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.