Class AlignerHelper

Method Details

• addAnchors

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

• getCuts

  public static AlignerHelper.Cut[] getCuts(int k, AlignerHelper.Subproblem subproblem, int[] dim, boolean anchor0)

• setCuts

  public static void setCuts(int x, AlignerHelper.Subproblem subproblem, AlignerHelper.Last[][] pointers, AlignerHelper.Cut[] cuts)

• 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:

• setSteps

  public static int[] setSteps(AlignerHelper.Last[][][] traceback, boolean local, int[] xyMax, AlignerHelper.Last last, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)

  Find alignment path through traceback matrix

  Parameters:

  traceback -

  local -

  xyMax -

  last -

  sx -

  sy -

  Returns:

• setSteps

  public static int[] setSteps(AlignerHelper.Last[][][] traceback, int[][][] scores, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)

  Find global alignment path through traceback matrix

  Parameters:

  traceback -

  scores -

  sx -

  sy -

  Returns:

• setSteps

  public static int[] setSteps(AlignerHelper.Last[][][] traceback, int[] xyMax, List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)

  Find local alignment path through traceback matrix

  Parameters:

  traceback -

  xyMax -

  sx -

  sy -

  Returns:

• tracebackToString

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