Package jebl.evolution.align

Class NeedlemanWunschAffine

  • public class NeedlemanWunschAffine
extends Align

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void allocateMatrices​(int n, int m)  
      void appendMatch​(jebl.evolution.align.AlignmentResult result1, jebl.evolution.align.AlignmentResult result2)  
      void doAlignment​(java.lang.String sq1, java.lang.String sq2)
      Performs the alignment.
      void doAlignment​(java.lang.String sequence1, java.lang.String sequence2, int startType, int endType)  
      void doAlignment​(jebl.evolution.align.Profile sequence1, jebl.evolution.align.Profile sequence2, int offset1, int offset2, int n, int m, int startType, int endType)  
      void doAlignment​(jebl.evolution.align.Profile sequence1, jebl.evolution.align.Profile sequence2, int offset1, int offset2, int n, int m, int startType, int endType, boolean freeStartGap, boolean freeEndGap)  
      java.lang.String[] getMatch()  
      java.lang.String[] getMatch​(char[] sq1, char[] sq2)  
      float getScore()  
      Traceback next​(Traceback tb)
      Get the next state in the traceback
      void prepareAlignment​(java.lang.String sq1, java.lang.String sq2)
      Initialises the matrices for the alignment.
      void printf​(Output out)
      Print matrix used to calculate this alignment.
      void setGapExtend​(float e)  

      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • NeedlemanWunschAffine

        public NeedlemanWunschAffine​(Scores sub,
                             float d,
                             float e)

    • Method Detail

      • doAlignment

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

      • allocateMatrices

        public void allocateMatrices​(int n,
                             int m)

      • prepareAlignment

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

      • doAlignment

        public void doAlignment​(java.lang.String sequence1,
                        java.lang.String sequence2,
                        int startType,
                        int endType)

      • doAlignment

        public void doAlignment​(jebl.evolution.align.Profile sequence1,
                        jebl.evolution.align.Profile sequence2,
                        int offset1,
                        int offset2,
                        int n,
                        int m,
                        int startType,
                        int endType)

      • doAlignment

        public void doAlignment​(jebl.evolution.align.Profile sequence1,
                        jebl.evolution.align.Profile sequence2,
                        int offset1,
                        int offset2,
                        int n,
                        int m,
                        int startType,
                        int endType,
                        boolean freeStartGap,
                        boolean freeEndGap)

      • appendMatch

        public void appendMatch​(jebl.evolution.align.AlignmentResult result1,
                        jebl.evolution.align.AlignmentResult result2)

      • getMatch

        public java.lang.String[] getMatch()
        Overrides:
        getMatch in class Align
        Returns:
        two-element array containing an alignment with maximal score

      • getMatch

        public java.lang.String[] getMatch​(char[] sq1,
                                   char[] sq2)

      • getScore

        public float getScore()
        Returns:
        score for this alignment

      • setGapExtend

        public void setGapExtend​(float e)

      • next

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

      • printf

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