last[][] setScoreVector​(int x,
                                                            int gop,
                                                            int gep,
                                                            int[] subs,
                                                            boolean storing,
                                                            int[][][] scores,
                                                            int[] xyMax,
                                                            int score)
        Score local alignment for a given position in the query sequence
        Parameters:
        x -
        gop -
        gep -
        subs -
        storing -
        scores -
        xyMax -
        score -
        Returns:
      • setScoreVector

        public static AlignerHelper.Last[][] setScoreVector​(int x,
                                                            int xb,
                                                            int yb,
                                                            int ye,
                                                            int gop,
                                                            int gep,
                                                            int[] subs,
                                                            boolean storing,
                                                            int[][][] scores,
                                                            int[] xyMax,
                                                            int score)
        Score local alignment for a given position in the query sequence
        Parameters:
        x -
        xb -
        yb -
        ye -
        gop -
        gep -
        subs -
        storing -
        scores -
        xyMax -
        score -
        Returns:
      • setScoreVector

        public static AlignerHelper.Last[][] setScoreVector​(int x,
                                                            int gep,
                                                            int[] subs,
                                                            boolean storing,
                                                            int[][][] scores,
                                                            int[] xyMax,
                                                            int score)
        Score local alignment for a given position in the query sequence for a linear gap penalty
        Parameters:
        x -
        gep -
        subs -
        storing -
        scores -
        xyMax -
        score -
        Returns:
      • setScoreVector

        public static AlignerHelper.Last[][] setScoreVector​(int x,
                                                            int xb,
                                                            int yb,
                                                            int ye,
                                                            int gep,
                                                            int[] subs,
                                                            boolean storing,
                                                            int[][][] scores,
                                                            int[] xyMax,
                                                            int score)
        Score local alignment for a given position in the query sequence for a linear gap penalty
        Parameters:
        x -
        xb -
        yb -
        ye -
        gep -
        subs -
        storing -
        scores -
        xyMax -
        score -
        Returns:
      • tracebackToString

        public static java.lang.String tracebackToString​(AlignerHelper.Last[][][] traceback)