Class NeedlemanWunsch

java.lang.Object
org.biojava.bio.alignment.AlignmentAlgorithm
org.biojava.bio.alignment.NeedlemanWunsch

public class NeedlemanWunsch extends AlignmentAlgorithm
Needleman and Wunsch defined the problem of global sequence alignments, from the first till the last symbol of a sequence. This class is able to perform such global sequence comparisons efficiently by dynamic programming. If inserts and deletes are equally expensive and as expensive as the extension of a gap, the alignment method of this class does not use affine gap penalties. Otherwise it does. Those costs need four times as much memory, which has significant effects on the run time, if the computer needs to swap.
Since:
1.5
Author:
Andreas Dräger, Gero Greiner, Mark Schreiber
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    protected int[][]
    A matrix with the size length(sequence1) times length(sequence2)
    A matrix with the size length(alphabet) times length(alphabet)
  • Constructor Summary

    Constructors
    Constructor
    Description
    NeedlemanWunsch(short match, short replace, short insert, short delete, short gapExtend, SubstitutionMatrix subMat)
    Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be taken from the given substitution matrix.
  • Method Summary

    Modifier and Type
    Method
    Description
    short
    Returns the current expenses of a single delete operation.
    int
    This gives the edit distance according to the given parameters of this certain object.
    short
    Returns the current expenses of any extension of a gap operation.
    short
    Returns the current expenses of a single insert operation.
    short
    Returns the current expenses of a single match operation.
    short
    Returns the current expenses of a single replace operation.
    protected static int
    min(int x, int y, int z)
    This just computes the minimum of three integer values.
    Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.
    static String
    printCostMatrix(int[][] CostMatrix, char[] queryChar, char[] targetChar)
    Prints a String representation of the CostMatrix for the given Alignment on the screen.
    void
    setDelete(short del)
    Sets the penalty for a delete operation to the specified value.
    void
    setGapExt(short ge)
    Sets the penalty for an extension of any gap (insert or delete) to the specified value.
    void
    setInsert(short ins)
    Sets the penalty for an insert operation to the specified value.
    void
    setMatch(short ma)
    Sets the penalty for a match operation to the specified value.
    void
    setReplace(short rep)
    Sets the penalty for a replace operation to the specified value.
    void
    Sets the substitution matrix to be used to the specified one.

    Methods inherited from class org.biojava.bio.alignment.AlignmentAlgorithm

    alignAll

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Field Details

    • CostMatrix

      protected int[][] CostMatrix
      A matrix with the size length(sequence1) times length(sequence2)
    • subMatrix

      A matrix with the size length(alphabet) times length(alphabet)
  • Constructor Details

    • NeedlemanWunsch

      public NeedlemanWunsch(short match, short replace, short insert, short delete, short gapExtend, SubstitutionMatrix subMat)
      Constructs a new Object with the given parameters based on the Needleman-Wunsch algorithm The alphabet of sequences to be aligned will be taken from the given substitution matrix.
      Parameters:
      match - This gives the costs for a match operation. It is only used, if there is no entry for a certain match of two symbols in the substitution matrix (default value).
      replace - This is like the match parameter just the default, if there is no entry in the substitution matrix object.
      insert - The costs of a single insert operation.
      delete - The expenses of a single delete operation.
      gapExtend - The expenses of an extension of a existing gap (that is a previous insert or delete. If the costs for insert and delete are equal and also equal to gapExtend, no affine gap penalties will be used, which saves a significant amount of memory.
      subMat - The substitution matrix object which gives the costs for matches and replaces.
  • Method Details

    • min

      protected static int min(int x, int y, int z)
      This just computes the minimum of three integer values.
      Parameters:
      x -
      y -
      z -
      Returns:
      Gives the minimum of three integers
    • printCostMatrix

      public static String printCostMatrix(int[][] CostMatrix, char[] queryChar, char[] targetChar)
      Prints a String representation of the CostMatrix for the given Alignment on the screen. This can be used to get a better understanding of the algorithm. There is no other purpose. This method also works for all extensions of this class with all kinds of matrices.
      Parameters:
      CostMatrix - The matrix that contains all expenses for swapping symbols.
      queryChar - a character representation of the query sequence ( mySequence.seqString().toCharArray()).
      targetChar - a character representation of the target sequence.
      Returns:
      a String representation of the matrix.
    • getDelete

      public short getDelete()
      Returns the current expenses of a single delete operation.
      Returns:
      delete
    • getEditDistance

      public int getEditDistance()
      This gives the edit distance according to the given parameters of this certain object. It returns just the last element of the internal cost matrix (left side down). So if you extend this class, you can just do the following: int myDistanceValue = foo; this.CostMatrix = new int[1][1]; this.CostMatrix[0][0] = myDistanceValue;
      Returns:
      returns the edit_distance computed with the given parameters.
    • getGapExt

      public short getGapExt()
      Returns the current expenses of any extension of a gap operation.
      Returns:
      gapExt
    • getInsert

      public short getInsert()
      Returns the current expenses of a single insert operation.
      Returns:
      insert
    • getMatch

      public short getMatch()
      Returns the current expenses of a single match operation.
      Returns:
      match
    • getReplace

      public short getReplace()
      Returns the current expenses of a single replace operation.
      Returns:
      replace
    • pairwiseAlignment

      Global pairwise sequence alignment of two BioJava-Sequence objects according to the Needleman-Wunsch-algorithm.
      Specified by:
      pairwiseAlignment in class AlignmentAlgorithm
      Parameters:
      query -
      subject -
      Returns:
      score of the alignment or the distance.
      Throws:
      BioException
      See Also:
    • setDelete

      public void setDelete(short del)
      Sets the penalty for a delete operation to the specified value.
      Parameters:
      del - costs for a single deletion operation
    • setGapExt

      public void setGapExt(short ge)
      Sets the penalty for an extension of any gap (insert or delete) to the specified value.
      Parameters:
      ge - costs for any gap extension
    • setInsert

      public void setInsert(short ins)
      Sets the penalty for an insert operation to the specified value.
      Parameters:
      ins - costs for a single insert operation
    • setMatch

      public void setMatch(short ma)
      Sets the penalty for a match operation to the specified value.
      Parameters:
      ma - costs for a single match operation
    • setReplace

      public void setReplace(short rep)
      Sets the penalty for a replace operation to the specified value.
      Parameters:
      rep - costs for a single replace operation
    • setSubstitutionMatrix

      Sets the substitution matrix to be used to the specified one. Afterwards it is only possible to align sequences of the alphabet of this substitution matrix.
      Parameters:
      matrix - an instance of a substitution matrix.